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1. NOTCH3 p.Arg1231Cys is markedly enriched in South Asians and associated with stroke

Author

Juan Lorenzo Rodriguez-Flores, Shareef Khalid, Neelroop Parikshak, Asif Rasheed, Bin Ye, Manav Kapoor, Joshua Backman, Farshid Sepehrband, Silvio Alessandro Di Gioia, Sahar Gelfman, Tanima De, Nilanjana Banerjee, Deepika Sharma, Hector Martinez, Sofia Castaneda, David D’Ambrosio, Xingmin A. Zhang, Pengcheng Xun, Ellen Tsai, I-Chun Tsai, Regeneron Genetics Center, Maleeha Zaman Khan, Muhammad Jahanzaib, Muhammad Rehan Mian, Muhammad Bilal Liaqat, Khalid Mahmood, Tanvir Us Salam, Muhammad Hussain, Javed Iqbal, Faizan Aslam, Michael N. Cantor, Gannie Tzoneva, John Overton, Jonathan Marchini, Jeffrey G. Reid, Aris Baras, Niek Verweij, Luca A. Lotta, Giovanni Coppola, Katia Karalis, Aris Economides, Sergio Fazio, Wolfgang Liedtke, John Danesh, Ayeesha Kamal, Philippe Frossard, Thomas Coleman, Alan R. Shuldiner, and Danish Saleheen

Subjects
Science
Abstract

Abstract The genetic factors of stroke in South Asians are largely unexplored. Exome-wide sequencing and association analysis (ExWAS) in 75 K Pakistanis identified NM_000435.3(NOTCH3):c.3691 C > T, encoding the missense amino acid substitution p.Arg1231Cys, enriched in South Asians (alternate allele frequency = 0.58% compared to 0.019% in Western Europeans), and associated with subcortical hemorrhagic stroke [odds ratio (OR) = 3.39, 95% confidence interval (CI) = [2.26, 5.10], p = 3.87 × 10−9), and all strokes (OR [CI] = 2.30 [1.77, 3.01], p = 7.79 × 10−10). NOTCH3 p.Arg231Cys was strongly associated with white matter hyperintensity on MRI in United Kingdom Biobank (UKB) participants (effect [95% CI] in SD units = 1.1 [0.61, 1.5], p = 3.0 × 10−6). The variant is attributable for approximately 2.0% of hemorrhagic strokes and 1.1% of all strokes in South Asians. These findings highlight the value of diversity in genetic studies and have major implications for genomic medicine and therapeutic development in South Asian populations.

Published
2024
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2. PMS2CL interference leading to erroneous identification of a pathogenic PMS2 variant in Black patients

Author

Jacqueline Cappadocia, Lisa B. Aiello, Michael J. Kelley, Bryson W. Katona, Kara N. Maxwell, Anurag Verma, Ph.D., Shefali S. Verma, Ph.D., Yuki Bradford, M.S., Ashlei Brock, Stephanie DerOhannessian, Scott Dudek, M.S., Joseph Dunn, Theodore Drivas, M.D., Ph.D., Ned Haubein, Khadijah Hu-Sain, Renae Judy, Ashley Kloter, Yi-An Ko, Meghan Livingstone, Linda Morrel, Colleen Morse, M.S., Afiya Poindexter, Marjorie Risman, M.S., Teo Tran, Fred Vadivieso, JoEllen Weaver, Daniel J. Rader, M.D., Marylyn D. Ritchie, Ph.D., Michael D. Feldman, M.D., Ph.D., Christina Beechert, Caitlin Forsythe, M.S., Erin D. Fuller, Zhenhua Gu, M.S., Michael Lattari, Alexander Lopez, M.S., John D. Overton, Ph.D., Maria Sotiropoulos Padilla, M.S., Manasi Pradhan, M.S., Kia Manoochehri, B.S., Thomas D. Schleicher, M.S., Louis Widom, Sarah E. Wolf, M.S., Ricardo H. Ulloa, B.S., Amelia Averitt, Ph.D., Nilanjana Banerjee, Ph.D., Michael Cantor, M.D., Dadong Li, Ph.D., Sameer Malhotra, M.D., Deepika Sharma, MHI, Jeffrey Staples, Ph.D., Xiaodong Bai, Ph.D., Suganthi Balasubramanian, Ph.D., Suying Bao, Ph.D., Boris Boutkov, Ph.D., Siying Chen, Ph.D., Gisu Eom, B.S., Lukas Habegger, Ph.D., Alicia Hawes, B.S., Shareef Khalid, Olga Krasheninina, M.S., Rouel Lanche, B.S., Adam J. Mansfield, B.A., Evan K. Maxwell, Ph.D., George Mitra, B.A., Mona Nafde, M.S., Sean O’Keeffe, Ph.D., Max Orelus, B.B.A., Razvan Panea, Ph.D., Tommy Polanco, B.A., Ayesha Rasool, M.S., Jeffrey G. Reid, Ph.D., William Salerno, Ph.D., Jeffrey C. Staples, Ph.D., Kathie Sun, Ph.D., Goncalo Abecasis, D.Phil., Joshua Backman, Ph.D., Amy Damask, Ph.D., Lee Dobbyn, Ph.D., Manuel Allen Revez Ferreira, Ph.D., Arkopravo Ghosh, M.S., Christopher Gillies, Ph.D., Lauren Gurski, B.S., Eric Jorgenson, Ph.D., Hyun Min Kang, Ph.D., Michael Kessler, Ph.D., Jack Kosmicki, Ph.D., Alexander Li, Ph.D., Nan Lin, Ph.D., Daren Liu, M.S., Adam Locke, Ph.D., Jonathan Marchini, Ph.D., Anthony Marcketta, M.S., Joelle Mbatchou, Ph.D., Arden Moscati, Ph.D., Charles Paulding, Ph.D., Carlo Sidore, Ph.D., Eli Stahl, Ph.D., Kyoko Watanabe, Ph.D., Bin Ye, Ph.D., Blair Zhang, Ph.D., Andrey Ziyatdinov, Ph.D., Ariane Ayer, B.S., Aysegul Guvenek, Ph.D., George Hindy, Ph.D., Giovanni Coppola, M.D., Jan Freudenberg, M.D., Jonas Bovijn, M.D., Katherine Siminovitch, M.D., Kavita Praveen, Ph.D., Luca A. Lotta, M.D., Manav Kapoor, Ph.D., Mary Haas, Ph.D., Moeen Riaz, Ph.D., Niek Verweij, Ph.D., Olukayode Sosina, Ph.D., Parsa Akbari, Ph.D., Priyanka Nakka, Ph.D., Sahar Gelfman, Ph.D., Sujit Gokhale, B.E., Tanima De, Ph.D., Veera Rajagopal, Ph.D., Alan Shuldiner, M.D., Gannie Tzoneva, Ph.D., Juan Rodriguez-Flores, Ph.D., Esteban Chen, M.S., Marcus B. Jones, Ph.D., Michelle G. LeBlanc, Ph.D., Jason Mighty, Ph.D., Lyndon J. Mitnaul, Ph.D., Nirupama Nishtala, Ph.D., Nadia Rana, Ph.D., Jaimee Hernandez, Goncalo Abecasis, PhD, Aris Baras, M.D., Andrew Deubler, Aris Economides, Ph.D., and Luca A. Lotta, M.D., Ph.D.

Subjects
PMS2, germline genetic testing, Lynch syndrome, PMS2CL, pseudogene interference, Genetics, QH426-470, Medicine
Abstract

This study investigates the frequency of a clinically reported variant in PMS2, NM_000535.7:c.2523G>A p.(W841∗), from next-generation sequencing studies in 2 racially diverse cohorts. We identified clinical reports of the PMS2 c.2523G>A p.(W841∗) variant in the National Precision Oncology Program’s somatic testing database (n = 25,168). We determined frequency of the variant in germline exome sequencing from the Penn Medicine BioBank (n = 44,256) and in gnomAD. The PMS2 c.2523G>A p.(W841∗) was identified as a homozygous variant on tumor testing in an adult patient of self-identified Black race/ethnicity with no evidence of constitutional mismatch repair deficiency. The variant was clinically reported on 35 total tumor and liquid biopsy tests (0.1%), and all individuals with the variant were of self-identified Black race/ethnicity (0.6% of n = 5787). In individuals of African genetic ancestry (AFR), the variant's germline frequency was reported to be 0.2% and 1.3% in the Penn Medicine BioBank (PMBB) and gnomAD, respectively. The variant cannot be found in any individuals of European genetic ancestry (EUR) from either of the databases. The variant is found in a region of PMS2 with 100% homology to the PMS2CL pseudogene. PMS2 c.2523G>A p.(W841∗), when identified, is typically an African-ancestry-specific PMS2CL pseudogene variant, which should be recognized to prevent misdiagnosis of Lynch syndrome in Blacks.

Published
2024
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3. Multiancestry exome sequencing reveals INHBE mutations associated with favorable fat distribution and protection from diabetes

Author

Parsa Akbari, Olukayode A. Sosina, Jonas Bovijn, Karl Landheer, Jonas B. Nielsen, Minhee Kim, Senem Aykul, Tanima De, Mary E. Haas, George Hindy, Nan Lin, Ian R. Dinsmore, Jonathan Z. Luo, Stefanie Hectors, Benjamin Geraghty, Mary Germino, Lampros Panagis, Prodromos Parasoglou, Johnathon R. Walls, Gabor Halasz, Gurinder S. Atwal, Regeneron Genetics Center, DiscovEHR Collaboration, Marcus Jones, Michelle G. LeBlanc, Christopher D. Still, David J. Carey, Alice Giontella, Marju Orho-Melander, Jaime Berumen, Pablo Kuri-Morales, Jesus Alegre-Díaz, Jason M. Torres, Jonathan R. Emberson, Rory Collins, Daniel J. Rader, Brian Zambrowicz, Andrew J. Murphy, Suganthi Balasubramanian, John D. Overton, Jeffrey G. Reid, Alan R. Shuldiner, Michael Cantor, Goncalo R. Abecasis, Manuel A. R. Ferreira, Mark W. Sleeman, Viktoria Gusarova, Judith Altarejos, Charles Harris, Aris N. Economides, Vincent Idone, Katia Karalis, Giusy Della Gatta, Tooraj Mirshahi, George D. Yancopoulos, Olle Melander, Jonathan Marchini, Roberto Tapia-Conyer, Adam E. Locke, Aris Baras, Niek Verweij, and Luca A. Lotta

Subjects
Science
Abstract

Fat distribution is associated with cardiometabolic disease, although it has been less well studied than overall obesity. In a multiancestry exome-sequencing study, the authors identified predicted loss-of-function mutations in INHBE associated with favorable fat distribution and protection from type 2 diabetes.

Published
2022
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4. Mutation spectrum of NOD2 reveals recessive inheritance as a main driver of Early Onset Crohn’s Disease

Author

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

Subjects
Medicine, Science
Abstract

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
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5. Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease

Author

Na Zhu, Carrie L. Welch, Jiayao Wang, Philip M. Allen, Claudia Gonzaga-Jauregui, Lijiang Ma, Alejandra K. King, Usha Krishnan, Erika B. Rosenzweig, D. Dunbar Ivy, Eric D. Austin, Rizwan Hamid, Michael W. Pauciulo, Katie A. Lutz, William C. Nichols, Jeffrey G. Reid, John D. Overton, Aris Baras, Frederick E. Dewey, Yufeng Shen, and Wendy K. Chung

Subjects
Pulmonary hypertension, Congenital heart disease, Exome sequencing, Genetic association study, Medicine, Genetics, QH426-470
Abstract

Abstract Background Pulmonary arterial hypertension (PAH) is a rare disease characterized by distinctive changes in pulmonary arterioles that lead to progressive pulmonary arterial pressures, right-sided heart failure, and a high mortality rate. Up to 30% of adult and 75% of pediatric PAH cases are associated with congenital heart disease (PAH-CHD), and the underlying etiology is largely unknown. There are no known major risk genes for PAH-CHD. Methods To identify novel genetic causes of PAH-CHD, we performed whole exome sequencing in 256 PAH-CHD patients. We performed a case-control gene-based association test of rare deleterious variants using 7509 gnomAD whole genome sequencing population controls. We then screened a separate cohort of 413 idiopathic and familial PAH patients without CHD for rare deleterious variants in the top association gene. Results We identified SOX17 as a novel candidate risk gene (p = 5.5e−7). SOX17 is highly constrained and encodes a transcription factor involved in Wnt/β-catenin and Notch signaling during development. We estimate that rare deleterious variants contribute to approximately 3.2% of PAH-CHD cases. The coding variants identified include likely gene-disrupting (LGD) and deleterious missense, with most of the missense variants occurring in a highly conserved HMG-box protein domain. We further observed an enrichment of rare deleterious variants in putative targets of SOX17, many of which are highly expressed in developing heart and pulmonary vasculature. In the cohort of PAH without CHD, rare deleterious variants of SOX17 were observed in 0.7% of cases. Conclusions These data strongly implicate SOX17 as a new risk gene contributing to PAH-CHD as well as idiopathic/familial PAH. Replication in other PAH cohorts and further characterization of the clinical phenotype will be important to confirm the precise role of SOX17 and better estimate the contribution of genes regulated by SOX17.

Published
2018
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6. Genetic inactivation of ANGPTL4 improves glucose homeostasis and is associated with reduced risk of diabetes

Author

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

Subjects
Science
Abstract

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
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7. Genetic Susceptibility to Mood Disorders and Risk of Stroke: A Polygenic Risk Score and Mendelian Randomization Study

Author

Jiangming Sun, Yan Borné, Andreas Edsfeldt, Yunpeng Wang, Mengyu Pan, Olle Melander, Gunnar Engström, Isabel Gonçalves, Goncalo Abecasis, Aris Baras, Michael Cantor, Giovanni Coppola, Aris Economides, Luca A. Lotta, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Karina Toledo, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H. Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Leland Barnard, Andrew Blumenfeld, Gisu Eom, Lukas Habegger, Young Hahn, Alicia Hawes, Shareef Khalid, Evan K. Maxwell, William Salerno, Jeffrey C. Staples, Ashish Yadav, Marcus B. Jones, and Lyndon J. Mitnaul

Subjects
Advanced and Specialized Nursing, Neurology (clinical), Cardiology and Cardiovascular Medicine
Abstract

Background: Mood disorders and strokes are often comorbid, and their health toll worldwide is huge. This study characterizes prognostic and causal roles of mood disorders in stroke. Methods: We tested if genetic susceptibilities for mood disorders were associated with all strokes, ischemic strokes in the Malmö Diet and Cancer cohort (24 631 individuals with a median follow-up of 21.3 (interquartile range: 16.6–23.2) years. We further examined the causal effects for mood disorders on all strokes and ischemic strokes using summary statistics from large genome-wide association studies of mood disorders (up to 609 424 individuals, Psychiatric Genomics Consortium), all strokes and ischemic strokes (up to 446 696 individuals, MEGASTROKE Consortium). Results: Among 24 366 stroke-free participants at baseline, 2632 individuals developed strokes, 2172 of them ischemic, during follow-up. After properly adjusting for well-known risk factors, participants in the highest quintile of polygenic risk scores for mood disorders had 1.45× (95% CI, 1.21–1.74) higher risk of strokes and 1.44× (95% CI, 1.18–1.76) higher risk of ischemic strokes compared with the lowest quintile in women. Mendelian randomization analyses suggested that mood disorders had a causal effect on strokes (odds ratio, 1.07 [95% CI, 1.03–1.11]) and ischemic strokes (odds ratio, 1.09 [95% CI, 1.04–1.13]). Conclusions: Our results suggest a causal role of mood disorders in the risk of stroke. High-risk women could be identified early in life using polygenic risk scores to ultimately prevent mood disorders and strokes.

Published
2023

9. Germline Mutations in CIDEB and Protection against Liver Disease

Author

Niek Verweij, Mary E. Haas, Jonas B. Nielsen, Olukayode A. Sosina, Minhee Kim, Parsa Akbari, Tanima De, George Hindy, Jonas Bovijn, Trikaldarshi Persaud, Lawrence Miloscio, Mary Germino, Lampros Panagis, Kyoko Watanabe, Joelle Mbatchou, Marcus Jones, Michelle LeBlanc, Suganthi Balasubramanian, Craig Lammert, Sofia Enhörning, Olle Melander, David J. Carey, Christopher D. Still, Tooraj Mirshahi, Daniel J. Rader, Prodromos Parasoglou, Johnathon R. Walls, John D. Overton, Jeffrey G. Reid, Aris Economides, Michael N. Cantor, Brian Zambrowicz, Andrew J. Murphy, Goncalo R. Abecasis, Manuel A.R. Ferreira, Eriks Smagris, Viktoria Gusarova, Mark Sleeman, George D. Yancopoulos, Jonathan Marchini, Hyun M. Kang, Katia Karalis, Alan R. Shuldiner, Giusy Della Gatta, Adam E. Locke, Aris Baras, and Luca A. Lotta

Subjects
General Medicine
Published
2022

10. Thrombotic risk determined by rare and common SERPINA1 variants in a population‐based cohort study

Author

Eric Manderstedt, Christer Halldén, Christina Lind‐Halldén, Johan Elf, Peter J. Svensson, Gunnar Engström, Olle Melander, Aris Baras, Luca A. Lotta, Bengt Zöller, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, Aris Economides, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Kia Manoochehri, Maria Sotiropoulos Padilla, Manasi Pradhan, Thomas D. Schleicher, Ricardo H. Ulloa, Louis Widom, Sarah E. Wolf, Xiaodong Bai, Suganthi Balasubramanian, Andrew Blumenfeld, Boris Boutkov, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Olga Krasheninina, Rouel Lanche, Adam J. Mansfield, Evan K. Maxwell, Mrunali Nafde, Sean O’Keeffe, Max Orelus, Razvan Panea, Tommy Polanco, Ayesha Rasool, William Salerno, Jeffrey C. Staples, Marcus B. Jones, Jason Mighty, and Lyndon J. Mitnaul

Subjects
Aged, 80 and over, Cohort Studies, Male, Genotype, Case-Control Studies, alpha 1-Antitrypsin, alpha 1-Antitrypsin Deficiency, Humans, Female, Thrombosis, Venous Thromboembolism, Hematology, Aged
Abstract

Severe alpha-1-antitrypsin deficiency (AATD), phenotype PiZZ, was associated with venous thromboembolism (VTE) in a case-control study.This study aimed to determine the genetic variation in the SERPINA1 gene and a possible thrombotic risk of these variants in a population-based cohort study.The coding sequence of SERPINA1 was analyzed for the Z (rs28929474), S (rs17580), and other qualifying variants in 28,794 subjects without previous VTE (born 1923-1950, 60% women), who participated in the Malmö Diet and Cancer study (1991-1996). Individuals were followed from baseline until the first event of VTE, death, or 2018.Resequencing the coding sequence of SERPINA1 identified 84 variants in the total study population, 21 synonymous, 62 missense, and 1 loss-of-function variant. Kaplan-Meier analysis showed that homozygosity for the Z allele increased the risk of VTE whereas heterozygosity showed no effect. The S (rs17580) variant was not associated with VTE. Thirty-one rare variants were qualifying and included in collapsing analysis using the following selection criteria, loss of function, in frame deletion or non-benign (PolyPhen-2) missense variants with minor allele frequency (MAF)0.1%. Combining the rare qualifying variants with the Z variant showed that carrying two alleles (ZZ or compound heterozygotes) showed increased risk. Cox regression analysis revealed an adjusted hazard ratio of 4.5 (95% confidence interval 2.0-10.0) for combinations of the Z variant and rare qualifying variants. One other variant (rs141620200; MAF = 0.002) showed an increased risk of VTE.The SERPINA1 ZZ genotype and compound heterozygotes for severe AATD are rare but associated with VTE in a population-based Swedish study.

