Search

Your search keyword '"Alan R Shuldiner"' showing total 232 results
Start Over Author "Alan R Shuldiner" Topic female
232 results on '"Alan R Shuldiner"'

1. Clinical case study meets population cohort: identification of a BRCA1 pathogenic founder variant in Orcadians

Author

Shona M. Kerr, Emma Cowan, Lucija Klaric, Christine Bell, Dawn O’Sullivan, David Buchanan, Joseph J. Grzymski, Cristopher V. van Hout, Gannie Tzoneva, Alan R. Shuldiner, James F. Wilson, and Zosia Miedzybrodzka

Subjects
Scotland/epidemiology, Breast Neoplasms/genetics, BRCA2 Protein/genetics, State Medicine, Gene Frequency, Haplotypes, Genetics, BRCA1 Protein/genetics, Humans, Female, Genetic Predisposition to Disease, Genetic Testing, Ovarian Neoplasms/epidemiology, Genetics (clinical)
Abstract

We multiply ascertained the BRCA1 pathogenic missense variant c.5207T > C; p.Val1736Ala (V1736A) in clinical investigation of breast and ovarian cancer families from Orkney in the Northern Isles of Scotland, UK. We sought to investigate the frequency and clinical relevance of this variant in those of Orcadian ancestry as an exemplar of the value of population cohorts in clinical care, especially in isolated populations. Oral history and birth, marriage and death registrations indicated genealogical linkage of the clinical cases to ancestors from the Isle of Westray, Orkney. Further clinical cases were identified through targeted testing for V1736A in women of Orcadian ancestry attending National Health Service (NHS) genetic clinics for breast and ovarian cancer family risk assessments. The variant segregates with female breast and ovarian cancer in clinically ascertained cases. Separately, exome sequence data from 2088 volunteer participants with three or more Orcadian grandparents, in the ORCADES research cohort, was interrogated to estimate the population prevalence of V1736A in Orcadians. The effects of the variant were assessed using Electronic Health Record (EHR) linkage. Twenty out of 2088 ORCADES research volunteers (~1%) carry V1736A, with a common haplotype around the variant. This allele frequency is ~480-fold higher than in UK Biobank participants. Cost-effectiveness of population screening for BRCA1 founder pathogenic variants has been demonstrated at a carrier frequency below the ~1% observed here. Thus we suggest that Orcadian women should be offered testing for the BRCA1 V1736A founder pathogenic variant, starting with those with known Westray ancestry.

Published
2023

2. The prevalence of prenatal sonographic findings in postnatal diagnostic exome sequencing performed for neurocognitive phenotypes: A cohort study

Author

Rivka, Sukenik-Halevy, Sharon, Perlman, Noa, Ruhrman-Shahar, Offra, Engel, Naama, Orenstein, Claudia, Gonzaga-Jauregui, Alan R, Shuldiner, Nurit, Magal, Ofir, Hagari, Noy, Azulay, Gabriel Arie, Lidzbarsky, Lily, Bazak, and Lina, Basel-Salmon

Subjects
Cohort Studies, Polyhydramnios, Fetal Growth Retardation, Phenotype, Pregnancy, Prenatal Diagnosis, Prevalence, Humans, Obstetrics and Gynecology, Exome, Female, Ultrasonography, Prenatal, Genetics (clinical)
Abstract

Prenatal exome sequencing (ES) is currently indicated for fetal malformations. Some neurocognitive genetic disorders may not have a prenatal phenotype. We assessed the prevalence of prenatally detectable phenotypes among patients with neurocognitive syndromes diagnosed postnatally by ES.The medical files of a cohort of 138 patients diagnosed postnatally with a neurocognitive disorder using ES were reviewed for prenatal sonographic data. The Online Mendelian Inheritance in Man (OMIM) database was searched for prenatally detectable phenotypes for all genes identified.Prenatal imaging data were available for 122 cases. Of these, 29 (23.75%) had fetal structural abnormalities and another 29 had other ultrasound abnormalities (fetal growth restriction, polyhydramnios, elevated nuchal translucency). In 30 patients, structural aberrations that were not diagnosed prenatally were detected at birth; in 21 (17.2%), the abnormalities could theoretically be detected prenatally by third-trimester/targeted scans. According to OMIM, 55.9% of the diagnosed genes were not associated with structural anomalies.Most patients (52.5%) with postnatally diagnosed neurocognitive disorders did not have prenatal sonographic findings indicating prenatal ES should be considered. The prevalence of specific prenatal phenotypes such as fetal growth restriction and polyhydramnios in our cohort suggests that additional prenatal findings should be assessed as possible indications for prenatal ES.

Published
2022

3. The Association between Factor XI Deficiency and the Risk of Bleeding, Cardiovascular, and Venous Thromboembolic Events

Author

Alan R. Shuldiner, Chalothorn Dan, Sarah Sharman Moser, Morton Lori C, Ming-Dauh Wang, Gabriel Chodick, Yan G. Ni, Ophira Salomon, and Jessica J. Jalbert

Subjects
Adult, Male, Venous Thrombosis, medicine.medical_specialty, Factor XI Deficiency, business.industry, MEDLINE, Hemorrhage, Retrospective cohort study, Venous Thromboembolism, Hematology, medicine.disease, Internal medicine, Humans, Medicine, Female, business, Factor XI, Stroke, Retrospective Studies
Abstract

The objective of this study was to assess the relationship between factor XI (FXI) deficiency and the risks of bleeding and cardiovascular (CV) events. We conducted a retrospective cohort study using data from Maccabi Healthcare Services (MHS). We identified adults with FXI deficiency (severe

Published
2021

4. The burden of pathogenic variants in clinically actionable genes in a founder population

Author

Elizabeth A. Streeten, Braxton D. Mitchell, Toni I. Pollin, Megan Lynch, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Kristin A. Maloney, Huichun Xu, and Cristopher V. Van Hout

Subjects
Adult, Male, medicine.medical_specialty, Population, Genomics, Biology, Genetic drift, Exome Sequencing, Genetics, medicine, Humans, Exome, Genetic Predisposition to Disease, Genetic Testing, Precision Medicine, education, Genetics (clinical), Exome sequencing, Genetic testing, education.field_of_study, medicine.diagnostic_test, Genetic Diseases, Inborn, Genetic Variation, Middle Aged, Old Order Amish, Medical genetics, Female, Amish, Founder effect
Abstract

Founder populations may be enriched with certain genetic variants of high clinical impact compared to nonfounder populations due to bottleneck events and genetic drift. Using exome sequencing (ES), we quantified the load of pathogenic variants that may be clinically actionable in 6136 apparently healthy adults living in the Lancaster, PA Old Order Amish settlement. We focused on variants in 78 genes deemed clinically actionable by the American College of Medical Genetics and Genomics (ACMG) or Geisinger's MyCode Health Initiative. ES revealed 3191 total variants among these genes including 480 nonsynonymous variants. After quality control and filtering, we applied the ACMG/AMP guidelines for variant interpretation and classified seven variants, across seven genes, as either pathogenic or likely pathogenic. Through genetic drift, all seven variants, are highly enriched in the Amish compared to nonfounder populations. In total, 14.7% of Lancaster Amish individuals carry at least one of these variants, largely explained by the 13% who harbor a copy of a single variant in APOB. Other studies report combined frequencies of pathogenic/likely pathogenic (P/LP) variants in actionable genes between 2.0% and 6.2% in outbred populations. The Amish population harbors fewer actionable variants compared to similarly characterized nonfounder populations but have a higher frequency of each variant identified, offering opportunities for efficient and cost-effective targeted precision medicine.

Published
2021

5. The diagnostic efficacy of exome data analysis using fixed neurodevelopmental gene lists: Implications for prenatal setting

Author

Rivka Sukenik-Halevy, Noa Ruhrman-Shahar, Lina Basel-Salmon, Noy Azulay, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Ofir Hagari, Lily Bazak, Nurit Magal, Gabriel Arie Lidzbarsky, and Naama Orenstein

Subjects
0301 basic medicine, Proband, Pediatrics, medicine.medical_specialty, Noninvasive Prenatal Testing, MEDLINE, Prenatal diagnosis, 030105 genetics & heredity, 03 medical and health sciences, Fetus, 0302 clinical medicine, Pregnancy, Exome Sequencing, Humans, Medicine, Exome, Genetics (clinical), Exome sequencing, 030219 obstetrics & reproductive medicine, business.industry, Obstetrics and Gynecology, Cohort, Female, business, Neurocognitive
Abstract

Objective Laboratories performing prenatal exome sequencing (ES) frequently limit analysis to predetermined gene lists. We used a diagnostic postnatal ES cohort to assess how many of the genes diagnosed are not included in a number of select fixed lists used for prenatal diagnosis. Methods Of 601 postnatal ES tests, pathogenic variants related to neurodevelopmental disorders were detected in 138 probands. We evaluated if causative genes were present in the following: (1) Developmental Disorders Genotype-Phenotype database list, (2) a commercial laboratory list for prenatal ES, (3) the PanelApp fetal anomalies panel, and (4) a published list used for prenatal diagnosis by ES (Prenatal Assessment of Genomes and Exomes study). Results The percentages of cases where the diagnosed gene was not included in the selected four lists were; 11.6%, 17.24%, 23.2%, and 10.9%, respectively. In 13/138 (9.4%) cases, the causative gene was not included in any of the lists; in 4/13 (∼30%) cases noninclusion was explained by a relatively recent discovery of gene-phenotype association. Conclusions A significant number of genes related to neurocognitive phenotypes are not included in some of the lists used for prenatal ES data interpretation. These are not only genes related to recently discovered disorders, but also genes with well-established gene-phenotype.

Published
2021

6. Exome sequencing and characterization of 49,960 individuals in the UK Biobank

Author

David J. Carey, Cristen J. Willer, Anthony Marcketta, Claudia Schurmann, Leland Barnard, John Penn, Suganthi Balasubramanian, Daren Liu, Joseph B. Leader, Gonçalo R. Abecasis, Marcus B. Jones, John C. Whittaker, Ashutosh K. Pandey, Ida Surakka, David H. Ledbetter, Evan Maxwell, John D. Overton, Andrew Blumenfeld, Michael N. Cantor, Robert A. Scott, Wendy K. Chung, Alexander H. Li, Alexander Lopez, Joshua D. Backman, Matthew R. Nelson, Jeffrey Staples, Giovanni Coppola, Jonathan Marchini, Xiaodong Bai, Kavita Praveen, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Aris N. Economides, Shareef Khalid, William J Salerno, Bin Ye, Cristopher V. Van Hout, Kristian Hveem, Jeffrey G. Reid, Colm O'Dushlaine, Joshua D. Hoffman, Laura M. Yerges-Armstrong, Nilanjana Banerjee, Sean O'Keeffe, Ioanna Tachmazidou, Lon R. Cardon, Alicia Hawes, Aris Baras, Ashish Yadav, George D. Yancopoulos, and Lukas Habegger

Subjects
Male, 0301 basic medicine, Genes, BRCA2, Genes, BRCA1, Hasso-Plattner-Institut für Digital Engineering GmbH, Penetrance, 030204 cardiovascular system & hematology, Ion Channels, 0302 clinical medicine, Bone Density, Loss of Function Mutation, Neoplasms, Databases, Genetic, Genetics research, Genotype, Exome, Exome sequencing, Biological Specimen Banks, education.field_of_study, Multidisciplinary, Genomics, Middle Aged, Biobank, Pedigree, Phenotype, ras GTPase-Activating Proteins, Female, Kidney Diseases, Population, Collagen Type VI, Computational biology, Biology, Article, DNA sequencing, Varicose Veins, 03 medical and health sciences, Exome Sequencing, Humans, education, Alleles, Aged, Demography, Rare variants, Peptide Fragments, United Kingdom, 030104 developmental biology, ddc:000, Next-generation sequencing
Abstract

The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1. Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenic BRCA1 and BRCA2 variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community., Exome sequences from the first 49,960 participants in the UK Biobank highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.

Published
2020

7. A novel mutation in MYCN gene causing congenital absence of the flexor pollicis longus tendon as an unusual presentation of Feingold syndrome 1

Author

Adi Mory, R Wollstein, Tamar Paperna, G Larom-Khan, Vardit Adir, Hagit Baris Feldman, Alina Kurolap, Lena Sagi-Dain, Noam Adir, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, and Amir Peleg

Subjects
Adult, Male, Models, Molecular, Microcephaly, Pathology, medicine.medical_specialty, Limb Deformities, Congenital, Thumb, Pathology and Forensic Medicine, Tendons, Structure-Activity Relationship, Intellectual Disability, Exome Sequencing, medicine, Feingold syndrome, Humans, Genetic Predisposition to Disease, Child, neoplasms, Exome, Gene, Genetic Association Studies, Genetics (clinical), Aged, N-Myc Proto-Oncogene Protein, business.industry, Eyelids, General Medicine, Middle Aged, medicine.disease, Pedigree, Tendon, Phenotype, medicine.anatomical_structure, Mutation, Pediatrics, Perinatology and Child Health, Female, Anatomy, Abnormality, business, N-Myc, Tracheoesophageal Fistula
Abstract

Feingold syndrome 1 (FGLDS1) is an autosomal dominant malformation syndrome, characterized by skeletal anomalies, microcephaly, facial dysmorphism, gastrointestinal atresias and learning disabilities. Mutations in the MYCN gene are known to be the cause of this syndrome. Congenital absence of the flexor pollicis longus (CAFPL) tendon is a rare hand anomaly. Most cases are sporadic and no genetic variants have been described associated with this abnormality. We describe here a pedigree combining familial CAFPL tendon as a feature of FGLDS1. Molecular analyses of whole exome sequence data in five affected family members spanning three generations of this family revealed a novel mutation in the MYCN gene (c.1171C>T; p.Arg391Cys). Variants in MYCN have not been published in association with isolated or syndromic CAFPL tendon, nor has this been described as a skeletal feature of Feingold syndrome. This report expands on the clinical and molecular spectrum of MYCN-related disorders and highlights the importance of MYCN protein in normal human thumb and foramen development.

Published
2020

8. Characterization of Exome Variants and Their Metabolic Impact in 6,716 American Indians from the Southwest US

Author

Robert L. Hanson, Leslie J. Baier, Nehal Gosalia, Hye In Kim, Çiğdem Köroğlu, Bin Ye, Alan R. Shuldiner, Clifton Bogardus, Cristopher V. Van Hout, Wen-Chi Hsueh, and William C. Knowler

Subjects
Male, 0301 basic medicine, Nonsynonymous substitution, Candidate gene, Population, 030209 endocrinology & metabolism, Genome-wide association study, Biology, Polymorphism, Single Nucleotide, Article, Body Mass Index, 03 medical and health sciences, 0302 clinical medicine, Southwestern United States, Genetics, Humans, Exome, Genetic Predisposition to Disease, Allele, education, Alleles, Genetics (clinical), Exome sequencing, Genetic association, education.field_of_study, Genetics, Population, Phenotype, 030104 developmental biology, Indians, North American, Female, Genome-Wide Association Study
Abstract

Applying exome sequencing to populations with unique genetic architecture has the potential to reveal novel genes and variants associated with traits and diseases. We sequenced and analyzed the exomes of 6,716 individuals from a Southwestern American Indian (SWAI) population with well-characterized metabolic traits. We found that the SWAI population has distinct allelic architecture compared to populations of European and East Asian ancestry, and there were many predicted loss-of-function (pLOF) and nonsynonymous variants that were highly enriched or private in the SWAI population. We used pLOF and nonsynonymous variants in the SWAI population to evaluate gene-burden associations of candidate genes from European genome-wide association studies (GWASs) for type 2 diabetes, body mass index, and four major plasma lipids. We found 19 significant gene-burden associations for 11 genes, providing additional evidence for prioritizing candidate effector genes of GWAS signals. Interestingly, these associations were mainly driven by pLOF and nonsynonymous variants that are unique or highly enriched in the SWAI population. Particularly, we found four pLOF or nonsynonymous variants in APOB, APOE, PCSK9, and TM6SF2 that are private or enriched in the SWAI population and associated with low-density lipoprotein (LDL) cholesterol levels. Their large estimated effects on LDL cholesterol levels suggest strong impacts on protein function and potential clinical implications of these variants in cardiovascular health. In summary, our study illustrates the utility and potential of exome sequencing in genetically unique populations, such as the SWAI population, to prioritize candidate effector genes within GWAS loci and to find additional variants in known disease genes with potential clinical impact.

Published
2020

9. Genetic Variation in PEAR1, Cardiovascular Outcomes and Effects of Aspirin in a Healthy Elderly Population

Author

Mark Nelson, Christopher M. Reid, Sophia Xie, Joshua P. Lewis, Alan R. Shuldiner, Andrew Tonkin, Paul Lacaze, Rory Wolfe, John J McNeil, Galina Polekhina, Anne M. Murray, and Moeen Riaz

Subjects
Blood Platelets, Male, medicine.medical_specialty, Time Factors, Pharmacogenomic Variants, Platelet Aggregation, Population, Hemorrhage, Receptors, Cell Surface, Placebo, Polymorphism, Single Nucleotide, Risk Assessment, 030226 pharmacology & pharmacy, Article, law.invention, 03 medical and health sciences, 0302 clinical medicine, Double-Blind Method, Randomized controlled trial, Risk Factors, law, Internal medicine, Post-hoc analysis, Humans, Medicine, Pharmacology (medical), Prospective Studies, Prospective cohort study, education, Stroke, Aged, Pharmacology, Aspirin, education.field_of_study, business.industry, Age Factors, Australia, medicine.disease, United States, Primary Prevention, Cardiovascular Diseases, Pharmacogenetics, 030220 oncology & carcinogenesis, Female, business, Platelet Aggregation Inhibitors, Mace, medicine.drug
Abstract

The platelet endothelial aggregation receptor-1 (PEAR1) rs12041331 variant has been identified as a genetic determinant of platelet aggregation in response to antiplatelet therapies, including aspirin. However, association with atherothrombotic cardiovascular events is less clear, with limited evidence from large trials. Here, we tested association of rs12041331 with cardiovascular events and aspirin use in a randomized trial population of healthy older individuals. We undertook post hoc analysis of 13,547 participants of the ASPirin in Reducing Events in the Elderly (ASPREE) trial, median age 74 years. Participants had no previous diagnosis of atherothrombotic cardiovascular disease at enrollment, and were randomized to either 100 mg daily low-dose aspirin or placebo for median 4.7 years follow-up. We used Cox proportional hazard regression to model the relationship between rs12041331 and the ASPREE primary cardiovascular disease (CVD) end point, and composites of major adverse cardiovascular events (MACE) and ischemic stroke (STROKE); and bleeding events; major hemorrhage (MHEM) and intracranial bleeding (ICB). We performed whole-population analysis using additive and dominant inheritance models, then stratified by treatment group. Interaction effects between genotypes and treatment group were examined. We observed no statistically significant association (P < 0.05) in the population, or by treatment group, between rs12041331 and cardiovascular or bleeding events in either model. We also found no significant interaction effects between rs12041331-A and treatment group, for CVD (P = 0.65), MACE (P = 0.32), STROKE (P = 0.56), MHEM (P = 0.59), or ICB (P = 0.56). The genetic variant PEAR1 rs12041331 is not associated with cardiovascular events in response to low-dose aspirin in a healthy elderly population.

Published
2020

10. Parkinson’s Disease-Related Motor and Nonmotor Symptoms in the Lancaster Amish

Author

Xuemei Huang, Toni I. Pollin, Alan R. Shuldiner, Lan Kong, Katherine A. Ryan, Honglei Chen, Richard B. Mailman, John W. Stiller, Mary Pavlovich, Teodor T. Postolache, Michael Goldenberg, and Braxton D. Mitchell

Subjects
Adult, Male, medicine.medical_specialty, Pediatrics, Sleepiness, Parkinson's disease, Adolescent, Epidemiology, Population, Pilot Projects, Disease, 030501 epidemiology, Article, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Surveys and Questionnaires, Prevalence, medicine, Humans, education, Aged, Aged, 80 and over, education.field_of_study, High prevalence, business.industry, Parkinsonism, Parkinson Disease, Middle Aged, Pennsylvania, medicine.disease, Screening questionnaire, Defecation, Female, Neurology (clinical), Amish, 0305 other medical science, business, Constipation, 030217 neurology & neurosurgery
Abstract

Introduction: Previous research has suggested that the Amish may experience a relatively high prevalence of Parkinson’s disease (PD) and/or parkinsonian motor signs. Methods: In a large sample from the Amish community in Lancaster County, Pennsylvania, age ≥18 years, we assessed the prevalence of self-reported PD diagnosis. For those without self-reported PD diagnosis, we assessed the frequency of PD-related motor symptoms using a 9-item questionnaire that was designed by the PD Epidemiology Research Group. Lastly, we queried study participants for the presence of 2 nonmotor symptoms that have been commonly linked to PD: bowel movement frequency and daytime sleepiness. Results: Among 2,025 subjects who answered the PD questionnaire, 430 were older than 60 years. Of 430 participants ≥60 years, 5 (1.2%) reported a PD diagnosis. Of those without a PD diagnosis, 10.5% reported ≥1 and 1.2% ≥ 4 motor symptoms for the 9-item PD screening questionnaire. Of the 3,789 subjects who answered the question about bowel movement frequency, 0.7% reported ≤3 bowel movements per week. Among 1,710 subjects who answered the question about daytime sleepiness, 8.1% of the participants reported “always” sleepy during the day. Discussion: These data neither support a markedly higher PD prevalence in the older Lancaster Amish nor do they show dramatically higher motor and/or selected nonmotor symptoms than the general population. Future studies that employ more rigorous procedures for case identification and PD-specific preclinical symptoms/tests are needed to determine the potential differences and similarities among different Amish populations and between Amish and non-Amish populations.

Published
2020

11. Genetic and functional evidence links a missense variant in

Author

May E, Montasser, Cristopher V, Van Hout, Lawrence, Miloscio, Alicia D, Howard, Avraham, Rosenberg, Myrasol, Callaway, Biao, Shen, Ning, Li, Adam E, Locke, Niek, Verweij, Tanima, De, Manuel A, Ferreira, Luca A, Lotta, Aris, Baras, Thomas J, Daly, Suzanne A, Hartford, Wei, Lin, Yuan, Mao, Bin, Ye, Derek, White, Guochun, Gong, James A, Perry, Kathleen A, Ryan, Qing, Fang, Gannie, Tzoneva, Evangelos, Pefanis, Charleen, Hunt, Yajun, Tang, Lynn, Lee, Carole, Sztalryd-Woodle, Braxton D, Mitchell, Matthew, Healy, Elizabeth A, Streeten, Simeon I, Taylor, Jeffrey R, O'Connell, Aris N, Economides, Giusy, Della Gatta, and Alan R, Shuldiner

Subjects
Male, Glycosylation, Whole Genome Sequencing, Mutation, Missense, Fibrinogen, Galactose, Cholesterol, LDL, Coronary Artery Disease, Galactosyltransferases, N-Acetylneuraminic Acid, Mice, Liver, Polysaccharides, Gene Knockdown Techniques, Animals, Humans, Female, Gene Knock-In Techniques, Glycoproteins
Abstract

Increased blood levels of low-density lipoprotein cholesterol (LDL-C) and fibrinogen are independent risk factors for cardiovascular disease. We identified associations between an Amish-enriched missense variant (p.Asn352Ser) in a functional domain of beta-1,4-galactosyltransferase 1 (

Published
2021

12. Mutation spectrum of NOD2 reveals recessive inheritance as a main driver of Early Onset Crohn’s Disease

Author

Nehal Gosalia, Cristopher V. Van Hout, John D. Overton, Omri Gottesman, Ryan Murchie, Aris Baras, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Gabriel Welch, Aleixo M. Muise, Jeffrey G. Reid, Julie E. Horowitz, Karoline Fiedler, Neil Warner, Anne M. Griffiths, Alejandra King, Eileen Crowley, and Jeffrey Staples

Subjects
0301 basic medicine, Adult, Male, Adolescent, Science, Nod2 Signaling Adaptor Protein, Disease, Inflammatory bowel disease, Article, 03 medical and health sciences, symbols.namesake, 0302 clinical medicine, Crohn Disease, NOD2, Immunogenetics, Medicine, Humans, Sequencing, Allele, Age of Onset, Child, Crohn's disease, Multidisciplinary, business.industry, Infant, Newborn, Infant, medicine.disease, Ulcerative colitis, digestive system diseases, 3. Good health, 030104 developmental biology, Child, Preschool, Immunology, Cohort, Mutation, Mendelian inheritance, symbols, 030211 gastroenterology & hepatology, Colitis, Ulcerative, Female, business, Medical genomics
Abstract

Inflammatory bowel disease (IBD), clinically defined as Crohn’s disease (CD), ulcerative colitis (UC), or IBD-unclassified, results in chronic inflammation of the gastrointestinal tract in genetically susceptible hosts. Pediatric onset IBD represents ≥ 25% of all IBD diagnoses and often presents with intestinal stricturing, perianal disease, and failed response to conventional treatments. NOD2 was the first and is the most replicated locus associated with adult IBD, to date. However, its role in pediatric onset IBD is not well understood. We performed whole-exome sequencing on a cohort of 1,183 patients with pediatric onset IBD (ages 0–18.5 years). We identified 92 probands with biallelic rare and low frequency NOD2 variants accounting for approximately 8% of our cohort, suggesting a Mendelian inheritance pattern of disease. Additionally, we investigated the contribution of recessive inheritance of NOD2 alleles in adult IBD patients from a large clinical population cohort. We found that recessive inheritance of NOD2 variants explains ~ 7% of cases in this adult IBD cohort, including ~ 10% of CD cases, confirming the observations from our pediatric IBD cohort. Exploration of EHR data showed that several of these adult IBD patients obtained their initial IBD diagnosis before 18 years of age, consistent with early onset disease. While it has been previously reported that carriers of more than one NOD2 risk alleles have increased susceptibility to Crohn’s Disease (CD), our data formally demonstrate that recessive inheritance of NOD2 alleles is a mechanistic driver of early onset IBD, specifically CD, likely due to loss of NOD2 protein function. Collectively, our findings show that recessive inheritance of rare and low frequency deleterious NOD2 variants account for 7–10% of CD cases and implicate NOD2 as a Mendelian disease gene for early onset Crohn’s Disease.