Published
2022

11. Inference of Causal Relationships Between Genetic Risk Factors for Cardiometabolic Phenotypes and Female‐Specific Health Conditions

Author

Brenda Xiao, Digna R. Velez Edwards, Anastasia Lucas, Theodore Drivas, Kathryn Gray, Brendan Keating, Chunhua Weng, Gail P. Jarvik, Hakon Hakonarson, Leah Kottyan, Noemie Elhadad, Wei‐Qi Wei, Yuan Luo, Dokyoon Kim, Marylyn Ritchie, Shefali Setia Verma, Goncalo Abecasis, Aris Baras, Michael Cantor, Giovanni Coppola, Andrew Deubler, Aris Economides, Katia Karalis, Luca A. Lotta, John D. Overton, Jeffrey G. Reid, Katherine Siminovitch, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Maria Sotiropoulos Padilla, Manasi Pradhan, Kia Manoochehri, Thomas D. Schleicher, Louis Widom, Sarah E. Wolf, Ricardo H. Ulloa, Amelia Averitt, Nilanjana Banerjee, Dadong Li, Sameer Malhotra, Deepika Sharma, Jeffrey Staples, Xiaodong Bai, Suganthi Balasubramanian, Suying Bao, Boris Boutkov, Siying Chen, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Olga Krasheninina, Rouel Lanche, Adam J. Mansfield, Evan K. Maxwell, George Mitra, Mona Nafde, Sean O’Keeffe, Max Orelus, Razvan Panea, Tommy Polanco, Ayesha Rasool, William Salerno, Jeffrey C. Staples, Kathie Sun, Joshua Backman, Amy Damask, Lee Dobbyn, Manuel Allen Revez Ferreira, Arkopravo Ghosh, Christopher Gillies, Lauren Gurski, Eric Jorgenson, Hyun Min Kang, Michael Kessler, Jack Kosmicki, Alexander Li, Nan Lin, Daren Liu, Adam Locke, Jonathan Marchini, Anthony Marcketta, Joelle Mbatchou, Arden Moscati, Charles Paulding, Carlo Sidore, Eli Stahl, Kyoko Watanabe, Bin Ye, Blair Zhang, Andrey Ziyatdinov, Ariane Ayer, Aysegul Guvenek, George Hindy, Jan Freudenberg, Jonas Bovijn, Kavita Praveen, Manav Kapoor, Mary Haas, Moeen Riaz, Niek Verweij, Olukayode Sosina, Parsa Akbari, Priyanka Nakka, Sahar Gelfman, Sujit Gokhale, Tanima De, Veera Rajagopal, Gannie Tzoneva, Juan Rodriguez‐Flores, Shek Man Chim, Valerio Donato, Daniel Fernandez, Giusy Della Gatta, Alessandro Di Gioia, Kristen Howell, Lori Khrimian, Minhee Kim, Hector Martinez, Lawrence Miloscio, Sheilyn Nunez, Elias Pavlopoulos, Trikaldarshi Persaud, Esteban Chen, Marcus B. Jones, Michelle G. LeBlanc, Jason Mighty, Lyndon J. Mitnaul, Nirupama Nishtala, and Nadia Rana

Subjects
Cardiology and Cardiovascular Medicine
Abstract

Background Cardiometabolic diseases are highly comorbid, but their relationship with female‐specific or overwhelmingly female‐predominant health conditions (breast cancer, endometriosis, pregnancy complications) is understudied. This study aimed to estimate the cross‐trait genetic overlap and influence of genetic burden of cardiometabolic traits on health conditions unique to women. Methods and Results Using electronic health record data from 71 008 ancestrally diverse women, we examined relationships between 23 obstetrical/gynecological conditions and 4 cardiometabolic phenotypes (body mass index, coronary artery disease, type 2 diabetes, and hypertension) by performing 4 analyses: (1) cross‐trait genetic correlation analyses to compare genetic architecture, (2) polygenic risk score–based association tests to characterize shared genetic effects on disease risk, (3) Mendelian randomization for significant associations to assess cross‐trait causal relationships, and (4) chronology analyses to visualize the timeline of events unique to groups of women with high and low genetic burden for cardiometabolic traits and highlight the disease prevalence in risk groups by age. We observed 27 significant associations between cardiometabolic polygenic scores and obstetrical/gynecological conditions (body mass index and endometrial cancer, body mass index and polycystic ovarian syndrome, type 2 diabetes and gestational diabetes, type 2 diabetes and polycystic ovarian syndrome). Mendelian randomization analysis provided additional evidence of independent causal effects. We also identified an inverse association between coronary artery disease and breast cancer. High cardiometabolic polygenic scores were associated with early development of polycystic ovarian syndrome and gestational hypertension. Conclusions We conclude that polygenic susceptibility to cardiometabolic traits is associated with elevated risk of certain female‐specific health conditions.

Published
2023

12. UGT1A1 genetic variants are associated with increases in bilirubin levels in rheumatoid arthritis patients treated with sarilumab

Author

Nan Lin, Amy Damask, Anita Boyapati, Jennifer D. Hamilton, Sara Hamon, Nils Ternes, Michael C. Nivens, John Penn, Alexander Lopez, Jeffrey G. Reid, John Overton, Alan R. Shuldiner, Goncalo Abecasis, Aris Baras, and Charles Paulding

Subjects
Adult, Arthritis, Rheumatoid, Pharmacology, Treatment Outcome, Antirheumatic Agents, Genetics, Humans, Molecular Medicine, Bilirubin, Glucuronosyltransferase, Antibodies, Monoclonal, Humanized, Genome-Wide Association Study
Abstract

Sarilumab is a human monoclonal antibody against interleukin (IL)-6Rα that has been approved for the treatment of adult patients with moderately to severely active rheumatoid arthritis (RA) and an inadequate response or intolerance to one or more disease-modifying antirheumatic drugs (DMARDs). Mild liver function test abnormalities have been observed in patients treated with sarilumab. We describe a genome-wide association study of bilirubin elevations in RA patients treated with sarilumab. Array genotyping and exome sequencing were performed on DNA samples from 1075 patients. Variants in the UGT1A1 gene were strongly associated with maximum bilirubin elevations in sarilumab-treated patients (rs4148325; p = 2.88 × 10−41) but were not associated with aminotransferase elevations. No other independent loci showed evidence of association with bilirubin elevations after sarilumab treatment. These findings suggest that most bilirubin increases during sarilumab treatment are related to genetic variation in UGT1A1 rather than underlying liver injury.

Published
2022

13. Genome‐wide association analysis of serum alanine and aspartate aminotransferase, and the modifying effects of BMI in 388k European individuals

Author

Chuan Gao, Anthony Marcketta, Joshua D. Backman, Colm O'Dushlaine, Jeffrey Staples, Manuel Allen Revez Ferreira, Luca A. Lotta, John D. Overton, Jeffrey G. Reid, Tooraj Mirshahi, null Regeneron Genetics Center, null Geisinger Regeneron Discovehr Collaboration, Aris Baras, Gonçalo Abecasis, Alan R. Shuldiner, Cristopher V. Van Hout, and Shane McCarthy

Subjects
ALT, Epidemiology, interaction, Physiology, Genome-wide association study, digestive system, Body Mass Index, 03 medical and health sciences, Liver disease, Genome-Wide Association Analysis, medicine, Humans, GWAS, Aspartate Aminotransferases, AST, Research Articles, Genetics (clinical), 030304 developmental biology, Genetic association, Alanine, 0303 health sciences, business.industry, 030305 genetics & heredity, Alanine Transaminase, medicine.disease, digestive system diseases, Genetic architecture, Minor allele frequency, liver disease, business, Body mass index, Genome-Wide Association Study, Research Article
Abstract

Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) are biomarkers for liver health. Here we report the largest genome‐wide association analysis to date of serum ALT and AST levels in over 388k people of European ancestry from UK biobank and DiscovEHR. Eleven million imputed markers with a minor allele frequency (MAF) ≥ 0.5% were analyzed. Overall, 300 ALT and 336 AST independent genome‐wide significant associations were identified. Among them, 81 ALT and 61 AST associations are reported for the first time. Genome‐wide interaction study identified 9 ALT and 12 AST independent associations significantly modified by body mass index (BMI), including several previously reported potential liver disease therapeutic targets, for example, PNPLA3, HSD17B13, and MARC1. While further work is necessary to understand the effect of ALT and AST‐associated variants on liver disease, the weighted burden of significant BMI‐modified signals is significantly associated with liver disease outcomes. In summary, this study identifies genetic associations which offer an important step forward in understanding the genetic architecture of serum ALT and AST levels. Significant interactions between BMI and genetic loci not only highlight the important role of adiposity in liver damage but also shed light on the genetic etiology of liver disease in obese individuals.

Published
2021

14. Germline Mutations in

Author

Niek, Verweij, Mary E, Haas, Jonas B, Nielsen, Olukayode A, Sosina, Minhee, Kim, Parsa, Akbari, Tanima, De, George, Hindy, Jonas, Bovijn, Trikaldarshi, Persaud, Lawrence, Miloscio, Mary, Germino, Lampros, Panagis, Kyoko, Watanabe, Joelle, Mbatchou, Marcus, Jones, Michelle, LeBlanc, Suganthi, Balasubramanian, Craig, Lammert, Sofia, Enhörning, Olle, Melander, David J, Carey, Christopher D, Still, Tooraj, Mirshahi, Daniel J, Rader, Prodromos, Parasoglou, Johnathon R, Walls, John D, Overton, Jeffrey G, Reid, Aris, Economides, Michael N, Cantor, Brian, Zambrowicz, Andrew J, Murphy, Goncalo R, Abecasis, Manuel A R, Ferreira, Eriks, Smagris, Viktoria, Gusarova, Mark, Sleeman, George D, Yancopoulos, Jonathan, Marchini, Hyun M, Kang, Katia, Karalis, Alan R, Shuldiner, Giusy, Della Gatta, Adam E, Locke, Aris, Baras, and Luca A, Lotta

Subjects
Liver, Liver Diseases, Exome Sequencing, Humans, Genetic Predisposition to Disease, Apoptosis Regulatory Proteins, Germ-Line Mutation, Transaminases
Abstract

Exome sequencing in hundreds of thousands of persons may enable the identification of rare protein-coding genetic variants associated with protection from human diseases like liver cirrhosis, providing a strategy for the discovery of new therapeutic targets.We performed a multistage exome sequencing and genetic association analysis to identify genes in which rare protein-coding variants were associated with liver phenotypes. We conducted in vitro experiments to further characterize associations.The multistage analysis involved 542,904 persons with available data on liver aminotransferase levels, 24,944 patients with various types of liver disease, and 490,636 controls without liver disease. We found that rare coding variants inRare germline mutations in

Published
2022

15. Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity

Author

Jack A. Kosmicki, Charles Paulding, Nan Lin, Andrew J. Murphy, Jerome I. Rotter, Brian Zambrowicz, Niek Verweij, Luca A. Lotta, Michal L. Schwartzman, Giusy Della Gatta, Yii-Der Ida Chen, Alexander H. Li, Suganthi Balasubramanian, Jason M. Torres, Hyun Min Kang, Rory Collins, Parsa Akbari, Michael E. Dunn, Gonçalo R. Abecasis, Christian Benner, David J. Carey, Svati H. Shah, Jonathan Marchini, Giovanni Coppola, Marcus B. Jones, Olle Melander, Christopher D. Still, Yi-Ya Fang, Olukayode A. Sosina, Manuel A. R. Ferreira, Roberto Tapia-Conyer, Michael Cantor, Aris N. Economides, Dylan Sun, Adam E. Locke, Jonathan V. Pascale, Daniel J. Rader, Ankit Gilani, Joelle Mbatchou, Jesus Alegre-Díaz, Mark W. Sleeman, Trikaldarshi Persaud, Jeffrey G. Reid, Pablo Kuri-Morales, Jaime Berumen-Campos, John D. Overton, Aris Baras, Ercument Dirice, Sakib Hossain, Alicia Hawes, George D. Yancopoulos, Jonathan Emberson, Victor Garcia, Judith Altarejos, Lori Khrimian, Katia Karalis, William E. Kraus, Tooraj Mirshahi, Kevin Agostinucci, Alan R. Shuldiner, Center, Regeneron Genetics, and Collaboration, DiscovEHR

Subjects
0301 basic medicine, Genetics, medicine.medical_specialty, Multidisciplinary, Body Weight, Genomics, Organ Size, Biology, medicine.disease, Obesity, Article, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Genetic variation, medicine, Medical genetics, Humans, medicine.symptom, Body mass index, Weight gain, 030217 neurology & neurosurgery, Exome sequencing, Glycemic
Abstract

Introduction Obesity accounts for a substantial and growing burden of disease globally. Body adiposity is highly heritable, and human genetic studies can lead to biological and therapeutic insights. Rationale Whole-exome sequencing of hundreds of thousands of individuals is complementary to approaches used to date in obesity genetics and has the potential to identify rare protein-coding variants with large phenotypic impact. We sequenced the exomes of 645,626 individuals from the UK, the US, and Mexico and estimated associations of rare coding variants with body mass index (BMI), a measure of overall adiposity used to define obesity in clinical practice. We complemented exome sequencing with fine-mapping of common alleles, polygenic score analysis, and in vitro and in vivo modeling work. Results We identified 16 genes for which the burden of rare nonsynonymous variants was associated with BMI at exome-wide statistical significance (inverse-variance weighted meta-analysis P < 3.6 × 10−7), including associations at five brain-expressed G protein–coupled receptors (CALCR, MC4R, GIPR, GPR151, and GPR75). We observed an overrepresentation of genes highly expressed in the hypothalamus, a key center for the neuroendocrine regulation of energy balance. Protein-truncating variants in GPR75 were found in ~4/10,000 sequenced people and were associated with 1.8 kg/m2 lower BMI, 5.3 kg lower bodyweight, and 54% lower odds of obesity in heterozygous carriers. Knock out of Gpr75 in mice resulted in resistance to weight gain in a high-fat diet model, which was allele-dose dependent (25% and 44% lower weight gain, respectively, for heterozygous Gpr75−/+ mice and knockout Gpr75−/− mice compared with wild type) and accompanied by improved glycemic control and insulin sensitivity. Protein-truncating variants in CALCR were associated with higher BMI and obesity risk, whereas protein-truncating variants in GIPR and two missense alleles [Arg190→Gln (Arg190Gln), Glu288Gly], which we show result in loss of function in vitro, were associated with lower adiposity. Among monogenic obesity genes in the leptin-melanocortin pathway, heterozygous predicted loss-of-function variants in LEP, POMC, PCSK1, and MC4R (but not LEPR) were associated with higher BMI. Rare protein-truncating variants in UBR2, ANO4, and PCSK1 were associated with more than twofold higher odds of obesity in heterozygous carriers, similar to predicted-deleterious nonsynonymous variants in MC4R, which are considered the most common cause of monogenic obesity. Polygenic predisposition due to >2 million common genetic variants influenced the penetrance of obesity in rare variant carriers in an additive fashion. Conclusion These results suggest that inhibition of GPR75 may be a therapeutic strategy for obesity and illustrate the power of massive-scale exome sequencing for the identification of large-effect coding variant associations and drug targets for complex traits.

Published
2022

16. 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

17. Classic Thrombophilias and Thrombotic Risk Among Middle-Aged and Older Adults: A Population-Based Cohort Study

Author

Eric Manderstedt, Christina Lind‐Halldén, Christer Halldén, Johan Elf, Peter J. Svensson, Björn Dahlbäck, Gunnar Engström, Olle Melander, Aris Baras, Luca A. Lotta, Bengt Zöller, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, Aris Economides, Luca A Lotta, John D Overton, Jeffrey G Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D Schleicher, Maria Sotiropoulos Padilla, Louis Widom, Sarah E Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Andrew Blumenfeld, Boris Boutkov, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Olga Krasheninina, Rouel Lanche, Adam J Mansfield, Evan K Maxwell, Mrunali Nafde, Sean O’Keeffe, Max Orelus, Razvan Panea, Tommy Polanco, Ayesha Rasool, William Salerno, Jeffrey C Staples, Marcus B Jones, Jason Mighty, and Lyndon J Mitnaul

Subjects
Male, Anticoagulants, Factor V, Thrombosis, Venous Thromboembolism, Middle Aged, Antithrombins, Protein S, Cohort Studies, Risk Factors, RC666-701, Mutation, natural anticoagulants, Diseases of the circulatory (Cardiovascular) system, Humans, Thrombophilia, epidemiology, genetics, Female, Prothrombin, Cardiology and Cardiovascular Medicine, Aged, Protein C
Abstract

Background Five classic thrombophilias have been recognized: factor V Leiden (rs6025), the prothrombin G20210A variant (rs1799963), and protein C, protein S, and antithrombin deficiencies. This study aimed to determine the thrombotic risk of classic thrombophilias in a cohort of middle‐aged and older adults. Methods and Results Factor V Leiden, prothrombin G20210A and protein‐coding variants in the PROC (protein C), PROS1 (protein S), and SERPINC1 (antithrombin) anticoagulant genes were determined in 29 387 subjects (born 1923–1950, 60% women) who participated in the Malmö Diet and Cancer study (1991–1996). The Human Gene Mutation Database was used to define 68 disease‐causing mutations. Patients were followed up from baseline until the first event of venous thromboembolism (VTE), death, or Dec 31, 2018. Carriership (n=908, 3.1%) for disease‐causing mutations in the PROC , PROS1 , and SERPINC1 genes was associated with incident VTE: Hazard ratio (HR) was 1.6 (95% CI, 1.3–1.9). Variants not in Human Gene Mutation Database were not linked to VTE (HR, 1.1; 95% CI, 0.8–1.5). Heterozygosity for rs6025 and rs1799963 was associated with incident VTE: HR, 1.8 (95% CI, 1.6–2.0) and HR, 1.6 (95% CI, 1.3–2.0), respectively. The HR for carrying 1 classical thrombophilia variant was 1.7 (95% CI, 1.6–1.9). HR was 3.9 (95% CI, 3.1–5.0) for carriers of ≥2 thrombophilia variants. Conclusions The 5 classic thrombophilias are associated with a dose‐graded risk of VTE in middle‐aged and older adults. Disease‐causing variants in the PROC , PROS1 , and SERPINC1 genes were more common than the rs1799963 variant but the conferred genetic risk was comparable with the rs6025 and rs1799963 variants.

Published
2022

18. 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

19. Medical manifestations and health care utilization among adult MyCode participants with neurodevelopmental psychiatric copy number variants

Author

Evan Maxwell, Lukas Habegger, David H. Ledbetter, S.M. Myers, Christa Leese Martin, H L Kirchner, A. Johns, Brenda M Finucane, Matthew T. Oetjens, Jeffrey G. Reid, and C. Fisher

Subjects
Adult, medicine.medical_specialty, DNA Copy Number Variations, business.industry, Patient Acceptance of Health Care, Article, Cohort Studies, Healthcare utilization, Prevalence, Medicine, Humans, Copy-number variation, business, Psychiatry, Child, Delivery of Health Care, Genetics (clinical)
Abstract

PURPOSE: Recurrent pathogenic copy number variants (pCNVs) have large-effect impacts on brain function and represent important etiologies of neurodevelopmental psychiatric disorders (NPDs), including autism and schizophrenia. Patterns of health care utilization in adults with pCNVs have gone largely unstudied and are likely to differ in significant ways from those of children. METHODS: We compared the prevalence of NPDs and electronic health record-based medical conditions in 928 adults with 26 pCNVs to a demographically-matched cohort of pCNV-negative controls from >135,000 patient-participants in Geisinger’s MyCode Community Health Initiative. We also evaluated 3 quantitative health care utilization measures (outpatient, inpatient, and emergency department (ED) visits) in both groups. RESULTS: Adults with pCNVs (24.9%) were more likely than controls (16.0%) to have a documented NPD. They had significantly higher rates of several chronic diseases, including diabetes (29.3% in participants with pCNVs vs. 20.4% in participants without pCNVs) and dementia (2.2% in participants with pCNVs vs. 1.0% in participants without pCNVs), and twice as many annual emergency department visits. CONCLUSION: These findings highlight the potential for genetic information – specifically, pCNVs - to inform the study of health care outcomes and utilization in adults. If, as our findings suggest, adults with pCNVs have poorer health and require disproportionate health care resources, early genetic diagnosis paired with patient-centered interventions may help to anticipate problems, improve outcomes, and reduce the associated economic burden.

Published
2021

20. Corrigendum to ‘An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs’ [J Hepatol 2021;75(3):572–581]

Author

Heather J. Cordell, James J. Fryett, Kazuko Ueno, Rebecca Darlay, Yoshihiro Aiba, Yuki Hitomi, Minae Kawashima, Nao Nishida, Seik-Soon Khor, Olivier Gervais, Yosuke Kawai, Masao Nagasaki, Katsushi Tokunaga, Ruqi Tang, Yongyong Shi, Zhiqiang Li, Brian D. Juran, Elizabeth J. Atkinson, Alessio Gerussi, Marco Carbone, Rosanna Asselta, Angela Cheung, Mariza de Andrade, Aris Baras, Julie Horowitz, Manuel A.R. Ferreira, Dylan Sun, David E. Jones, Steven Flack, Ann Spicer, Victoria L. Mulcahy, Jinyoung Byun, Younghun Han, Richard N. Sandford, Konstantinos N. Lazaridis, Christopher I. Amos, Gideon M. Hirschfield, Michael F. Seldin, Pietro Invernizzi, Katherine A. Siminovitch, Xiong Ma, Minoru Nakamura, George F. Mells, Andrew Mason, Catherine Vincent, Gang Xie, Jinyi Zhang, Andrea Affronti, Piero L. Almasio, Domenico Alvaro, Pietro Andreone, Angelo Andriulli, Francesco Azzaroli, Pier Maria Battezzati, Antonio Benedetti, Maria Consiglia Bragazzi, Maurizia Brunetto, Savino Bruno, Vincenza Calvaruso, Vincenzo Cardinale, Giovanni Casella, Nora Cazzagon, Antonio Ciaccio, Barbara Coco, Agostino Colli, Guido Colloredo, Massimo Colombo, Silvia Colombo, Laura Cristoferi, Carmela Cursaro, Lory Saveria Crocè, Andrea Crosignani, Daphne D’Amato, Francesca Donato, Gianfranco Elia, Luca Fabris, Stefano Fagiuoli, Carlo Ferrari, Annarosa Floreani, Andrea Galli, Edoardo Giannini, Ignazio Grattagliano, Pietro Lampertico, Ana Lleo, Federica Malinverno, Clara Mancuso, Fabio Marra, Marco Marzioni, Sara Massironi, Alberto Mattalia, Luca Miele, Chiara Milani, Lorenzo Morini, Filomena Morisco, Luigi Muratori, Paolo Muratori, Grazia A. Niro, Sarah O’Donnell, Antonio Picciotto, Piero Portincasa, Cristina Rigamonti, Vincenzo Ronca, Floriano Rosina, Giancarlo Spinzi, Mario Strazzabosco, Mirko Tarocchi, Claudio Tiribelli, Pierluigi Toniutto, Luca Valenti, Maria Vinci, Massimo Zuin, Hitomi Nakamura, Seigo Abiru, Shinya Nagaoka, Atsumasa Komori, Hiroshi Yatsuhashi, Hiromi Ishibashi, Masahiro Ito, Kiyoshi Migita, Hiromasa Ohira, Shinji Katsushima, Atsushi Naganuma, Kazuhiro Sugi, Tatsuji Komatsu, Tomohiko Mannami, Kouki Matsushita, Kaname Yoshizawa, Fujio Makita, Toshiki Nikami, Hideo Nishimura, Hiroshi Kouno, Hirotaka Kouno, Hajime Ota, Takuya Komura, Yoko Nakamura, Masaaki Shimada, Noboru Hirashima, Toshiki Komeda, Keisuke Ario, Makoto Nakamuta, Tsutomu Yamashita, Kiyoshi Furuta, Masahiro Kikuchi, Noriaki Naeshiro, Hironao Takahashi, Yutaka Mano, Seiji Tsunematsu, Iwao Yabuuchi, Yusuke Shimada, Kazuhiko Yamauchi, Rie Sugimoto, Hironori Sakai, Eiji Mita, Masaharu Koda, Satoru Tsuruta, Hiroshi Kamitsukasa, Takeaki Sato, Naohiko Masaki, Tatsuro Kobata, Nobuyoshi Fukushima, Yukio Ohara, Toyokichi Muro, Eiichi Takesaki, Hitoshi Takaki, Tetsuo Yamamoto, Michio Kato, Yuko Nagaoki, Shigeki Hayashi, Jinya Ishida, Yukio Watanabe, Masakazu Kobayashi, Michiaki Koga, Takeo Saoshiro, Michiyasu Yagura, Keisuke Hirata, Atsushu Tanaka, Hajime Takikawa, Mikio Zeniya, Masanori Abe, Morikazu Onji, Shuichi Kaneko, Masao Honda, Kuniaki Arai, Teruko Arinaga-Hino, Etsuko Hashimoto, Makiko Taniai, Takeji Umemura, Satoru Joshita, Kazuhiko Nakao, Tatsuki Ichikawa, Hidetaka Shibata, Satoshi Yamagiwa, Masataka Seike, Koichi Honda, Shotaro Sakisaka, Yasuaki Takeyama, Masaru Harada, Michio Senju, Osamu Yokosuka, Tatsuo Kanda, Yoshiyuki Ueno, Kentaro Kikuchi, Hirotoshi Ebinuma, Takashi Himoto, Michio Yasunami, Kazumoto Murata, Masashi Mizokami, Kazuhito Kawata, Shinji Shimoda, Yasuhiro Miyake, Akinobu Takaki, Kazuhide Yamamoto, Katsuji Hirano, Takafumi Ichida, Akio Ido, Hirohito Tsubouchi, Kazuaki Chayama, Kenichi Harada, Yasuni Nakanuma, Yoshihiko Maehara, Akinobu Taketomi, Ken Shirabe, Yuji Soejima, Akira Mori, Shintaro Yagi, Shinji Uemoto, Egawa H, Tomohiro Tanaka, Noriyo Yamashiki, Sumito Tamura, Yasuhiro Sugawara, Norihiro Kokudo, Naga Chalasani, Vel Luketic, Joseph Odin, Kapil Chopra, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, Aris Economides, Luca A. Lotta, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Karina Toledo, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H. Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Leland Barnard, Andrew Blumenfeld, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Evan K. Maxwell, William Salerno, Jeffrey C. Staples, Marcus B. Jones, Lyndon J. Mitnaul, Richard Sturgess, Christopher Healey, Andrew Yeoman, Anton V.J. Gunasekera, Paul Kooner, Kapil Kapur, V. Sathyanarayana, Yiannis Kallis, Javaid Subhani, Rory Harvey, Roger McCorry, Paul Rooney, David Ramanaden, Richard Evans, Thiriloganathan Mathialahan, Jaber Gasem, Christopher Shorrock, Mahesh Bhalme, Paul Southern, Jeremy A. Tibble, David A. Gorard, Susan Jones, George Mells, Victoria Mulcahy, Brijesh Srivastava, Matthew R. Foxton, Carole E. Collins, David Elphick, Mazn Karmo, Francisco Porras-Perez, Michael Mendall, Tom Yapp, Minesh Patel, Roland Ede, Joanne Sayer, James Jupp, Neil Fisher, Martyn J. Carter, Konrad Koss, Jayshri Shah, Andrzej Piotrowicz, Glyn Scott, Charles Grimley, Ian R. Gooding, Simon Williams, Judith Tidbury, Guan Lim, Kuldeep Cheent, Sass Levi, Dina Mansour, Matilda Beckley, Coral Hollywood, Terry Wong, Richard Marley, John Ramage, Harriet M. Gordon, Jo Ridpath, Theodore Ngatchu, Vijay Paul Bob Grover, Ray G. Shidrawi, George Abouda, L. Corless, Mark Narain, Ian Rees, Ashley Brown, Simon Taylor-Robinson, Joy Wilkins, Leonie Grellier, Paul Banim, Debasish Das, Michael A. Heneghan, Howard Curtis, Helen C. Matthews, Faiyaz Mohammed, Mark Aldersley, Raj Srirajaskanthan, Giles Walker, Alistair McNair, Amar Sharif, Sambit Sen, George Bird, Martin I. Prince, Geeta Prasad, Paul Kitchen, Adrian Barnardo, Chirag Oza, Nurani N. Sivaramakrishnan, Prakash Gupta, Amir Shah, Chris D.J. Evans, Subrata Saha, Katharine Pollock, Peter Bramley, Ashis Mukhopadhya, Stephen T. Barclay, Natasha McDonald, Andrew J. Bathgate, Kelvin Palmer, John F. Dillon, Simon M. Rushbrook, Robert Przemioslo, Chris McDonald, Andrew Millar, Cheh Tai, Stephen Mitchell, Jane Metcalf, Syed Shaukat, Mary Ninkovic, Udi Shmueli, Andrew Davis, Asifabbas Naqvi, Tom J.W. Lee, Stephen Ryder, Jane Collier, Howard Klass, Matthew E. Cramp, Nichols Sharer, Richard Aspinall, Deb Ghosh, Andrew C. Douds, Jonathan Booth, Earl Williams, Hyder Hussaini, John Christie, Steven Mann, Douglas Thorburn, Aileen Marshall, Imran Patanwala, Aftab Ala, Julia Maltby, Ray Matthew, Chris Corbett, Sam Vyas, Saket Singhal, Dermot Gleeson, Sharat Misra, Jeff Butterworth, Keith George, Tim Harding, Andrew Douglass, Harriet Mitchison, Simon Panter, Jeremy Shearman, Gary Bray, Michael Roberts, Graham Butcher, Daniel Forton, Zahid Mahmood, Matthew Cowan, Debashis Das, Chin Lye Ch'ng, Mesbah Rahman, Gregory C.A. Whatley, Emma Wesley, Aditya Mandal, Sanjiv Jain, Stephen P. Pereira, Mark Wright, Palak Trivedi, Fiona H. Gordon, Esther Unitt, Altaf Palejwala, Andrew Austin, Vishwaraj Vemala, Allister Grant, Andrew D. Higham, Alison Brind, Ray Mathew, Mark Cox, Subramaniam Ramakrishnan, Alistair King, Simon Whalley, Jocelyn Fraser, S.J. Thomson, Andrew Bell, Voi Shim Wong, Richard Kia, Ian Gee, Richard Keld, Rupert Ransford, James Gotto, and Charles Millson

Subjects
Science & Technology, Hepatology, Gastroenterology & Hepatology, Italian PBC Study Group, Japan-PBC-GWAS Consortium, UK-PBC Consortium, Chinese PBC Consortium, 1103 Clinical Sciences, US PBC Consortium, Canadian PBC Consortium, Life Sciences & Biomedicine, PBC Consortia, 1117 Public Health and Health Services
Published
2021

21. Thrombotic Risk Determined by STAB 2 Variants in a Population-Based Cohort Study

Author

Eric Manderstedt, Christer Halldén, Christina Lind-Halldén, Johan Elf, Peter J. Svensson, Gunnar Engström, Olle Melander, Aris Baras, Luca A Lotta, Bengt Zöller, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Katia Karalis, Katherine Siminovitch, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H. Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Andrew Blumenfeld, Boris Boutkov, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Olga Krasheninina, Rouel Lanche, Adam J. Mansfield, Evan K. Maxwell, Mrunali Nafde, Sean O’Keeffe, Max Orelus, Razvan Panea, Tommy Polanco, Ayesha Rasool, William Salerno, Jeffrey C. Staples, Niek Verweij, Jonas Nielsen, Tanima De, Marcus B. Jones, Jason Mighty, Michelle G. LeBlanc, and Lyndon J. Mitnaul

Subjects
Thrombotic risk, medicine.medical_specialty, education.field_of_study, business.industry, Population, General Medicine, medicine.disease, Thrombosis, Population based cohort, Internal medicine, Medicine, business, education, Venous thromboembolism
Published
2021

22. Genetic variation of the blood coagulation regulator tissue factor pathway inhibitor and venous thromboembolism among middle‐aged and older adults: A population‐based cohort study

Author

Eric Manderstedt, Christina Lind‐Halldén, Christer Halldén, Johan Elf, Peter J. Svensson, Gunnar Engström, Olle Melander, Aris Baras, Luca A. Lotta, Bengt Zöller, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, Aris Economides, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H. Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Andrew Blumenfeld, Boris Boutkov, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Olga Krasheninina, Rouel Lanche, Adam J. Mansfield, Evan K. Maxwell, Mrunali Nafde, Sean O’Keeffe, Max Orelus, Razvan Panea, Tommy Polanco, Ayesha Rasool, William Salerno, Jeffrey C. Staples, Marcus B. Jones, Jason Mighty, and Lyndon J. Mitnaul

Subjects
Hematology
Abstract

Tissue factor is the main initiator of blood coagulation, and tissue factor pathway inhibitor (TFPI) is the primary inhibitor of the initiation of blood coagulation.The genetic variation ofThe exomes ofNo common variant was associated with VTE. Nine rare variants (two loss-of-function and seven nonbenign missense) were classified as qualifying and included in collapsing analysis. Prevalence of qualifying variants was 0.09%. Five individuals with VTE compared to 17 individuals without VTE carried one qualifying variant. Cox multivariate regression analysis adjusted for age, sex, body mass index, systolic blood pressure, smoking and alcohol consumption, rs6025, rs1799963, and ancestry showed a hazard ratio of 2.9 (95% CI, 1.2-7.1) for rare qualifying variants.Rare qualifying

Published
2022

23. Erratum: Azimuthal Anisotropy of KS0 and Λ+Λ¯ Production at Midrapidity from Au+Au Collisions at sNN=130 GeV [Phys. Rev. Lett. 89 , 132301 (2002)]