Published
2021

13. Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability

Author

Tove Fall, Anubha Mahajan, Dmitry Shungin, B. Balkau, Gerjan Navis, A. Metspalu, Anneli Pouta, Andrew A. Hicks, Ilja M. Nolte, Ian Ford, Aroon D. Hingorani, Stefan R Bornstein, Anuj Goel, Rona J. Strawbridge, Niek Verweij, Sarah H. Wild, Patricia B. Munroe, T.B. Harris, Jaana Lindström, Johnson Pcd., Nita G. Forouhi, Pierre Meneton, Patricia A. Peyser, Sarin A-P., Andrea Ganna, Timothy M. Frayling, Patrik K. E. Magnusson, Joanne M. Meyer, Yongmei Liu, Jeanette M. Stafford, Christian Herder, L Zudina, Maria G. Stathopoulou, May E. Montasser, Nicholas D. Hastie, Inês Barroso, Schwarz Peh., James B. Meigs, Perttu Salo, George Davey Smith, Gonneke Willemsen, Christopher J. Groves, Erik P A Van Iperen, M. A. Province, Veikko Salomaa, Naveed Sattar, Serena Sanna, Maria Dimitriou, Joop Jukema, Ulrika Krus, Albert V. Smith, Markku Laakso, James F. Wilson, George Nicholson, Loic Yengo, Tatijana Zemunik, Per Eriksson, Harold Snieder, Peter P. Pramstaller, Claudia Langenberg, R. Rauramaa, Alan R. Shuldiner, Pau Navarro, Veronique Vitart, Ross M. Fraser, Aaron Isaacs, C. Lecoeur, Jesper R. Gådin, Jackie F. Price, Letizia Marullo, L.F. Bielak, Sirkka Keinänen-Kiukaanniemi, Amélie Bonnefond, Michael Stumvoll, Alessia Faggian, Anke Tönjes, Tomohiro Tanaka, Wieland Kiess, Harry Campbell, Josée Dupuis, David Altshuler, João Fadista, Winfried März, G K Hovingh, Thomas Illig, Toby Johnson, H Grallert, Kari Stefansson, Reedik Mägi, Palmer Cna., de Geus Ejcn., Martina Müller-Nurasyid, Karen Kapur, Philippe Froguel, Dorret I. Boomsma, Anders Franco-Cereceda, Marcus E. Kleber, Boehnke M, Olga D. Carlson, Ozren Polasek, Andrew P. Morris, Alex S. F. Doney, Najaf Amin, Sara M. Willems, Vilmundur Gudnason, Jose C. Florez, Jeffery R. O'Connell, Nancy L. Pedersen, T. Saaristo, Wolffenbuttel Bhr., M. I. J. Uusitupa, Longda Jiang, Iva Miljkovic, James S. Pankow, Caroline Hayward, Hugh Watkins, Vasiliki Lagou, Johanna Kuusisto, Jaakko Tuomilehto, Alan F. Wright, Josephine M. Egan, Perry Jrb., C M van Duijn, Valeriya Lyssenko, Leif Groop, Stefania Bandinelli, Nigel W. Rayner, Tõnu Esko, Stela McLachlan, Momoko Horikoshi, Eric Boerwinkle, Rick Jansen, Richard N. Bergman, Gudmar Thorleifsson, Lyle J. Palmer, Vilmantas Giedraitis, Peter Kovacs, Nicholas J. Wareham, Luigi Ferrucci, N J Timpson, D Rybin, Anne U. Jackson, Tiinamaija Tuomi, Gonçalo R. Abecasis, Harst Pvd., Meena Kumari, Albert Hofman, Chiara Scapoli, Evelin Mihailov, Josine L. Min, Anders Hamsten, Hottenga J-J., Loos Rjf., Lars Lind, Ulf de Faire, Jaakko Kaprio, Guo Li, Beate St Pourcain, C Gieger, Amanda J. Bennett, Anna Ulrich, Nabila Bouatia-Naji, Satu Männistö, Antigone S. Dimas, Jarvelin M-R., Günther Silbernagel, F Karpe, A. Körner, David S. Siscovick, M Blüher, Rebecca J. Webster, Erik Ingelsson, Susan Campbell, Mika Kivimäki, Laura J. Rasmussen-Torvik, Heikki A. Koistinen, Sophie Visvikis-Siest, Bernhard O. Boehm, Inga Prokopenko, Ping An, Emmanouil T. Dermitzakis, Cecilia M. Lindgren, Kardia Slr., Richa Saxena, Igor Rudan, Richard M. Watanabe, Jian'an Luan, Marika Kaakinen, Shin S-Y., George Dedoussis, Panagiotis Deloukas, Mark I. McCarthy, Barbara Thorand, B.W.J.H. Penninx, Peter Vollenweider, Paul W. Franks, Leena Kinnunen, Markus Perola, Yvonne Boettcher, Timo A. Lakka, Nicole Soranzo, Stavroula Kanoni, Bakker Sjl., Winkelmann Br, The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford [Oxford], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Institute of Genomics [Tartu, Estonia], University of Tartu, Vrije Universiteit Amsterdam [Amsterdam] (VU), Vrije Universiteit Medical Centre (VUMC), Helmholtz-Zentrum München (HZM), University of Cambridge [UK] (CAM), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Università degli Studi di Ferrara (UniFE), Boston University [Boston] (BU), VU University Medical Center [Amsterdam], University of Bristol [Bristol], Biomedical Sciences Research Centre Alexander Fleming [Vari, Greece] (BSRC), Imperial College London, Karolinska Institutet [Stockholm], Institute for Molecular Bioscience, University of Queensland [Brisbane], Statens Serum Institut [Copenhagen], Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire (IGE-PCV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Cardiovascular Research Institute Maastricht (CARIM), Maastricht University [Maastricht], MRC Institute of Genetics and Molecular Medicine [Edinburgh] (IGMM), University of Edinburgh-Medical Research Council, National Institute on Aging [Baltimore, MD, USA] (NIH), University of Michigan [Ann Arbor], University of Michigan System, University of Maryland School of Medicine, University of Maryland System, The University of Western Australia (UWA), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Massachusetts General Hospital [Boston], Harvard Medical School [Boston] (HMS), Wake Forest University, National Institute for Health and Welfare [Helsinki], The Wellcome Trust Sanger Institute [Cambridge], University of Iceland [Reykjavik], University of Washington [Seattle], University of Groningen [Groningen], University of Glasgow, William Harvey Research Institute, Barts and the London Medical School, Université de Lausanne (UNIL), deCODE genetics [Reykjavik], Northwestern University Feinberg School of Medicine, Uppsala Universitet [Uppsala], University of Edinburgh, Medical Faculty [Mannheim], University of Graz, Ludwig-Maximilians-Universität München (LMU), Johannes Gutenberg - Universität Mainz (JGU), Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Umeå University, Skane University Hospital [Malmo], Lund University [Lund], RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche [Roma] (CNR), University Medical Center Groningen [Groningen] (UMCG), Universität Leipzig [Leipzig], Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Split, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA), University of Eastern Finland, Harokopio University of Athens, European Academy Bozen/Bolzano (EURAC), University of Kuopio, German Center for Diabetes Research - Deutsches Zentrum für Diabetesforschung [Neuherberg] (DZD), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Ninewells Hospital and Medical School [Dundee], University College of London [London] (UCL), University of Essex, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], University of Helsinki, Leiden University Medical Center (LUMC), Institute of Cardiovascular and Medical Sciences [Glasgow], University of Oulu, The University of Texas Health Science Center at Houston (UTHealth), University of Minnesota Medical School, University of Minnesota System, Keck School of Medicine [Los Angeles], University of Southern California (USC), Amsterdam UMC, University Hospital Carl Gustav Carus [Dresden, Germany], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), Universität Heidelberg [Heidelberg], King Abdulaziz University, Pirkanmaa Hospital District, Tampere University Hospital, Cedars-Sinai Medical Center, Danube University Krems, Harvard School of Public Health, Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Institute of Epidemiology [Neuherberg] (EPI), German Research Center for Environmental Health - Helmholtz Center München (GmbH), Hannover Medical School [Hannover] (MHH), Universität zu Lübeck [Lübeck], University of Exeter, Regeneron Pharmaceuticals [Tarrytown], University of Adelaide, Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Harvard T.H. Chan School of Public Health, John Radcliffe Hospital [Oxford University Hospital], Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Université de Genève (UNIGE), Big Data Institute, University of Surrey (UNIS), University of Bergen (UiB), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Stanford Cardiovascular Institute, University of Liverpool, University of Manchester [Manchester], Institute of Biochemistry and Genetics of Ufa Scientific Centre, Russian Academy of Sciences [Moscow] (RAS), Experimental Vascular Medicine, Vascular Medicine, ACS - Atherosclerosis & ischemic syndromes, SIEST, Sofia, PreciDIAB Institute, the holistic approach of personal diabets care - - PreciDIAB2018 - ANR-18-IBHU-0001 - IBHU - VALID, Understanding the dynamic determinants of glucose homeostasis and social capability to promote Healthy and active aging - DYNAHEALTH - - H20202015-04-01 - 2019-03-31 - 633595 - VALID, Beyond the Genetics of Addiction - ADDICTION - - EC:FP7:ERC2011-12-01 - 2017-05-31 - 284167 - VALID, Rise of scientific excellence and collaboration for implementing personalised medicine in Estonia - ePerMed - - H20202016-01-01 - 2018-12-31 - 692145 - VALID, University of Oxford, Helmholtz Zentrum München = German Research Center for Environmental Health, Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Università degli Studi di Ferrara = University of Ferrara (UniFE), Université de Lausanne = University of Lausanne (UNIL), Karl-Franzens-Universität Graz, Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Amsterdam UMC - Amsterdam University Medical Center, Nanyang Technological University [Singapour], Universität zu Lübeck = University of Lübeck [Lübeck], Laboratoire d'Informatique Médicale et Ingénierie des Connaissances en e-Santé (LIMICS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Sorbonne Paris Nord, Université de Genève = University of Geneva (UNIGE), ANR-18-IBHU-0001,PreciDIAB,PreciDIAB Institute, the holistic approach of personal diabets care(2018), European Project: 633595,H2020,H2020-PHC-2014-two-stage,DYNAHEALTH(2015), European Project: 284167,EC:FP7:ERC,ERC-2011-StG_20101124,ADDICTION(2011), European Project: 692145,H2020,H2020-TWINN-2015,ePerMed(2016), Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, Functional Genomics, APH - Mental Health, Sociology and Social Gerontology, APH - Methodology, Hottenga, Jouke- Jan [0000-0002-5668-2368], Bouatia-Naji, Nabila [0000-0001-5424-2134], Jansen, Rick [0000-0002-3333-6737], Min, Josine L. [0000-0003-4456-9824], Faggian, Alessia [0000-0002-3799-9722], Bonnefond, Amélie [0000-0001-9976-3005], Isaacs, Aaron [0000-0001-5037-4834], Willems, Sara M. [0000-0002-6803-3007], Navarro, Pau [0000-0001-5576-8584], Jackson, Anne U. [0000-0002-9672-2547], Bielak, Lawrence F. [0000-0002-3443-8030], Saxena, Richa [0000-0003-2233-1065], Smith, Albert V. [0000-0003-1942-5845], Verweij, Niek [0000-0002-4303-7685], Goel, Anuj [0000-0003-2307-4021], Johnson, Paul C. D. [0000-0001-6663-7520], Strawbridge, Rona J. [0000-0001-8506-3585], Fall, Tove [0000-0003-2071-5866], Fraser, Ross M. [0000-0003-0488-2592], Kanoni, Stavroula [0000-0002-1691-9615], Giedraitis, Vilmantas [0000-0003-3423-2021], Kleber, Marcus E. [0000-0003-0663-7275], Müller-Nurasyid, Martina [0000-0003-3793-5910], Luan, Jian’an [0000-0003-3137-6337], Sanna, Serena [0000-0002-3768-1749], Nolte, Ilja M. [0000-0001-5047-4077], Zemunik, Tatijana [0000-0001-8120-2891], Kovacs, Peter [0000-0002-0290-5423], Wild, Sarah H. [0000-0001-7824-2569], McLachlan, Stela [0000-0003-0480-6143], Egan, Josephine [0000-0002-8945-0053], Hicks, Andrew A. [0000-0001-6320-0411], Thorand, Barbara [0000-0002-8416-6440], Hingorani, Aroon [0000-0001-8365-0081], Kivimaki, Mika [0000-0002-4699-5627], Koistinen, Heikki A. [0000-0001-7870-070X], Bakker, Stephan J. L. [0000-0003-3356-6791], Palmer, Colin N. A. [0000-0002-6415-6560], Jukema, J. Wouter [0000-0002-3246-8359], Sattar, Naveed [0000-0002-1604-2593], Snieder, Harold [0000-0003-1949-2298], Magnusson, Patrik K. [0000-0002-7315-7899], Blüher, Matthias [0000-0003-0208-2065], Wolffenbuttel, Bruce H. R. [0000-0001-9262-6921], Abecasis, Goncalo R. [0000-0003-1509-1825], Meigs, James B. [0000-0002-2439-2657], Wilson, James F. [0000-0001-5751-9178], Schwarz, Peter E. H. [0000-0001-6317-7880], Boehm, Bernhard O. [0000-0002-2706-7710], Metspalu, Andres [0000-0002-3718-796X], Deloukas, Panos [0000-0001-9251-070X], Körner, Antje [0000-0001-6001-0356], Wareham, Nicholas J. [0000-0003-1422-2993], Langenberg, Claudia [0000-0002-5017-7344], Männistö, Satu [0000-0002-8668-3046], Franks, Paul W. [0000-0002-0520-7604], Hayward, Caroline [0000-0002-9405-9550], Vitart, Veronique [0000-0002-4991-3797], Kaprio, Jaakko [0000-0002-3716-2455], Visvikis-Siest, Sophie [0000-0001-8104-8425], Altshuler, David [0000-0002-7250-4107], Rudan, Igor [0000-0001-6993-6884], van Duijn, Cornelia M. [0000-0002-2374-9204], Pramstaller, Peter P. [0000-0002-9831-8302], Boehnke, Michael [0000-0002-6442-7754], Frayling, Timothy M. [0000-0001-8362-2603], Peyser, Patricia A. [0000-0002-9717-8459], Harst, Pim van der [0000-0002-2713-686X], Smith, George Davey [0000-0002-1407-8314], Forouhi, Nita G. [0000-0002-5041-248X], Loos, Ruth J. F. [0000-0002-8532-5087], Salomaa, Veikko [0000-0001-7563-5324], Soranzo, Nicole [0000-0003-1095-3852], Boomsma, Dorret I. [0000-0002-7099-7972], Groop, Leif [0000-0002-0187-3263], Tuomi, Tiinamaija [0000-0002-8306-6202], Munroe, Patricia B. [0000-0002-4176-2947], Gudnason, Vilmundur [0000-0001-5696-0084], Lecoeur, Cecile [0000-0003-0075-6417], Jarvelin, Marjo-Riitta [0000-0002-2149-0630], Stefansson, Kari [0000-0003-1676-864X], Dermitzakis, Emmanouil T. [0000-0002-9302-6490], Lindgren, Cecilia M. [0000-0002-4903-9374], Froguel, Philippe [0000-0003-2972-0784], Kaakinen, Marika A. [0000-0002-9228-0462], Watanabe, Richard M. [0000-0003-1015-0531], Ingelsson, Erik [0000-0003-2256-6972], Dupuis, Josée [0000-0003-2871-3603], Barroso, Inês [0000-0001-5800-4520], Apollo - University of Cambridge Repository, Epidemiology, University Hospital Mannheim | Universitätsmedizin Mannheim, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Universität Leipzig, Universiteit Leiden, Universität Heidelberg [Heidelberg] = Heidelberg University, Karl-Franzens-Universität [Graz, Autriche], Psychiatry, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, General practice, APH - Digital Health, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Life Course Epidemiology (LCE), Lifestyle Medicine (LM), Groningen Institute for Organ Transplantation (GIOT), Groningen Kidney Center (GKC), Center for Liver, Digestive and Metabolic Diseases (CLDM), Value, Affordability and Sustainability (VALUE), Cardiovascular Centre (CVC), Hottenga, Jouke-Jan [0000-0002-5668-2368], Min, Josine L [0000-0003-4456-9824], Willems, Sara M [0000-0002-6803-3007], Jackson, Anne U [0000-0002-9672-2547], Bielak, Lawrence F [0000-0002-3443-8030], Smith, Albert V [0000-0003-1942-5845], Johnson, Paul CD [0000-0001-6663-7520], Strawbridge, Rona J [0000-0001-8506-3585], Fraser, Ross M [0000-0003-0488-2592], Kleber, Marcus E [0000-0003-0663-7275], Luan, Jian'an [0000-0003-3137-6337], Nolte, Ilja M [0000-0001-5047-4077], Wild, Sarah H [0000-0001-7824-2569], Hicks, Andrew A [0000-0001-6320-0411], Koistinen, Heikki A [0000-0001-7870-070X], Bakker, Stephan JL [0000-0003-3356-6791], Palmer, Colin NA [0000-0002-6415-6560], Jukema, J Wouter [0000-0002-3246-8359], Magnusson, Patrik K [0000-0002-7315-7899], Wolffenbuttel, Bruce HR [0000-0001-9262-6921], Abecasis, Goncalo R [0000-0003-1509-1825], Meigs, James B [0000-0002-2439-2657], Wilson, James F [0000-0001-5751-9178], Schwarz, Peter EH [0000-0001-6317-7880], Boehm, Bernhard O [0000-0002-2706-7710], Wareham, Nicholas J [0000-0003-1422-2993], Franks, Paul W [0000-0002-0520-7604], van Duijn, Cornelia M [0000-0002-2374-9204], Pramstaller, Peter P [0000-0002-9831-8302], Frayling, Timothy M [0000-0001-8362-2603], Peyser, Patricia A [0000-0002-9717-8459], Forouhi, Nita G [0000-0002-5041-248X], Loos, Ruth JF [0000-0002-8532-5087], Boomsma, Dorret I [0000-0002-7099-7972], Munroe, Patricia B [0000-0002-4176-2947], Dermitzakis, Emmanouil T [0000-0002-9302-6490], Lindgren, Cecilia M [0000-0002-4903-9374], Kaakinen, Marika A [0000-0002-9228-0462], Watanabe, Richard M [0000-0003-1015-0531], Tampere University, Tays Research Services, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC), Fysiologie, RS: FHML MaCSBio, and RS: Carim - B01 Blood proteins & engineering

Subjects
Male, Anorexia Nervosa, medicine.medical_treatment, 45/43, Insulin Resistance/genetics, SUSCEPTIBILITY, Quantitative trait, Impaired glucose tolerance, 0302 clinical medicine, Architecture, LS2_1, IMPUTATION, Insulin, ComputingMilieux_MISCELLANEOUS, Fasting, Publisher Correction, 3. Good health, [SDV] Life Sciences [q-bio], Kruppel-Like Transcription Factors/blood, Endokrinologi och diabetes, Science & Technology - Other Topics, Adult, Blood Glucose, European Continental Ancestry Group, Female, Gene Expression, Genetic Loci, Genome-Wide Association Study, Glucose Intolerance, Humans, Insulin Receptor Substrate Proteins, Insulin Resistance, Kruppel-Like Transcription Factors, Middle Aged, Phenotype, Sex Characteristics, Sex Factors, Waist-Hip Ratio, Sex characteristics, medicine.medical_specialty, Science, 631/208/205/2138, Endocrinology and Diabetes, General Biochemistry, Genetics and Molecular Biology, White People, Gender-differences, 03 medical and health sciences, SDG 3 - Good Health and Well-being, 692/53/2421, GLYCEMIC TRAITS, GENOME-WIDE ASSOCIATION, Glycemic, GENDER-DIFFERENCES, Science & Technology, IDENTIFICATION, 692/699/2743/2815, Blood Glucose/metabolism, Diagnostic markers, medicine.disease, Anorexia Nervosa/blood, 030104 developmental biology, Endocrinology, Glucose, Insulin/blood, Anorexia Nervosa/ethnology, Anorexia Nervosa/genetics, Anorexia Nervosa/physiopathology, Fasting/blood, Glucose Intolerance/blood, Glucose Intolerance/ethnology, Glucose Intolerance/genetics, Glucose Intolerance/physiopathology, Insulin Receptor Substrate Proteins/blood, Insulin Receptor Substrate Proteins/genetics, Kruppel-Like Transcription Factors/genetics, 0301 basic medicine, Identification, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Genome-wide association studies, Waist–hip ratio, LS4_5, RISK, ARCHITECTURE, Multidisciplinary, article, Type 2 diabetes, Multidisciplinary Sciences, MENDELIAN RANDOMIZATION, Pre-diabetes, Medical Genetics, Risk, PATHOPHYSIOLOGY, 030209 endocrinology & metabolism, 3121 Internal medicine, 692/163/2743/137/773, NO, Insulin resistance, Internal medicine, Diabetes mellitus, medicine, Mendelian randomization, 631/208/480, Medicinsk genetik, business.industry, General Chemistry, Impaired fasting glucose, business
Abstract

Differences between sexes contribute to variation in the levels of fasting glucose and insulin. Epidemiological studies established a higher prevalence of impaired fasting glucose in men and impaired glucose tolerance in women, however, the genetic component underlying this phenomenon is not established. We assess sex-dimorphic (73,089/50,404 women and 67,506/47,806 men) and sex-combined (151,188/105,056 individuals) fasting glucose/fasting insulin genetic effects via genome-wide association study meta-analyses in individuals of European descent without diabetes. Here we report sex dimorphism in allelic effects on fasting insulin at IRS1 and ZNF12 loci, the latter showing higher RNA expression in whole blood in women compared to men. We also observe sex-homogeneous effects on fasting glucose at seven novel loci. Fasting insulin in women shows stronger genetic correlations than in men with waist-to-hip ratio and anorexia nervosa. Furthermore, waist-to-hip ratio is causally related to insulin resistance in women, but not in men. These results position dissection of metabolic and glycemic health sex dimorphism as a steppingstone for understanding differences in genetic effects between women and men in related phenotypes., Sex differences in fasting glucose and insulin have been identified, but the genetic loci underlying these differences have not. Here, the authors perform a meta-analysis of genome-wide association studies to detect sex-specific and sex-dimorphic loci associated with fasting glucose and insulin.