Author

S. P. Chernenko, W. J. Llope, A. Cardenas, H. Long, R. Lednický, V. A. Nikitin, K. E. Shestermanov, A. Stolpovsky, R. S. Longacre, W. Christie, L. Kotchenda, H. Bichsel, P. Seyboth, V. Trofimov, Guy Paic, A. Chikanian, A. V. Brandin, S. S. Shimanskii, A. I. Kulikov, Masashi Kaneta, W. M. Zhang, L. C. Bland, Y. Panebratsev, R.Kh. Kutuev, Andrey Vasiliev, Joram Berger, T. Todoroki, Adam Ryszard Kisiel, J. B. Carroll, A. E. Yakutin, G. Igo, M. Oldenburg, H. J. Crawford, M. Castro, M. Calderon De La Barca Sanchez, G. Rai, J. W. Mitchell, N. Schmitz, Janet Elizabeth Seger, VL Rykov, B. D. Anderson, V. Petrov, E. Shahaliev, A. Boucham, T. J. Humanic, V. B. Dunin, A. C. Saulys, Z. Z. Xu, Q. Li, R. Witt, S. E. Vigdor, T. W. Henry, Christian Claude Kuhn, W. S. Deng, V. Ghazikhanian, Nikita Smirnov, I.A. Savin, M. Csanád, A. I. Pavlinov, F. Liu, M. B. Tonjes, J. W. Harris, B. E. Bonner, N. T. Porile, O. D. Tsai, J. L. Romero, Mirko Planinic, H. M. Spinka, C. E. Allgower, G. Eppley, S. Bekele, V. Morozov, Michael Kramer, M. Cherney, B. Lasiuk, E. Finch, Thomas Michael Cormier, R. Willson, D. G. Underwood, Michael W. Anderson, E. Gushin, P. Yepes, V. Eckardt, R. Ma, P. Nevski, J. H. Thomas, D. Hardtke, F. Laue, A. H. Tang, R. D. Majka, J. Pluta, L. Liu, V. M. Leontiev, Olivier Ravel, G. LoCurto, C. O. Blyth, E. Hjort, I. Zborovský, Yu A. Matulenko, M. Horsley, G. Skoro, B. Stringfellow, T. S. McShane, Rene Bellwied, C. P. Lansdell, R. E. Tribble, R.J.M. Snellings, Gerald W Hoffmann, J. N. Marx, B. Choi, J. G. Cramer, Thomas Dietel, Alexander Kovalenko, L. V. Nogach, A. P. Meschanin, Y. Fisyak, Ian Johnson, Christophe Pierre Suire, J. Sowinski, J. Schambach, D. Reichhold, T. J. M. Symons, T. Niida, A. Lebedev, M. M. de Moura, A. Szanto de Toledo, T. Pawlak, Morton Kaplan, P. Sorensen, G. Van Buren, Sevil Salur, Saurabh Pandey, A. Tai, T. W. Ludlam, J. Amonett, J. M. Nelson, V. Emelianov, D. Keane, W. Peryt, R. Stock, L. G. Efimov, D. Seliverstov, A. Schüttauf, G. S. Averichev, J. Porter, C. Roy, A. Klyachko, Vladimir Tikhomirov, P. Chaloupka, S. Trentalange, A. Ishihara, Yu Chen, Gregory Rakness, B. K. Srivastava, I. M. Vasilevski, F. Retiere, J. Gans, Boris Hippolyte, J. C. Dunlop, Zubayer Ahammed, M. J. LeVine, H. G. Ritter, A. S. Konstantinov, B. Norman, A. A. Kuznetsov, S. Y. Panitkin, E. Yamamoto, J. Engelage, David Lynn, J. G. Ma, J. Takahashi, M. A. C. Lamont, S. B. Nurushev, Z. Milosevich, N. G. Minaev, Sergey Voloshin, K. J. Foley, V. S. Shvetcov, Q. J. Liu, C. A. Whitten, J. Baudot, A. Rose, Y. V. Zanevski, S. Lange, S. J. Lindenbaum, Yu. Ivanshin, N. Xu, John N. Wood, M. Guedon, A. M. Poskanzer, A. M. VanderMolen, Russell Wells, J. M. Landgraf, M. Strikhanov, A. Billmeier, J. Putschke, J. W. Watson, A. Ogawa, Thomas A. Trainor, R. P. Scharenberg, Christina Markert, H. S. Matis, G. Odyniec, J. Sandweiss, Z. Liu, W. W. Jacobs, G. D. Westfall, H. Ward, L. S. Schroeder, S. V. Razin, L. Gaudichet, H. Zhang, Jay Roberts, Jinghui Yang, Malgorzata Anna Janik, C. L. Kunz, K. Krueger, C. F. Moore, C. Struck, M. Lopez-Noriega, I. Sakrejda, M. L. Miller, Fuqiang Wang, P. Szarwas, A. S. Hirsch, P. M. Jacobs, P. Kravtsov, C. Adler, E. G. Judd, Michael A. Thompson, Michal Sumbera, Jeffrey G. Reid, A. A. P. Suaide, E. Sugarbaker, S. R. Klein, V. Faine, J. Castillo, S. W. Wissink, J. E. Draper, H. Z. Huang, N.D. Gagunashvili, O. Barannikova, D. L. Olson, Sukalyan Chattopadhyay, T. J. Hallman, V. Perevoztchikov, K. Filimonov, A. A. Derevschikov, Marie Germain, V. I. Yurevich, A. N. Zubarev, M. Messer, P. Fachini, V. V. Belaga, Peter Graham Jones, Lee Stuart Barnby, F. Meissner, L. Didenko, M. Kopytine, J. Fu, M. Tokarev, K. Schweda, H. H. Wieman, J. Kiryluk, Rajarshi Ray, L. Lakehal-Ayat, W. A. Love, Vitaly Okorokov, Bernd Surrow, J. L. Klay, C. A. Gagliardi, A. Ridiger, T. Herston, R. V. Cadman, S. Heppelmann, D. Flierl, Frank Jm Geurts, L. Martin, J. P. Coffin, O. V. Rogachevski, V. A. Moiseenko, Marcelo Gameiro Munhoz, D. J. Prindle, E. J. Stephenson, M. A. Lisa, S. Margetis, O. A. Grachov, B. Erazmus, Gerd Joachim Kunde, D. Cebra, A. Bravar, Yu Melnick, J. Balewski, Claude Andre Pruneau, T. Ullrich, R. Zoulkarneev, V. Grigoriev, E. Potrebenikova, T. Ljubicic, and H. Caines

Subjects
Physics, Nuclear physics, Azimuth, General Physics and Astronomy, Anisotropy
Published
2021

24. Erratum: Azimuthal Anisotropy at the Relativistic Heavy Ion Collider: The First and Fourth Harmonics [Phys. Rev. Lett. 92 , 062301 (2004)]

Author

J. W. Harris, R. Willson, D. G. Underwood, D. Thein, R. V. Cadman, C. Roy, P. Seyboth, M. Kopytine, J. Fu, E. Gushin, P. Yepes, V. Eckardt, D. Reichhold, Jianhong Wu, Frank Jm Geurts, I.A. Savin, N. T. Porile, A. H. Tang, T. J. M. Symons, A. Klyachko, J. H. Thomas, M. Tokarev, C-Q. Li, P. Sorensen, M. Shao, G. Van Buren, S. P. Chernenko, Vladimir Tikhomirov, R. Witt, V. Trofimov, R. P. Scharenberg, Christina Markert, W. T. Waggoner, Yu A. Matulenko, M. Horsley, T. W. Henry, W. J. Llope, P. Chaloupka, V. Yu Khodyrev, B. K. Srivastava, J. C. Dunlop, J. Gans, H. S. Matis, Zubayer Ahammed, M. J. LeVine, S. K. Badyal, S. Trentalange, L. S. Schroeder, S. Bhardwaj, Boris Hippolyte, S. V. Razin, M. Calderon De La Barca Sanchez, H. H. Wieman, B. Stringfellow, L. Gaudichet, H. Long, Sukalyan Chattopadhyay, W. W. Jacobs, J. Lauret, M. S. Ganti, R.Kh. Kutuev, Joram Berger, J. E. Gonzalez, Bedangadas Mohanty, T. W. Ludlam, J. M. Nelson, A. Ridiger, G. S. Averichev, K. Schweda, Guy Paic, A. Chikanian, S. S. Shimanskii, Jay Roberts, S. Stanislaus, V. B. Dunin, S. Mahajan, Q. Li, M. Heinz, Michael Kramer, I. Zborovský, L. K. Mangotra, T. J. Hallman, Y. G. Ma, W. Peryt, D. K. Mishra, S. Heppelmann, D. Flierl, J. Porter, V. Ghazikhanian, J. L. Romero, R. Lednický, L. Martin, J. Engelage, John N. Wood, Premomoy Ghosh, J. M. Landgraf, M. Strikhanov, C. Perkins, T. Niida, A. Lebedev, M. M. de Moura, J. G. Cramer, R. Manweiler, T. S. McShane, Y. Fisyak, Ian Johnson, T. Todoroki, Adam Ryszard Kisiel, J. B. Carroll, Christophe Pierre Suire, H. J. Crawford, G. Wang, V. A. Nikitin, K. E. Shestermanov, A. Boucham, T. J. Humanic, D. Arkhipkin, S. Bekele, A. Ishihara, H. Jiang, Basanta Kumar Nandi, M. Guedon, A. M. Poskanzer, A. M. VanderMolen, Russell Wells, J. P. Coffin, O. V. Rogachevski, C. P. Lansdell, E. Sugarbaker, R.J.M. Snellings, H. Z. Huang, C. Struck, M. Lopez-Noriega, F. Meissner, J. Kiryluk, Rajarshi Ray, D. A. Morozov, J. L. Klay, M. Botje, A. Billmeier, G. Odyniec, J. Sandweiss, Z. Liu, R. Fatemi, C. O. Blyth, R. S. Longacre, P. Bhaskar, V. Perevoztchikov, K. Filimonov, Q. J. Liu, C. A. Whitten, L. Ruan, M. J. Mora-Corral, A. Rose, S. Lange, S. J. Lindenbaum, H. Ward, Sergey Voloshin, K. J. Foley, D. Seliverstov, J. Takahashi, M. A. C. Lamont, S. B. Nurushev, Z. Milosevich, X. L. Wang, B. I. Bezverkhny, S. Margetis, O. A. Grachov, X. Dong, S. K. Pal, A. Bravar, V. Grigoriev, E. Potrebenikova, V. V. Belaga, B. Erazmus, Gerd Joachim Kunde, D. Cebra, M. Estienne, E. Finch, A. Szanto de Toledo, T. Pawlak, A. Stolpovsky, L. Kotchenda, J. R. Adams, M. Castro, L. C. Bland, C. L. Kunz, K. Krueger, C. F. Moore, Y. Panebratsev, D. Grosnick, G. Rai, R. Picha, N. Xu, P. Filip, Debasish Das, G. D. Westfall, S. C. Phatak, A. Kumar, T. Ljubicic, M. Cherney, E. G. Judd, Thomas Michael Cormier, S. Das, P. Nevski, A. Gupta, B. Norman, Malgorzata Anna Janik, J. Baudot, Y. V. Zanevski, Saroj K. Nayak, Morton Kaplan, X. Z. Cai, Peter Graham Jones, Yu Melnick, H. Bichsel, Raghunath Sahoo, S. M. Guertin, D. P. Mahapatra, Yu Chen, M. Csanád, J. N. Marx, Mirko Planinic, P. A. Żołnierczuk, N.D. Gagunashvili, Michael W. Anderson, L. Liu, B. Choi, F. Du, S. Kabana, Olivier Ravel, Y. P. Viyogi, H. Caines, Sudhir Raniwala, Camelia Mironov, Michal Sumbera, A. A. P. Suaide, G. Renault, Thomas Dietel, Zhongyukun Xu, M. Potekhin, G. Igo, Alexander Kovalenko, L. V. Nogach, V. I. Kravtsov, M. R. Dutta Majumdar, M. Oldenburg, J. Zoulkarneeva, V. Faine, J. W. Mitchell, Z. P. Zhang, V. Petrov, J. Castillo, S. W. Wissink, Anand Kumar Dubey, L. Didenko, F. Retiere, A. S. Hirsch, P. M. Jacobs, J. Balewski, Rashmi Raniwala, Claude Andre Pruneau, P. Kravtsov, C. Adler, B. V. K. S. Potukuchi, David Lynn, J. E. Draper, N. G. Minaev, N. Schmitz, E. Shahaliev, T. Ullrich, R. Zoulkarneev, H. G. Ritter, Jeffrey G. Reid, D. Magestro, J. Putschke, J. W. Watson, E. Hjort, Gregory Rakness, H. M. Spinka, A. Ogawa, H. F. Chen, Shengli Huang, Thomas A. Trainor, G. Skoro, J. G. Ma, R. N. Singaraju, Marcelo Gameiro Munhoz, D. J. Prindle, Z. Z. Xu, A. P. Meschanin, S. R. Klein, Manish Sharma, M. A. Lisa, W. J. Dong, O. Barannikova, D. L. Olson, Nikita Smirnov, A. A. Derevschikov, Vitaly Okorokov, Bernd Surrow, Marie Germain, A. Tai, G. Sood, C. A. Gagliardi, J. Amonett, T. Herston, Madan M. Aggarwal, A. N. Zubarev, Fuqiang Wang, M. Messer, V. Emelianov, V. I. Yurevich, Frank Simon, P. Fachini, A. K. Bhati, D. Keane, S. Gronstal, Lee Stuart Barnby, R. Stock, L. G. Efimov, W. A. Love, D. D. Koetke, T. K. Nayak, B. E. Bonner, O. D. Tsai, B. Lasiuk, M. A. Vasiliev, Sevil Salur, Saurabh Pandey, W. Christie, A. I. Kulikov, Masashi Kaneta, W. M. Zhang, Andrey Vasiliev, Janet Elizabeth Seger, T. Kollegger, A. I. Pavlinov, F. Liu, M. B. Tonjes, V. Morozov, T. D. Gutierrez, D. Hardtke, F. Laue, R. D. Majka, J. Sowinski, Z. M. Wang, J. Schambach, Julien Faivre, A. V. Brandin, S. E. Vigdor, Christian Claude Kuhn, R. Ma, B. D. Anderson, H. Zhang, G. Eppley, I. Sakrejda, J. Pluta, M. L. Miller, L. Molnar, P. Szarwas, Rene Bellwied, R. E. Tribble, A. A. Kuznetsov, S. Y. Panitkin, Gerald W Hoffmann, E. Yamamoto, and M. D. Trivedi

Subjects
Nuclear physics, Physics, Azimuth, Harmonics, General Physics and Astronomy, Anisotropy, Relativistic Heavy Ion Collider
Published
2021

25. Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals

Author

Martin I. Jones, Joseph D. Szustakowski, Giorgio Sirugo, Lukas Habegger, Adam J. Mansfield, Will Salerno, Joshua D. Backman, Athanasios Kousathanas, David J. Carey, Yi-Pin Lai, James F. Wilson, Alison M. Meynert, Anne E. Justice, Alexander H. Li, Jack A. Kosmicki, Anthony Marcketta, Sándor Szalma, Shane McCarthy, A. R. Shuldiner, A. Baras, Daniel J. Rader, Michael N. Cantor, Ashish Yadav, Manuel A. R. Ferreira, F. S. P. Kury, Konrad Rawlik, Loukas Moutsianas, Gonçalo R. Abecasis, Susan P. Walker, Xing Chen, Albert Tenesa, Paul Nioi, Adam E. Locke, Guillaume Butler-Laporte, E. N. Smith, Richard H Scott, Gundula Povysil, Joseph B. Leader, Lauren Gurski, Dorota Pasko, Marylyn D. Ritchie, A. Cordova-Palomera, Kyoko Watanabe, Colm O'Dushlaine, A. O'Neill, Tomoko Nakanishi, Erola Pairo-Castineira, Xiuwen Zheng, Emily Wong, Jeffrey G. Reid, Slavé Petrovski, Julie E. Horowitz, Anurag Verma, Justin W. Davis, Dylan Sun, Sahar Esmaeeli, Heiko Runz, Quanli Wang, John D. Overton, Shareef Khalid, Tooraj Mirshahi, Evan Maxwell, Mark J. Caulfield, Mark Lathrop, Olympe Chazara, Deepika Sharma, David Goldstein, Jonathan Marchini, Xiaodong Bai, Suganthi Balasubramanian, Krzysztof Kiryluk, Nilanjana Banerjee, Rouel Lanche, J. B. Richards, Hyun Min Kang, J. K. Baillie, Yunfeng Huang, Sean O'Keeffe, Erika Kvikstad, Margaret M. Parker, and Joelle Mbatchou

Subjects
Male, 0301 basic medicine, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Biology, 03 medical and health sciences, Current sample, 0302 clinical medicine, Data sequences, Report, Exome Sequencing, Genetics, Humans, Exome, Genetic Predisposition to Disease, 030212 general & internal medicine, Gene, Genetics (clinical), SARS-CoV-2, COVID-19, Prognosis, Hospitalization, 030104 developmental biology, Sample Size, Multiple comparisons problem, Susceptibility locus, Female, Interferons
Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that can result in hospitalization or death. We used exome sequence data to investigate associations between rare genetic variants and seven COVID-19 outcomes in 586,157 individuals, including 20,952 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome wide or when specifically focusing on (1) 13 interferon pathway genes in which rare deleterious variants have been reported in individuals with severe COVID-19, (2) 281 genes located in susceptibility loci identified by the COVID-19 Host Genetics Initiative, or (3) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, and results are publicly available through the Regeneron Genetics Center COVID-19 Results Browser.

Published
2021

26. Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank

Author

Lukas Habegger, Max Orelus, Marcus B. Jones, Anurag Verma, Aris Economides, Shareef Khalid, William J Salerno, Adam J. Mansfield, Luca A. Lotta, Maria Sotiropoulos Padilla, Louis Widom, Michael Cantor, Giovanni Coppola, Katherine L. Nathanson, Suganthi Balasubramanian, Razvan Panea, John D. Overton, Alicia Hawes, Anh D. Le, Jeffrey C. Staples, Danielle L. Mowery, Jason Mighty, Kara N. Maxwell, Renae Judy, Andrew Blumenfeld, Manasi Pradhan, Peter Gabriel, Heena Desai, Caitlin Forsythe, Jeffrey G. Reid, Lyndon J. Mitnaul, Christina Beechert, Xiaodong Bai, Olga Krasheninina, Zhenhua Gu, Abigail Doucette, Mrunali Nafde, Boris Boutkov, Kia Manoochehri, Marylyn D. Ritchie, Tommy Polanco, Rouel Lanche, Alexander E. Lopez, Ryan Hausler, Alan R. Shuldiner, Sarah E. Wolf, Thomas D. Schleicher, Gisu Eom, Shefali S. Verma, Sean O’Keeffe, Ayesha Rasool, Rachel L. Kember, Evan Maxwell, Michael Lattari, Erin D. Fuller, Scott M. Damrauer, Ricardo H. Ulloa, Gonçalo R. Abecasis, Louise Wang, and Aris Baras

Subjects
Gerontology, business.industry, Medicine, Cancer, Polygenic risk score, business, medicine.disease, Biobank
Abstract

PurposeGenome-wide association studies (GWAS) have identified hundreds of single nucleotide polymorphisms (SNPs) significantly associated with several cancers, but the predictive ability of polygenic risk scores (PRS) is unclear, especially among non-Whites.MethodsGenome-wide genotype data was available for 20,079 individuals enrolled in an academic biobank. PRS were derived from significant DNA variants for 15 cancers. We determined the discriminatory accuracy of each cancer-specific PRS in patients of genetically-determined African and European ancestry separately.ResultsAmong individuals of European genetic ancestry, PRS for breast, colon, melanoma, and prostate were significantly associated with their respective cancers (OR 1.25-1.47). Among individuals of African genetic ancestry, PRS for breast, colon, and prostate were significantly associated with their respective cancers. The AUC of a model comprised of age, sex, and principal components was 0.617–0.709 and increased by 1-4% with the PRS in individuals of European genetic ancestry. In individuals of African genetic ancestry, AUC was overall higher in the model without PRS (0.740-0.811) but increased < 1% with the PRS in the majority of cancers.ConclusionPRS constructed from SNPs moderately increased discriminatory ability for cancer status in individuals of European but not African ancestry. Further large-scale studies are needed to identify ancestry-specific genetic factors in non-White populations to incorporate PRS into cancer risk assessment.

Published
2021

27. Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank

Author

Louise Wang, Heena Desai, Shefali S. Verma, Anh Le, Ryan Hausler, Anurag Verma, Renae Judy, Abigail Doucette, Peter E. Gabriel, Katherine L. Nathanson, Scott M. Damrauer, Danielle L. Mowery, Marylyn D. Ritchie, Rachel L. Kember, Kara N. Maxwell, Goncalo Abecasis, Xiaodong Bai, Suganthi Balasubramanian, Aris Baras, Andrew Blumenfeld, Boris Boutkov, Michael Cantor, Giovanni Coppola, Aris Economides, Gisu Eom, Lukas Habegger, Alicia Hawes, Marcus B. Jones, Shareef Khalid, Olga Krasheninina, Rouel Lanche, Luca A. Lotta, Adam J. Mansfield, Evan K. Maxwell, Jason Mighty, Lyndon J. Mitnaul, Mrunali Nafde, Sean O’Keeffe, Max Orelus, John D. Overton, Razvan Panea, Tommy Polanco, Ayesha Rasool, Jeffrey G. Reid, William Salerno, Jeffrey C. Staples, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Kia Manoochehri, Manasi Pradhan, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Ricardo H. Ulloa, Louis Widom, and Sarah E. Wolf

Subjects
Male, Multifactorial Inheritance, Risk Factors, Neoplasms, Black People, Humans, Female, Genetic Predisposition to Disease, Genetics (clinical), White People, Biological Specimen Banks, Genome-Wide Association Study
Abstract

Genome-wide association studies have identified hundreds of single nucleotide variations (formerly single nucleotide polymorphisms) associated with several cancers, but the predictive ability of polygenic risk scores (PRSs) is unclear, especially among non-Whites.PRSs were derived from genome-wide significant single-nucleotide variations for 15 cancers in 20,079 individuals in an academic biobank. We evaluated the improvement in discriminatory accuracy by including cancer-specific PRS in patients of genetically-determined African and European ancestry.Among the individuals of European genetic ancestry, PRSs for breast, colon, melanoma, and prostate were significantly associated with their respective cancers. Among the individuals of African genetic ancestry, PRSs for breast, colon, prostate, and thyroid were significantly associated with their respective cancers. The area under the curve of the model consisting of age, sex, and principal components was 0.621 to 0.710, and it increased by 1% to 4% with the inclusion of PRS in individuals of European genetic ancestry. In individuals of African genetic ancestry, area under the curve was overall higher in the model without the PRS (0.723-0.810) but increased by1% with the inclusion of PRS for most cancers.PRS moderately increased the ability to discriminate the cancer status in individuals of European but not African ancestry. Further large-scale studies are needed to identify ancestry-specific genetic factors in non-White populations to incorporate PRS into cancer risk assessment.

Published
2021

28. Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline

Author

Lukas Habegger, Charumathi Sabanayagam, Michael Preuss, Laura M. Raffield, Mary F. Feitosa, Bamidele O. Tayo, Kevin Ho, Leo-Pekka Lyytikäinen, Florian Kronenberg, Valencia Hui Xian Foo, Adrienne Tin, Michael Cantor, Nisha Bansal, Tarunveer S. Ahluwalia, Melanie Waldenberger, Sarah A. Pendergrass, Behrooz Z. Alizadeh, Wolfgang Koenig, Qiong Yang, Xiaodong Bai, Christoph Wanner, Ben Schöttker, Giovanni Coppola, A. R. Shuldiner, Leslie A. Lange, Piyush Gampawar, Markus Scholz, Tien Yin Wong, Mary L. Biggs, Morris Swertz, Alicia Hawes, Girish N. Nadkarni, Christina-Alexandra Schulz, Chiea Chuen Khor, Ricardo H. Ulloa, Jeffrey C. Staples, Miao-Li Chee, Laura M. Yerges-Armstrong, Andrew Blumenfeld, Karlhans Endlich, Bernhard Banas, Bruce H.R. Wolffenbuttel, Kai-Uwe Eckardt, Pavel Hamet, Carsten A. Böger, Harold Snieder, Marcus B. Jones, Judy Wang, Shih-Jen Hwang, Mathias Gorski, Anselm Hoppmann, Josyf C. Mychaleckyj, Bernd Holleczek, Pamela R. Matias-Garcia, Rainer Rettig, Karsten B. Sieber, Manasi Pradhan, Pashupati P. Mishra, Peter Rossing, Matthias Wuttke, Miao-Ling Chee, H. Marike Boezen, Yong Li, M. Arfan Ikram, Jeffrey G. Reid, Teresa Nutile, Maria Sotiropoulos Padilla, Lude Franke, Robert J. Carroll, Luca A. Lotta, Bernhard K. Krämer, Kjell Nikus, Jerome I. Rotter, Thomas Meitinger, Lars Wallentin, Cisca Wijmenga, Kent D. Taylor, Holly Kramer, Louis Widom, Olli T. Raitakari, Marcus E. Kleber, Man Li, Nina Hutri-Kähönen, Massimiliano Cocca, Reinhold Schmidt, John D. Overton, Cristian Pattaro, Michael Lattari, Sarah E. Wolf, Jin-Fang Chai, Karina Toledo, Brigitte Kühnel, Zhenhua Gu, Peter Almgren, Caitlin Forsythe, Yuri Milaneschi, Stephan J. L. Bakker, Layal Chaker, Dawn M. Waterworth, Silke Szymczak, James G. Wilson, Peter J. van der Most, Michelle L. O'Donoghue, William Salerno, Masayuki Yasuda, Sahar Ghasemi, Eric Boerwinkle, Josef Coresh, Ilja M. Nolte, Kia Manoochehri, Konstantin Strauch, Thomas D. Schleicher, Myriam Rheinberger, Audrey Y. Chu, Sanaz Sedaghat, Sandra Freitag-Wolf, Boting Ning, Matthias Nauck, Christina Beechert, Helena Schmidt, Harvey D. White, Nina Mononen, Johanne Tremblay, Navya Shilpa Josyula, Mika Kähönen, Katrin Horn, Andre Franke, Marianne Rots, Bettina Jung, Alexander R. Rosenkranz, Christian M. Shaffer, Mary Ann Lukas, Gerjan Navis, Christian Gieger, John Chalmers, Shareef Khalid, Uwe Völker, Marju Orho-Melander, Iris M. Heid, Brenda W.J.H. Penninx, A. Baras, Alexander Lopez, Evan Maxwell, Ruth J. F. Loos, Erin D. Fuller, Christa Meisinger, Gonçalo R. Abecasis, Suganthi Balasubramanian, Chris H. L. Thio, Martin H. de Borst, Stefan Coassin, Ching-Yu Cheng, Wolfgang Lieb, Kenneth Rice, Alexander Teumer, Mark Woodward, Gisu Eom, Hermann Brenner, Thomas W. Winkler, Anna Köttgen, Edith Hofer, Aris Economides, Ron T. Gansevoort, Pim van der Harst, Lyndon J. Mitnaul, Bruce M. Psaty, Erwin P. Bottinger, Olle Melander, Niek Verweij, Frauke Degenhardt, Yan Zhang, Mohsen Ghanbari, Veronika Wanner, Terho Lehtimäki, Leland Barnard, Tampere University, Primary Health Care, Department of Paediatrics, Clinical Medicine, Department of Clinical Physiology and Nuclear Medicine, Department of Clinical Chemistry, TAYS Heart Centre, Groningen Institute for Organ Transplantation (GIOT), Groningen Kidney Center (GKC), Cardiovascular Centre (CVC), Life Course Epidemiology (LCE), Department of Marketing Management, Epidemiology, Internal Medicine, Psychiatry, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Mental Health, and APH - Digital Health

Subjects
0301 basic medicine, medicine.medical_specialty, Genome-wide association study, 030232 urology & nephrology, Protein Disulfide-Isomerases, Hasso-Plattner-Institut für Digital Engineering GmbH, Renal function, Locus (genetics), Biology, AMP-Activated Protein Kinases, Kidney, 3121 Internal medicine, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, end-stage kidney disease, rapid eGFRcrea decline, Urologi och njurmedicin, medicine, Humans, Urology and Nephrology, ddc:610, Allele, Genetic association, Genetics, Creatinine, genome-wide association study, Acute kidney injury, acute kidney injury, medicine.disease, United Kingdom, ddc, 030104 developmental biology, chemistry, Nephrology, Medical genetics, 3111 Biomedicine, 610 Medizin und Gesundheit, Glomerular Filtration Rate
Abstract

Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m(2)/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m(2) at follow-up among those with eGFRcrea 60 mL/min/1.73m(2) or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or (LARP4B). Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function., Zweitveröffentlichungen der Universität Potsdam : Reihe der Digital Engineering Fakultät; 19

Published
2021

29. Exome-wide evaluation of rare coding variants using electronic health records identifies new gene-phenotype associations

Author

Manuel A. R. Ferreira, Ali Naji, Todd L. Edwards, Anne E. Justice, Marylyn D. Ritchie, John D. Overton, Theodore G. Drivas, Nathan Katz, Ying H. Shen, Yanming Li, Renae Judy, Anastasia Lucas, Amanda Dobbyn, Anurag Verma, Scott M. Damrauer, Daniel J. Rader, Geetha Chittoor, Maria Fasolino, Xinyuan Zhang, Jinbo Chen, Scott A. LeMaire, Alexander H. Li, Joseph H. Breeyear, Rachel L. Kember, Kumardeep Chaudhary, Joseph Park, JoEllen Weaver, Shadi Ahmadmehrabi, Alan Daugherty, Hisashi Sawada, Yuki Bradford, Klaus H. Kaestner, Jeffrey G. Reid, Ron Do, Navya Shilpa Josyula, Golnaz Vahedi, Girish N. Nadkarni, Judy H. Cho, Chen Zhang, Aris Baras, and Venkata R M Chavali

Subjects
0301 basic medicine, Male, Genotype, Population, Genome-wide association study, Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, 0302 clinical medicine, Genetic variation, Exome Sequencing, Electronic Health Records, Humans, Exome, education, Exome sequencing, Aged, Genetics, education.field_of_study, Computational Biology, General Medicine, Biobank, Phenotype, 030104 developmental biology, 030220 oncology & carcinogenesis, Female, Genome-Wide Association Study
Abstract

The clinical impact of rare loss-of-function variants has yet to be determined for most genes. Integration of DNA sequencing data with electronic health records (EHRs) could enhance our understanding of the contribution of rare genetic variation to human disease1. By leveraging 10,900 whole-exome sequences linked to EHR data in the Penn Medicine Biobank, we addressed the association of the cumulative effects of rare predicted loss-of-function variants for each individual gene on human disease on an exome-wide scale, as assessed using a set of diverse EHR phenotypes. After discovering 97 genes with exome-by-phenome-wide significant phenotype associations (P