Published
2021

14. A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids

Author

Rui Xia, Jordana T. Bell, Roby Joehanes, Abbas Dehghan, Sharon L.R. Kardia, Erin B. Ware, Deugi Zhi, Devin Absher, Annette Peters, Martina Müller-Nurasyid, Daniel Levy, Nona Sotoodehnia, Wei Chen, Coleen M. Damcott, Lifang Hou, Donna K. Arnett, Weihua Guan, Jincheng Shen, Steve Horvath, Rory P. Wilson, Kim Valeska Emilie Braun, Lars Lind, Wei Zhao, Myriam Fornage, Shengxu Li, Mina A. Jhun, Paula Singmann, Elena Carnero-Montoro, Michael M. Mendelson, Jennifer A. Smith, Xiaoping Zhao, Marguerite R. Irvin, Bruce M. Psaty, Andrea A. Baccarelli, Jeffrey R. O'Connell, Mohammad Arfan Ikram, Traci M. Bartz, Erik Ingelsson, Klodian Dhana, Melanie Waldenberger, Stefan Gustafsson, Yii-Der Ida Chen, Thomas Meitinger, Themistocles L. Assimes, Elias Salfati, Tao Zhang, Pfeiffer Liliane, Dianjianyi Sun, Rahul Gondalia, Eric Boerwinkle, Philip S. Tsao, Christian Gieger, Eric A. Whitsel, Chen Yao, Tim D. Spector, Alan R. Shuldiner, Åsa K. Hedman, Joyce B. J. van Meurs, May E. Montasser, Anh N. Do, Mohsen Ghanbari, André G. Uitterlinden, Megan L. Grove, Jennifer A. Brody, Epidemiology, and Internal Medicine

Subjects
Adult, Epigenomics, Male, 0301 basic medicine, Science, Concordance, Quantitative Trait Loci, Ethnic group, General Physics and Astronomy, Blood lipids, 030204 cardiovascular system & hematology, Biology, Article, White People, General Biochemistry, Genetics and Molecular Biology, Epigenesis, Genetic, Epigenome, 03 medical and health sciences, 0302 clinical medicine, Genetics, Leukocytes, Humans, Dyslipidaemias, Aged, Medicinsk genetik, Genetic association, Multidisciplinary, Carnitine O-Palmitoyltransferase, Hispanic or Latino, General Chemistry, DNA Methylation, Middle Aged, Lipids, Black or African American, 030104 developmental biology, Meta-analysis, DNA methylation, Epigenetics, CpG Islands, Female, Lipoproteins, HDL, Medical Genetics
Abstract

Here we examine the association between DNA methylation in circulating leukocytes and blood lipids in a multi-ethnic sample of 16,265 subjects. We identify 148, 35, and 4 novel associations among Europeans, African Americans, and Hispanics, respectively, and an additional 186 novel associations through a trans-ethnic meta-analysis. We observe a high concordance in the direction of effects across racial/ethnic groups, a high correlation of effect sizes between high-density lipoprotein and triglycerides, a modest overlap of associations with epigenome-wide association studies of other cardio-metabolic traits, and a largely non-overlap with lipid loci identified to date through genome-wide association studies. Thirty CpGs reached significance in at least 2 racial/ethnic groups including 7 that showed association with the expression of an annotated gene. CpGs annotated to CPT1A showed evidence of being influenced by triglycerides levels. DNA methylation levels of circulating leukocytes show robust and consistent association with blood lipid levels across multiple racial/ethnic groups., Abnormal blood lipid levels are important risk factors for cardiovascular and other various diseases. Here the authors conduct a large-scale multi-ethnic epigenome-wide association study combined with epigenetic (cis-QTL and eQTM) data, and identify CpG-lipid traits associations that are specific to or common across racial/ethnic groups.

Published
2021

15. Self-Reported Sleep Duration and Pattern in Old Order Amish and Non-Amish Adults

Author

Soren Snitker, Braxton D. Mitchell, Melanie Daue, Teodor T. Postolache, Kathleen A. Ryan, Toni I. Pollin, Huichun Xu, Alan R. Shuldiner, Man Zhang, and Emerson M. Wickwire

Subjects
Adult, Male, Pulmonary and Respiratory Medicine, Time Factors, Adolescent, Young Adult, 03 medical and health sciences, Sex Factors, 0302 clinical medicine, Surveys and Questionnaires, Humans, Medicine, Aged, business.industry, digestive, oral, and skin physiology, Age Factors, Middle Aged, Pennsylvania, Scientific Investigations, Sleep in non-human animals, humanities, Cross-Sectional Studies, Neurology, Old Order Amish, Female, Self Report, Neurology (clinical), Amish, Sleep, business, 030217 neurology & neurosurgery, Clinical psychology, Sleep duration
Abstract

STUDY OBJECTIVES: We hypothesized that sleep duration in the Amish would be longer than in non-Amish. METHODS: Sleep duration was obtained by questionnaire administered to Amish individuals (n = 3,418) and from the 2015–2016 National Health and Nutrition Examination Survey (NHANES; n = 1,912). Self-reported sleep duration was calculated as the difference in usual times that the participants went to bed at night and woke up in the morning. RESULTS: In Amish (43.7 ± 16.7 years) and NHANES (50.0 ± 20.6 years), women had a longer sleep duration than men (P < .0001 in both groups) and sleep was significantly longer in those aged 18–29 years and ≥ 70 years, compared to those aged 30–69 years. Seasonal-adjusted sleep duration was shorter in Amish than that in NHANES (7.8 minutes shorter, age- and sex-adjusted P < .0001). However, Amish were less likely to report sleeping fewer than 7 hours per night (15.4% in Amish versus 20.5% in NHANES, P < .0001). Amish went to bed 80.4 minutes earlier than NHANES and arose 87.6 minutes earlier (age-, sex-, and season-adjusted P < .0001 for both). In the Amish, sleep duration was longer in clerks than in farmers (P < .0001) and was significantly correlated among household members (.15 < r < .62, P < .001), although there was no evidence that this trait was heritable (h(2) approximately 0) after adjustment for household. CONCLUSIONS: The lower frequency of short sleepers in the Amish may contribute to the relatively lower risks of cardiometabolic diseases observed in this population. CITATION: Zhang M, Ryan KA, Wickwire E, Postolache TT, Xu H, Daue M, Snitker S, Pollin TI, Shuldiner AR, Mitchell BD. Self-reported sleep duration and pattern in old order amish and non-amish adults. J Clin Sleep Med. 2019;15(9):1321–1328.

Published
2019

16. Paediatric systemic lupus erythematosus as a manifestation of constitutional mismatch repair deficiency

Author

Melyssa Aronson, Helen Toledano, Lili Bazak, Efrat Sofrin, Gil Amarilyo, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Noa Ruhrman-Shahar, Katharina Wimmer, Lina Basel-Salmon, Naama Orenstein, Hibs Al-tarrah, Pola Smirin-Yosef, Yael Goldberg, and Uri Tabori

Subjects
0301 basic medicine, medicine.medical_specialty, Neurofibromatosis 1, Childhood cancer, MLH1, DNA Mismatch Repair, Pediatrics, 03 medical and health sciences, 0302 clinical medicine, Neoplastic Syndromes, Hereditary, Genetics, PMS2, Humans, Lupus Erythematosus, Systemic, Medicine, Neurofibromatosis, Child, Genetics (clinical), Brain Neoplasms, business.industry, medicine.disease, Dermatology, DNA-Binding Proteins, MSH6, Phenotype, 030104 developmental biology, MSH2, Child, Preschool, 030220 oncology & carcinogenesis, Mutation, MISMATCH REPAIR DEFICIENCY, Female, DNA mismatch repair, Colorectal Neoplasms, business
Abstract

Biallelic mutations in any of the four mismatch repair genes MSH2, MSH6, MLH1 and PMS2 result in one of the most aggressive childhood cancer predisposition syndromes, termed constitutional mismatch repair deficiency (CMMRD) syndrome. In addition to a very high tumour risk, the CMMRD phenotype is often characterised by the presence of signs reminiscent of neurofibromatosis type 1. Although paediatric systemic lupus erythematosus (pSLE) has been reported so far in three patients with CMMRD, it has not been considered a diagnostic feature of the syndrome. We report here two additional female patients with pSLE and CMMRD due to biallelic pathogenic variants in MSH6. Hence, there are a total of five out of approximately 200 (2.5%) currently reported patients with CMMRD that also have pSLE, suggesting pSLE should raise the suspicion of a diagnosis of CMMRD, especially if supported by additional indicative features

Published
2019

17. Clinical and genetic validity of quantitative bipolarity

Author

Kevin A. Strauss, Laura M. Rowland, Chamindi Seneviratne, Xiaoming Du, Feven Fisseha, Hemalatha Sampath, Teodor T. Postolache, Alan R. Shuldiner, Braxton D. Mitchell, Francis J. McMahon, Alfredo Bellon, Shuo Chen, Thangavelu Kavita, Krista Wisner, Heather Bruce, Seth A. Ament, Peter Kochunov, Mark D. Kvarta, Joshua Chiappelli, and L. Elliot Hong

Subjects
Adult, Male, Bipolar Disorder, Genotype, Pedigree chart, Article, lcsh:RC321-571, 03 medical and health sciences, Cellular and Molecular Neuroscience, Young Adult, 0302 clinical medicine, Medicine, Humans, Genetic Predisposition to Disease, Bipolar disorder, Clinical genetics, Allele, lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry, Biological Psychiatry, Alleles, Subclinical infection, Psychiatric Status Rating Scales, Depressive Disorder, Major, business.industry, Medical genetics, Family aggregation, Heritability, Middle Aged, medicine.disease, 030227 psychiatry, Pedigree, Psychiatry and Mental health, Phenotype, Old Order Amish, Trait, Female, business, 030217 neurology & neurosurgery, Clinical psychology
Abstract

Research has yet to provide a comprehensive understanding of the genetic basis of bipolar disorder (BP). In genetic studies, defining the phenotype by diagnosis may miss risk-allele carriers without BP. The authors aimed to test whether quantitatively detected subclinical symptoms of bipolarity identifies a heritable trait that infers risk for BP. The Quantitative Bipolarity Scale (QBS) was administered to 310 Old Order Amish or Mennonite individuals from multigenerational pedigrees; 110 individuals had psychiatric diagnoses (20 BP, 61 major depressive disorders (MDD), 3 psychotic disorders, 26 other psychiatric disorders). Familial aggregation of QBS was calculated using the variance components method to derive heritability and shared household effects. The QBS score was significantly higher in BP subjects (31.5 ± 3.6) compared to MDD (16.7 ± 2.0), other psychiatric diagnoses (7.0 ± 1.9), and no psychiatric diagnosis (6.0 ± 0.65) (all p 2 = 0.46 ± 0.15, p p = 0.073). When subjects with psychiatric illness were removed, the QBS heritability was similar (h2 = 0.59 ± 0.18, p

Published
2019

18. A novel TUFM homozygous variant in a child with mitochondrial cardiomyopathy expands the phenotype of combined oxidative phosphorylation deficiency 4

Author

Alina Kurolap, Hagit Baris Feldman, John D. Overton, Ann Saada, Adi Mory, Tova Hershkovitz, Tamar Paperna, Sarah Wolf, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, and Hanna Mandel

Subjects
Male, 0301 basic medicine, Mitochondrial DNA, Mitochondrial Diseases, Mitochondrial disease, Disease, Oxidative phosphorylation, Peptide Elongation Factor Tu, 030105 genetics & heredity, Bioinformatics, DNA, Mitochondrial, Oxidative Phosphorylation, Mitochondrial Proteins, Consanguinity, 03 medical and health sciences, Exome Sequencing, Genetics, medicine, Humans, Missense mutation, Amino Acid Sequence, Genetics (clinical), business.industry, Homozygote, Infant, Dilated cardiomyopathy, medicine.disease, Phenotype, Mitochondria, 030104 developmental biology, Lactic acidosis, Mutation, Acidosis, Lactic, Female, Cardiomyopathies, business, Metabolism, Inborn Errors
Abstract

Translation of mitochondrial-specific DNA is required for proper mitochondrial function and energy production. For this purpose, an elaborate network of dedicated molecular machinery including initiation, elongation and termination factors exists. We describe a patient with an unusual phenotype and a novel homozygous missense variant in TUFM (c.344A>C; p.His115Pro), encoding mtDNA translation elongating factor Tu (EFTu). To date, only four patients have been reported with bi-allelic mutations in TUFM, leading to combined oxidative phosphorylation deficiency 4 (COXPD4) characterized by severe early-onset lactic acidosis and progressive fatal infantile encephalopathy. The patient presented here expands the phenotypic features of TUFM-related disease, exhibiting lactic acidosis and dilated cardiomyopathy without progressive encephalopathy. This warrants the inclusion of TUFM in differential diagnosis of metabolic cardiomyopathy. Cases that further refine genotype-phenotype associations and characterize the molecular basis of mitochondrial disorders allow clinicians to predict disease prognosis, greatly impacting patient care, as well as provide families with reproductive planning options.

Published
2019

19. Homozygosity for CHEK2 p.Gly167Arg leads to a unique cancer syndrome with multiple complex chromosomal translocations in peripheral blood karyotype

Author

Adi Mory, Tamar Paperna, Gili Reznick-Levi, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Miora Feinstien, Lina Basel-Salmon, Nivin Moustafa, Hagit Baris Feldman, Alina Kurolap, Yael Goldberg, Nitzan Sharon-Shwartzman, Elizabeth E. Half, Yishai Ofran, and Yariv Carasso

Subjects
Adult, Male, 0301 basic medicine, Protein Conformation, DNA repair, Karyotype, Chromosomal translocation, Translocation, Genetic, Cancer syndrome, 03 medical and health sciences, symbols.namesake, 0302 clinical medicine, Neoplasms, Chromosome instability, Genetics, medicine, Humans, Missense mutation, Genetic Predisposition to Disease, CHEK2, Genetics (clinical), Aged, Sanger sequencing, business.industry, Homozygote, Cancer, Middle Aged, medicine.disease, Pedigree, Checkpoint Kinase 2, 030104 developmental biology, 030220 oncology & carcinogenesis, Cancer research, symbols, Female, business
Abstract

BackgroundChromosomal instability, as reflected by structural or copy-number changes, is a known cancer characteristic but are rarely observed in healthy tissue. Mutations in DNA repair genes disrupt the maintenance of DNA integrity and predispose to hereditary cancer syndromes.ObjectiveTo clinically characterise and genetically diagnose two reportedly unrelated patients with unique cancer syndromes, including multiorgan tumourogenesis (patient 1) and early-onset acute myeloid leukaemia (patient 2), both displaying unique peripheral blood karyotypes.MethodsGenetic analysis in patient 1 included TruSight One panel and whole-exome sequencing, while patient 2 was diagnosed by FoundationOne Heme genomic analysis; Sanger sequencing was used for mutation confirmation in both patients. Karyotype analysis was performed on peripheral blood, bone marrow and other available tissues.ResultsBoth patients were found homozygous for CHEK2 c.499G>A; p.Gly167Arg and exhibited multiple different chromosomal translocations in 30%–60% peripheral blood lymphocytes. This karyotype phenotype was not observed in other tested tissues or in an ovarian cancer patient with a different homozygous missense mutation in CHEK2 (c.1283C>T; p.Ser428Phe).ConclusionsThe multiple chromosomal translocations in patient lymphocytes highlight the role of CHK2 in DNA repair. We suggest that homozygosity for p.Gly167Arg increases patients' susceptibility to non-accurate correction of DNA breaks and possibly explains their increased susceptibility to either multiple primary tumours during their lifetime or early-onset tumourigenesis.

Published
2019

20. Two intronic cis-acting variants in both alleles of the POLR3A gene cause progressive spastic ataxia with hypodontia

Author

Alan R. Shuldiner, Malak Darawshe, Avi Fellner, Claudia Gonzaga-Jauregui, Alexander Lossos, Zohar Argov, Gabriel Arie Lidzbarsky, Noam Shomron, Elena Kogan, Lina Basel-Salmon, Lily Bazak, and Yael Goldberg

Subjects
0301 basic medicine, Male, DNA Mutational Analysis, 030105 genetics & heredity, Biology, Compound heterozygosity, 03 medical and health sciences, Intellectual Disability, Genotype, Genetics, medicine, Humans, Spinocerebellar Ataxias, Allele, Frameshift Mutation, Gene, Genetics (clinical), Exome sequencing, Alleles, Anodontia, Progeria, RNA Polymerase III, Middle Aged, medicine.disease, Phenotype, Introns, Hypodontia, Optic Atrophy, 030104 developmental biology, Muscle Spasticity, Female
Abstract

POLR3A encodes the largest subunit of the DNA-dependent RNA polymerase III. Pathogenic variants in this gene are associated with dysregulation of tRNA production and other non-coding RNAs. POLR3A-related disorders include variable phenotypes. The genotype-phenotype correlation is still unclear. Phenotypic analysis and exome sequencing were performed in four affected siblings diagnosed clinically with hereditary spastic ataxia, two healthy siblings and their unaffected mother. All four affected siblings (ages 46-55) had similar clinical features of early childhood-onset hypodontia and adolescent-onset progressive spastic ataxia. None had progeria, gonadal dysfunction or dysmorphism. All affected individuals had biallelic POLR3A pathogenic variants composed by two cis-acting intronic splicing-altering variants, c.1909 + 22G > A and c.3337-11 T > C. The two healthy siblings had wild-type alleles. The mother and another unaffected sibling were heterozygous for the allele containing both variants. This is the first report addressing the clinical consequence associated with homozygosity for a unique pathogenic intronic allele in the POLR3A gene. This allele was previously reported in compound heterozygous combinations in patients with Wiedemann-Rautenstrauch syndrome, a severe progeroid POLR3A-associated phenotype. We show that homozygosity for this allele is associated with spastic ataxia with hypodontia, and not with progeroid features. These findings contribute to the characterization of genotype-phenotype correlation in POLR3A-related disorders.

Published
2021

21. Exome Sequencing of 21 Bardet-Biedl Syndrome (BBS) Genes to Identify Obesity Variants in 6,851 American Indians

Author

Leslie J. Baier, William C. Knowler, Clifton Bogardus, Sayuko Kobes, Samantha E. Day, Alan R. Shuldiner, Hye In Kim, Darin Mahkee, Nehal Gosalia, Yunhua L. Muller, Kim Wiedrich, Cris Van Hout, Robert L. Hanson, Bin Ye, and Çiğdem Köroğlu

Subjects
Male, congenital, hereditary, and neonatal diseases and abnormalities, Endocrinology, Diabetes and Metabolism, Medicine (miscellaneous), 030209 endocrinology & metabolism, BBS9, Biology, In vitro analysis, 03 medical and health sciences, 0302 clinical medicine, Endocrinology, Bardet–Biedl syndrome, Genetic variation, medicine, Humans, Exome, 030212 general & internal medicine, Obesity, Allele, Gene, Bardet-Biedl Syndrome, Exome sequencing, American Indian or Alaska Native, Genetics, Nutrition and Dietetics, Epidemiology/Genetics, Original Articles, medicine.disease, Female, Original Article
Abstract

Objective In an ongoing effort to identify the genetic variation that contributes to obesity in American Indians, known Bardet–Biedl syndrome (BBS) genes were analyzed for an effect on BMI and leptin signaling. Methods Potentially deleterious variants (Combined Annotation Dependent Depletion score > 20) in BBS genes were identified in whole‐exome sequence data from 6,851 American Indians informative for BMI. Common variants (detected in ≥ 10 individuals) were analyzed for association with BMI; rare variants (detected in 40 kg/m2), four were in BBS9. In vitro analysis of BBS9 found the Ile allele at Thr549Ile had a 20% increase in STAT3 activity compared with the Thr allele (P = 0.01). Western blot analysis showed the Ile allele had a 15% increase in STAT3 phosphorylation (P = 0.006). Comparable functional results were observed with Ser545Gly and Val209Leu but not Leu665Phe and Lys810Glu. Conclusions Potentially functional variants in BBS genes in American Indians are reported. However, functional evidence supporting a causal role for BBS9 in obesity is inconclusive.

Published
2020

22. Genetic versus stress and mood determinants of sleep in the Amish

Author

Alan R. Shuldiner, Anya Savransky, Heather Bruce, Francis J. McMahon, Jeffrey R. O'Connell, Braxton D. Mitchell, Teodor T. Postolache, Seth A. Ament, Kathleen Carino, Mark D. Kvarta, Jessica Sewell, Joshua Chiappelli, Peter Kochunov, L. Elliot Hong, and Wyatt Marshall

Subjects
0301 basic medicine, Adult, Male, Sleep Wake Disorders, Evening, 030105 genetics & heredity, Bedtime, Article, Pittsburgh Sleep Quality Index, 03 medical and health sciences, Cellular and Molecular Neuroscience, Surveys and Questionnaires, Medicine, Humans, Genetics (clinical), business.industry, Mood Disorders, Heritability, Mental health, Sleep in non-human animals, United States, Psychiatry and Mental health, 030104 developmental biology, Mood, Case-Control Studies, Female, Sleep onset, business, Amish, Stress, Psychological, Clinical psychology
Abstract

Sleep is essential to the human brain and is regulated by genetics with many features conserved across species. Sleep is also influenced by health and environmental factors; identifying replicable genetic variants contributing to sleep may require accounting for these factors. We examined how stress and mood disorder contribute to sleep and impact its heritability. Our sample included 326 Amish/Mennonite individuals with a lifestyle with limited technological interferences with sleep. Sleep measures included Pittsburgh Sleep Quality Index (PSQI), bedtime, wake time, and time to sleep onset. Current stress level, cumulative life stressors, and mood disorder were also evaluated. We estimated the heritability of sleep features and examined the impact of current stress, lifetime stress, mood diagnosis on sleep quality. The results showed current stress, lifetime stress, and mood disorder were independently associated with PSQI score (p < .05). Heritability of PSQI was low (0-0.23) before and after accounting for stress and mood. Bedtime, wake time, and minutes to sleep time did show significant heritability at 0.44, 0.42, and 0.29. However, after adjusting for shared environment, only heritability of wake time remained significant. Sleep is affected by environmental stress and mental health factors even in a society with limited technological interference with sleep. Wake time may be a more biological marker of sleep as compared to the evening measures which are more influenced by other household members. Accounting for nongenetic and partially genetic determinants of sleep particularly stress and mood disorder is likely important for improving the precision of genetic studies of sleep.

Published
2020

23. Effect of serum zinc and copper levels on insulin secretion, insulin resistance and pancreatic β cell dysfunction in US adults: Findings from the National Health and Nutrition Examination Survey (NHANES) 2011-2012

Author

Rahul Chaudhary, Alan R. Shuldiner, Ravi Kant, Kashif M. Munir, Rashmi Chandra, Vipin Verma, and Siddharth Patel

Subjects
Adult, Male, medicine.medical_specialty, National Health and Nutrition Examination Survey, Endocrinology, Diabetes and Metabolism, Cell, 030209 endocrinology & metabolism, History, 21st Century, Pathogenesis, 03 medical and health sciences, 0302 clinical medicine, Endocrinology, Insulin resistance, Diabetes mellitus, Internal medicine, Insulin Secretion, Internal Medicine, medicine, Humans, 030212 general & internal medicine, Prediabetes, business.industry, Confounding, General Medicine, Middle Aged, medicine.disease, Nutrition Surveys, United States, Zinc, medicine.anatomical_structure, Treatment Outcome, Homeostatic model assessment, Female, Insulin Resistance, business, Copper
Abstract

Aim To compare zinc (Zn) and copper (Cu) levels in US adults with normoglycemia, prediabetes and diabetes, and study the association of serum Zn and Cu levels with pancreatic β cell insulin secretion, pancreatic dysfunction and insulin resistance in US adults with normoglycemia and prediabetes. Method Homeostatic Model Assessment (HOMA2) calculator was used to compute estimates of steady state β cell insulin secretion (HOMA2-B), peripheral insulin sensitivity (HOMA2-S), insulin resistance (HOMA-IR), and disposition index (HOMA-DI) in 804 adult individuals from the National Health and Nutrition Examination Survey (NHANES 2011–2012). Results There was no significant difference between serum Zn and Cu levels among subjects with normoglycemia, prediabetes, and diabetes. After adjusting for multiple possible confounders, higher serum Zn concentrations were associated with lower β cell insulin secretion (HOMA2-B; p = 0.01) and lower insulin resistance (HOMA-IR; p = 0.04) in the prediabetic subjects. In normoglycemic group, higher serum Zn levels were associated with improved pancreatic function (HOMA-DI; P = 0.02). On the other hand, higher serum Cu levels were associated with increased β cell insulin secretion (HOMA2-B, P = 0.03) only in the subjects with prediabetes. Conclusion These findings support the need for further studies to investigate the role of trace elements in diabetes pathogenesis.

Published
2020

24. Heterozygosity for a Pathogenic Variant in

Author

Xuesi, Wan, James, Perry, Haichen, Zhang, Feng, Jin, Kathleen A, Ryan, Cristopher, Van Hout, Jeffrey, Reid, John, Overton, Aris, Baras, Zhe, Han, Elizabeth, Streeten, Yanbing, Li, Braxton D, Mitchell, Alan R, Shuldiner, Mao, Fu, and Lyndon J, Mitnaul

Subjects
Adult, Male, Heterozygote, Genetic Drift, Mutation, Missense, Genetic Variation, Genes, Recessive, Middle Aged, Pennsylvania, Polymorphism, Single Nucleotide, Cohort Studies, Electrolytes, Amino Acid Substitution, Clinical Research, Exome Sequencing, Potassium, Homeostasis, Humans, Female, Solute Carrier Family 12, Member 3, Amish, Gitelman Syndrome, Chromosomes, Human, Pair 16
Abstract

BACKGROUND: Potassium levels regulate multiple physiologic processes. The heritability of serum potassium level is moderate, with published estimates varying from 17% to 60%, suggesting genetic influences. However, the genetic determinants of potassium levels are not generally known. METHODS: A whole-exome sequencing association study of serum potassium levels in 5812 subjects of the Old Order Amish was performed. A dietary salt intervention in 533 Amish subjects estimated interaction between p.R642G and sodium intake. RESULTS: A cluster of variants, spanning approximately 537 kb on chromosome 16q13, was significantly associated with serum potassium levels. Among the associated variants, a known pathogenic variant of autosomal recessive Gitelman syndrome (p.R642G SLC12A3) was most likely causal; there were no homozygotes in our sample. Heterozygosity for p.R642G was also associated with lower chloride levels, but not with sodium levels. Notably, p.R642G showed a novel association with lower serum BUN levels. Heterozygotes for p.R642G had a two-fold higher rate of self-reported bone fractures and had higher resting heart rates on a low-salt diet compared with noncarriers. CONCLUSIONS: This study provides evidence that heterozygosity for a pathogenic variant in SLC12A3 causing Gitelman syndrome, a canonically recessive disorder, contributes to serum potassium concentration. The findings provide insights into SLC12A3 biology and the effects of heterozygosity on electrolyte homeostasis and related subclinical phenotypes that may have implications for personalized medicine and nutrition.