Published
2021

30. An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs

Author

Heather J. Cordell, James J. Fryett, Kazuko Ueno, Rebecca Darlay, Yoshihiro Aiba, Yuki Hitomi, Minae Kawashima, Nao Nishida, Seik-Soon Khor, Olivier Gervais, Yosuke Kawai, Masao Nagasaki, Katsushi Tokunaga, Ruqi Tang, Yongyong Shi, Zhiqiang Li, Brian D. Juran, Elizabeth J. Atkinson, Alessio Gerussi, Marco Carbone, Rosanna Asselta, Angela Cheung, Mariza de Andrade, Aris Baras, Julie Horowitz, Manuel A.R. Ferreira, Dylan Sun, David E. Jones, Steven Flack, Ann Spicer, Victoria L. Mulcahy, Jinyoung Byan, Younghun Han, Richard N. Sandford, Konstantinos N. Lazaridis, Christopher I. Amos, Gideon M. Hirschfield, Michael F. Seldin, Pietro Invernizzi, Katherine A. Siminovitch, Xiong Ma, Minoru Nakamura, George F. Mells, Andrew Mason, Catherine Vincent, Gang Xie, Jinyi Zhang, Andrea Affronti, Piero L. Almasio, Domenico Alvaro, Pietro Andreone, Angelo Andriulli, Francesco Azzaroli, Pier Maria Battezzati, Antonio Benedetti, MariaConsiglia Bragazzi, Maurizia Brunetto, Savino Bruno, Vincenza Calvaruso, Vincenzo Cardinale, Giovanni Casella, Nora Cazzagon, Antonio Ciaccio, Barbara Coco, Agostino Colli, Guido Colloredo, Massimo Colombo, Silvia Colombo, Laura Cristoferi, Carmela Cursaro, Lory Saveria Crocè, Andrea Crosignani, Daphne D’Amato, Francesca Donato, Gianfranco Elia, Luca Fabris, Stefano Fagiuoli, Carlo Ferrari, Annarosa Floreani, Andrea Galli, Edoardo Giannini, Ignazio Grattagliano, Pietro Lampertico, Ana Lleo, Federica Malinverno, Clara Mancuso, Fabio Marra, Marco Marzioni, Sara Massironi, Alberto Mattalia, Luca Miele, Chiara Milani, Lorenzo Morini, Filomena Morisco, Luigi Muratori, Paolo Muratori, Grazia A. Niro, Sarah O’Donnell, Antonio Picciotto, Piero Portincasa, Cristina Rigamonti, Vincenzo Ronca, Floriano Rosina, Giancarlo Spinzi, Mario Strazzabosco, Mirko Tarocchi, Claudio Tiribelli, Pierluigi Toniutto, Luca Valenti, Maria Vinci, Massimo Zuin, Hitomi Nakamura, Seigo Abiru, Shinya Nagaoka, Atsumasa Komori, Hiroshi Yatsuhashi, Hiromi Ishibashi, Masahiro Ito, Kiyoshi Migita, Hiromasa Ohira, Shinji Katsushima, Atsushi Naganuma, Kazuhiro Sugi, Tatsuji Komatsu, Tomohiko Mannami, Kouki Matsushita, Kaname Yoshizawa, Fujio Makita, Toshiki Nikami, Hideo Nishimura, Hiroshi Kouno, Hirotaka Kouno, Hajime Ota, Takuya Komura, Yoko Nakamura, Masaaki Shimada, Noboru Hirashima, Toshiki Komeda, Keisuke Ario, Makoto Nakamuta, Tsutomu Yamashita, Kiyoshi Furuta, Masahiro Kikuchi, Noriaki Naeshiro, Hironao Takahashi, Yutaka Mano, Seiji Tsunematsu, Iwao Yabuuchi, Yusuke Shimada, Kazuhiko Yamauchi, Rie Sugimoto, Hironori Sakai, Eiji Mita, Masaharu Koda, Satoru Tsuruta, Hiroshi Kamitsukasa, Takeaki Sato, Naohiko Masaki, Tatsuro Kobata, Nobuyoshi Fukushima, Yukio Ohara, Toyokichi Muro, Eiichi Takesaki, Hitoshi Takaki, Tetsuo Yamamoto, Michio Kato, Yuko Nagaoki, Shigeki Hayashi, Jinya Ishida, Yukio Watanabe, Masakazu Kobayashi, Michiaki Koga, Takeo Saoshiro, Michiyasu Yagura, Keisuke Hirata, Atsushu Tanaka, Hajime Takikawa, Mikio Zeniya, Masanori Abe, Morikazu Onji, Shuichi Kaneko, Masao Honda, Kuniaki Arai, Teruko Arinaga-Hino, Etsuko Hashimoto, Makiko Taniai, Takeji Umemura, Satoru Joshita, Kazuhiko Nakao, Tatsuki Ichikawa, Hidetaka Shibata, Satoshi Yamagiwa, Masataka Seike, Koichi Honda, Shotaro Sakisaka, Yasuaki Takeyama, Masaru Harada, Michio Senju, Osamu Yokosuka, Tatsuo Kanda, Yoshiyuki Ueno, Kentaro Kikuchi, Hirotoshi Ebinuma, Takashi Himoto, Michio Yasunami, Kazumoto Murata, Masashi Mizokami, Kazuhito Kawata, Shinji Shimoda, Yasuhiro Miyake, Akinobu Takaki, Kazuhide Yamamoto, Katsuji Hirano, Takafumi Ichida, Akio Ido, Hirohito Tsubouchi, Kazuaki Chayama, Kenichi Harada, Yasuni Nakanuma, Yoshihiko Maehara, Akinobu Taketomi, Ken Shirabe, Yuji Soejima, Akira Mori, Shintaro Yagi, Shinji Uemoto, Egawa H, Tomohiro Tanaka, Noriyo Yamashiki, Sumito Tamura, Yasuhiro Sugawara, Norihiro Kokudo, Naga Chalasani, Vel Luketic, Joseph Odin, Kapil Chopra, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, Aris Economides, Luca A. Lotta, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Karina Toledo, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H. Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Leland Barnard, Andrew Blumenfeld, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Evan K. Maxwell, William Salerno, Jeffrey C. Staples, Marcus B. Jones, Lyndon J. Mitnaul, Richard Sturgess, Christopher Healey, Andrew Yeoman, Anton VJ. Gunasekera, Paul Kooner, Kapil Kapur, V. Sathyanarayana, Yiannis Kallis, Javaid Subhani, Rory Harvey, Roger McCorry, Paul Rooney, David Ramanaden, Richard Evans, Thiriloganathan Mathialahan, Jaber Gasem, Christopher Shorrock, Mahesh Bhalme, Paul Southern, Jeremy A. Tibble, David A. Gorard, Susan Jones, George Mells, Victoria Mulcahy, Brijesh Srivastava, Matthew R. Foxton, Carole E. Collins, David Elphick, Mazn Karmo, Francisco Porras-Perez, Michael Mendall, Tom Yapp, Minesh Patel, Roland Ede, Joanne Sayer, James Jupp, Neil Fisher, Martyn J. Carter, Konrad Koss, Jayshri Shah, Andrzej Piotrowicz, Glyn Scott, Charles Grimley, Ian R. Gooding, Simon Williams, Judith Tidbury, Guan Lim, Kuldeep Cheent, Sass Levi, Dina Mansour, Matilda Beckley, Coral Hollywood, Terry Wong, Richard Marley, John Ramage, Harriet M. Gordon, Jo Ridpath, Theodore Ngatchu, Vijay Paul Bob Grover, Ray G. Shidrawi, George Abouda, L. Corless, Mark Narain, Ian Rees, Ashley Brown, Simon Taylor-Robinson, Joy Wilkins, Leonie Grellier, Paul Banim, Debasish Das, Michael A. Heneghan, Howard Curtis, Helen C. Matthews, Faiyaz Mohammed, Mark Aldersley, Raj Srirajaskanthan, Giles Walker, Alistair McNair, Amar Sharif, Sambit Sen, George Bird, Martin I. Prince, Geeta Prasad, Paul Kitchen, Adrian Barnardo, Chirag Oza, Nurani N. Sivaramakrishnan, Prakash Gupta, Amir Shah, Chris DJ. Evans, Subrata Saha, Katharine Pollock, Peter Bramley, Ashis Mukhopadhya, Stephen T. Barclay, Natasha McDonald, Andrew J. Bathgate, Kelvin Palmer, John F. Dillon, Simon M. Rushbrook, Robert Przemioslo, Chris McDonald, Andrew Millar, Cheh Tai, Stephen Mitchell, Jane Metcalf, Syed Shaukat, Mary Ninkovic, Udi Shmueli, Andrew Davis, Asifabbas Naqvi, Tom JW. Lee, Stephen Ryder, Jane Collier, Howard Klass, Matthew E. Cramp, Nichols Sharer, Richard Aspinall, Deb Ghosh, Andrew C. Douds, Jonathan Booth, Earl Williams, Hyder Hussaini, John Christie, Steven Mann, Douglas Thorburn, Aileen Marshall, Imran Patanwala, Aftab Ala, Julia Maltby, Ray Matthew, Chris Corbett, Sam Vyas, Saket Singhal, Dermot Gleeson, Sharat Misra, Jeff Butterworth, Keith George, Tim Harding, Andrew Douglass, Harriet Mitchison, Simon Panter, Jeremy Shearman, Gary Bray, Michael Roberts, Graham Butcher, Daniel Forton, Zahid Mahmood, Matthew Cowan, Debashis Das, Chin Lye Ch’ng, Mesbah Rahman, Gregory C.A. Whatley, Emma Wesley, Aditya Mandal, Sanjiv Jain, Stephen P. Pereira, Mark Wright, Palak Trivedi, Fiona H. Gordon, Esther Unitt, Altaf Palejwala, Andrew Austin, Vishwaraj Vemala, Allister Grant, Andrew D. Higham, Alison Brind, Ray Mathew, Mark Cox, Subramaniam Ramakrishnan, Alistair King, Simon Whalley, Jocelyn Fraser, S.J. Thomson, Andrew Bell, Voi Shim Wong, Richard Kia, Ian Gee, Richard Keld, Rupert Ransford, James Gotto, Charles Millson, Cordell, H. J., Fryett, J. J., Ueno, K., Darlay, R., Aiba, Y., Hitomi, Y., Kawashima, M., Nishida, N., Khor, S. -S., Gervais, O., Kawai, Y., Nagasaki, M., Tokunaga, K., Tang, R., Shi, Y., Li, Z., Juran, B. D., Atkinson, E. J., Gerussi, A., Carbone, M., Asselta, R., Cheung, A., de Andrade, M., Baras, A., Horowitz, J., Ferreira, M. A. R., Sun, D., Jones, D. E., Flack, S., Spicer, A., Mulcahy, V. L., Byan, J., Han, Y., Sandford, R. N., Lazaridis, K. N., Amos, C. I., Hirschfield, G. M., Seldin, M. F., Invernizzi, P., Siminovitch, K. A., Ma, X., Nakamura, M., Mells, G. F., Mason, A., Vincent, C., Xie, G., Zhang, J., Affronti, A., Almasio, P. L., Alvaro, D., Andreone, P., Andriulli, A., Azzaroli, F., Battezzati, P. M., Benedetti, A., Bragazzi, M., Brunetto, M., Bruno, S., Calvaruso, V., Cardinale, V., Casella, G., Cazzagon, N., Ciaccio, A., Coco, B., Colli, A., Colloredo, G., Colombo, M., Colombo, S., Cristoferi, L., Cursaro, C., Croce, L. S., Crosignani, A., D'Amato, D., Donato, F., Elia, G., Fabris, L., Fagiuoli, S., Ferrari, C., Floreani, A., Galli, A., Giannini, E., Grattagliano, I., Lampertico, P., Lleo, A., Malinverno, F., Mancuso, C., Marra, F., Marzioni, M., Massironi, S., Mattalia, A., Miele, L., Milani, C., Morini, L., Morisco, F., Muratori, L., Muratori, P., Niro, G. A., O'Donnell, S., Picciotto, A., Portincasa, P., Rigamonti, C., Ronca, V., Rosina, F., Spinzi, G., Strazzabosco, M., Tarocchi, M., Tiribelli, C., Toniutto, P., Valenti, L., Vinci, M., Zuin, M., Nakamura, H., Abiru, S., Nagaoka, S., Komori, A., Yatsuhashi, H., Ishibashi, H., Ito, M., Migita, K., Ohira, H., Katsushima, S., Naganuma, A., Sugi, K., Komatsu, T., Mannami, T., Matsushita, K., Yoshizawa, K., Makita, F., Nikami, T., Nishimura, H., Kouno, H., Ota, H., Komura, T., Nakamura, Y., Shimada, M., Hirashima, N., Komeda, T., Ario, K., Nakamuta, M., Yamashita, T., Furuta, K., Kikuchi, M., Naeshiro, N., Takahashi, H., Mano, Y., Tsunematsu, S., Yabuuchi, I., Shimada, Y., Yamauchi, K., Sugimoto, R., Sakai, H., Mita, E., Koda, M., Tsuruta, S., Kamitsukasa, H., Sato, T., Masaki, N., Kobata, T., Fukushima, N., Ohara, Y., Muro, T., Takesaki, E., Takaki, H., Yamamoto, T., Kato, M., Nagaoki, Y., Hayashi, S., Ishida, J., Watanabe, Y., Kobayashi, M., Koga, M., Saoshiro, T., Yagura, M., Hirata, K., Tanaka, A., Takikawa, H., Zeniya, M., Abe, M., Onji, M., Kaneko, S., Honda, M., Arai, K., Arinaga-Hino, T., Hashimoto, E., Taniai, M., Umemura, T., Joshita, S., Nakao, K., Ichikawa, T., Shibata, H., Yamagiwa, S., Seike, M., Honda, K., Sakisaka, S., Takeyama, Y., Harada, M., Senju, M., Yokosuka, O., Kanda, T., Ueno, Y., Kikuchi, K., Ebinuma, H., Himoto, T., Yasunami, M., Murata, K., Mizokami, M., Kawata, K., Shimoda, S., Miyake, Y., Takaki, A., Yamamoto, K., Hirano, K., Ichida, T., Ido, A., Tsubouchi, H., Chayama, K., Harada, K., Nakanuma, Y., Maehara, Y., Taketomi, A., Shirabe, K., Soejima, Y., Mori, A., Yagi, S., Uemoto, S., H, E., Tanaka, T., Yamashiki, N., Tamura, S., Sugawara, Y., Kokudo, N., Chalasani, N., Luketic, V., Odin, J., Chopra, K., Abecasis, G., Cantor, M., Coppola, G., Economides, A., Lotta, L. A., Overton, J. D., Reid, J. G., Shuldiner, A., Beechert, C., Forsythe, C., Fuller, E. D., Gu, Z., Lattari, M., Lopez, A., Schleicher, T. D., Padilla, M. S., Toledo, K., Widom, L., Wolf, S. E., Pradhan, M., Manoochehri, K., Ulloa, R. H., Bai, X., Balasubramanian, S., Barnard, L., Blumenfeld, A., Eom, G., Habegger, L., Hawes, A., Khalid, S., Maxwell, E. K., Salerno, W., Staples, J. C., Jones, M. B., Mitnaul, L. J., Sturgess, R., Healey, C., Yeoman, A., Gunasekera, A. V., Kooner, P., Kapur, K., Sathyanarayana, V., Kallis, Y., Subhani, J., Harvey, R., Mccorry, R., Rooney, P., Ramanaden, D., Evans, R., Mathialahan, T., Gasem, J., Shorrock, C., Bhalme, M., Southern, P., Tibble, J. A., Gorard, D. A., Jones, S., Mells, G., Mulcahy, V., Srivastava, B., Foxton, M. R., Collins, C. E., Elphick, D., Karmo, M., Porras-Perez, F., Mendall, M., Yapp, T., Patel, M., Ede, R., Sayer, J., Jupp, J., Fisher, N., Carter, M. J., Koss, K., Shah, J., Piotrowicz, A., Scott, G., Grimley, C., Gooding, I. R., Williams, S., Tidbury, J., Lim, G., Cheent, K., Levi, S., Mansour, D., Beckley, M., Hollywood, C., Wong, T., Marley, R., Ramage, J., Gordon, H. M., Ridpath, J., Ngatchu, T., Bob Grover, V. P., Shidrawi, R. G., Abouda, G., Corless, L., Narain, M., Rees, I., Brown, A., Taylor-Robinson, S., Wilkins, J., Grellier, L., Banim, P., Das, D., Heneghan, M. A., Curtis, H., Matthews, H. C., Mohammed, F., Aldersley, M., Srirajaskanthan, R., Walker, G., Mcnair, A., Sharif, A., Sen, S., Bird, G., Prince, M. I., Prasad, G., Kitchen, P., Barnardo, A., Oza, C., Sivaramakrishnan, N. N., Gupta, P., Shah, A., Evans, C. D., Saha, S., Pollock, K., Bramley, P., Mukhopadhya, A., Barclay, S. T., Mcdonald, N., Bathgate, A. J., Palmer, K., Dillon, J. F., Rushbrook, S. M., Przemioslo, R., Mcdonald, C., Millar, A., Tai, C., Mitchell, S., Metcalf, J., Shaukat, S., Ninkovic, M., Shmueli, U., Davis, A., Naqvi, A., Lee, T. J., Ryder, S., Collier, J., Klass, H., Cramp, M. E., Sharer, N., Aspinall, R., Ghosh, D., Douds, A. C., Booth, J., Williams, E., Hussaini, H., Christie, J., Mann, S., Thorburn, D., Marshall, A., Patanwala, I., Ala, A., Maltby, J., Matthew, R., Corbett, C., Vyas, S., Singhal, S., Gleeson, D., Misra, S., Butterworth, J., George, K., Harding, T., Douglass, A., Mitchison, H., Panter, S., Shearman, J., Bray, G., Roberts, M., Butcher, G., Forton, D., Mahmood, Z., Cowan, M., Ch'Ng, C. L., Rahman, M., Whatley, G. C. A., Wesley, E., Mandal, A., Jain, S., Pereira, S. P., Wright, M., Trivedi, P., Gordon, F. H., Unitt, E., Palejwala, A., Austin, A., Vemala, V., Grant, A., Higham, A. D., Brind, A., Mathew, R., Cox, M., Ramakrishnan, S., King, A., Whalley, S., Fraser, J., Thomson, S. J., Bell, A., Wong, V. S., Kia, R., Gee, I., Keld, R., Ransford, R., Gotto, J., Millson, C., Cordell H.J., Fryett J.J., Ueno K., Darlay R., Aiba Y., Hitomi Y., Kawashima M., Nishida N., Khor S.-S., Gervais O., Kawai Y., Nagasaki M., Tokunaga K., Tang R., Shi Y., Li Z., Juran B.D., Atkinson E.J., Gerussi A., Carbone M., Asselta R., Cheung A., de Andrade M., Baras A., Horowitz J., Ferreira M.A.R., Sun D., Jones D.E., Flack S., Spicer A., Mulcahy V.L., Byan J., Han Y., Sandford R.N., Lazaridis K.N., Amos C.I., Hirschfield G.M., Seldin M.F., Invernizzi P., Siminovitch K.A., Ma X., Nakamura M., Mells G.F., Mason A., Vincent C., Xie G., Zhang J., Affronti A., Almasio P.L., Alvaro D., Andreone P., Andriulli A., Azzaroli F., Battezzati P.M., Benedetti A., Bragazzi M., Brunetto M., Bruno S., Calvaruso V., Cardinale V., Casella G., Cazzagon N., Ciaccio A., Coco B., Colli A., Colloredo G., Colombo M., Colombo S., Cristoferi L., Cursaro C., Croce L.S., Crosignani A., D'Amato D., Donato F., Elia G., Fabris L., Fagiuoli S., Ferrari C., Floreani A., Galli A., Giannini E., Grattagliano I., Lampertico P., Lleo A., Malinverno F., Mancuso C., Marra F., Marzioni M., Massironi S., Mattalia A., Miele L., Milani C., Morini L., Morisco F., Muratori L., Muratori P., Niro G.A., O'Donnell S., Picciotto A., Portincasa P., Rigamonti C., Ronca V., Rosina F., Spinzi G., Strazzabosco M., Tarocchi M., Tiribelli C., Toniutto P., Valenti L., Vinci M., Zuin M., Nakamura H., Abiru S., Nagaoka S., Komori A., Yatsuhashi H., Ishibashi H., Ito M., Migita K., Ohira H., Katsushima S., Naganuma A., Sugi K., Komatsu T., Mannami T., Matsushita K., Yoshizawa K., Makita F., Nikami T., Nishimura H., Kouno H., Ota H., Komura T., Nakamura Y., Shimada M., Hirashima N., Komeda T., Ario K., Nakamuta M., Yamashita T., Furuta K., Kikuchi M., Naeshiro N., Takahashi H., Mano Y., Tsunematsu S., Yabuuchi I., Shimada Y., Yamauchi K., Sugimoto R., Sakai H., Mita E., Koda M., Tsuruta S., Kamitsukasa H., Sato T., Masaki N., Kobata T., Fukushima N., Ohara Y., Muro T., Takesaki E., Takaki H., Yamamoto T., Kato M., Nagaoki Y., Hayashi S., Ishida J., Watanabe Y., Kobayashi M., Koga M., Saoshiro T., Yagura M., Hirata K., Tanaka A., Takikawa H., Zeniya M., Abe M., Onji M., Kaneko S., Honda M., Arai K., Arinaga-Hino T., Hashimoto E., Taniai M., Umemura T., Joshita S., Nakao K., Ichikawa T., Shibata H., Yamagiwa S., Seike M., Honda K., Sakisaka S., Takeyama Y., Harada M., Senju M., Yokosuka O., Kanda T., Ueno Y., Kikuchi K., Ebinuma H., Himoto T., Yasunami M., Murata K., Mizokami M., Kawata K., Shimoda S., Miyake Y., Takaki A., Yamamoto K., Hirano K., Ichida T., Ido A., Tsubouchi H., Chayama K., Harada K., Nakanuma Y., Maehara Y., Taketomi A., Shirabe K., Soejima Y., Mori A., Yagi S., Uemoto S., H E., Tanaka T., Yamashiki N., Tamura S., Sugawara Y., Kokudo N., Chalasani N., Luketic V., Odin J., Chopra K., Abecasis G., Cantor M., Coppola G., Economides A., Lotta L.A., Overton J.D., Reid J.G., Shuldiner A., Beechert C., Forsythe C., Fuller E.D., Gu Z., Lattari M., Lopez A., Schleicher T.D., Padilla M.S., Toledo K., Widom L., Wolf S.E., Pradhan M., Manoochehri K., Ulloa R.H., Bai X., Balasubramanian S., Barnard L., Blumenfeld A., Eom G., Habegger L., Hawes A., Khalid S., Maxwell E.K., Salerno W., Staples J.C., Jones M.B., Mitnaul L.J., Sturgess R., Healey C., Yeoman A., Gunasekera A.V., Kooner P., Kapur K., Sathyanarayana V., Kallis Y., Subhani J., Harvey R., McCorry R., Rooney P., Ramanaden D., Evans R., Mathialahan T., Gasem J., Shorrock C., Bhalme M., Southern P., Tibble J.A., Gorard D.A., Jones S., Mells G., Mulcahy V., Srivastava B., Foxton M.R., Collins C.E., Elphick D., Karmo M., Porras-Perez F., Mendall M., Yapp T., Patel M., Ede R., Sayer J., Jupp J., Fisher N., Carter M.J., Koss K., Shah J., Piotrowicz A., Scott G., Grimley C., Gooding I.R., Williams S., Tidbury J., Lim G., Cheent K., Levi S., Mansour D., Beckley M., Hollywood C., Wong T., Marley R., Ramage J., Gordon H.M., Ridpath J., Ngatchu T., Bob Grover V.P., Shidrawi R.G., Abouda G., Corless L., Narain M., Rees I., Brown A., Taylor-Robinson S., Wilkins J., Grellier L., Banim P., Das D., Heneghan M.A., Curtis H., Matthews H.C., Mohammed F., Aldersley M., Srirajaskanthan R., Walker G., McNair A., Sharif A., Sen S., Bird G., Prince M.I., Prasad G., Kitchen P., Barnardo A., Oza C., Sivaramakrishnan N.N., Gupta P., Shah A., Evans C.D., Saha S., Pollock K., Bramley P., Mukhopadhya A., Barclay S.T., McDonald N., Bathgate A.J., Palmer K., Dillon J.F., Rushbrook S.M., Przemioslo R., McDonald C., Millar A., Tai C., Mitchell S., Metcalf J., Shaukat S., Ninkovic M., Shmueli U., Davis A., Naqvi A., Lee T.J., Ryder S., Collier J., Klass H., Cramp M.E., Sharer N., Aspinall R., Ghosh D., Douds A.C., Booth J., Williams E., Hussaini H., Christie J., Mann S., Thorburn D., Marshall A., Patanwala I., Ala A., Maltby J., Matthew R., Corbett C., Vyas S., Singhal S., Gleeson D., Misra S., Butterworth J., George K., Harding T., Douglass A., Mitchison H., Panter S., Shearman J., Bray G., Roberts M., Butcher G., Forton D., Mahmood Z., Cowan M., Ch'ng C.L., Rahman M., Whatley G.C.A., Wesley E., Mandal A., Jain S., Pereira S.P., Wright M., Trivedi P., Gordon F.H., Unitt E., Palejwala A., Austin A., Vemala V., Grant A., Higham A.D., Brind A., Mathew R., Cox M., Ramakrishnan S., King A., Whalley S., Fraser J., Thomson S.J., Bell A., Wong V.S., Kia R., Gee I., Keld R., Ransford R., Gotto J., Millson C., Medical Research Council (MRC), LiveR North, Cordell, H, Fryett, J, Ueno, K, Darlay, R, Aiba, Y, Hitomi, Y, Kawashima, M, Nishida, N, Khor, S, Gervais, O, Kawai, Y, Nagasaki, M, Tokunaga, K, Tang, R, Shi, Y, Li, Z, Juran, B, Atkinson, E, Gerussi, A, Carbone, M, Asselta, R, Cheung, A, de Andrade, M, Baras, A, Horowitz, J, Ferreira, M, Sun, D, Jones, D, Flack, S, Spicer, A, Mulcahy, V, Byan, J, Han, Y, Sandford, R, Lazaridis, K, Amos, C, Hirschfield, G, Seldin, M, Invernizzi, P, Siminovitch, K, Ma, X, Nakamura, M, Mells, G, Mason, A, Vincent, C, Xie, G, Zhang, J, Affronti, A, Almasio, P, Alvaro, D, Andreone, P, Andriulli, A, Azzaroli, F, Battezzati, P, Benedetti, A, Bragazzi, M, Brunetto, M, Bruno, S, Calvaruso, V, Cardinale, V, Casella, G, Cazzagon, N, Ciaccio, A, Coco, B, Colli, A, Colloredo, G, Colombo, M, Colombo, S, Cristoferi, L, Cursaro, C, Croce, L, Crosignani, A, D'Amato, D, Donato, F, Elia, G, Fabris, L, Fagiuoli, S, Ferrari, C, Floreani, A, Galli, A, Giannini, E, Grattagliano, I, Lampertico, P, Lleo, A, Malinverno, F, Mancuso, C, Marra, F, Marzioni, M, Massironi, S, Mattalia, A, Miele, L, Milani, C, Morini, L, Morisco, F, Muratori, L, Muratori, P, Niro, G, O'Donnell, S, Picciotto, A, Portincasa, P, Rigamonti, C, Ronca, V, Rosina, F, Spinzi, G, Strazzabosco, M, Tarocchi, M, Tiribelli, C, Toniutto, P, Valenti, L, Vinci, M, Zuin, M, Nakamura, H, Abiru, S, Nagaoka, S, Komori, A, Yatsuhashi, H, Ishibashi, H, Ito, M, Migita, K, Ohira, H, Katsushima, S, Naganuma, A, Sugi, K, Komatsu, T, Mannami, T, Matsushita, K, Yoshizawa, K, Makita, F, Nikami, T, Nishimura, H, Kouno, H, Ota, H, Komura, T, Nakamura, Y, Shimada, M, Hirashima, N, Komeda, T, Ario, K, Nakamuta, M, Yamashita, T, Furuta, K, Kikuchi, M, Naeshiro, N, Takahashi, H, Mano, Y, Tsunematsu, S, Yabuuchi, I, Shimada, Y, Yamauchi, K, Sugimoto, R, Sakai, H, Mita, E, Koda, M, Tsuruta, S, Kamitsukasa, H, Sato, T, Masaki, N, Kobata, T, Fukushima, N, Ohara, Y, Muro, T, Takesaki, E, Takaki, H, Yamamoto, T, Kato, M, Nagaoki, Y, Hayashi, S, Ishida, J, Watanabe, Y, Kobayashi, M, Koga, M, Saoshiro, T, Yagura, M, Hirata, K, Tanaka, A, Takikawa, H, Zeniya, M, Abe, M, Onji, M, Kaneko, S, Honda, M, Arai, K, Arinaga-Hino, T, Hashimoto, E, Taniai, M, Umemura, T, Joshita, S, Nakao, K, Ichikawa, T, Shibata, H, Yamagiwa, S, Seike, M, Honda, K, Sakisaka, S, Takeyama, Y, Harada, M, Senju, M, Yokosuka, O, Kanda, T, Ueno, Y, Kikuchi, K, Ebinuma, H, Himoto, T, Yasunami, M, Murata, K, Mizokami, M, Kawata, K, Shimoda, S, Miyake, Y, Takaki, A, Yamamoto, K, Hirano, K, Ichida, T, Ido, A, Tsubouchi, H, Chayama, K, Harada, K, Nakanuma, Y, Maehara, Y, Taketomi, A, Shirabe, K, Soejima, Y, Mori, A, Yagi, S, Uemoto, S, H, E, Tanaka, T, Yamashiki, N, Tamura, S, Sugawara, Y, Kokudo, N, Chalasani, N, Luketic, V, Odin, J, Chopra, K, Abecasis, G, Cantor, M, Coppola, G, Economides, A, Lotta, L, Overton, J, Reid, J, Shuldiner, A, Beechert, C, Forsythe, C, Fuller, E, Gu, Z, Lattari, M, Lopez, A, Schleicher, T, Padilla, M, Toledo, K, Widom, L, Wolf, S, Pradhan, M, Manoochehri, K, Ulloa, R, Bai, X, Balasubramanian, S, Barnard, L, Blumenfeld, A, Eom, G, Habegger, L, Hawes, A, Khalid, S, Maxwell, E, Salerno, W, Staples, J, Jones, M, Mitnaul, L, Sturgess, R, Healey, C, Yeoman, A, Gunasekera, A, Kooner, P, Kapur, K, Sathyanarayana, V, Kallis, Y, Subhani, J, Harvey, R, Mccorry, R, Rooney, P, Ramanaden, D, Evans, R, Mathialahan, T, Gasem, J, Shorrock, C, Bhalme, M, Southern, P, Tibble, J, Gorard, D, Jones, S, Srivastava, B, Foxton, M, Collins, C, Elphick, D, Karmo, M, Porras-Perez, F, Mendall, M, Yapp, T, Patel, M, Ede, R, Sayer, J, Jupp, J, Fisher, N, Carter, M, Koss, K, Shah, J, Piotrowicz, A, Scott, G, Grimley, C, Gooding, I, Williams, S, Tidbury, J, Lim, G, Cheent, K, Levi, S, Mansour, D, Beckley, M, Hollywood, C, Wong, T, Marley, R, Ramage, J, Gordon, H, Ridpath, J, Ngatchu, T, Bob Grover, V, Shidrawi, R, Abouda, G, Corless, L, Narain, M, Rees, I, Brown, A, Taylor-Robinson, S, Wilkins, J, Grellier, L, Banim, P, Das, D, Heneghan, M, Curtis, H, Matthews, H, Mohammed, F, Aldersley, M, Srirajaskanthan, R, Walker, G, Mcnair, A, Sharif, A, Sen, S, Bird, G, Prince, M, Prasad, G, Kitchen, P, Barnardo, A, Oza, C, Sivaramakrishnan, N, Gupta, P, Shah, A, Evans, C, Saha, S, Pollock, K, Bramley, P, Mukhopadhya, A, Barclay, S, Mcdonald, N, Bathgate, A, Palmer, K, Dillon, J, Rushbrook, S, Przemioslo, R, Mcdonald, C, Millar, A, Tai, C, Mitchell, S, Metcalf, J, Shaukat, S, Ninkovic, M, Shmueli, U, Davis, A, Naqvi, A, Lee, T, Ryder, S, Collier, J, Klass, H, Cramp, M, Sharer, N, Aspinall, R, Ghosh, D, Douds, A, Booth, J, Williams, E, Hussaini, H, Christie, J, Mann, S, Thorburn, D, Marshall, A, Patanwala, I, Ala, A, Maltby, J, Matthew, R, Corbett, C, Vyas, S, Singhal, S, Gleeson, D, Misra, S, Butterworth, J, George, K, Harding, T, Douglass, A, Mitchison, H, Panter, S, Shearman, J, Bray, G, Roberts, M, Butcher, G, Forton, D, Mahmood, Z, Cowan, M, Ch'Ng, C, Rahman, M, Whatley, G, Wesley, E, Mandal, A, Jain, S, Pereira, S, Wright, M, Trivedi, P, Gordon, F, Unitt, E, Palejwala, A, Austin, A, Vemala, V, Grant, A, Higham, A, Brind, A, Mathew, R, Cox, M, Ramakrishnan, S, King, A, Whalley, S, Fraser, J, Thomson, S, Bell, A, Wong, V, Kia, R, Gee, I, Keld, R, Ransford, R, Gotto, J, Millson, C, Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MAR, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byan J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF, PBC Consortia, Canadian PBC Consortium, Chinese PBC Consortium, Italian PBC Study Group, Japan-PBC-GWAS Consortium, US PBC Consortium, UK-PBC Consortium, and Calvaruso V. .

Subjects
Liver Cirrhosis, ALSPAC, ERN RARE-LIVER, Genomic co-localization, Network-based in silico drug efficacy screening, UK-PBC, 0301 basic medicine, Candidate gene, Genome-Wide Association Study, Humans, Liver Cirrhosis, Biliary, Italian PBC Study Group, LD SCORE REGRESSION, Japan-PBC-GWAS Consortium, Genome-wide association study, Locus (genetics), Disease, SUSCEPTIBILITY, PBC, Chronic liver disease, Bioinformatics, GENETIC ASSOCIATION, 1117 Public Health and Health Services, 03 medical and health sciences, 0302 clinical medicine, UK-PBC Consortium, Genotype, Medicine, Genetic association, Science & Technology, Gastroenterology & Hepatology, Hepatology, business.industry, Biliary, Chinese PBC Consortium, 1103 Clinical Sciences, medicine.disease, PBC Consortia, 030104 developmental biology, Meta-analysis, ERN RARE LIVER, 030211 gastroenterology & hepatology, US PBC Consortium, Canadian PBC Consortium, business, Life Sciences & Biomedicine, Human
Abstract

[BACKGROUND & AIMS] Primary biliary cholangitis (PBC) is a chronic liver disease in which autoimmune destruction of the small intra-hepatic bile ducts eventually leads to cirrhosis. Many patients have inadequate response to licensed medications, motivating the search for novel therapies. Previous genome-wide association studies (GWAS) and meta-analyses (GWMA) of PBC have identified numerous risk loci for this condition, providing insight into its aetiology. We undertook the largest GWMA of PBC to date, aiming to identify additional risk loci and prioritise candidate genes for in silico drug efficacy screening. [METHODS] We combined new and existing genotype data for 10, 516 cases and 20, 772 controls from five European and two East Asian cohorts. [RESULTS] We identified 56 genome-wide significant loci (20 novel) including 46 in European, 13 in Asian, and 41 in combined cohorts; and a 57th genome-wide significant locus (also novel) in conditional analysis of the European cohorts. Candidate genes at newly identified loci include FCRL3, INAVA, PRDM1, IRF7, CCR6, CD226, and IL12RB1, each having key roles in immunity. Pathway analysis reiterated the likely importance of pattern recognition receptor and TNF signalling, Jak-STAT signalling, and differentiation of TH1 and TH17 cells in the pathogenesis of this disease. Drug efficacy screening identified several medications predicted to be therapeutic in PBC, some well-established in the treatment of other autoimmune disorders. [CONCLUSIONS] This study has identified additional risk loci for PBC, provided a hierarchy of agents that could be trialled in this condition, and emphasised the value of genetic and genomic approaches to drug discovery in complex disorders. [Lay summary] Primary biliary cholangitis (PBC) is a chronic liver disease that eventually leads to cirrhosis. In this study, we analysed genetic information from 10, 516 people with PBC and 20, 772 healthy individuals recruited in Canada, China, Italy, Japan, UK, or USA. We identified several genetic regions associated with PBC. Each of these regions contains several genes. For each region, we used diverse sources of evidence to help us choose the gene most likely to be involved in causing PBC. We used these ‘candidate genes’ to help us identify medications that are currently used for treatment of other conditions, which might also be useful for treatment of PBC., 原発性胆汁性胆管炎のゲノムワイド関連解析 --国際メタ解析による新規疾患感受性遺伝子と治療薬候補の同定--. 京都大学プレスリリース. 2021-06-28.

Published
2021

31. Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations

Author

Cindy G. Boer, Konstantinos Hatzikotoulas, Lorraine Southam, Lilja Stefánsdóttir, Yanfei Zhang, Rodrigo Coutinho de Almeida, Tian T. Wu, Jie Zheng, April Hartley, Maris Teder-Laving, Anne Heidi Skogholt, Chikashi Terao, Eleni Zengini, George Alexiadis, Andrei Barysenka, Gyda Bjornsdottir, Maiken E. Gabrielsen, Arthur Gilly, Thorvaldur Ingvarsson, Marianne B. Johnsen, Helgi Jonsson, Margreet Kloppenburg, Almut Luetge, Sigrun H. Lund, Reedik Mägi, Massimo Mangino, Rob R.G.H.H. Nelissen, Manu Shivakumar, Julia Steinberg, Hiroshi Takuwa, Laurent F. Thomas, Margo Tuerlings, George C. Babis, Jason Pui Yin Cheung, Jae Hee Kang, Peter Kraft, Steven A. Lietman, Dino Samartzis, P. Eline Slagboom, Kari Stefansson, Unnur Thorsteinsdottir, Jonathan H. Tobias, André G. Uitterlinden, Bendik Winsvold, John-Anker Zwart, George Davey Smith, Pak Chung Sham, Gudmar Thorleifsson, Tom R. Gaunt, Andrew P. Morris, Ana M. Valdes, Aspasia Tsezou, Kathryn S.E. Cheah, Shiro Ikegawa, Kristian Hveem, Tõnu Esko, J. Mark Wilkinson, Ingrid Meulenbelt, Ming Ta Michael Lee, Joyce B.J. van Meurs, Unnur Styrkársdóttir, Eleftheria Zeggini, John Loughlin, Nigel Arden, Fraser Birrell, Andrew Carr, Panos Deloukas, Michael Doherty, Andrew W. McCaskie, William E.R. Ollier, Ashok Rai, Stuart H. Ralston, Tim D. Spector, Gillian A. Wallis, Amy E. Martinsen, Cristen Willer, Egil Andreas Fors, Ingunn Mundal, Knut Hagen, Kristian Bernhard Nilsen, Marie Udnesseter Lie, Sigrid Børte, Ben Brumpton, Jonas Bille Nielsen, Lars G. Fritsche, Wei Zhou, Ingrid Heuch, Kjersti Storheim, Evangelos Tyrpenou, Athanasios Koukakis, Dimitrios Chytas, Dimitrios Stergios Evangelopoulos, Chronopoulos Efstathios, Spiros Pneumaticos, Vasileios S. Nikolaou, Konstantinos Malizos, Lydia Anastasopoulou, Goncalo Abecasis, Aris Baras, Michael Cantor, Giovanni Coppola, Andrew Deubler, Aris Economides, Luca A. Lotta, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Katia Karalis, Katherine Siminovitch, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Xiaodong Bai, Suganthi Balasubramanian, Boris Boutkov, Gisu Eom, Lukas Habegger, Alicia Hawes, Olga Krasheninina, Rouel Lanche, Adam J. Mansfield, Evan K. Maxwell, Mona Nafde, Sean O’Keeffe, Max Orelus, Razvan Panea, Tommy Polanco, Ayesha Rasool, William Salerno, Jeffrey C. Staples, Dadong Li, Deepika Sharma, Ilanjana Banerjee, Jonas Bovijn, Adam Locke, Niek Verweij, Mary Haas, George Hindy, Tanima De, Parsa Akbari, Olukayode Sosina, Manuel A.R. Ferreira, Marcus B. Jones, Jason Mighty, Michelle G. LeBlanc, Lyndon J. Mitnaul, and Internal Medicine

Subjects
Resource, genome-wide association meta-analysis, Disease, Osteoarthritis, effector genes, Biology, Bioinformatics, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Drug Targets, Effector Genes, Functional Genomics, Genetic Architecture, Genome-wide Association Meta-analysis, Spine osteoarthritis, Risk Factors, drug targets, medicine, Humans, Genetic Predisposition to Disease, Sex Characteristics, Cartilage, Correction, medicine.disease, Phenotype, genetic architecture, Genetic architecture, ddc, osteoarthritis, Genetics, Population, medicine.anatomical_structure, Subchondral bone, Female, Functional genomics, functional genomics, Genome-Wide Association Study, Signal Transduction
Abstract

Summary Osteoarthritis affects over 300 million people worldwide. Here, we conduct a genome-wide association study meta-analysis across 826,690 individuals (177,517 with osteoarthritis) and identify 100 independently associated risk variants across 11 osteoarthritis phenotypes, 52 of which have not been associated with the disease before. We report thumb and spine osteoarthritis risk variants and identify differences in genetic effects between weight-bearing and non-weight-bearing joints. We identify sex-specific and early age-at-onset osteoarthritis risk loci. We integrate functional genomics data from primary patient tissues (including articular cartilage, subchondral bone, and osteophytic cartilage) and identify high-confidence effector genes. We provide evidence for genetic correlation with phenotypes related to pain, the main disease symptom, and identify likely causal genes linked to neuronal processes. Our results provide insights into key molecular players in disease processes and highlight attractive drug targets to accelerate translation., Graphical abstract, Highlights • A multicohort study identifies 52 previously unknown osteoarthritis genetic risk variants • Similarities and differences in osteoarthritis genetic risk depend on joint sites • Osteoarthritis genetic components are associated with pain-related phenotypes • High-confidence effector genes highlight potential targets for drug intervention, A multicohort genome-wide association meta-analysis of osteoarthritis highlights the impact of joint site types on the features of genetic risk variants and the link between osteoarthritis genetics and pain-related phenotypes, pointing toward potential targets for therapeutic intervention.