Published
2020

25. The role of phenotype-based search approaches using public online databases in diagnostics of Mendelian disorders

Author

Avi, Fellner, Noa, Ruhrman-Shahar, Naama, Orenstein, Gabriel, Lidzbarsky, Alan R, Shuldiner, Claudia, Gonzaga-Jauregui, Hadar, Brown-Shalev, Ofir, Hagari-Bechar, Lily, Bazak, and Lina, Basel-Salmon

Subjects
Phenotype, Databases, Factual, Genotype, Databases, Genetic, Exome Sequencing, Humans, Exome, Female, Child
Abstract

To investigate the effectiveness of phenotype-based search approaches using publicly available online databases.We included consecutively solved cases from our exome database. For each case, the combination of Human Phenotype Ontology terms reported by the referring clinician was used to perform a search in three commonly used databases: OMIM (first 300 results), Phenolyzer (first 300 results), and Mendelian (all 100 results).One hundred cases were included (43 females; mean age: 10 years). The actual molecular diagnosis identified through exome sequencing was not included in the search results of any of the queried databases in 33% of cases. In 85% of cases it was not found within the top five search results. When included, its median rank was 61 (range: 1-295), 21 (1-270), and 29 (1-92) in OMIM, Phenolyzer and Mendelian, respectively.This study demonstrates that, in most cases, phenotype-based search approaches using public online databases is ineffective in providing a probable diagnosis for Mendelian conditions. Genotype-first approach through molecular-guided diagnostics with backward phenotyping may be a more appropriate approach for these disorders, unless a specific diagnosis is considered a priori based on highly unique phenotypic features or a specific facial gestalt.

Published
2020

26. Genomewide Association Study of Platelet Reactivity and Cardiovascular Response in Patients Treated With Clopidogrel: A Study by the International Clopidogrel Pharmacogenomics Consortium

Author

Jae-Gook Shin, Dan M. Roden, Stefan Winter, Paul A. Gurbel, Michiaki Kubo, Braxton D. Mitchell, Joshua P. Lewis, Yuki Bradford, Daniel Aradi, Kevin P. Bliden, Jurriën M. ten Berg, Thomas O. Bergmeijer, Kiyuk Chang, Ruth E. Pakyz, Alan R. Shuldiner, Ho-Sook Kim, Jean-Luc Reny, Meinrad Gawaz, Tobias Geisler, Gianluca Campo, Marco Valgimigli, Elke Schaeffeler, Jolanta M. Siller-Matula, Gian Franco Gensini, Lene Holmvang, Willibald Hochholzer, Rossella Marcucci, Betti Giusti, Ming Ta Michael Lee, Jean-Pierre Déry, Dietmar Trenk, Ming-Shien Wen, John M. Wallace, Marylyn D. Ritchie, Teri E. Klein, Israel Fernandez-Cadenas, Dimitrios Alexopoulos, Matthias Schwab, Ryan Whaley, John H. Cleator, Pierre Fontana, Joshua D. Backman, Russ B. Altman, Shefali S. Verma, Eun Young Kim, Nadia Paarup Dridi, Li Gong, and Joan Montaner

Subjects
Male, Pharmacogenomic Variants, medicine.medical_treatment, Coronary Artery Disease, 030226 pharmacology & pharmacy, Coronary artery disease, Cytochrome P-450 CYP2C19/genetics/metabolism, 0302 clinical medicine, Risk Factors, Platelet Aggregation Inhibitors/adverse effects/therapeutic use, Pharmacology (medical), Myocardial infarction, pharmacokinetic, ddc:616, Clopidogrel/adverse effects/therapeutic use, Articles, Middle Aged, Clopidogrel, clinical outcomes, 3. Good health, Treatment Outcome, Cardiovascular Diseases, 030220 oncology & carcinogenesis, Cardiology, Female, percutaneous coronary intervention, clinical outcomes, CYP2C19, pharmacokinetic, medicine.drug, Blood Platelets, medicine.medical_specialty, Acute coronary syndrome, CYP2C19, Polymorphism, Single Nucleotide, Risk Assessment, Blood Platelets/drug effects/metabolism, Article, NO, 03 medical and health sciences, Internal medicine, medicine, Humans, Cardiovascular Diseases/blood/genetics/mortality/prevention & control, cardiovascular diseases, Aged, Pharmacology, Coronary Artery Disease/mortality/therapy, business.industry, Research, Percutaneous Coronary Intervention/adverse effects/mortality, percutaneous coronary intervention, Percutaneous coronary intervention, medicine.disease, Cytochrome P-450 CYP2C19, Pharmacogenetics, Pharmacogenomics, ddc:618.97, business, Platelet Aggregation Inhibitors, Genome-Wide Association Study
Abstract

Antiplatelet response to clopidogrel shows wide variation, and poor response is correlated with adverse clinical outcomes. CYP2C19 loss-of-function alleles play an important role in this response, but account for only a small proportion of variability in response to clopidogrel. An aim of the International Clopidogrel Pharmacogenomics Consortium (ICPC) is to identify other genetic determinants of clopidogrel pharmacodynamics and clinical response. A genomewide association study (GWAS) was performed using DNA from 2,750 European ancestry individuals, using adenosine diphosphate-induced platelet reactivity and major cardiovascular and cerebrovascular events as outcome parameters. GWAS for platelet reactivity revealed a strong signal for CYP2C19*2 (P value = 1.67e−33). After correction for CYP2C19*2 no other single-nucleotide polymorphism reached genomewide significance. GWAS for a combined clinical end point of cardiovascular death, myocardial infarction, or stroke (5.0% event rate), or a combined end point of cardiovascular death or myocardial infarction (4.7% event rate) showed no significant results, although in coronary artery disease, percutaneous coronary intervention, and acute coronary syndrome subgroups, mutations in SCOS5P1, CDC42BPA, and CTRAC1 showed genomewide significance (lowest P values: 1.07e−09, 4.53e−08, and 2.60e−10, respectively). CYP2C19*2 is the strongest genetic determinant of on-clopidogrel platelet reactivity. We identified three novel associations in clinical outcome subgroups, suggestive for each of these outcomes.

Published
2020

27. Exome sequencing identifies a nonsense variant in DAO associated with reduced energy expenditure in American Indians

Author

Pankaj Kumar, Clifton Bogardus, Hye In Kim, Jeff Sutherland, Cristopher V. Van Hout, Jonathan Krakoff, Paolo Piaggi, Alan R. Shuldiner, Çiğdem Köroğlu, Sayuko Kobes, William C. Knowler, Yunhua L. Muller, Leslie J. Baier, Nehal Gosalia, Marcus B. Jones, Robert L. Hanson, Anup K. Nair, and Wen-Chi Hsueh

Subjects
Adult, D-Amino-Acid Oxidase, Male, medicine.medical_specialty, Adolescent, Endocrinology, Diabetes and Metabolism, media_common.quotation_subject, Clinical Biochemistry, Nonsense, Nonsense mutation, Energy metabolism, Protein degradation, Biology, Biochemistry, Young Adult, Endocrinology, Gene Frequency, Internal medicine, Exome Sequencing, energy expenditure, energy metabolism, medicine, Humans, Exome, Obesity, whole-exome sequencing, Allele, Online Only Articles, Exome sequencing, Alleles, American Indian or Alaska Native, media_common, Genetic association, respiratory quotient, Biochemistry (medical), thrifty metabolic phenotype, Glucose Tolerance Test, Middle Aged, medicine.disease, Codon, Nonsense, Female
Abstract

Background Obesity and energy expenditure (EE) are heritable and genetic variants influencing EE may contribute to the development of obesity. We sought to identify genetic variants that affect EE in American Indians, an ethnic group with high prevalence of obesity. Methods Whole-exome sequencing was performed in 373 healthy Pima Indians informative for 24-hour EE during energy balance. Genetic association analyses of all high-quality exonic variants (≥5 carriers) was performed, and those predicted to be damaging were prioritized. Results Rs752074397 introduces a premature stop codon (Cys264Ter) in DAO and demonstrated the strongest association for 24-hour EE, where the Ter allele associated with substantially lower 24-hour EE (mean lower by 268 kcal/d) and sleeping EE (by 135 kcal/d). The Ter allele has a frequency = 0.5% in Pima Indians, whereas is extremely rare in most other ethnic groups (frequency < 0.01%). In vitro functional analysis showed reduced protein levels for the truncated form of DAO consistent with increased protein degradation. DAO encodes D-amino acid oxidase, which is involved in dopamine synthesis which might explain its role in modulating EE. Conclusion Our results indicate that a nonsense mutation in DAO may influence EE in American Indians. Identification of variants that influence energy metabolism may lead to new pathways to treat human obesity. Clinical Trial Registration Number NCT00340132.

Published
2020

28. Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction

Author

Dennis O. Mook-Kanamori, Yalda Jamshidi, Peter K. Joshi, Seung Hoan Choi, Henry J. Lin, Rebecca D. Jackson, Alison D. Murray, May E. Montasser, Veikko Salomaa, Charles Kooperberg, Moritz F. Sinner, Gianfranco Sinagra, Luisa Foco, James G. Wilson, Johan Sundström, Kathleen A. Ryan, Eric A. Whitsel, Bruno H. Stricker, Sandosh Padmanabhan, Christopher Newton-Cheh, Ozren Polasek, Unnur Thorsteinsdottir, Niek Verweij, Pier D. Lambiase, Nathan R. Tucker, Stefan Kääb, Jun Ding, Stefan Weiss, Daniel F. Gudbjartsson, David Conen, Lars Lind, Ivana Kolcic, Lu-Chen Weng, J. Wouter Jukema, Kirill V. Tarasov, Xiuqing Guo, Stella Trompet, Patricia B. Munroe, Albert V. Smith, Elsayed Z. Soliman, Andrew Tinker, Antti Jula, J. Gustav Smith, Alexander P. Reiner, Sébastien Thériault, Kathryn L. Lunetta, Vilmundur Gudnason, Mika Kähönen, Massimo Mangino, Raymond Noordam, Joshua C. Bis, Alan R. Shuldiner, Tim D. Spector, Borbala Mifsud, Stefan van Duijvenboden, Jeffrey R. O'Connell, Emelia J. Benjamin, M. Benjamin Shoemaker, Stephan B. Felix, Peter W. Macfarlane, Lorenz Risch, Uwe Völker, Stephanie M. Gogarten, Maria Fernanda Lima-Costa, Julia Ramirez, Morten S. Olesen, Konstantin Strauch, Annette Peters, Aaron Isaacs, Steven A. Lubitz, Eric Boerwinkle, Carolina Roselli, James H. Cartwright, Nathalia M. Araujo, Ruth J. F. Loos, Diane Fatkin, Harry Campbell, Blair H. Smith, Thomas Meitinger, André G. Uitterlinden, Paul L. Huang, Tamara B. Harris, Kathleen F. Kerr, David J. Porteous, Martina Müller-Nurasyid, Francesco Cucca, Michiel Rienstra, Davíð O. Arnar, Amanda A. Seyerle, Caroline Hayward, M. Abdullah Said, Catriona L. K. Barnes, Kent D. Taylor, Nona Sotoodehnia, Nina Mononen, Dan M. Roden, Jonathan Marten, Terho Lehtimäki, Dan E. Arking, Anna F. Dominiczak, Jan A. Kors, Olli T. Raitakari, Igor Rudan, Yordi J. van de Vegte, Christopher P. Nelson, Erik Ingelsson, Ulrike Peters, Girish N. Nadkarni, Eduardo Tarazona-Santos, Edward G. Lakatta, Nina Hutri-Kähönen, Bruce M. Psaty, Patrick T. Ellinor, Christian Fuchsberger, Katharina Schramm, Amelia W. Hall, M. Yldau van der Ende, Alvaro Alonso, James F. Wilson, Sheila Ulivi, Rosa B. Thorolfsdottir, Stefanie Aeschbacher, Mary L. Biggs, Marten E. van den Berg, Nilesh J. Samani, Thibaud Boutin, Vilmantas Giedraitis, Honghuang Lin, Kjell Nikus, Helen R. Warren, Arie C. Maan, James J. Cranley, Adolfo Correa, Martin Gögele, Ian Ford, Katri Sääksjärvi, Georg Ehret, Michele Orini, Susan R. Heckbert, Cecilia M. Lindgren, Jie Yao, Maria Pina Concas, Pim van der Harst, Ioanna Ntalla, Jeffrey Haessler, Jerome I. Rotter, Pashupati P. Mishra, Michael J. Cutler, Erwin P. Bottinger, Cornelia M. van Duijn, Jennifer A. Brody, Paolo Gasparini, Lenore J. Launer, Andrew P. Morris, Renée de Mutsert, Aki S. Havulinna, James P. Cook, Hilma Holm, Patrick Sulem, Alessandro De Grandi, Cristian Pattaro, Gardar Sveinbjornsson, Antonio Luiz Pinho Ribeiro, Mark J. Caulfield, Gudmar Thorleifsson, Marcus Dörr, Muhammad B. Riaz, Peter P. Pramstaller, Yong Qian, Anubha Mahajan, Cathy C. Laurie, Kenneth Rice, Mark Chaffin, Kari Stefansson, Andrew A. Hicks, Solmaz Assa, Hao Mei, Leo-Pekka Lyytikäinen, Fabiola Del Greco M, Renan P. Souza, Michael Preuss, Adrienne M. Stilp, Barry London, Melanie Waldenberger, Christy L. Avery, Daniel Levy, Michael R. Barnes, Medical Informatics, Epidemiology, Internal Medicine, Weng, Lu-Chen [0000-0003-1475-4930], Hall, Amelia Weber [0000-0002-7915-0313], Tucker, Nathan R [0000-0002-5071-4218], Chaffin, Mark D [0000-0002-1234-5562], Roselli, Carolina [0000-0001-5267-6756], Barnes, Michael R [0000-0001-9097-7381], Mifsud, Borbala [0000-0003-3429-3094], Hayward, Caroline [0000-0002-9405-9550], Concas, Maria Pina [0000-0003-3598-2537], Boutin, Thibaud [0000-0003-4754-1675], Kolcic, Ivana [0000-0001-7918-6052], Rudan, Igor [0000-0001-6993-6884], Souza, Renan P [0000-0002-9479-4432], Giedraitis, Vilmantas [0000-0003-3423-2021], Ingelsson, Erik [0000-0003-2256-6972], Mahajan, Anubha [0000-0001-5585-3420], Morris, Andrew P [0000-0002-6805-6014], Hicks, Andrew A [0000-0001-6320-0411], Sundström, Johan [0000-0003-2247-8454], Nelson, Christopher P [0000-0001-8025-2897], Riaz, Muhammad B [0000-0002-5512-1745], Sinagra, Gianfranco [0000-0003-2700-8478], Mishra, Pashupati P [0000-0001-5177-3431], Caulfield, Mark J [0000-0001-9295-3594], Dominiczak, Anna [0000-0003-4913-3608], Risch, Lorenz [0000-0003-2692-6699], Joshi, Peter K [0000-0002-6361-5059], Wilson, James F [0000-0001-5751-9178], Isaacs, Aaron [0000-0001-5037-4834], van Duijn, Cornelia M [0000-0002-2374-9204], Gudnason, Vilmundur [0000-0001-5696-0084], Smith, Albert V [0000-0003-1942-5845], Loos, Ruth JF [0000-0002-8532-5087], Preuss, Michael H [0000-0001-5266-8465], Correa, Adolfo [0000-0002-9501-600X], Müller-Nurasyid, Martina [0000-0003-3793-5910], Waldenberger, Melanie [0000-0003-0583-5093], Mangino, Massimo [0000-0002-2167-7470], Rienstra, Michiel [0000-0002-2581-070X], van der Harst, Pim [0000-0002-2713-686X], Verweij, Niek [0000-0002-4303-7685], Fatkin, Diane [0000-0002-9010-9856], Brody, Jennifer A [0000-0001-8509-148X], Rice, Kenneth [0000-0002-3071-7278], Pattaro, Cristian [0000-0002-4119-0109], Wouter Jukema, J [0000-0002-3246-8359], Weiss, Stefan [0000-0002-3553-4315], Havulinna, Aki S [0000-0002-4787-8959], Sääksjärvi, Katri [0000-0002-5061-4911], Salomaa, Veikko [0000-0001-7563-5324], Rotter, Jerome I [0000-0001-7191-1723], Taylor, Kent D [0000-0002-2756-4370], Lakatta, Edward G [0000-0002-4772-0035], Lin, Honghuang [0000-0003-3043-3942], Lunetta, Kathryn L [0000-0002-9268-810X], Murray, Alison D [0000-0003-4915-4847], Porteous, David J [0000-0003-1249-6106], Smith, Blair H [0000-0002-5362-9430], Uitterlinden, André [0000-0002-7276-3387], Peters, Ulrike [0000-0001-5666-9318], Alonso, Alvaro [0000-0002-2225-8323], Ehret, Georg B [0000-0002-5730-0675], Soliman, Elsayed Z [0000-0001-5632-8150], Gogarten, Stephanie M [0000-0002-7231-9745], Kerr, Kathleen F [0000-0002-6438-9583], Abdullah Said, M [0000-0003-2920-7745], Orini, Michele [0000-0001-5773-0344], Ramirez, Julia [0000-0003-4130-5866], Van Duijvenboden, Stefan [0000-0001-8897-558X], Gudbjartsson, Daniel F [0000-0002-5222-9857], Sulem, Patrick [0000-0001-7123-6123], Thorolfsdottir, Rosa B [0000-0001-7475-0398], Benjamin, Emelia J [0000-0003-4076-2336], Stefansson, Kari [0000-0003-1676-864X], Ellinor, Patrick T [0000-0002-2067-0533], Jamshidi, Yalda [0000-0003-0151-6482], Lubitz, Steven A [0000-0002-9599-4866], Munroe, Patricia B [0000-0002-4176-2947], Apollo - University of Cambridge Repository, Medicum, Institute for Molecular Medicine Finland, Complex Disease Genetics, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Cardiovascular Centre (CVC), Ntalla, I., Weng, L. -C., Cartwright, J. H., Hall, A. W., Sveinbjornsson, G., Tucker, N. R., Choi, S. H., Chaffin, M. D., Roselli, C., Barnes, M. R., Mifsud, B., Warren, H. R., Hayward, C., Marten, J., Cranley, J. J., Concas, M. P., Gasparini, P., Boutin, T., Kolcic, I., Polasek, O., Rudan, I., Araujo, N. M., Lima-Costa, M. F., Ribeiro, A. L. P., Souza, R. P., Tarazona-Santos, E., Giedraitis, V., Ingelsson, E., Mahajan, A., Morris, A. P., Del Greco M, F., Foco, L., Gogele, M., Hicks, A. A., Cook, J. P., Lind, L., Lindgren, C. M., Sundstrom, J., Nelson, C. P., Riaz, M. B., Samani, N. J., Sinagra, G., Ulivi, S., Kahonen, M., Mishra, P. P., Mononen, N., Nikus, K., Caulfield, M. J., Dominiczak, A., Padmanabhan, S., Montasser, M. E., O'Connell, J. R., Ryan, K., Shuldiner, A. R., Aeschbacher, S., Conen, D., Risch, L., Theriault, S., Hutri-Kahonen, N., Lehtimaki, T., Lyytikainen, L. -P., Raitakari, O. T., Barnes, C. L. K., Campbell, H., Joshi, P. K., Wilson, J. F., Isaacs, A., Kors, J. A., van Duijn, C. M., Huang, P. L., Gudnason, V., Harris, T. B., Launer, L. J., Smith, A. V., Bottinger, E. P., Loos, R. J. F., Nadkarni, G. N., Preuss, M. H., Correa, A., Mei, H., Wilson, J., Meitinger, T., Muller-Nurasyid, M., Peters, A., Waldenberger, M., Mangino, M., Spector, T. D., Rienstra, M., van de Vegte, Y. J., van der Harst, P., Verweij, N., Kaab, S., Schramm, K., Sinner, M. F., Strauch, K., Cutler, M. J., Fatkin, D., London, B., Olesen, M., Roden, D. M., Benjamin Shoemaker, M., Gustav Smith, J., Biggs, M. L., Bis, J. C., Brody, J. A., Psaty, B. M., Rice, K., Sotoodehnia, N., De Grandi, A., Fuchsberger, C., Pattaro, C., Pramstaller, P. P., Ford, I., Wouter Jukema, J., Macfarlane, P. W., Trompet, S., Dorr, M., Felix, S. B., Volker, U., Weiss, S., Havulinna, A. S., Jula, A., Saaksjarvi, K., Salomaa, V., Guo, X., Heckbert, S. R., Lin, H. J., Rotter, J. I., Taylor, K. D., Yao, J., de Mutsert, R., Maan, A. C., Mook-Kanamori, D. O., Noordam, R., Cucca, F., Ding, J., Lakatta, E. G., Qian, Y., Tarasov, K. V., Levy, D., Lin, H., Newton-Cheh, C. H., Lunetta, K. L., Murray, A. D., Porteous, D. J., Smith, B. H., Stricker, B. H., Uitterlinden, A., van den Berg, M. E., Haessler, J., Jackson, R. D., Kooperberg, C., Peters, U., Reiner, A. P., Whitsel, E. A., Alonso, A., Arking, D. E., Boerwinkle, E., Ehret, G. B., Soliman, E. Z., Avery, C. L., Gogarten, S. M., Kerr, K. F., Laurie, C. C., Seyerle, A. A., Stilp, A., Assa, S., Abdullah Said, M., Yldau van der Ende, M., Lambiase, P. D., Orini, M., Ramirez, J., Van Duijvenboden, S., Arnar, D. O., Gudbjartsson, D. F., Holm, H., Sulem, P., Thorleifsson, G., Thorolfsdottir, R. B., Thorsteinsdottir, U., Benjamin, E. J., Tinker, A., Stefansson, K., Ellinor, P. T., Jamshidi, Y., Lubitz, S. A., Munroe, P. B., Fysiologie, RS: FHML MaCSBio, RS: Carim - B01 Blood proteins & engineering, Læknadeild (HÍ), Faculty of Medicine (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), School of Engineering and Natural Sciences (UI), Háskóli Íslands, and University of Iceland

Subjects
0301 basic medicine, Male, Multifactorial Inheritance, General Physics and Astronomy, Gene Expression, Genome-wide association study, 030204 cardiovascular system & hematology, Arrhythmias, Genome-wide association studies, CALCINEURIN, Electrocardiography, 0302 clinical medicine, Cardiovascular Disease, Multi-ancestry GWAS, ELEMENTS, Medicine, Cardiac and Cardiovascular Systems, Blóðrásarsjúkdómar, lcsh:Science, RISK, DECREASE, education.field_of_study, Multidisciplinary, Kardiologi, medicine.diagnostic_test, 1184 Genetics, developmental biology, physiology, Atrial fibrillation, 3142 Public health care science, environmental and occupational health, 3. Good health, Endophenotype, Arrhythmias, Cardiac, Cardiovascular Diseases, Endophenotypes, Female, Genetic Loci, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Humans, Quantitative Trait Loci, cardiovascular system, Cardiology, medicine.symptom, Erfðarannsóknir, Cardiac, Medical Genetics, Human, Bradycardia, medicine.medical_specialty, Science, GENOME-WIDE ASSOCIATION, ATRIAL-FIBRILLATION, MUTATIONS, DURATION, CARDIOMYOPATHY, BRADYCARDIA, Population, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Internal medicine, Cardiac conduction, PR interval, education, Medicinsk genetik, business.industry, Cardiovascular genetics, General Chemistry, Arfgengi, medicine.disease, 030104 developmental biology, lcsh:Q, business
Abstract

Publisher's version (útgefin grein), The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N = 293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease., We provide all investigator and study-specific acknowledgements in Supplementary Note 1, and funding sources in Supplementary Note 2.

Published
2020

29. Genetic inactivation of ANGPTL4 improves glucose homeostasis and is associated with reduced risk of diabetes

Author

Teresa Tusié-Luna, Svati H. Shah, Wen-Jane Lee, Amit Khera, Gonçalo R. Abecasis, Olle Melander, Alan R. Shuldiner, Connor A. Emdin, Kari Stefansson, Jesper Gromada, Andrew P. Morris, Lee-Ming Chuang, Omri Gottesman, Lars G. Fritsche, Pradeep Natarajan, Marju Orho-Melander, Daniel F. Gudbjartsson, Anubha Mahajan, Marylyn D. Ritchie, William E. Kraus, Tooraj Mirshahi, Colm O'Dushlaine, Jason Flannick, Nicholas J. Wareham, Anne Tybjærg-Hansen, Anders Berg Wulff, Rashmi B. Prasad, Aris Baras, Jonas B. Nielsen, Valgerdur Steinthorsdottir, Yii-Der Ida Chen, Jerome I. Rotter, Lukas Habegger, Samantha N. Fetterolf, David Altshuler, Om Prakash Dwivedi, Tanya M. Teslovich, Cristen J. Willer, Luca A. Lotta, Andrew J. Murphy, Joseph B. Leader, Cristopher V. Van Hout, Christopher D. Still, Ola Hansson, David Birtwell, Alexander Lopez, Daniel J. Rader, John D. Overton, Anthony Marcketta, Patrick Sulem, Peter N. Benotti, Jose C. Florez, Lydia Coulter Kwee, David J. Carey, Oddgeir L. Holmen, Kristian Hveem, Leif Groop, Sekar Kathiresan, Viktoria Gusarova, Unnur Thorsteinsdottir, Cassandra M. Hartle, Uyenlinh L. Mirshahi, H. Lester Kirchner, Shannon Bruse, Robert A. Scott, Michael F. Murray, Marketa Sjögren, Jeffrey G. Reid, Aeron Small, Børge G. Nordestgaard, Amr H. Wardeh, Chad M. Brummett, Mark I. McCarthy, Frederick E. Dewey, David H. Ledbetter, John Penn, Ingrid B. Borecki, Scott M. Damrauer, Hilma Holm, Michael Boehnke, George D. Yancopoulos, Institute for Molecular Medicine Finland, University of Helsinki, Centre of Excellence in Complex Disease Genetics, and HUS Abdominal Center

Subjects
Blood Glucose, Male, 0301 basic medicine, Insulin Resistance/genetics, General Physics and Astronomy, Type 2 diabetes, 030204 cardiovascular system & hematology, Inbred C57BL, Cardiovascular, HAN CHINESE, Whole Exome Sequencing, Mice, 0302 clinical medicine, Risk Factors, ANGPTL4, Homeostasis, Glucose homeostasis, lcsh:Science, Mice, Knockout, Lipoprotein lipase, Multidisciplinary, Diabetes, Lipoprotein Lipase/metabolism, REMNANT CHOLESTEROL, ADIPOSE-TISSUE, Female, Type 2, Heterozygote, medicine.medical_specialty, Knockout, Science, LIPOPROTEIN-LIPASE, HEART-DISEASE, Diabetes Mellitus, Type 2/etiology, Article, General Biochemistry, Genetics and Molecular Biology, Angiopoietin-like 4 Protein/deficiency, 03 medical and health sciences, Internal medicine, Diabetes mellitus, Exome Sequencing, Diabetes Mellitus, Genetics, medicine, Angiopoietin-Like Protein 4, Animals, Humans, Gene Silencing, GENOME-WIDE ASSOCIATION, Metabolic and endocrine, Genetic Association Studies, CHINESE POPULATION, Blood Glucose/metabolism, PLASMA-LIPIDS, business.industry, Case-control study, Genetic Variation, General Chemistry, Odds ratio, Atherosclerosis, medicine.disease, Mice, Inbred C57BL, Lipoprotein Lipase, 030104 developmental biology, Endocrinology, Diabetes Mellitus, Type 2, Amino Acid Substitution, Case-Control Studies, lcsh:Q, 3111 Biomedicine, ANGIOPOIETIN-LIKE PROTEIN-4, Insulin Resistance, business
Abstract

Angiopoietin-like 4 (ANGPTL4) is an endogenous inhibitor of lipoprotein lipase that modulates lipid levels, coronary atherosclerosis risk, and nutrient partitioning. We hypothesize that loss of ANGPTL4 function might improve glucose homeostasis and decrease risk of type 2 diabetes (T2D). We investigate protein-altering variants in ANGPTL4 among 58,124 participants in the DiscovEHR human genetics study, with follow-up studies in 82,766 T2D cases and 498,761 controls. Carriers of p.E40K, a variant that abolishes ANGPTL4 ability to inhibit lipoprotein lipase, have lower odds of T2D (odds ratio 0.89, 95% confidence interval 0.85–0.92, p = 6.3 × 10−10), lower fasting glucose, and greater insulin sensitivity. Predicted loss-of-function variants are associated with lower odds of T2D among 32,015 cases and 84,006 controls (odds ratio 0.71, 95% confidence interval 0.49–0.99, p = 0.041). Functional studies in Angptl4-deficient mice confirm improved insulin sensitivity and glucose homeostasis. In conclusion, genetic inactivation of ANGPTL4 is associated with improved glucose homeostasis and reduced risk of T2D., Genetic variation in ANGPTL4 is associated with lipid traits. Here, the authors find that predicted loss-of-function variants in ANGPTL4 are associated with glucose homeostasis and reduced risk of type 2 diabetes and that Angptl4−/− mice on a high-fat diet show improved insulin sensitivity.

Published
2018

30. Monogenic diabetes in overweight and obese youth diagnosed with type 2 diabetes: the TODAY clinical trial

Author

Morey W. Haymond, Lynne L. Levitsky, Kenneth C. Copeland, Barbara Linder, Neil H. White, Alan R. Shuldiner, Toni I. Pollin, Jeffrey W. Kleinberger, Rachelle Gandica, and Sherida E. Tollefsen

Subjects
Male, obesity, Pediatrics, medicine.medical_specialty, Adolescent, 030209 endocrinology & metabolism, Type 2 diabetes, Protein Serine-Threonine Kinases, Overweight, Article, Body Mass Index, Germinal Center Kinases, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Diabetes mellitus, medicine, Humans, Hepatocyte Nuclear Factor 1-alpha, 030212 general & internal medicine, Child, Genetics (clinical), 2. Zero hunger, youth, business.industry, clinical trial, medicine.disease, Obesity, 3. Good health, HNF1A, Diabetes Mellitus, Type 2, Hepatocyte Nuclear Factor 4, monogenic diabetes, Cohort, Female, type 2 diabetes, medicine.symptom, business, Body mass index, Cohort study
Abstract

PurposeMonogenic diabetes accounts for 1-2% of diabetes cases. It is often undiagnosed, which may lead to inappropriate treatment. This study was performed to estimate the prevalence of monogenic diabetes in a cohort of overweight/obese adolescents diagnosed with type 2 diabetes (T2D).MethodsSequencing using a custom monogenic diabetes gene panel was performed on a racially/ethnically diverse cohort of 488 overweight/obese adolescents with T2D in the Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) clinical trial. Associations between having a monogenic diabetes variant and clinical characteristics and time to treatment failure were analyzed.ResultsMore than 4% (22/488) had genetic variants causing monogenic diabetes (seven GCK, seven HNF4A, five HNF1A, two INS, and one KLF11). Patients with monogenic diabetes had a statistically, but not clinically, significant lower body mass index (BMI) z-score, lower fasting insulin, and higher fasting glucose. Most (6/7) patients with HNF4A variants rapidly failed TODAY treatment across study arms (hazard ratio = 5.03, P = 0.0002), while none with GCK variants failed treatment.ConclusionThe finding of 4.5% of patients with monogenic diabetes in an overweight/obese cohort of children and adolescents with T2D suggests that monogenic diabetes diagnosis should be considered in children and adolescents without diabetes-associated autoantibodies and maintained C-peptide, regardless of BMI, as it may direct appropriate clinical management.

Published
2018

31. Alcohol Consumption and Risk of Coronary Artery Disease (from the Million Veteran Program)

Author

Rebecca J. Song, Xuan-Mai T. Nguyen, Rachel Quaden, Yuk-Lam Ho, Amy C. Justice, David R. Gagnon, Kelly Cho, Christopher J. O'Donnell, John Concato, J. Michael Gaziano, Luc Djoussé, Ildiko Halasz, Daniel Federman, Jean Beckham, Scott E. Sherman, Peruvemba Sriram, Philip S. Tsao, Edward J. Boyko, Junzhe Xu, Frank Lederle, Louis J. Dellitalia, Rachel McArdle, Laurence Kaminsky, Alan C. Swann, Mark B. Hamner, Hermes J. Florez, Prashant Pandya, Gerardo Villarreal, Peter Wilson, Timothy R. Morgan, Lori Davis, Robin A. Hurley, Laurence Meyer, Sunil K. Ahuja, Eric P. Konicki, David Cohen, Jack Lichy, Jeffrey Whittle, Kathlyn Sue Haddock, Karl D. Straub, John T. Callaghan, Samuel M. Aguayo, Samir Gupta, Ronald G. Washburn, Mary E. Oehlert, Adriana M. Hung, Agnes Wallbom, Robert Keith, Elif Sonel, Ronald B. Schifman, Richard D. Childress, Michael F. Godschalk, Alan R. Shuldiner, Padmashri Rastogi, Salvador Gutierrez, Ronald Fernando, Pran R. Iruvanti, Darshana Jhala, Carlos Rosado-Rodriguez, Stephen M. Mastorides, John B. Harley, Kristin Mattocks, Brooks Robey, Robert T. Striker, Michael Rauchman, John Wells, Zuhair K. Ballas, Susan S. Woods, Shing Shing Yeh, Nora R. Ratcliffe, Jon B. Klein, Adam G. Golden, Harold M. Ginzburg, Satish Sharma, Kris Ann K. Oursler, Mary A. Whooley, Gretchen Gibson, and null Heinz

Subjects
Male, medicine.medical_specialty, Alcohol Drinking, Population, Coronary Artery Disease, Alcohol use disorder, 030204 cardiovascular system & hematology, Lower risk, Article, Coronary artery disease, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Internal medicine, medicine, Humans, 030212 general & internal medicine, education, Aged, Proportional Hazards Models, Veterans, education.field_of_study, Proportional hazards model, business.industry, Alcoholic Beverages, Hazard ratio, Middle Aged, Protective Factors, medicine.disease, United States, Confidence interval, Alcoholism, Cardiology, Female, Self Report, Cardiology and Cardiovascular Medicine, business, Body mass index, Demography
Abstract

Moderate alcohol consumption has been associated with a lower risk of coronary artery disease (CAD) in the general population but has not been well studied in US veterans. We obtained self-reported alcohol consumption from Million Veteran Program participants. Using electronic health records, CAD events were defined as 1 inpatient or 2 outpatient diagnosis codes for CAD, or 1 code for a coronary procedure. We excluded participants with prevalent CAD (n = 69,995) or incomplete alcohol information (n = 8,449). We used a Cox proportional hazards model to estimate hazard ratios and 95% confidence intervals for CAD, adjusting for age, gender, body mass index, race, smoking, education, and exercise. Among 156,728 participants, the mean age was 65.3 years (standard deviation = 12.1) and 91% were men. There were 6,153 CAD events during a mean follow-up of 2.9 years. Adjusted hazard ratios (95% confidence intervals) for CAD were 1.00 (reference), 1.02 (0.92 to 1.13), 0.83 (0.74 to 0.93), 0.77 (0.67 to 0.87), 0.71 (0.62 to 0.81), 0.62 (0.51 to 0.76), 0.58 (0.46 to 0.74), and 0.95 (0.85 to 1.06) for categories of never drinker; former drinker; current drinkers of ≤0.5 drink/day, >0.5 to 1 drink/day, >1 to 2 drinks/day, >2 to 3 drinks/day, and >3 to 4 drinks/day; and heavy drinkers (>4 drinks/day) or alcohol use disorder, respectively. For a fixed amount of ethanol, intake at ≥3 days/week was associated with lower CAD risk compared with ≤1 day/week. Beverage preference (beer, wine, or liquor) did not influence the alcohol-CAD relation. Our data show a lower risk of CAD with light-to-moderate alcohol consumption among US veterans, and drinking frequency may provide a further reduction in risk.

Published
2018

32. Profiling and Leveraging Relatedness in a Precision Medicine Cohort of 92,455 Exomes

Author

Shane McCarthy, David H. Ledbetter, Frederick E. Dewey, Lukas Habegger, John Penn, David J. Carey, George D. Yancoupolos, Cristopher V. Van Hout, H. Lester Kirchner, Suganthi Balasubramanian, Joseph B. Leader, Tanya M. Teslovich, Xiaodong Bai, Colm O'Dushlaine, Aris Baras, John D. Overton, Michael F. Murray, Nehal Gosalia, Jeffrey G. Reid, Evan Maxwell, Alan R. Shuldiner, Alexander Lopez, Claudia Gonzaga-Jauregui, Christopher Snyder, Jeffrey Staples, Ricardo Ulloa, and Alicia Hawes

Subjects
Male, 0301 basic medicine, Heterozygote, Population, Genomics, Pedigree chart, Biology, Compound heterozygosity, Article, Cohort Studies, 03 medical and health sciences, Genetics, Electronic Health Records, Humans, Computer Simulation, Exome, Family, Precision Medicine, education, Nuclear family, Genetics (clinical), Exome sequencing, education.field_of_study, Geography, Reproducibility of Results, Exons, Human genetics, Pedigree, Genetics, Population, Phenotype, 030104 developmental biology, Evolutionary biology, Mutation, Cohort, Female, Tandem exon duplication
Abstract

Large-scale human genetics studies are ascertaining increasing proportions of populations as they continue growing in both number and scale. As a result, the amount of cryptic relatedness within these study cohorts is growing rapidly and has significant implications on downstream analyses. We demonstrate this growth empirically among the first 92,455 exomes from the DiscovEHR cohort and, via a custom simulation framework we developed called SimProgeny, show that these measures are in-line with expectations given the underlying population and ascertainment approach. For example, we identified ∼66,000 close (first- and second-degree) relationships within DiscovEHR involving 55.6% of study participants. Our simulation results project that >70% of the cohort will be involved in these close relationships as DiscovEHR scales to 250,000 recruited individuals. We reconstructed 12,574 pedigrees using these relationships (including 2,192 nuclear families) and leveraged them for multiple applications. The pedigrees substantially improved the phasing accuracy of 20,947 rare, deleterious compound heterozygous mutations. Reconstructed nuclear families were critical for identifying 3,415 de novo mutations in ∼1,783 genes. Finally, we demonstrate the segregation of known and suspected disease-causing mutations through reconstructed pedigrees, including a tandem duplication in LDLR causing familial hypercholesterolemia. In summary, this work highlights the prevalence of cryptic relatedness expected among large healthcare population genomic studies and demonstrates several analyses that are uniquely enabled by large amounts of cryptic relatedness.

Published
2018

33. Genomic diagnostics within a medically underserved population: efficacy and implications

Author

Donna L. Robinson, Cristopher V. Van Hout, Mindy Kuebler, Millie Young, Kavita Praveen, Erik G. Puffenberger, Scott Mellis, Aris Baras, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Karlla W. Brigatti, Kevin A. Strauss, Alejandra King, Robert N. Jinks, Jeffrey G. Reid, John D. Overton, Frederick E. Dewey, Katie B. Williams, Ian Finnegan, and Adam D. Heaps

Subjects
Adult, Male, 0301 basic medicine, Proband, medicine.medical_specialty, Adolescent, Genetics, Medical, Population, Disease, Pharmacology, Vulnerable Populations, Workflow, Young Adult, 03 medical and health sciences, Underserved Population, 0302 clinical medicine, Internal medicine, Humans, Medicine, Genetic Predisposition to Disease, Genetic Testing, Healthcare Disparities, Allele, Child, education, Exome, Genetic Association Studies, Genetics (clinical), Exome sequencing, Incidental Findings, education.field_of_study, business.industry, Infant, Newborn, Infant, Genomics, Middle Aged, Pedigree, 030104 developmental biology, Child, Preschool, Population Surveillance, Etiology, Female, business, Algorithms, 030217 neurology & neurosurgery
Abstract

PurposeWe integrated whole-exome sequencing (WES) and chromosomal microarray analysis (CMA) into a clinical workflow to serve an endogamous, uninsured, agrarian community.MethodsSeventy-nine probands (newborn to 49.8 years) who presented between 1998 and 2015 remained undiagnosed after biochemical and molecular investigations. We generated WES data for probands and family members and vetted variants through rephenotyping, segregation analyses, and population studies.ResultsThe most common presentation was neurological disease (64%). Seven (9%) probands were diagnosed by CMA. Family WES data were informative for 37 (51%) of the 72 remaining individuals, yielding a specific genetic diagnosis (n = 32) or revealing a novel molecular etiology (n = 5). For five (7%) additional subjects, negative WES decreased the likelihood of genetic disease. Compared to trio analysis, "family" WES (average seven exomes per proband) reduced filtered candidate variants from 22 ± 6 to 5 ± 3 per proband. Nineteen (51%) alleles were de novo and 17 (46%) inherited; the latter added to a population-based diagnostic panel. We found actionable secondary variants in 21 (4.2%) of 502 subjects, all of whom opted to be informed.ConclusionCMA and family-based WES streamline and economize diagnosis of rare genetic disorders, accelerate novel gene discovery, and create new opportunities for community-based screening and prevention in underserved populations.

Published
2018

34. Publisher Correction: A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids

Author

Myriam Fornage, Thomas Meitinger, Elena Carnero-Montoro, Donna K. Arnett, Rory P. Wilson, Steve Horvath, Mina A. Jhun, Tao Zhang, Elias Salfati, Devin Absher, Marguerite R. Irvin, Melanie Waldenberger, Nona Sotoodehnia, Mohsen Ghanbari, Klodian Dhana, Christian Gieger, Stefan Gustafsson, Wei Chen, Andrea A. Baccarelli, Lifang Hou, Jeffrey R. O'Connell, Rui Xia, Jordana T. Bell, Bruce M. Psaty, Lars Lind, Yii-Der Ida Chen, Mohammad Arfan Ikram, May E. Montasser, Weihua Guan, Paula Singmann, Jincheng Shen, Eric Boerwinkle, Martina Müller-Nurasyid, Anh N. Do, Shengxu Li, Traci M. Bartz, Dianjianyi Sun, Eric A. Whitsel, Erik Ingelsson, Annette Peters, Jennifer A. Smith, Daniel Levy, Coleen M. Damcott, Xiaoping Zhao, Wei Zhao, Philip S. Tsao, Alan R. Shuldiner, Themistocles L. Assimes, Michael M. Mendelson, Tim D. Spector, Åsa K. Hedman, Chen Yao, Pfeiffer Liliane, Joyce B. J. van Meurs, Rahul Gondalia, Abbas Dehghan, Kim Valeska Emilie Braun, Roby Joehanes, Sharon L.R. Kardia, Erin B. Ware, Deugi Zhi, Megan L. Grove, Jennifer A. Brody, and André G. Uitterlinden

Subjects
Epigenomics, Adult, Male, Science, Quantitative Trait Loci, Ethnic group, General Physics and Astronomy, Blood lipids, Biology, General Biochemistry, Genetics and Molecular Biology, White People, Epigenesis, Genetic, Epigenome, Genetics, Leukocytes, Humans, Epigenetics, Dyslipidaemias, Aged, Multidisciplinary, Carnitine O-Palmitoyltransferase, General Chemistry, Hispanic or Latino, DNA Methylation, Middle Aged, Publisher Correction, Lipids, Black or African American, DNA methylation, CpG Islands, Female, Lipoproteins, HDL
Abstract

Here we examine the association between DNA methylation in circulating leukocytes and blood lipids in a multi-ethnic sample of 16,265 subjects. We identify 148, 35, and 4 novel associations among Europeans, African Americans, and Hispanics, respectively, and an additional 186 novel associations through a trans-ethnic meta-analysis. We observe a high concordance in the direction of effects across racial/ethnic groups, a high correlation of effect sizes between high-density lipoprotein and triglycerides, a modest overlap of associations with epigenome-wide association studies of other cardio-metabolic traits, and a largely non-overlap with lipid loci identified to date through genome-wide association studies. Thirty CpGs reached significance in at least 2 racial/ethnic groups including 7 that showed association with the expression of an annotated gene. CpGs annotated to CPT1A showed evidence of being influenced by triglycerides levels. DNA methylation levels of circulating leukocytes show robust and consistent association with blood lipid levels across multiple racial/ethnic groups.

Published
2021

35. TM6SF2 rs58542926 impacts lipid processing in liver and small intestine

Author

Elizabeth A. O'Hare, Janet D. Robishaw, Kathy Ryan, Shilpa Narina, Laura M. Yerges-Armstrong, Glenn S. Gerhard, Rongze Yang, Rebecca McFarland, Alan R. Shuldiner, Norann A. Zaghloul, Alexis Gorden, Christopher D. Still, Steve A. Farber, Meredith H. Wilson, Urmila Sreenivasan, G. Craig Wood, Carmen C. Leitch, and Carole Sztalryd

Subjects
Male, 0301 basic medicine, medicine.medical_specialty, Molecular Sequence Data, Biology, Polymorphism, Single Nucleotide, Article, Mice, 03 medical and health sciences, Fibrosis, Internal medicine, Intestine, Small, Nonalcoholic fatty liver disease, medicine, Animals, Homeostasis, Humans, Triglycerides, Zebrafish, Base Sequence, Hepatology, Tunicamycin, Endoplasmic reticulum, Membrane Proteins, Middle Aged, Endoplasmic Reticulum Stress, Lipid Metabolism, Postprandial Period, medicine.disease, Small intestine, Fatty Liver, Enterocytes, 030104 developmental biology, Endocrinology, medicine.anatomical_structure, Postprandial, Liver, Hepatocytes, Female, Caco-2 Cells, Lipoprotein, TM6SF2
Abstract

The transmembrane 6 superfamily member 2 (TM6SF2) loss-of-function variant rs58542926 is a genetic risk factor for nonalcoholic fatty liver disease and progression to fibrosis but is paradoxically associated with lower levels of hepatically derived triglyceride-rich lipoproteins. TM6SF2 is expressed predominantly in liver and small intestine, sites for triglyceride-rich lipoprotein biogenesis and export. In light of this, we hypothesized that TM6SF2 may exhibit analogous effects on both liver and intestine lipid homeostasis. To test this, we genotyped rs58542926 in 983 bariatric surgery patients from the Geisinger Medical Center for Nutrition and Weight Management, Geisinger Health System, in Pennsylvania and from 3,556 study participants enrolled in the Amish Complex Disease Research Program. Although these two cohorts have different metabolic profiles, carriers in both cohorts had improved fasting lipid profiles. Importantly, following a high-fat challenge, carriers in the Amish Complex Disease Research Program cohort exhibited significantly lower postprandial serum triglycerides, suggestive of a role for TM6SF2 in the small intestine. To gain further insight into this putative role, effects of TM6SF2 deficiency were studied in a zebrafish model and in cultured human Caco-2 enterocytes. In both systems TM6SF2 deficiency resulted in defects in small intestine metabolism in response to dietary lipids, including significantly increased lipid accumulation, decreased lipid clearance, and increased endoplasmic reticulum stress. CONCLUSIONS These data strongly support a role of TM6SF2 in the regulation of postprandial lipemia, potentially through a similar function for TM6SF2 in the lipidation and/or export of both hepatically and intestinally derived triglyceride-rich lipoproteins. (Hepatology 2017;65:1526-1542).

Published
2017

36. Cardiovascular risks impact human brain

Author

Joshua, Chiappelli, Laura M, Rowland, S Andrea, Wijtenburg, Hongji, Chen, Andrew A, Maudsley, Sulaiman, Sheriff, Shuo, Chen, Anya, Savransky, Wyatt, Marshall, Meghann C, Ryan, Heather A, Bruce, Alan R, Shuldiner, Braxton D, Mitchell, Peter, Kochunov, and L Elliot, Hong

Subjects
Adult, Male, Aspartic Acid, Echo-Planar Imaging, Blood Pressure, Middle Aged, Biological Sciences, White Matter, Young Adult, nervous system, Cardiovascular Diseases, Risk Factors, Humans, Female, Gray Matter
Abstract

Cardiovascular risk factors such as dyslipidemia and hypertension increase the risk for white matter pathology and cognitive decline. We hypothesize that white matter levels of N-acetylaspartate (NAA), a chemical involved in the metabolic pathway for myelin lipid synthesis, could serve as a biomarker that tracks the influence of cardiovascular risk factors on white matter prior to emergence of clinical changes. To test this, we measured levels of NAA across white matter and gray matter in the brain using echo planar spectroscopic imaging (EPSI) in 163 individuals and examined the relationship of regional NAA levels and cardiovascular risk factors as indexed by the Framingham Cardiovascular Risk Score (FCVRS). NAA was strongly and negatively correlated with FCVRS across the brain, but, after accounting for age and sex, the association was found primarily in white matter regions, with additional effects found in the thalamus, hippocampus, and cingulate gyrus. FCVRS was also negatively correlated with creatine levels, again primarily in white matter. The results suggest that cardiovascular risks are related to neurochemistry with a predominantly white matter pattern and some subcortical and cortical gray matter involvement. NAA mapping of the brain may provide early surveillance for the potential subclinical impact of cardiovascular and metabolic risk factors on the brain.

Published
2019

37. Clinical and Molecular Prevalence of Lipodystrophy in an Unascertained Large Clinical Care Cohort

Author

David J. Carey, Aris Baras, H. Lester Kirchner, Wenzhen Ge, Ryan Colonie, Jesper Gromada, Jeffrey Staples, Ashish Yadav, Joseph B. Leader, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Judith Altarejos, Michael F. Murray, Jeffrey G. Reid, Cristopher V. Van Hout, John D. Overton, Omri Gottesman, and Steve Gao

Subjects
0301 basic medicine, Adult, Male, Pediatrics, medicine.medical_specialty, Dunnigan familial partial lipodystrophy, Lipodystrophy, Endocrinology, Diabetes and Metabolism, Population, 030209 endocrinology & metabolism, Disease, LMNA, 03 medical and health sciences, 0302 clinical medicine, Internal Medicine, Medicine, Electronic Health Records, Humans, Genetic Predisposition to Disease, education, education.field_of_study, business.industry, Partial Lipodystrophy, Genomics, medicine.disease, United States, 030104 developmental biology, Population Surveillance, Cohort, Female, Diagnosis code, business
Abstract

Lipodystrophies are a group of disorders characterized by absence or loss of adipose tissue and abnormal fat distribution, commonly accompanied by metabolic dysregulation. Although considered rare disorders, their prevalence in the general population is not well understood. We aimed to evaluate the clinical and genetic prevalence of lipodystrophy disorders in a large clinical care cohort. We interrogated the electronic health record (EHR) information of >1.3 million adults from the Geisinger Health System for lipodystrophy diagnostic codes. We estimate a clinical prevalence of disease of 1 in 20,000 individuals. We performed genetic analyses in individuals with available genomic data to identify variants associated with inherited lipodystrophies and examined their EHR for comorbidities associated with lipodystrophy. We identified 16 individuals carrying the p.R482Q pathogenic variant in LMNA associated with Dunnigan familial partial lipodystrophy. Four had a clinical diagnosis of lipodystrophy, whereas the remaining had no documented clinical diagnosis despite having accompanying metabolic abnormalities. We observed a lipodystrophy-associated variant carrier frequency of 1 in 3,082 individuals in our cohort with substantial burden of metabolic dysregulation. We estimate a genetic prevalence of disease of ∼1 in 7,000 in the general population. Partial lipodystrophy is an underdiagnosed condition. and its prevalence, as defined molecularly, is higher than previously reported. Genetically guided stratification of patients with common metabolic disorders, like diabetes and dyslipidemia, is an important step toward precision medicine.

Published
2019

38. Circulating sex hormone binding globulin levels are modified with intensive lifestyle intervention, but their changes did not independently predict diabetes risk in the Diabetes Prevention Program

Author

Mike Reidy, Christine Lee, Michael Brändle, Sherita Hill Golden, Samuel Dagogo-Jack, David Kessler, Elizabeth Barrett-Connor, Steve Jones, Ling Chen, Judith Wylie-Rosett, Ping Zhang, Paula Williamson, Carlos Lorenzo, Leigh Perreault, Dana Dabelea, Santica Marcovina, Rachel Williams, Marie Smith, Carmen Pal, Patricia Katz, William H. Herman, Sharon L Edelstein, Yong Ma, Vanita R Aroda, Costas A Christophi, Catherine Kim, Sherita H Golden, Edward Horton, Kieren J Mather, George A. Bray, Kishore Gadde, Iris W. Culbert, Jennifer Arceneaux, Annie Chatellier, Amber Dragg, Catherine M. Champagne, Crystal Duncan, Barbara Eberhardt, Frank Greenway, Fonda G. Guillory, April A. Herbert, Michael L. Jeffirs, Betty M. Kennedy, Erma Levy, Monica Lockett, Jennifer C. Lovejoy, Laura H. Morris, Lee E. Melancon, Donna H. Ryan, Deborah A. Sanford, Kenneth G. Smith, Lisa L. Smith, Julia A. St, Richard T. Tulley Amant, Paula C. Vicknair, Donald Williamson, Jeffery J. Zachwieja, Kenneth S. Polonsky, Janet Tobian, David A. Ehrmann, Margaret J. Matulik, Bart Clark, Kirsten Czech, Catherine DeSandre, Ruthanne Hilbrich, Wylie McNabb, Ann R. Semenske, Jose F. Caro, Kevin Furlong, Barry J. Goldstein, Pamela G. Watson, Kellie A. Smith, Jewel Mendoza, Wendi Wildman, Renee Liberoni, John Spandorfer, Constance Pepe, Richard P. Donahue, Ronald B. Goldberg, Ronald Prineas, Jeanette Calles, Juliet Ojito, Patricia Rowe, Paul Cassanova-Romero, Sumaya Castillo-Florez, Hermes J. Florez, Anna Giannella, Lascelles Kirby, Carmen Larreal, Olga Lara, Valerie McLymont, Jadell Mendez, Arlette Perry, Patrice Saab, Beth Veciana, Steven M. Haffner, Helen P. Hazuda, Maria G. Montez, Kathy Hattaway, Arlene Martinez, Tatiana Walker, Richard F. Hamman, Patricia V. Nash, Sheila C. Steinke, Lisa Testaverde, Denise R. Anderson, Larry B. Ballonoff, Alexis Bouffard, Brian Bucca, B. Ned Calonge, Lynne Delve, Martha Farago, James O. Hill, Shelley R. Hoyer, Tonya Jenkins, Bonnie T. Jortberg, Dione Lenz, Marsha Miller, David W. Price, Judith G. Regensteiner, Helen Seagle, Carissa M. Smith, Brent VanDorsten, Edward S. Horton, Kathleen E. Lawton, Catherine S. Poirier, Kati Swift, Ronald A. Arky, Marybeth Bryant, Jacqueline P. Burke, Enrique Caballero, Karen M. Callaphan, Barbara Fargnoli, Therese Franklin, Om P. Ganda, Ashley Guidi, Mathew Guido, Sharon D. Jackson, Alan M. Jacobsen, Lori Lambert, Sarah Ledbury, Margaret Kocal, Lyn M. Kula, Maureen A. Malloy, Maryanne Nicosia, Cathryn F. Oldmixon, Jocelyn Pan, Marizel Quitingon, Stacy Rubtchinsky, Jessica Sansoucy, Dana Schweizer, Ellen W. Seely, Donald Simonson, Fannie Smith, Caren G. Solomon, Jeanne Spellman, James Warram, Steven E. Kahn, Brenda K. Montgomery, Wilfred Fujimoto, Robert H. Knopp, Edward W. Lipkin, Michelle Marr, Ivy Morgan-Taggart, Anne Murillo, Dace Trence, Lonnese Taylor, April Thomas, Elaine C. Tsai, Abbas E. Kitabchi, Mary E. Murphy, Laura Taylor, Jennifer Dolgoff, William B. Applegate, Michael Bryer-Ash, Debra Clark, Sandra L. Frieson, Uzoma Ibebuogu, Raed Imseis, Helen Lambeth, Lynne C. Lichtermann, Hooman Oktaei, Harriet Ricks, Lily M.K. Rutledge, Amy R. Sherman, Clara M. Smith, Judith E. Soberman, Beverly Williams-Cleaves, Boyd E. Metzger, Mark E. Molitch, Mariana K. Johnson, Daphne T. Adelman, Catherine Behrends, Michelle Cook, Marian Fitzgibbon, Mimi M. Giles, Deloris Heard, Cheryl K.H. Johnson, Diane Larsen, Anne Lowe, Megan Lyman, David McPherson, Samsam C. Penn, Thomas Pitts, Renee Reinhart, Susan Roston, Pamela A. Schinleber, David M. Nathan, Charles McKitrick, Heather Turgeon, Mary Larkin, Kathy Abbott, Ellen Anderson, Laurie Bissett, Kristy Bondi, Enrico Cagliero, Jose C. Florez, Kali D’Anna, Linda Delahanty, Valerie Goldman, Peter Lou, Alexandra Poulos, Elyse Raymond, Christine Stevens, Beverly Tseng, Jerrold M. Olefsky, Mary Lou Carrion-Petersen, Madeline Beltran, Lauren N. Claravall, Jonalle M. Dowden, Steven V. Edelman, Robert R. Henry, Javiva Horne, Marycie Lamkin, Simona Szerdi Janesch, Diana Leos, Sunder Mudaliar, William Polonsky, Jean Smith, Jennifer Torio-Hurley, Karen Vejvoda, F. Xavier Pi-Sunyer, Jane E. Lee, David B. Allison, Nnenna Agharanya, Nancy J. Aronoff, Maria Baldo, Jill P. Crandall, Sandra T. Foo, Susan Hagamen, Jose A. Luchsinger, Kathy Parkes, Mary Beth Pena, Ellen S. Rooney, Gretchen E.H. Van Wye, Kristine A. Viscovich, David G. Marrero, Kieren J. Mather, Melvin J. Prince, Susie M. Kelly, Marcia A. Jackson, Gina McAtee, Paula Putenney, Ronald T. Ackermann, Carolyn M. Cantrell, Yolanda F. Dotson, Edwin S. Fineberg, Megan Fultz, John C. Guare, Angela Hadden, James M. Ignaut, Marion S. Kirkman, Erin O’Kelly Phillips, Beverly D. Porter, Paris J. Roach, Nancy D. Rowland, Madelyn L. Wheeler, Vanita Aroda, Robert E. Ratner, Gretchen Youssef, Sue Shapiro, Catherine Bavido-Arrage, Geraldine Boggs, Marjorie Bronsord, Ernestine Brown, Wayman W. Cheatham, Susan Cola, Cindy Evans, Peggy Gibbs, Tracy Kellum, Renee Wiggins, Milvia Lagarda, Lilia Leon, Claresa Levatan, Milajurine Lindsay, Asha K. Nair, Maureen Passaro, Angela Silverman, Gabriel Uwaifo, Debra Wells-Thayer, Mohammed F. Saad, Karol Watson, Maria Budget, Sujata Jinagouda, Medhat Botrous, Khan Akbar, Claudia Conzues, Perpetua Magpuri, Kathy Ngo, Amer Rassam, Debra Waters, Kathy Xapthalamous, Julio V. Santiago, Neil H. White, Angela L. Brown, Samia Das, Prajakta Khare-Ranade, Tamara Stich, Ana Santiago, Edwin Fisher, Emma Hurt, Tracy Jones, Michelle Kerr, Lucy Ryder, Cormarie Wernimont, Christopher D. Saudek, Vanessa Bradley, Emily Sullivan, Tracy Whittington, Caroline Abbas, Adrienne Allen, Frederick L. Brancati, Sharon Cappelli, Jeanne M. Clark, Jeanne B. Charleston, Janice Freel, Katherine Horak, Alicia Greene, Dawn Jiggetts, Deloris Johnson, Hope Joseph, Kimberly Loman, Henry Mosley, John Reusing, Richard R. Rubin, Alafia Samuels, Thomas Shields, Shawne Stephens, Kerry J. Stewart, LeeLana Thomas, Evonne Utsey, David S. Schade, Karwyn S. Adams, Janene L. Canady, Carolyn Johannes, Claire Hemphill, Penny Hyde, Leslie F. Atler, Patrick J. Boyle, Mark R. Burge, Lisa Chai, Kathleen Colleran, Ysela Gonzales, Doris A. Hernandez-McGinnis, Carolyn King, Sofya Rubinchik, Willette Senter, Jill Crandall, Harry Shamoon, Janet O. Brown, Gilda Trandafirescu, Elsie Adorno, Liane Cox, Helena Duffy, Samuel Engel, Allison Friedler, Angela Goldstein, Crystal J. Howard-Century, Jennifer Lukin, Stacey Kloiber, Nadege Longchamp, Helen Martinez, Dorothy Pompi, Jonathan Scheindlin, Elissa Violino, Elizabeth A. Walker, Elise Zimmerman, Joel Zonszein, Trevor Orchard, Rena R. Wing, Susan Jeffries, Gaye Koenning, M. Kaye Kramer, Susan Barr, Catherine Benchoff, Miriam Boraz, Lisa Clifford, Rebecca Culyba, Marlene Frazier, Ryan Gilligan, Stephanie Guimond, Susan Harrier, Louann Harris, Andrea Kriska, Bonny Rockette-Wagner, Qurashia Manjoo, Monica Mullen, Alicia Noel, Amy Otto, Jessica Pettigrew, Debra Rubinstein, Linda Semler, Cheryl F. Smith, Elizabeth Venditti, Valarie Weinzierl, Katherine V. Williams, Tara Wilson, Richard F. Arakaki, Renee W. Latimer, Narleen K. Baker-Ladao, Mae K. Isonaga, Ralph Beddow, Nina E. Bermudez, Lorna Dias, Jillian Inouye, Marjorie K. Mau, John S. Melish, Kathy Mikami, Pharis Mohideen, Sharon K. Odom, Raynette U. Perry, Robin E. Yamamoto, William C. Knowler, Norman Cooeyate, Mary A. Hoskin, Carol A. Percy, Alvera Enote, Camille Natewa, Kelly J. Acton, Vickie L. Andre, Rosalyn Barber, Shandiin Begay, Peter H. Bennett, Mary Beth Benson, Evelyn C. Bird, Brenda A. Broussard, Brian C. Bucca, Marcella Chavez, Sherron Cook, Jeff Curtis, Tara Dacawyma, Matthew S. Doughty, Roberta Duncan, Charlotte Dodge, Cyndy Edgerton, Jacqueline M. Ghahate, Justin Glass, Martia Glass, Dorothy Gohdes, Wendy Grant, Robert L. Hanson, Ellie Horse, Louise E. Ingraham, Merry Jackson, Priscilla Jay, Roylen S. Kaskalla, Kathleen M. Kobus, Jonathan Krakoff, Jason Kurland, Catherine Manus, Cherie McCabe, Sara Michaels, Tina Morgan, Yolanda Nashboo, Julie A. Nelson, Steven Poirier, Evette Polczynski, Christopher Piromalli, Jeanine Roumain, Debra Rowse, Robert J. Roy, Sandra Sangster, Janet Sewenemewa, Miranda Smart, Darryl Tonemah, Charlton Wilson, Michelle Yazzie, Raymond Bain, Sarah Fowler, Marinella Temprosa, Michael D. Larsen, Tina Brenneman, Sharon L. Edelstein, Solome Abebe, Julie Bamdad, Melanie Barkalow, Joel Bethepu, Tsedenia Bezabeh, Nicole Butler, Jackie Callaghan, Caitlin E. Carter, Costas Christophi, Gregory M. Dwyer, Mary Foulkes, Yuping Gao, Robert Gooding, Adrienne Gottlieb, Kristina L. Grimes, Nisha Grover-Fairchild, Lori Haffner, Heather Hoffman, Kathleen Jablonski, Tara L. Jones, Richard Katz, Preethy Kolinjivadi, John M. Lachin, Pamela Mucik, Robert Orlosky, Qing Pan, Susan Reamer, James Rochon, Alla Sapozhnikova, Hanna Sherif, Charlotte Stimpson, Ashley Hogan Tjaden, Fredricka Walker-Murray, Elizabeth M. Venditti, Andrea M. Kriska, Valerie Weinzierl, Jessica Harting, F. Alan Aldrich, John Albers, Greg Strylewicz, R. Eastman, Judith Fradkin, Sanford Garfield, Edward Gregg, Morton B. Brown, David Altshuler, Liana K. Billings, Maegan Harden, Toni I. Pollin, Alan R. Shuldiner, Paul W. Franks, and Marie-France Hivert

Subjects
Male, Aging, Endocrinology, Diabetes and Metabolism, primary prevention, Overweight, Cardiovascular, Medical and Health Sciences, lcsh:Diseases of the endocrine glands. Clinical endocrinology, law.invention, Impaired glucose tolerance, 0302 clinical medicine, Sex hormone-binding globulin, Randomized controlled trial, law, Sex Hormone-Binding Globulin, polycyclic compounds, skin and connective tissue diseases, reproductive and urinary physiology, biology, DPP Research Group, Diabetes, Metformin, type 2, 030220 oncology & carcinogenesis, diabetes mellitus, Female, Clinical care/Education/Nutrition, medicine.symptom, hormones, hormone substitutes, and hormone antagonists, medicine.drug, medicine.medical_specialty, Diabetes risk, hormone, Clinical Trials and Supportive Activities, Clinical Sciences, 030209 endocrinology & metabolism, Placebo, 03 medical and health sciences, Clinical Research, Internal medicine, Diabetes mellitus, Health Sciences, Glucose Intolerance, Diabetes Mellitus, medicine, Humans, Obesity, Life Style, Metabolic and endocrine, Nutrition, lcsh:RC648-665, business.industry, Prevention, life style, medicine.disease, Estrogen, Diabetes Mellitus, Type 2, biology.protein, 3.1 Primary prevention interventions to modify behaviours or promote wellbeing, sense organs, business
Abstract

IntroductionSex hormone binding globulin (SHBG) levels are reported to be inversely associated with diabetes risk. It is unknown whether diabetes prevention interventions increase SHBG and whether resultant changes in SHBG affect diabetes risk. The purpose of this analysis was to determine whether intensive lifestyle intervention (ILS) or metformin changed circulating SHBG and if resultant changes influenced diabetes risk in the Diabetes Prevention Program (DPP).Research design and methodsThis is a secondary analysis from the DPP (1996–2001), a randomized trial of ILS or metformin versus placebo on diabetes risk over a mean follow-up of 3.2 years. The DPP was conducted across 27 academic study centers in the USA. Men, premenopausal and postmenopausal women without hormone use in the DPP were evaluated. The DPP included overweight/obese persons with elevated fasting glucose and impaired glucose tolerance. Main outcomes measures were changes in SHBG levels at 1 year and risk of diabetes over 3 years.ResultsILS resulted in significantly higher increases (postmenopausal women: pConclusionsLifestyle intervention may be associated with favorable changes in circulating SHBG, which is largely due to changes in adiposity. Changes in circulating SHBG do not independently predict reductions in diabetes incidence.

Published
2020

39. From Genotype to Phenotype: Nonsense Variants in SLC13A1 Are Associated with Decreased Serum Sulfate and Increased Serum Aminotransferases

Author

James A. Perry, Leslie E. Anforth, Laura M. Yerges-Armstrong, Joshua P. Lewis, Alan R. Shuldiner, Kathleen A. Ryan, Christina G. Tise, Joshua D. Backman, Mary Pavlovich, and Jeffrey R. O'Connell

Subjects
Male, 0301 basic medicine, Genome-wide association study, QH426-470, 030204 cardiovascular system & hematology, Kidney, 0302 clinical medicine, Bone Density, Missense mutation, Intestinal Mucosa, Cation Transport Proteins, Exome, Genetics (clinical), media_common, Genetics, education.field_of_study, Old Order Amish, Symporters, Sulfates, Middle Aged, Liver, Codon, Nonsense, Sulfate Transporters, Female, Chemical and Drug Induced Liver Injury, SLC13A1, Adult, Heterozygote, medicine.medical_specialty, media_common.quotation_subject, Nonsense, Population, Investigations, Biology, loss-of-function variants, Polymorphism, Single Nucleotide, 03 medical and health sciences, Dogs, Internal medicine, GWAS/ExWAS, medicine, Animals, Humans, education, Molecular Biology, Allele frequency, Transaminases, Acetaminophen, Aged, Sodium Sulfate Cotransporter, Sheep, Membrane Transport Proteins, serum sulfate, 030104 developmental biology, Endocrinology, Calcium, Amish, Founder effect
Abstract

Using genomic applications to glean insights into human biology, we systematically searched for nonsense single nucleotide variants (SNVs) that are rare in the general population but enriched in the Old Order Amish (Amish) due to founder effect. We identified two nonlinked, nonsense SNVs (R12X and W48X) in SLC13A1 (allele frequencies 0.29% and 0.74% in the Amish; enriched 1.2-fold and 3.7-fold, compared to the outbred Caucasian population, respectively). SLC13A1 encodes the apical sodium-sulfate cotransporter (NaS1) responsible for sulfate (re)absorption in the kidneys and intestine. SLC13A1 R12X and W48X were independently associated with a 27.6% (P = 2.7 × 10−8) and 27.3% (P = 6.9 × 10−14) decrease in serum sulfate, respectively (P = 8.8 × 10-20 for carriers of either SLC13A1 nonsense SNV). We further performed the first exome- and genome-wide association study (ExWAS/GWAS) of serum sulfate and identified a missense variant (L348P) in SLC26A1, which encodes the basolateral sulfate-anion transporter (Sat1), that was associated with decreased serum sulfate (P = 4.4 × 10−12). Consistent with sulfate’s role in xenobiotic detoxification and protection against acetaminophen-induced hepatotoxicity, SLC13A1 nonsense SNV carriers had higher aminotransferase levels compared to noncarriers. Furthermore, SLC26A1 L348P was associated with lower whole-body bone mineral density (BMD) and higher serum calcium, consistent with the osteochondrodysplasia exhibited by dogs and sheep with naturally occurring, homozygous, loss-of-function mutations in Slc13a1. This study demonstrates the power and translational potential of systematic identification and characterization of rare, loss-of-function variants and warrants additional studies to better understand the importance of sulfate in human physiology, disease, and drug toxicity.

Published
2016

40. Cognitive profiles and heritability estimates in the Old Order Amish

Author

Anya Savransky, Katie L. Nugent, Deanna E. Jurius, Braxton D. Mitchell, Ryan M. Kuehner, Alan R. Shuldiner, L. Elliot Hong, Christopher Gaudiot, James M. Gold, Heather Bruce, and Peter Kochunov

Subjects
Adult, Male, 050103 clinical psychology, Repeatable Battery for the Assessment of Neuropsychological Status, Psychometrics, Population, Neuropsychological Tests, Article, 03 medical and health sciences, Cognition, 0302 clinical medicine, Genetics, Humans, 0501 psychology and cognitive sciences, education, Biological Psychiatry, Genetics (clinical), education.field_of_study, 05 social sciences, Neuropsychology, Reproducibility of Results, Middle Aged, Pennsylvania, Heritability, Psychiatry and Mental health, Old Order Amish, Normative, Female, Amish, Cognition Disorders, Psychology, 030217 neurology & neurosurgery, Clinical psychology
Abstract

OBJECTIVE This study aimed to establish the applicability of the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) in the Old Order Amish (OOA) and to assess the genetic contribution toward the RBANS total score and its cognitive domains using a large family-based sample of OOA. PARTICIPANTS AND METHODS RBANS data were collected in 103 OOA individuals from Lancaster County, Pennsylvania, including 85 individuals without psychiatric illness and 18 individuals with current psychiatric diagnoses. RESULTS The RBANS total score and all five cognitive domains of in nonpsychiatric OOA were within half a SD of the normative data of the general population. The RBANS total score was highly heritable (h=0.51, P=0.019). OOA with psychiatric diagnoses had a numerically lower RBANS total score and domain scores compared with the nonpsychiatric participants. CONCLUSION The RBANS appears to be a suitable cognitive battery for the OOA population as measurements obtained from the OOA are comparable with normative data in the US population. The heritability estimated from the OOA is in line with heritabilities of other cognitive batteries estimated in other populations. These results support the use of RBANS in cognitive assessment, clinical care, and behavioral genetic studies of neuropsychological functioning in this population.

Published
2016

41. Gene Expression Differences Between Offspring of Long-Lived Individuals and Controls in Candidate Longevity Regions: Evidence forPAPSS2as a Longevity Gene

Author

Coleen M. Damcott, Braxton D. Mitchell, Laura M. Yerges-Armstrong, Joanne E. Curran, Sumbul Chai, John Blangero, Alan R. Shuldiner, and Jeffery R. O'Connell

Subjects
Male, 0301 basic medicine, Premature aging, Aging, Offspring, media_common.quotation_subject, Longevity, Gene Expression, Locus (genetics), Single-nucleotide polymorphism, Genome-wide association study, 030105 genetics & heredity, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Multienzyme Complexes, Humans, SNP, Gene, media_common, Aged, 80 and over, Genetics, Brief Report, Middle Aged, Pennsylvania, Sulfate Adenylyltransferase, 030104 developmental biology, Evolutionary biology, Case-Control Studies, Female, Geriatrics and Gerontology, Amish, Genome-Wide Association Study
Abstract

Although there is compelling evidence for a genetic contribution to longevity, identification of specific genes that robustly associate with longevity has been a challenge. In order to identify longevity-enhancing genes, we measured differential gene expression between offspring of long-lived Amish (older than 90 years; cases, n = 128) and spouses of these offspring (controls, n = 121) and correlated differentially expressed transcripts with locations of longevity-associated variants detected in a prior genome-wide association study (GWAS) of survival to age 90. Expression of one of these transcripts, 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (PAPSS2), was significantly higher in offspring versus controls (4×10(-4)) and this association was replicated using quantitative real-time polymerase chain reaction. PAPSS2, a sulfation enzyme located on chromosome 10, is ~80kb upstream of the PAPSS2 transcription start site. We found evidence of cis-expression for the originally reported GWAS SNP and PAPSS2 Monogenic conditions linked to PAPSS2 include andrenocortical androgen excess resulting in premature pubarche and skeletal dysplasias, both of which have premature aging features. In summary, these findings provide novel evidence for PAPSS2 as a longevity locus and illustrate the value of harnessing multiple "-omic" approaches to identify longevity candidates.

Published
2016

42. Increased usual physical activity is associated with a blunting of the triglyceride response to a high-fat meal

Author

Soren Snitker, Joshua P. Lewis, Nanette I. Steinle, Gurmannat Kalra, Michael Miller, Simeon I. Taylor, Man Zhang, Huichun Xu, Alan R. Shuldiner, Kathleen A. Ryan, Braxton D. Mitchell, and Carole Sztalryd

Subjects
Adult, Male, Risk, medicine.medical_specialty, Endocrinology, Diabetes and Metabolism, Cardiovascular health, Physical activity, Coronary Disease, Hyperlipidemias, 030204 cardiovascular system & hematology, Diet, High-Fat, Article, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Internal medicine, Internal Medicine, medicine, Humans, 030212 general & internal medicine, Significant risk, Exercise, Fasting state, Triglycerides, Meal, Nutrition and Dietetics, Triglyceride, business.industry, Age Factors, Middle Aged, Postprandial Period, Coronary heart disease, Endocrinology, Postprandial, Cross-Sectional Studies, chemistry, Female, Cardiology and Cardiovascular Medicine, business, Amish
Abstract

BACKGROUND: Post-prandial lipemia (PPL), defined as a prolonged or elevated rise in triglycerides that accompanies fat feeding, is a significant risk factor for coronary heart disease (CHD) and associated comorbidities. The impact of PPL on CHD risk is underscored by the preponderance of each day spent in the post-prandial state. OBJECTIVE: In this study, we evaluated cross-sectionally the association between usual (i.e., non-interventional) physical activity and the 6-hour triglyceride response to a standardized high-fat meal. METHODS: The high-fat meal intervention was carried out in 671 apparently healthy individuals as part of the Hereditary and Phenotype Intervention (HAPI) Heart Study. Triglyceride levels were measured in the fasting state and during six hours following administration of a standardized fat challenge. We defined PPL response as the triglyceride area under the fat load curve (AUC) and measured physical activity using accelerometers that were worn continuously over a 7-day period. RESULTS: Physical activity levels decreased with increasing age and were higher in men than women (both p < 0.001). The triglyceride AUC increased with increasing age in both men and women (both p

Published
2018

43. Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders

Author

Symen Ligthart, Ahmad Vaez, Urmo Võsa, Maria G. Stathopoulou, Paul S. de Vries, Bram P. Prins, Peter J. Van der Most, Toshiko Tanaka, Elnaz Naderi, Lynda M. Rose, Ying Wu, Robert Karlsson, Maja Barbalic, Honghuang Lin, René Pool, Gu Zhu, Aurélien Macé, Carlo Sidore, Stella Trompet, Massimo Mangino, Maria Sabater-Lleal, John P. Kemp, Ali Abbasi, Tim Kacprowski, Niek Verweij, Albert V. Smith, Tao Huang, Carola Marzi, Mary F. Feitosa, Kurt K. Lohman, Marcus E. Kleber, Yuri Milaneschi, Christian Mueller, Mahmudul Huq, Efthymia Vlachopoulou, Leo-Pekka Lyytikäinen, Christopher Oldmeadow, Joris Deelen, Markus Perola, Jing Hua Zhao, Bjarke Feenstra, Marzyeh Amini, Jari Lahti, Katharina E. Schraut, Myriam Fornage, Bhoom Suktitipat, Wei-Min Chen, Xiaohui Li, Teresa Nutile, Giovanni Malerba, Jian’an Luan, Tom Bak, Nicholas Schork, Fabiola Del Greco M., Elisabeth Thiering, Anubha Mahajan, Riccardo E. Marioni, Evelin Mihailov, Joel Eriksson, Ayse Bilge Ozel, Weihua Zhang, Maria Nethander, Yu-Ching Cheng, Stella Aslibekyan, Wei Ang, Ilaria Gandin, Loïc Yengo, Laura Portas, Charles Kooperberg, Edith Hofer, Kumar B. Rajan, Claudia Schurmann, Wouter den Hollander, Tarunveer S. Ahluwalia, Jing Zhao, Harmen H.M. Draisma, Ian Ford, Nicholas Timpson, Alexander Teumer, Hongyan Huang, Simone Wahl, YongMei Liu, Jie Huang, Hae-Won Uh, Frank Geller, Peter K. Joshi, Lisa R. Yanek, Elisabetta Trabetti, Benjamin Lehne, Diego Vozzi, Marie Verbanck, Ginevra Biino, Yasaman Saba, Ingrid Meulenbelt, Jeff R. O’Connell, Markku Laakso, Franco Giulianini, Patrik K.E. Magnusson, Christie M. Ballantyne, Jouke Jan Hottenga, Grant W. Montgomery, Fernando Rivadineira, Rico Rueedi, Maristella Steri, Karl-Heinz Herzig, David J. Stott, Cristina Menni, Mattias Frånberg, Beate St. Pourcain, Stephan B. Felix, Tune H. Pers, Stephan J.L. Bakker, Peter Kraft, Annette Peters, Dhananjay Vaidya, Graciela Delgado, Johannes H. Smit, Vera Großmann, Juha Sinisalo, Ilkka Seppälä, Stephen R. Williams, Elizabeth G. Holliday, Matthijs Moed, Claudia Langenberg, Katri Räikkönen, Jingzhong Ding, Harry Campbell, Michele M. Sale, Yii-Der I. Chen, Alan L. James, Daniela Ruggiero, Nicole Soranzo, Catharina A. Hartman, Erin N. Smith, Gerald S. Berenson, Christian Fuchsberger, Dena Hernandez, Carla M.T. Tiesler, Vilmantas Giedraitis, David Liewald, Krista Fischer, Dan Mellström, Anders Larsson, Yunmei Wang, William R. Scott, Matthias Lorentzon, John Beilby, Kathleen A. Ryan, Craig E. Pennell, Dragana Vuckovic, Beverly Balkau, Maria Pina Concas, Reinhold Schmidt, Carlos F. Mendes de Leon, Erwin P. Bottinger, Margreet Kloppenburg, Lavinia Paternoster, Michael Boehnke, A.W. Musk, Gonneke Willemsen, David M. Evans, Pamela A.F. Madden, Mika Kähönen, Zoltán Kutalik, Magdalena Zoledziewska, Ville Karhunen, Stephen B. Kritchevsky, Naveed Sattar, Genevieve Lachance, Robert Clarke, Tamara B. Harris, Olli T. Raitakari, John R. Attia, Diana van Heemst, Eero Kajantie, Rossella Sorice, Giovanni Gambaro, Robert A. Scott, Andrew A. Hicks, Luigi Ferrucci, Marie Standl, Cecilia M. Lindgren, John M. Starr, Magnus Karlsson, Lars Lind, Jun Z. Li, John C. Chambers, Trevor A. Mori, Eco J.C.N. de Geus, Andrew C. Heath, Nicholas G. Martin, Juha Auvinen, Brendan M. Buckley, Anton J.M. de Craen, Melanie Waldenberger, Konstantin Strauch, Thomas Meitinger, Rodney J. Scott, Mark McEvoy, Marian Beekman, Cristina Bombieri, Paul M. Ridker, Karen L. Mohlke, Nancy L. Pedersen, Alanna C. Morrison, Dorret I. Boomsma, John B. Whitfield, David P. Strachan, Albert Hofman, Peter Vollenweider, Francesco Cucca, Marjo-Riitta Jarvelin, J. Wouter Jukema, Tim D. Spector, Anders Hamsten, Tanja Zeller, André G. Uitterlinden, Matthias Nauck, Vilmundur Gudnason, Lu Qi, Harald Grallert, Ingrid B. Borecki, Jerome I. Rotter, Winfried März, Philipp S. Wild, Marja-Liisa Lokki, Michael Boyle, Veikko Salomaa, Mads Melbye, Johan G. Eriksson, James F. Wilson, Brenda W.J.H. Penninx, Diane M. Becker, Bradford B. Worrall, Greg Gibson, Ronald M. Krauss, Marina Ciullo, Gianluigi Zaza, Nicholas J. Wareham, Albertine J. Oldehinkel, Lyle J. Palmer, Sarah S. Murray, Peter P. Pramstaller, Stefania Bandinelli, Joachim Heinrich, Erik Ingelsson, Ian J. Deary, Reedik Mägi, Liesbeth Vandenput, Pim van der Harst, Karl C. Desch, Jaspal S. Kooner, Claes Ohlsson, Caroline Hayward, Terho Lehtimäki, Alan R. Shuldiner, Donna K. Arnett, Lawrence J. Beilin, Antonietta Robino, Philippe Froguel, Mario Pirastu, Tine Jess, Wolfgang Koenig, Ruth J.F. Loos, Denis A. Evans, Helena Schmidt, George Davey Smith, P. Eline Slagboom, Gudny Eiriksdottir, Andrew P. Morris, Bruce M. Psaty, Russell P. Tracy, Ilja M. Nolte, Eric Boerwinkle, Sophie Visvikis-Siest, Alex P. Reiner, Myron Gross, Joshua C. Bis, Lude Franke, Oscar H. Franco, Emelia J. Benjamin, Daniel I. Chasman, Josée Dupuis, Harold Snieder, Abbas Dehghan, Behrooz Z. Alizadeh, H. Marike Boezen, Gerjan Navis, Marianne Rots, Morris Swertz, Bruce H.R. Wolffenbuttel, Cisca Wijmenga, Emelia Benjamin, Tarunveer Singh Ahluwalia, James Meigs, Russell Tracy, Josh Bis, Nathan Pankratz, Alex Rainer, James G. Wilson, Josee Dupuis, Bram Prins, Urmo Vaso, Maria Stathopoulou, Terho Lehtimaki, Yalda Jamshidi, Sophie Siest, Andre G. Uitterlinden, Mohammadreza Abdollahi, Renate Schnabel, Ursula M. Schick, Aldi Kraja, Yi-Hsiang Hsu, Daniel S. Tylee, Alyson Zwicker, Rudolf Uher, George Davey-Smith, Andrew Hicks, Cornelia M. van Duijn, Cavin Ward-Caviness, J. Rotter, Ken Rice, Leslie Lange, Eco de Geus, Kari Matti Makela, David Stacey, Johan Eriksson, Tim M. Frayling, Eline P. Slagboom, Erasmus University Medical Center [Rotterdam] (Erasmus MC), University Medical Center Groningen [Groningen] (UMCG), University of Isfahan, University of Tartu, Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire (IGE-PCV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), The University of Texas Health Science Center at Houston (UTHealth), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Brigham and Women's Hospital [Boston], University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], University of Split, Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Process & Energy Laboratory, Delft University of Technology (TU Delft), Grand Lyon : communauté urbaine de Lyon, Interuniversity Cardiology Institute Netherlands, Department of Twin Research and Genetic Epidemiology, King's College London, London, Huazhong University of Science and Technology [Wuhan] (HUST), Division of Statistical Genomics, Washington University School of Medicine, Department of Psychiatry, VU University Medical Center [Amsterdam], Institut fuer Theoretische Physik (Institut fuer Theoretische Physik), Universität Heidelberg [Heidelberg] = Heidelberg University, Molecular Epidemiology, MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Mahidol University [Bangkok], Northwest A and F University, Laboratoire d'Optimisation des Systèmes Industriels (LOSI), Institut Charles Delaunay (ICD), Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS), Institute of Genetics and Biophysics, CNR, Naples, Università degli studi di Verona = University of Verona (UNIVR), Department of Molecular Medicine [Scripps Research Institute], The Scripps Research Institute [La Jolla, San Diego], Department of Physics, Indian Institute of Technology Kanpur (IIT Kanpur), Deptartment of Medical Biochemistry and Microbiology, Uppsala University, Department of Electrical and Computer Engineering [Waterloo] (ECE), University of Waterloo [Waterloo], University of Maryland School of Medicine, University of Maryland System, Institut National de l'Environnement Industriel et des Risques (INERIS), Institute of Pop. Genetics, CNR, Sassari, Interfaculty Institute for Genetics and Functional Genomics, Universität Greifswald - University of Greifswald, IT University of Copenhagen (ITU), Robertson Centre for Biostatistics, University of Glasgow, Centre for Causal Analyses in Translational Epidemiology, University of Bristol [Bristol]-Medical Research Council, King‘s College London, Jinan University [Guangzhou], Institute of Oceanology [China], School Medicine, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), General Internal Medicine, Johns Hopkins School of Medicine, Johns Hopkins University School of Medicine [Baltimore], Shardna life science Pula Cagliari, Section Molecular Epidemiology, Leiden University Medical Center (LUMC), Department of Medicine, University of Eastern Finland-Kuopio University Hospital, Medstar Research Institute, Department of Cardiology, Ernst-Moritz-Arndt University, Center for Biological Sequence Analysis [Lyngby], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Department of Internal Medicine, University of Groningen and University Medical Center Groningen, Department of Epidemiology, Harvard School of Public Health, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Metacohorts Consortium, INEOS Technologies (SWITZERLAND), MRC Epidemiology Unit, University of Cambridge [UK] (CAM)-Institute of Metabolic Science, University of Edinburgh, School of Population Health [Crawley, Western Australia], The University of Western Australia (UWA), Institute of Genetics and Biophysics, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), The Scripps Translational Science Institute and Scripps Health, Tulane Center for Cardiovascular Health, Tulane University Health Sciences Center, Centre for Population Health Sciences, Genomic Research Laboratory, Service of Infectious Disease, Hôpitaux Universitaires de Genève (HUG), Infectious diseases division, Department of internal medicine, Washington University in Saint Louis (WUSTL), Luleå University of Technology (LUT), Recherche en épidémiologie et biostatistique, Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Austrian Institute of Technology [Vienna] (AIT), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Department of Rheumatology and Clinical Epidemiology, Leiden University Medical Center (LUMC), Department of Rheumatology and Clinical Epidemiology [Leiden University Medical Center] (LUMC), Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden-Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Department of Biostatistics and Center for Statistical Genetics, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, University of Virginia, Tampere University Hospital, Department of Medical Genetics, Université de Lausanne = University of Lausanne (UNIL), Department of Pathological Biochemistry, Royal Infirmary, Oxford University, University of Oxford, University of Newcastle [Callaghan, Australia] (UoN), Department of neurology, Institute of Metabolic Science, MRC, The Wellcome Trust Centre for Human Genetics [Oxford], Uppsala Universitet [Uppsala], QIMR Berghofer Medical Research Institute, Institute of Genetic Epidemiology [Neuherberg, Germany], Institute of Human Genetics, Helmholtz Zentrum München = German Research Center for Environmental Health, Schizophrenia Research Institute [Sydney], Department of Genetics, University of North Carolina System (UNC)-University of North Carolina System (UNC), Vrije Universiteit Brussel (VUB), Population Health Sciences and Education, St George's University of London, Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Institute of Health Sciences and Biocenter Oulu, University of Oulu, Medizinische Klinik und Poliklinik, Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Institute of Clinical Chemistry and Laboratory Medicine, Icelandic Heart Association, Heart Preventive Clinic and Research Institute, Departments of Epidemiology and Nutrition, Institute of Epidemiology [Neuherberg] (EPI), Medical University Graz, Transplantation Laboratory [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Chronic Disease Prevention, National Institute for Health and Welfare [Helsinki], Dept. of Epidemiology Research, Statens Serum Institut [Copenhagen], CLinical Psychology, Genetics and Pathology, Geriatric Rehabilitation Unit, Azienda Sanitaria Firenze, Center For Narcolepsy, Stanford University, Centre for Bone and Arthritis Research, University of Gothenburg (GU)-Institute of Medicine, MRC Human Gentics Unit, Inst Genet and Mol Med, Western General Hospital, Edinburgh, University of Maryland School of Medicine [Baltimore, MD, USA], Génétique des maladies multifactorielles (GMM), Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Stockholm], Stockholm University, University of Bristol [Bristol], Universiteit Leiden, Department of Epidemiology, University of Washington, University of Washington [Seattle], Department of Epidemiology [Rotterdam], University of Groningen [Groningen], Dutch Initiative on Crohn and Colitis (ICC), Icelandic Heart Association [Kopavogur, Iceland] (IHA), Department of Physiology and Biophysics [Jackson, MS, USA], University of Southern Mississippi (USM), Human Genetics Branch, National Institutes of Health [Bethesda] (NIH)-National Institute of Mental Health (NIMH), Faculty of Medicine and Life Sciences [Tampere], University of Tampere [Finland], German Center for Cardiovascular Research (DZHK), Berlin Institute of Health (BIH), MRC Centre for Neuropsychiatric Genetics and Genomics, Medical Research Council-Cardiff University, Department of Social Medicine, School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Department of Medicine [Aurora, CO, USA], University of Colorado [Denver], Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), Mathematical Institute [Oxford] (MI), Institute of Psychiatry, Psychology & Neuroscience, King's College London, LifeLines Cohort Study, CHARGE Inflammation Working Group, Ligthart, S., Vaez, A., Vosa, U., Stathopoulou, M. G., de Vries, P. S., Prins, B. P., Van der Most, P. J., Tanaka, T., Naderi, E., Rose, L. M., Wu, Y., Karlsson, R., Barbalic, M., Lin, H., Pool, R., Zhu, G., Mace, A., Sidore, C., Trompet, S., Mangino, M., Sabater-Lleal, M., Kemp, J. P., Abbasi, A., Kacprowski, T., Verweij, N., Smith, A. V., Huang, T., Marzi, C., Feitosa, M. F., Lohman, K. K., Kleber, M. E., Milaneschi, Y., Mueller, C., Huq, M., Vlachopoulou, E., Lyytikainen, L. -P., Oldmeadow, C., Deelen, J., Perola, M., Zhao, J. H., Feenstra, B., Alizadeh, B. Z., Boezen, H. M., Franke, L., van der Harst, P., Navis, G., Rots, M., Snieder, H., Swertz, M., Wolffenbuttel, B. H. R., Wijmenga, C., Amini, M., Benjamin, E., Chasman, D. I., Dehghan, A., Ahluwalia, T. S., Meigs, J., Tracy, R., Bis, J., Eiriksdottir, G., Pankratz, N., Gross, M., Rainer, A., Wilson, J. G., Psaty, B. M., Dupuis, J., Prins, B., Vaso, U., Stathopoulou, M., Lehtimaki, T., Koenig, W., Jamshidi, Y., Siest, S., Uitterlinden, A. G., Abdollahi, M., Schnabel, R., Schick, U. M., Nolte, I. M., Kraja, A., Hsu, Y. -H., Tylee, D. S., Zwicker, A., Uher, R., Davey-Smith, G., Morrison, A. C., Hicks, A., van Duijn, C. M., Ward-Caviness, C., Boerwinkle, E., Rotter, J., Rice, K., Lange, L., de Geus, E., Morris, A. P., Makela, K. M., Stacey, D., Eriksson, J., Frayling, T. M., Slagboom, E. P., Lahti, J., Schraut, K. E., Fornage, M., Suktitipat, B., Chen, W. -M., Li, X., Nutile, T., Malerba, G., Luan, J., Bak, T., Schork, N., Del Greco, M. F., Thiering, E., Mahajan, A., Marioni, R. E., Mihailov, E., Ozel, A. B., Zhang, W., Nethander, M., Cheng, Y. -C., Aslibekyan, S., Ang, W., Gandin, I., Yengo, L., Portas, L., Kooperberg, C., Hofer, E., Rajan, K. B., Schurmann, C., den Hollander, W., Zhao, J., Draisma, H. H. M., Ford, I., Timpson, N., Teumer, A., Huang, H., Wahl, S., Liu, Y., Huang, J., Uh, H. -W., Geller, F., Joshi, P. K., Yanek, L. R., Trabetti, E., Lehne, B., Vozzi, D., Verbanck, M., Biino, G., Saba, Y., Meulenbelt, I., O'Connell, J. R., Laakso, M., Giulianini, F., Magnusson, P. K. E., Ballantyne, C. M., Hottenga, J. J., Montgomery, G. W., Rivadineira, F., Rueedi, R., Steri, M., Herzig, K. -H., Stott, D. J., Menni, C., Franberg, M., S, t. Pourcain B., Felix, S. B., Pers, T. H., Bakker, S. J. L., Kraft, P., Peters, A., Vaidya, D., Delgado, G., Smit, J. H., Grossmann, V., Sinisalo, J., Seppala, I., Williams, S. R., Holliday, E. G., Moed, M., Langenberg, C., Raikkonen, K., Ding, J., Campbell, H., Sale, M. M., Chen, Y. -D. I., James, A. L., Ruggiero, D., Soranzo, N., Hartman, C. A., Smith, E. N., Berenson, G. S., Fuchsberger, C., Hernandez, D., Tiesler, C. M. T., Giedraitis, V., Liewald, D., Fischer, K., Mellstrom, D., Larsson, A., Wang, Y., Scott, W. R., Lorentzon, M., Beilby, J., Ryan, K. A., Pennell, C. E., Vuckovic, D., Balkau, B., Concas, M. P., Schmidt, R., Mendes de Leon, C. F., Bottinger, E. P., Kloppenburg, M., Paternoster, L., Boehnke, M., Musk, A. W., Willemsen, G., Evans, D. M., Madden, P. A. F., Kahonen, M., Kutalik, Z., Zoledziewska, M., Karhunen, V., Kritchevsky, S. B., Sattar, N., Lachance, G., Clarke, R., Harris, T. B., Raitakari, O. T., Attia, J. R., van Heemst, D., Kajantie, E., Sorice, R., Gambaro, G., Scott, R. A., Hicks, A. A., Ferrucci, L., Standl, M., Lindgren, C. M., Starr, J. M., Karlsson, M., Lind, L., Li, J. Z., Chambers, J. C., Mori, T. A., de Geus, E. J. C. N., Heath, A. C., Martin, N. G., Auvinen, J., Buckley, B. M., de Craen, A. J. M., Waldenberger, M., Strauch, K., Meitinger, T., Scott, R. J., Mcevoy, M., Beekman, M., Bombieri, C., Ridker, P. M., Mohlke, K. L., Pedersen, N. L., Boomsma, D. I., Whitfield, J. B., Strachan, D. P., Hofman, A., Vollenweider, P., Cucca, F., Jarvelin, M. -R., Jukema, J. W., Spector, T. D., Hamsten, A., Zeller, T., Nauck, M., Gudnason, V., Qi, L., Grallert, H., Borecki, I. B., Rotter, J. I., Marz, W., Wild, P. S., Lokki, M. -L., Boyle, M., Salomaa, V., Melbye, M., Eriksson, J. G., Wilson, J. F., Penninx, B. W. J. H., Becker, D. M., Worrall, B. B., Gibson, G., Krauss, R. M., Ciullo, M., Zaza, G., Wareham, N. J., Oldehinkel, A. J., Palmer, L. J., Murray, S. S., Pramstaller, P. P., Bandinelli, S., Heinrich, J., Ingelsson, E., Deary, I. J., Magi, R., Vandenput, L., Desch, K. C., Kooner, J. S., Ohlsson, C., Hayward, C., Shuldiner, A. R., Arnett, D. K., Beilin, L. J., Robino, A., Froguel, P., Pirastu, M., Jess, T., Loos, R. J. F., Evans, D. A., Schmidt, H., Slagboom, P. E., Tracy, R. P., Visvikis-Siest, S., Reiner, A. P., Bis, J. C., Franco, O. H., Benjamin, E. J., AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, Graduate School, Epidemiology, Internal Medicine, Groningen Institute for Organ Transplantation (GIOT), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Cardiovascular Centre (CVC), Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Stem Cell Aging Leukemia and Lymphoma (SALL), Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), VU University medical center, Psychiatry, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Mental Health, APH - Methodology, APH - Digital Health, Biological Psychology, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, Universität Heidelberg [Heidelberg], University of Verona (UNIVR), Department of Molecular and Experimental Medicine, The Scripps Research Institute, The Scripps Research Institute, Université Grenoble Alpes - UFR Sciences de l'Homme et de la Société (UGA UFR SHS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), IT University of Copenhagen, Technical University of Denmark [Lyngby] (DTU), Consiglio Nazionale delle Ricerche (CNR), University of Virginia [Charlottesville], Université de Lausanne (UNIL), University of Oxford [Oxford], University of Newcastle [Australia] (UoN), Centre d'économie industrielle i3 (CERNA i3), Centre National de la Recherche Scientifique (CNRS)-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Helmholtz-Zentrum München (HZM), Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA (UMR_7583)), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Universitätsmedizin der Johannes-Gutenberg Universität Mainz, University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Cardiff University-Medical Research Council, University of California-University of California, and DE CARVALHO, Philippe

Subjects
0301 basic medicine, Male, Netherlands Twin Register (NTR), Bipolar Disorder, LD SCORE REGRESSION, [SDV]Life Sciences [q-bio], Genome-wide association study, [SDV.GEN] Life Sciences [q-bio]/Genetics, Body Mass Index, inflammatory disorder, 80 and over, WIDE ASSOCIATION, EPIDEMIOLOGY, ta318, International HapMap Project, Child, Genetics (clinical), 2. Zero hunger, Genetics, Genetics & Heredity, Aged, 80 and over, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, C-reactive proteingenome-wide association studyinflammationMendelian randomizationinflammatory disordersDEPICTcoronary artery diseaseschizophreniasystem biology, system biology, DEPICT, Mendelian Randomization Analysis, 11 Medical And Health Sciences, Middle Aged, C-reactive protein, coronary artery disease, genome-wide association study, inflammation, inflammatory disorders, Mendelian randomization, schizophrenia, Adolescent, Adult, Aged, Biomarkers, C-Reactive Protein, Female, Genetic Loci, Genome-Wide Association Study, Humans, Inflammation, Liver, Metabolic Networks and Pathways, Schizophrenia, Young Adult, 3. Good health, [SDV] Life Sciences [q-bio], Medical genetics, Biomarker (medicine), Life Sciences & Biomedicine, Human, medicine.medical_specialty, CHARGE Inflammation Working Group, Biology, IMMUNITY, ta3111, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, medicine, CORONARY-HEART-DISEASE, Mendelian Randomization Analysi, 1000 Genomes Project, METAANALYSIS, Genetic association, [SDV.GEN]Life Sciences [q-bio]/Genetics, Science & Technology, ta1184, Metabolic Networks and Pathway, Biomarker, INSTRUMENTS, 06 Biological Sciences, 030104 developmental biology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, LifeLines Cohort Study
Abstract

International audience; C-reactive protein (CRP) is a sensitive biomarker of chronic low-grade inflammation and is associated with multiple complex diseases. The genetic determinants of chronic inflammation remain largely unknown, and the causal role of CRP in several clinical outcomes is debated. We performed two genome-wide association studies (GWASs), on HapMap and 1000 Genomes imputed data, of circulating amounts of CRP by using data from 88 studies comprising 204,402 European individuals. Additionally, we performed in silico functional analyses and Mendelian randomization analyses with several clinical outcomes. The GWAS meta-analyses of CRP revealed 58 distinct genetic loci (p < 5 × 10-8). After adjustment for body mass index in the regression analysis, the associations at all except three loci remained. The lead variants at the distinct loci explained up to 7.0% of the variance in circulating amounts of CRP. We identified 66 gene sets that were organized in two substantially correlated clusters, one mainly composed of immune pathways and the other characterized by metabolic pathways in the liver. Mendelian randomization analyses revealed a causal protective effect of CRP on schizophrenia and a risk-increasing effect on bipolar disorder. Our findings provide further insights into the biology of inflammation and could lead to interventions for treating inflammation and its clinical consequences.Copyright © 2018 American Society of Human Genetics. All rights reserved.

Published
2018

44. Loss of Function ABCC8 Mutations in Pulmonary Arterial Hypertension

Author

Michael S. Bohnen, Charaka Hadinnapola, Joanna Pepke-Zaba, Anton Vonk Noordegraaf, David G. Kiely, Stephen J. Wort, Andrew J. Peacock, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Erika B. Rosenzweig, Frederick E. Dewey, Wendy K. Chung, Kevin J. Sampson, Mélanie Eyries, Paul A. Corris, Robert S. Kass, Lijiang Ma, Allan Lawrie, Yufeng Shen, Colin G. Nichols, Mark Toshner, Katherine Yates, Jeffrey G. Reid, Christophe Guignabert, Matthias Haimel, J. Simon R. Gibbs, Gerry Coghlan, Marc Humbert, John D. Overton, Harm Jan Bogaard, Arjan C. Houweling, Colin Church, Jennifer M. Martin, Robert V. MacKenzie Ross, Stefan Gräf, Barbara Girerd, Martin R. Wilkins, John Wharton, David Montani, Na Zhu, Marta Bleda, Aris Baras, Florent Soubrier, Conor McClenaghan, Nicholas W. Morrell, Usha Krishnan, Hongjian Qi, Jay Suntharalingam, Richard C. Trembath, Carmen M. Treacy, Pulmonary medicine, ACS - Pulmonary hypertension & thrombosis, Human genetics, ACS - Atherosclerosis & ischemic syndromes, and APH - Quality of Care

Subjects
0301 basic medicine, Adult, Male, medicine.medical_specialty, DNA Mutational Analysis, Mutation, Missense, 030204 cardiovascular system & hematology, Sulfonylurea Receptors, ABCC8, Article, 03 medical and health sciences, 0302 clinical medicine, medicine.artery, Internal medicine, medicine, Humans, Exome, Familial Primary Pulmonary Hypertension, Child, Pathological, Loss function, biology, business.industry, General Medicine, medicine.disease, Pulmonary hypertension, 030104 developmental biology, medicine.anatomical_structure, Amino Acid Substitution, Pulmonary artery, biology.protein, Vascular resistance, Cardiology, Female, business
Abstract

Background: In pulmonary arterial hypertension (PAH), pathological changes in pulmonary arterioles progressively raise pulmonary artery pressure and increase pulmonary vascular resistance, leading to right heart failure and high mortality rates. Recently, the first potassium channelopathy in PAH, because of mutations in KCNK3 , was identified as a genetic cause and pharmacological target. Methods: Exome sequencing was performed to identify novel genes in a cohort of 99 pediatric and 134 adult-onset group I PAH patients. Novel rare variants in the gene identified were independently identified in a cohort of 680 adult-onset patients. Variants were expressed in COS cells and function assessed by patch-clamp and rubidium flux analysis. Results: We identified a de novo novel heterozygous predicted deleterious missense variant c.G2873A (p.R958H) in ABCC8 in a child with idiopathic PAH. We then evaluated all individuals in the original and a second cohort for rare or novel variants in ABCC8 and identified 11 additional heterozygous predicted damaging ABCC8 variants. ABCC8 encodes SUR1 (sulfonylurea receptor 1)—a regulatory subunit of the ATP-sensitive potassium channel. We observed loss of ATP-sensitive potassium channel function for all ABCC8 variants evaluated and pharmacological rescue of all channel currents in vitro by the SUR1 activator, diazoxide. Conclusions: Novel and rare missense variants in ABCC8 are associated with PAH. Identified ABCC8 mutations decreased ATP-sensitive potassium channel function, which was pharmacologically recovered.

Published
2018

45. Evaluation of WISP1 as a candidate gene for bone mineral density in the Old Order Amish

Author

Zhizhen Li, Dongfang Liu, James A. Perry, Zhongliang Deng, Mao Fu, Kathleen A. Ryan, Elizabeth A. Streeten, Shabnam Salimi, Xing Wang, and Alan R. Shuldiner

Subjects
Adult, Male, musculoskeletal diseases, 0301 basic medicine, Candidate gene, Adolescent, Science, 030209 endocrinology & metabolism, Biology, Polymorphism, Single Nucleotide, Article, CCN Intercellular Signaling Proteins, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Bone Density, Osteogenesis, Proto-Oncogene Proteins, Genetic variation, Humans, Genetic Predisposition to Disease, Wnt Signaling Pathway, Gene, Aged, Genetic association, Aged, 80 and over, Bone mineral, Genetics, Multidisciplinary, Wnt signaling pathway, Middle Aged, 030104 developmental biology, Multiple comparisons problem, Old Order Amish, Medicine, Osteoporosis, Female, Amish, Genome-Wide Association Study
Abstract

Wnt1-inducible signaling pathway protein-1 (WISP1) is a novel target of the Wnt pathway for modulating osteogenesis and improving bone strength. However, it is not clear if genetic variants in the WISP1 region are associated with bone mineral density (BMD) in human. The aim of this study is to investigate the role of genetic variation in WISP1 gene as a determinant of BMD in 1,510 Old Order Amish (OOA). We performed regional association analysis of 58 tag variants within 5 kb upstream and downstream to WISP1 with BMD and found 5 variants that were associated with BMD at multiple skeletal sites (P values from 2.89 × 10−6 to 1.62 × 10−2), with some significant associations even after adjustment for multiple comparisons. To replicate these results in an independent dataset, we performed a look-up of BMD associations with these variants in European ancestry subjects from the large GEFOS Consortium and observed the nominal associations of two of these variants with BMD (P values: 0.031 to 0.048). In conclusion, we have demonstrated that genetic variants surrounding WISP1 are associated with BMD at multiple skeletal sites in the OOA, thus influencing osteoporosis risk. These results support a role for the WISP1 gene on influencing variation in BMD.

Published
2018

46. DASH Score and Subsequent Risk of Coronary Artery Disease: The Findings From Million Veteran Program

Author

Luc Djoussé, Yuk‐Lam Ho, Xuan‐Mai T. Nguyen, David R. Gagnon, Peter W.F. Wilson, Kelly Cho, J. Michael Gaziano, Ildiko Halasz, Daniel Federman, Jean Beckham, Scott E. Sherman, Peruvemba Sriram, Philip S. Tsao, Edward J. Boyko, Junzhe Xu, Frank Lederle, Louis J. Dellitalia, Rachel McArdle, Laurence Kaminsky, Alan C. Swann, Mark B. Hamner, Hermes J. Florez, Prashant Pandya, Gerardo Villarreal, Peter Wilson, Timothy R. Morgan, Lori Davis, Robin A. Hurley, Laurence Meyer, Sunil K. Ahuja, Eric P. Konicki, David Cohen, Jack Lichy, Jeffrey Whittle, Kathlyn Sue Haddock, Karl D. Straub, John T. Callaghan, Samuel M. Aguayo, Samir Gupta, Ronald G. Washburn, Mary E. Oehlert, Adriana M. Hung, Agnes Wallbom, Robert Keith, Elif Sonel, Ronald B. Schifman, Richard D. Childress, Michael F. Godschalk, Alan R. Shuldiner, Padmashri Rastogi, Salvador Gutierrez, Ronald Fernando, Pran R. Iruvanti, Darshana Jhala, Carlos Rosado‐Rodriguez, Stephen M. Mastorides, John B. Harley, Kristin Mattocks, Robert T. Striker, Michael Rauchman, John Wells, Zuhair K. Ballas, Susan S. Woods, Shing Yeh, Nora R. Ratcliffe, Jon B. Klein, Adam G. Golden, Harold M. Ginzburg, Satish Sharma, Kris Ann K. Oursler, Mary A. Whooley, and Gretchen Gibson

Subjects
0301 basic medicine, Male, medicine.medical_specialty, Time Factors, Dietary Approaches To Stop Hypertension, Epidemiology, Population, Veterans Health, Coronary Artery Disease, Lower risk, Risk Assessment, Coronary artery disease, 03 medical and health sciences, Risk Factors, Internal medicine, Cardiovascular Disease, Dash, medicine, Humans, Prospective Studies, education, Aged, Original Research, education.field_of_study, 030109 nutrition & dietetics, business.industry, Incidence (epidemiology), Incidence, Hazard ratio, Middle Aged, Protective Factors, medicine.disease, Prognosis, Lifestyle, Confidence interval, United States, nutrition, Patient Compliance, Female, Diet, Healthy, Cardiology and Cardiovascular Medicine, business, Body mass index, Risk Reduction Behavior
Abstract

Background While adherence to healthful dietary patterns has been associated with a lower risk of coronary artery disease (CAD) in the general population, limited data are available among US veterans. We tested the hypothesis that adherence to Dietary Approach to Stop Hypertension (DASH) food pattern is associated with a lower risk of developing CAD among veterans. Methods and Results We analyzed data on 153 802 participants of the Million Veteran Program enrolled between 2011 and 2016. Information on dietary habits was obtained using a food frequency questionnaire at enrollment. We used electronic health records to assess the development of CAD during follow‐up. Of the 153 802 veterans who provided information on diet and were free of CAD at baseline, the mean age was 64.0 (SD=11.8) years and 90.4% were men. During a mean follow‐up of 2.8 years, 5451 CAD cases occurred. The crude incidence rate of CAD was 14.0, 13.1, 12.6, 12.3, and 11.1 cases per 1000 person‐years across consecutive quintiles of Dietary Approach to Stop Hypertension score. Hazard ratios (95% confidence interval) for CAD were 1.0 (ref), 0.91 (0.84–0.99), 0.87 (0.80–0.95), 0.86 (0.79–0.94), and 0.80 (0.73–0.87) from the lowest to highest quintile of Dietary Approach to Stop Hypertension score controlling for age, sex, body mass index, race, smoking, exercise, alcohol intake, and statin use ( P linear trend, Conclusions Our data are consistent with an inverse association between Dietary Approach to Stop Hypertension diet score and incidence of CAD among US veterans.

Published
2018

47. A Protein-Truncating HSD17B13 Variant and Protection from Chronic Liver Disease

Author

Shane McCarthy, Jonathan C. Cohen, Frederick E. Dewey, Claudia Schurmann, Matthew D. Still, Panayiotis Stevis, Xin Chu, Daniel J. Rader, David J. Carey, Alan R. Shuldiner, Noura S. Abul-Husn, Semanti Mukherjee, Jonathan S. Packer, Xiping Cheng, Ann Stepanchick, Brian Zambrowicz, Helen H. Hobbs, John Penn, Uyenlinh L. Mirshahi, Scott M. Damrauer, Ingrid B. Borecki, Yurong Xin, G. Craig Wood, Jesper Gromada, Suganthi Balasubramanian, Tanya M. Teslovich, Andrew J. Murphy, Erin D. Fuller, Christopher D. Still, Tooraj Mirshahi, Jonathan Z. Luo, John D. Overton, George D. Yancopoulos, Yashu Liu, Alexander H. Li, Aeron Small, Omri Gottesman, Julia Kozlitina, Jeffrey G. Reid, Stefan Stender, David Esopi, William C. Olson, Michael Feldman, Colm O'Dushlaine, Alexander E. Lopez, Nehal Gosalia, Sun Y. Kim, and Aris Baras

Subjects
0301 basic medicine, Male, medicine.medical_specialty, 17-Hydroxysteroid Dehydrogenases, Genotype, Chronic liver disease, Gastroenterology, Article, 03 medical and health sciences, Liver disease, 0302 clinical medicine, Non-alcoholic Fatty Liver Disease, Loss of Function Mutation, Internal medicine, Exome Sequencing, Medicine, Humans, Exome, Genetic Predisposition to Disease, Aspartate Aminotransferases, Exome sequencing, biology, business.industry, Sequence Analysis, RNA, Liver Diseases, Fatty liver, Genetic Variation, Alanine Transaminase, General Medicine, medicine.disease, Human genetics, Fatty Liver, 030104 developmental biology, Alanine transaminase, Liver, Chronic Disease, biology.protein, Disease Progression, Linear Models, 030211 gastroenterology & hepatology, Female, business, Biomarkers, TM6SF2
Abstract

BACKGROUND: Elucidation of the genetic factors underlying chronic liver disease may reveal new therapeutic targets. METHODS: We used exome sequence data and electronic health records from 46,544 participants in the DiscovEHR human genetics study to identify genetic variants associated with serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Variants that were replicated in three additional cohorts (12,527 persons) were evaluated for association with clinical diagnoses of chronic liver disease in DiscovEHR study participants and two independent cohorts (total of 37,173 persons) and with histopathological severity of liver disease in 2391 human liver samples. RESULTS: A splice variant (rs72613567:TA) in HSD17B13, encoding the hepatic lipid droplet protein hydroxysteroid 17-beta dehydrogenase 13, was found to be associated with reduced levels of ALT (P=4.20×10(−12)) and AST (P=6.2×10(−10)). Among DiscovEHR study participants, this variant was found to be associated with a reduced risk of alcoholic liver disease (by 42% [95% confidence interval {CI}, 20 to 58] among heterozygotes and by 53% [95% CI, 3 to 77] among homozygotes), nonalcoholic liver disease (by 17% [95% CI, 8 to 25] among heterozygotes and by 30% [95% CI, 13 to 43] among homozygotes), alcoholic cirrhosis (by 42% [95% CI, 14 to 61] among heterozygotes and by 73% [95% CI, 15 to 91] among homozygotes), and nonalcoholic cirrhosis (by 26% [95% CI, 7 to 40] among heterozygotes and by 49% [95% CI, 15 to 69] among homozygotes). Associations were confirmed in two independent cohorts. The rs72613567:TA variant was associated with a reduced risk of nonalcoholic steatohepatitis, but not steatosis, in human liver samples. The rs72613567:TA variant mitigated liver injury associated with the risk-increasing PNPLA3 p.I148M allele and resulted in an unstable and truncated protein with reduced enzymatic activity. CONCLUSIONS: A loss-of-function variant in HSD17B13 is associated with a reduced risk of chronic liver disease and of progression from steatosis to steatohepatitis. (Funded by Regeneron Pharmaceuticals and others.)

Published
2018

48. Establishing the role of

Author

Alina, Kurolap, Orly, Eshach-Adiv, Claudia, Gonzaga-Jauregui, Katya, Dolnikov, Adi, Mory, Tamar, Paperna, Tova, Hershkovitz, John D, Overton, Marielle, Kaplan, Fabian, Glaser, Yaniv, Zohar, Alan R, Shuldiner, Gidon, Berger, and Hagit N, Baris

Subjects
Adult, Male, Models, Molecular, Protein Conformation, Biopsy, Protein-Losing Enteropathies, Homozygote, Infant, Newborn, Mutation, Missense, Computational Biology, Membrane Proteins, Pedigree, Consanguinity, Structure-Activity Relationship, Young Adult, Phenotype, Amino Acid Substitution, Humans, Female, Carrier Proteins, Biomarkers, Genetic Association Studies
Abstract

Intestinal integrity is essential for proper nutrient absorption and tissue homeostasis, with damage leading to enteric protein loss, that is, protein-losing enteropathy (PLE). Recently, homozygous nonsense variants in the plasmalemma vesicle-associated protein gene (To genetically diagnose two first-degree cousins once removed, who presented with PLE at ages 22 and 2.5 years.Family-based whole exome sequencing was performed based on an autosomal recessive inheritance model.We identified a rare homozygous variant (NM_031310.2:c.101TC;p.Leu34Pro) inBiallelic missense variants in

Published
2018

49. Genome-wide association study of triglyceride response to a high-fat meal among participants of the NHLBI Genetics of Lipid Lowering Drugs and Diet Network (GOLDN)

Author

Jose M. Ordovas, Michael A. Province, Donna K. Arnett, Kathy Ryan, Alexis C. Frazier-Wood, Mary K. Wojczynski, Quince Gibson, Chao Q. Lai, Hemant K. Tiwari, Jeffrey R. O'Connell, Mary F. Feitosa, Alan R. Shuldiner, Toni I. Pollin, Laurence D. Parnell, Ingrid B. Borecki, and Stella Aslibekyan

Subjects
Adult, Male, medicine.medical_specialty, Linkage disequilibrium, Genotype, Endocrinology, Diabetes and Metabolism, Single-nucleotide polymorphism, Genome-wide association study, Biology, Diet, High-Fat, Polymorphism, Single Nucleotide, Article, chemistry.chemical_compound, Endocrinology, High-density lipoprotein, Meta-Analysis as Topic, Internal medicine, medicine, Humans, Meals, Triglycerides, Aged, Hypolipidemic Agents, Genetics, Meal, Triglyceride, Lipid metabolism, Middle Aged, Lipid Metabolism, Postprandial Period, Lipids, United States, Postprandial, chemistry, Female, National Heart, Lung, and Blood Institute (U.S.), Genome-Wide Association Study
Abstract

The triglyceride (TG) response to a high-fat meal (postprandial lipemia, PPL) affects cardiovascular disease risk and is influenced by genes and environment. Genes involved in lipid metabolism have dominated genetic studies of PPL TG response. We sought to elucidate common genetic variants through a genome-wide association (GWA) study in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN).The GOLDN GWAS discovery sample consisted of 872 participants within families of European ancestry. Genotypes for 2,543,887 variants were measured or imputed from HapMap. Replication of our top results was performed in the Heredity and Phenotype Intervention (HAPI) Heart Study (n = 843). PPL TG response phenotypes were constructed from plasma TG measured at baseline (fasting, 0 hour), 3.5 and 6 hours after a high-fat meal, using a random coefficient regression model. Association analyses were adjusted for covariates and principal components, as necessary, in a linear mixed model using the kinship matrix; additional models further adjusted for fasting TG were also performed. Meta-analysis of the discovery and replication studies (n = 1715) was performed on the top SNPs from GOLDN.GOLDN revealed 111 suggestive (p1E-05) associations, with two SNPs meeting GWA significance level (p5E-08). Of the two significant SNPs, rs964184 demonstrated evidence of replication (p = 1.20E-03) in the HAPI Heart Study and in a joint analysis, was GWA significant (p = 1.26E-09). Rs964184 has been associated with fasting lipids (TG and HDL) and is near ZPR1 (formerly ZNF259), close to the APOA1/C3/A4/A5 cluster. This association was attenuated upon additional adjustment for fasting TG.This is the first report of a genome-wide significant association with replication for a novel phenotype, namely PPL TG response. Future investigation into response phenotypes is warranted using pathway analyses, or newer genetic technologies such as metabolomics.

Published
2015

50. Multi-site Investigation of Outcomes with Implementation of CYP2C19 Genotype-Guided Antiplatelet Therapy after Percutaneous Coronary Intervention

Author

Issam Hamadeh, Devon C. Nwaba, Nita A. Limdi, Amer Ardati, Josh F. Peterson, James M. Stevenson, Russell A. Wilke, Craig R. Lee, Kristin Weitzel, Tameka D. Alestock, Yan Gong, Kathleen Palmer, Joshua C. Denny, Stephen E. Kimmel, Almut G. Winterstein, Richard B. Horenstein, Mark R. Vesely, Todd C. Skaar, Caitrin W. McDonough, Supatat Chumnumwat, Dyson T. Wake, James H. Willig, Petr Starostik, Larisa H. Cavallari, Linda J. B. Jeng, Karen E. Weck, Chrisly Dillon, Michael J. Clare-Salzler, D. Max Smith, Jorge A. Alsip, Vindhya B. Sriramoju, Rolf P. Kreutz, Chintan V. Dave, Julie A. Johnson, William B. Hillegass, Victoria M. Pratt, Toni I. Pollin, R. David Anderson, Rhonda M. Cooper-DeHoff, Richard Y. Zhao, Yee Ming Lee, Shawn W. Robinson, Brigitta C. Brott, Deepak Voora, Tomasz Stys, Lindsay J. Hines, Alan R. Shuldiner, Ruth E. Pakyz, Mark D. Kelemen, Alison H. Quinn, Edith A. Nutescu, Shuko Harada, Lawrence Brown, David R. Nelson, Oyunbileg Magvanjav, Philip E. Empey, Lucius A. Howell, Amanda R. Elsey, May E. Montasser, Nicholas Varunok, James C. Coons, Amber L. Beitelshees, George A. Stouffer, Julio D. Duarte, and Jamie Schub

Subjects
Male, Ticagrelor, medicine.medical_specialty, Time Factors, Prasugrel, Ticlopidine, Pharmacogenomic Variants, Genotype, medicine.medical_treatment, Clinical Decision-Making, Drug Resistance, 030204 cardiovascular system & hematology, Risk Assessment, Article, 03 medical and health sciences, 0302 clinical medicine, Percutaneous Coronary Intervention, Predictive Value of Tests, Risk Factors, Internal medicine, Humans, Medicine, cardiovascular diseases, 030212 general & internal medicine, Aged, business.industry, Patient Selection, Hazard ratio, Percutaneous coronary intervention, Middle Aged, Clopidogrel, United States, Confidence interval, Pharmacogenomic Testing, Surgery, Cytochrome P-450 CYP2C19, Treatment Outcome, Pharmacogenetics, Conventional PCI, Platelet aggregation inhibitor, Female, Cardiology and Cardiovascular Medicine, business, Prasugrel Hydrochloride, Platelet Aggregation Inhibitors, medicine.drug
Abstract

Objectives This multicenter pragmatic investigation assessed outcomes following clinical implementation of CYP2C19 genotype–guided antiplatelet therapy after percutaneous coronary intervention (PCI). Background CYP2C19 loss-of-function alleles impair clopidogrel effectiveness after PCI. Methods After clinical genotyping, each institution recommended alternative antiplatelet therapy (prasugrel, ticagrelor) in PCI patients with a loss-of-function allele. Major adverse cardiovascular events (defined as myocardial infarction, stroke, or death) within 12 months of PCI were compared between patients with a loss-of-function allele prescribed clopidogrel versus alternative therapy. Risk was also compared between patients without a loss-of-function allele and loss-of-function allele carriers prescribed alternative therapy. Cox regression was performed, adjusting for group differences with inverse probability of treatment weights. Results Among 1,815 patients, 572 (31.5%) had a loss-of-function allele. The risk for major adverse cardiovascular events was significantly higher in patients with a loss-of-function allele prescribed clopidogrel versus alternative therapy (23.4 vs. 8.7 per 100 patient-years; adjusted hazard ratio: 2.26; 95% confidence interval: 1.18 to 4.32; p = 0.013). Similar results were observed among 1,210 patients with acute coronary syndromes at the time of PCI (adjusted hazard ratio: 2.87; 95% confidence interval: 1.35 to 6.09; p = 0.013). There was no difference in major adverse cardiovascular events between patients without a loss-of-function allele and loss-of-function allele carriers prescribed alternative therapy (adjusted hazard ratio: 1.14; 95% confidence interval: 0.69 to 1.88; p = 0.60). Conclusions These data from real-world observations demonstrate a higher risk for cardiovascular events in patients with a CYP2C19 loss-of-function allele if clopidogrel versus alternative therapy is prescribed. A future randomized study of genotype-guided antiplatelet therapy may be of value.

Published
2017

Catalog

Books, media, physical & digital resources
See catalog results