Published
2021

32. Genome-wide analysis in 756,646 individuals provides first genetic evidence that ACE2 expression influences COVID-19 risk and yields genetic risk scores predictive of severe disease

Author

Marie V. Coignet, Dylan Sun, Lukas Habegger, Evan Maxwell, Daniel J. Rader, David J. Carey, Katherine A. Siminovitch, Giorgio Sirugo, Anne E. Justice, Joelle Mbatchou, Eli A. Stahl, Gonçalo R. Abecasis, Alexander H. Li, David A. Turissini, Adam E. Locke, Kristin A. Rand, Aris Baras, Joseph B. Leader, Genevieve H.L. Roberts, Ahna R. Girshick, Deepika Sharma, Nilanjana Banerjee, Fabricio S. P. Kury, John D. Overton, Shane McCarthy, Jonathan Marchini, Xiaodong Bai, Eurie L. Hong, Rouel Lanche, Amy Damask, Ashish Yadav, Raghavendran Partha, Shannon R. McCurdy, Miao Zhang, Suganthi Balasubramanian, Hyun Min Kang, Anurag Verma, Marcus B. Jones, Marylyn D. Ritchie, Colm O'Dushlaine, Manuel A. R. Ferreira, Adam J. Mansfield, Anthony Marcketta, Joshua D. Backman, Alan R. Shuldiner, Michael N. Cantor, Tooraj Mirshahi, Lee Dobbyn, Spencer C. Knight, William J Salerno, Harenda Guturu, Jeffrey G. Reid, Julie E. Horowitz, Lauren Gurski, Danny S. Park, Kyoko Watanabe, Catherine A. Ball, Asher K. Haug Baltzell, and Jack A. Kosmicki

Subjects
2019-20 coronavirus outbreak, Increased risk, Coronavirus disease 2019 (COVID-19), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Genetic variants, MEDLINE, Severe disease, Medicine, Bioinformatics, business
Abstract

SARS-CoV-2 enters host cells by binding angiotensin-converting enzyme 2 (ACE2). Through a genome-wide association study, we show that a rare variant (MAF = 0.3%, odds ratio 0.60, P=4.5x10-13) that down-regulates ACE2 expression reduces risk of COVID-19 disease, providing human genetics support for the hypothesis that ACE2 levels influence COVID-19 risk. Further, we show that common genetic variants define a risk score that predicts severe disease among COVID-19 cases.

Published
2020

33. Open-source mapping and variant calling for large-scale NGS data from original base-quality scores

Author

Olga Krasheninina, Zalcman A, Hwang Y, Evan Maxwell, William J Salerno, Jeffrey G. Reid, and Xiaodong Bai

Subjects
Protocol (science), Open source, Computer science, Scale (chemistry), media_common.quotation_subject, Quality (business), Data mining, Standard methods, computer.software_genre, Base (topology), computer, media_common
Abstract

Standardized genome informatics protocols minimize reprocessing costs and facilitate harmonization across studies if implemented in a transparent, accessible and reproducible manner. Here we define the OQFE protocol, a lossless read-mapping protocol that retains key features of existing NGS standard methods. We demonstrate that variants can be called directly from NovaSeq OQFE data without the need for base quality score recalibration and describe a large-scale variant calling protocol for OQFE data. The OQFE protocol is open-source and a containerized implementation is provided.

Published
2020

34. Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank

Author

Joseph D, Szustakowski, Suganthi, Balasubramanian, Erika, Kvikstad, Shareef, Khalid, Paola G, Bronson, Ariella, Sasson, Emily, Wong, Daren, Liu, J, Wade Davis, Carolina, Haefliger, A, Katrina Loomis, Rajesh, Mikkilineni, Hyun Ji, Noh, Samir, Wadhawan, Xiaodong, Bai, Alicia, Hawes, Olga, Krasheninina, Ricardo, Ulloa, Alex E, Lopez, Erin N, Smith, Jeffrey F, Waring, Christopher D, Whelan, Ellen A, Tsai, John D, Overton, William J, Salerno, Howard, Jacob, Sandor, Szalma, Heiko, Runz, Gregory, Hinkle, Paul, Nioi, Slavé, Petrovski, Melissa R, Miller, Aris, Baras, Lyndon J, Mitnaul, Jeffrey G, Reid, and Zhan, Ye

Subjects
Research, Drug Discovery, Exome Sequencing, Humans, Human Genetics, Genomics, United Kingdom, Biological Specimen Banks
Abstract

The UK Biobank Exome Sequencing Consortium (UKB-ESC) is a private-public partnership between the UK Biobank (UKB) and eight biopharmaceutical companies that will complete the sequencing of exomes for all ~500,000 UKB participants. Here, we describe the early results from ~200,000 UKB participants and the features of this project that enabled its success. The biopharmaceutical industry has increasingly used human genetics to improve success in drug discovery. Recognizing the need for large-scale human genetics data, as well as the unique value of the data access and contribution terms of the UKB, the UKB-ESC was formed. As a result, exome data from 200,643 UKB enrollees are now available. These data include ~10 million exonic variants-a rich resource of rare coding variation that is particularly valuable for drug discovery. The UKB-ESC precompetitive collaboration has further strengthened academic and industry ties and has provided teams with an opportunity to interact with and learn from the wider research community.

Published
2020

35. Advancing Human Genetics Research and Drug Discovery through Exome Sequencing of the UK Biobank

Author

Xiaodong Bai, Samir Wadhawan, Howard J. Jacob, Carolina Haefliger, Ariella Sasson, Rajesh Mikkilineni, Daren Liu, William J. Salerno, Jeffrey F. Waring, Joseph D. Szustakowski, Emily Wong, Paola G. Bronson, Ellen A. Tsai, Gregory Hinkle, Suganthi Balasubramanian, Alex Lopez, Olga Krasheninina, A. Katrina Loomis, E. N. Smith, Melissa R. Miller, Sándor Szalma, Hyun Ji Noh, Heiko Runz, Paul Nioi, Shareef Khalid, Christopher D. Whelan, Jeffrey G. Reid, Slavé Petrovski, Alicia Hawes, Lyndon J. Mitnaul, Ricardo Ulloa, John D. Overton, J. Wade Davis, Aris Baras, and Erika Kvikstad

Subjects
0303 health sciences, business.industry, Drug discovery, Genomics, Computational biology, Biology, Data science, Biobank, Human genetics, 03 medical and health sciences, Open data, 0302 clinical medicine, Drug development, General partnership, Genetics, business, Indel, Exome, 030217 neurology & neurosurgery, Biomedicine, Exome sequencing, 030304 developmental biology
Abstract

The UK Biobank Exome Sequencing Consortium (UKB-ESC) is a unique private/public partnership between the UK Biobank and eight biopharma companies that will sequence the exomes of all ∼500,000 UK Biobank participants. Here we describe early results from the exome sequence data generated by this consortium for the first ∼200,000 UKB subjects and the key features of this project that enabled the UKB-ESC to come together and generate this data.Exome sequencing data from the first 200,643 UKB enrollees are now accessible to the research community. Approximately 10M variants were observed within the targeted regions, including: 8,086,176 SNPs, 370,958 indels and 1,596,984 multi-allelic variants. Of the ∼8M variants observed, 84.5% are coding variants and include 2,139,318 (25.3%) synonymous, 4,549,694 (53.8%) missense, 453,733 (5.4%) predicted loss-of-function (LOF) variants (initiation codon loss, premature stop codons, stop codon loss, splicing and frameshift variants) affecting at least one coding transcript. This open access data provides a rich resource of coding variants for rare variant genetic studies, and is particularly valuable for drug discovery efforts that utilize rare, functionally consequential variants.Over the past decade, the biopharma industry has increasingly leveraged human genetics as part of their drug discovery and development strategies. This shift was motivated by technical advances that enabled cost-effective human genetics research at scale, the emergence of electronic health records and biobanks, and a maturing understanding of how human genetics can increase the probability of successful drug development. Recognizing the need for large-scale human genetics data to drive drug discovery, and the unique value of the open data access policies and contribution terms of the UK Biobank, the UKB-ESC was formed. This precompetitive collaboration has further strengthened the ties between academia and industry and provided teams an unprecedented opportunity to interact with and learn from the wider research community.

Published
2020

36. Validating gene-phenotype associations using relationships in the UMLS

Author

Lukas Habegger, Suganthi Balasubramanian, Michael N. Cantor, Deepika Sharma, Jeffrey Staples, Ashish Yadav, Claudia Gonzaga-Jauregui, Jeffrey G. Reid, Shareef Khalid, and Andrew Blumenfeld

Subjects
Set (abstract data type), education.field_of_study, Computer science, Unified Medical Language System, Population, Cohort, Computational biology, Disease, Health records, education, Gene, Phenotype, Exome sequencing
Abstract

ObjectiveLarge scale next-generation sequencing of population cohorts paired with patients’ electronic health records (EHR) provides an excellent resource for the study of gene-disease associations. To validate those associations, researchers often consult databases that identify relationships between genes of interest and relevant disease phenotypes, which we refer to as simply “phenotypes”. However, most of these databases contain phenotypes that are not suited for automated analysis of EHR data, which often captured these phenotypes in the form of International Classification of Diseases (ICD) codes. There is a need for a resource that comprehensively provides gene-phenotype mappings in a format that can be used to evaluate phenotypes from EHR.MethodsWe built a directed graph database of genes, medical concepts and ICD codes based on a subset of the National Library of Medicine’s Unified Medical Language System (UMLS) and other resources. To obtain associations between genes and ICD codes, we traversed the defined relationships from gene, variant and disease concepts to ICD codes, resulting in a set of mappings that link specific genes and variants to these ICD codes.ResultsOur method created 249,764 mappings between genes and ICD codes, including 27,226 “disease” phenotypes and 222,538 “symptom” phenotypes, and provided mappings for 4,456 unique genes. Paths were validated by manual review of a diverse sample of paths. In a cohort of 92,455 samples, we used these mappings to validate gene-phenotype associations in 32,786 samples where a person had a potentially disease-causing genetic mutation and at least one corresponding diagnosis in their EHR.ConclusionThe concepts and relationships in the UMLS can be used to generate gene-ICD phenotype mappings that are not explicit in the source vocabularies. We were able use these mappings to validate gene-disease associations in a large cohort of sequenced exomes paired with EHR.

Published
2020

37. Polygenic Risk of Psychiatric Disorders Exhibits Cross-trait Associations in Electronic Health Record Data From European Ancestry Individuals

Author

Rachel L. Kember, Alison K. Merikangas, Shefali S. Verma, Anurag Verma, Renae Judy, Scott M. Damrauer, Marylyn D. Ritchie, Daniel J. Rader, Maja Bućan, Goncalo Abecasis, Aris Baras, Michael Cantor, Giovanni Coppola, Aris Economides, Luca Lotta, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Karina Toledo, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H. Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Leland Barnard, Andrew Blumenfeld, Gisu Eom, Lukas Habegger, Young Hahn, Alicia Hawes, Shareef Khalid, Evan K. Maxwell, William Salerno, Jeffrey C. Staples, Ashish Yadav, Marcus B. Jones, and Lyndon J. Mitnaul

Subjects
0301 basic medicine, medicine.medical_specialty, Multifactorial Inheritance, Bipolar Disorder, Disease, Article, 03 medical and health sciences, 0302 clinical medicine, medicine, Electronic Health Records, Humans, Genetic Predisposition to Disease, Bipolar disorder, Psychiatry, Biological Psychiatry, Depressive Disorder, Major, business.industry, Odds ratio, medicine.disease, Biobank, Genetic architecture, 030104 developmental biology, Phenotype, Schizophrenia, Anorexia nervosa (differential diagnoses), Major depressive disorder, business, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Background Prediction of disease risk is a key component of precision medicine. Common traits such as psychiatric disorders have a complex polygenic architecture, making the identification of a single risk predictor difficult. Polygenic risk scores (PRSs) denoting the sum of an individual’s genetic liability for a disorder are a promising biomarker for psychiatric disorders, but they require evaluation in a clinical setting. Methods We developed PRSs for 6 psychiatric disorders (schizophrenia, bipolar disorder, major depressive disorder, cross disorder, attention-deficit/hyperactivity disorder, and anorexia nervosa) and 17 nonpsychiatric traits in more than 10,000 individuals from the Penn Medicine Biobank with accompanying electronic health records. We performed phenome-wide association analyses to test their association across disease categories. Results Four of the 6 psychiatric PRSs were associated with their primary phenotypes (odds ratios from 1.2 to 1.6). Cross-trait associations were identified both within the psychiatric domain and across trait domains. PRSs for coronary artery disease and years of education were significantly associated with psychiatric disorders, largely driven by an association with tobacco use disorder. Conclusions We demonstrated that the genetic architecture of electronic health record–derived psychiatric diagnoses is similar to ascertained research cohorts from large consortia. Psychiatric PRSs are moderately associated with psychiatric diagnoses but are not yet clinically predictive in naive patients. Cross-trait associations for these PRSs suggest a broader effect of genetic liability beyond traditional diagnostic boundaries. As identification of genetic markers increases, including PRSs alongside other clinical risk factors may enhance prediction of psychiatric disorders and associated conditions in clinical registries.

Published
2020

38. Homozygosity for a mutation affecting the catalytic domain of tyrosyl-tRNA synthetase (YARS) causes multisystem disease

Author

Karlla W. Brigatti, John D. Overton, Mark Yoder, Anthony Antonellis, Vincent J Carson, Erick D Martinez, Lili Miles, Kadakkal Radhakrishnan, Vinay Kandula, Aris Baras, Claudia Gonzaga-Jauregui, Laurie B. Griffin, Jeffrey G. Reid, Robert N. Jinks, Erik G. Puffenberger, Katie B. Williams, Katryn N. Furuya, Olivia Wenger, Kevin A. Strauss, Matthew M Demczko, Laura Poskitt, and Michael D Fox

Subjects
Adult, Male, 0301 basic medicine, Heterozygote, Hearing Loss, Sensorineural, 030105 genetics & heredity, Biology, Hypoglycemia, medicine.disease_cause, Severity of Illness Index, 03 medical and health sciences, Loss of Function Mutation, Tyrosine-tRNA Ligase, Catalytic Domain, Yeasts, Exome Sequencing, Genetics, medicine, Humans, Genetic Predisposition to Disease, Allele, Molecular Biology, Genetics (clinical), Exome sequencing, Mutation, Homozygote, Genetic Diseases, Inborn, Infant, Newborn, Infant, Heterozygote advantage, General Medicine, medicine.disease, Pedigree, Complementation, Phenotype, Peripheral neuropathy, Child, Preschool, Female, Sensorineural hearing loss, General Article
Abstract

Aminoacyl-tRNA synthetases (ARSs) are critical for protein translation. Pathogenic variants of ARSs have been previously associated with peripheral neuropathy and multisystem disease in heterozygotes and homozygotes, respectively. We report seven related children homozygous for a novel mutation in tyrosyl-tRNA synthetase (YARS, c.499C > A, p.Pro167Thr) identified by whole exome sequencing. This variant lies within a highly conserved interface required for protein homodimerization, an essential step in YARS catalytic function. Affected children expressed a more severe phenotype than previously reported, including poor growth, developmental delay, brain dysmyelination, sensorineural hearing loss, nystagmus, progressive cholestatic liver disease, pancreatic insufficiency, hypoglycemia, anemia, intermittent proteinuria, recurrent bloodstream infections and chronic pulmonary disease. Related adults heterozygous for YARS p.Pro167Thr showed no evidence of peripheral neuropathy on electromyography, in contrast to previous reports for other YARS variants. Analysis of YARS p.Pro167Thr in yeast complementation assays revealed a loss-of-function, hypomorphic allele that significantly impaired growth. Recombinant YARS p.Pro167Thr demonstrated normal subcellular localization, but greatly diminished ability to homodimerize in human embryonic kidney cells. This work adds to a rapidly growing body of research emphasizing the importance of ARSs in multisystem disease and significantly expands the allelic and clinical heterogeneity of YARS-associated human disease. A deeper understanding of the role of YARS in human disease may inspire innovative therapies and improve care of affected patients.

Published
2018

39. Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease

Author

Eric D. Austin, Rizwan Hamid, William C. Nichols, Jiayao Wang, Philip M. Allen, Frederick E. Dewey, Yufeng Shen, Erika B. Rosenzweig, Wendy K. Chung, Lijiang Ma, John D. Overton, Alejandra King, Katie A. Lutz, Claudia Gonzaga-Jauregui, Carrie L. Welch, Jeffrey G. Reid, Michael W. Pauciulo, Usha Krishnan, D. Dunbar Ivy, Aris Baras, and Na Zhu

Subjects
0301 basic medicine, Adult, Heart Defects, Congenital, Male, Exome sequencing, Heart disease, Adolescent, lcsh:QH426-470, Hypertension, Pulmonary, Population, lcsh:Medicine, Bioinformatics, Pulmonary hypertension, 03 medical and health sciences, Risk Factors, Genetics, medicine, SOXF Transcription Factors, Missense mutation, Humans, Genetic Predisposition to Disease, Amino Acid Sequence, education, Child, Molecular Biology, Gene, Genetics (clinical), Congenital heart disease, Genetic association study, education.field_of_study, business.industry, Research, lcsh:R, Genetic Variation, Infant, medicine.disease, 3. Good health, lcsh:Genetics, 030104 developmental biology, Heart failure, Child, Preschool, Molecular Medicine, Female, business, Rare disease
Abstract

Background Pulmonary arterial hypertension (PAH) is a rare disease characterized by distinctive changes in pulmonary arterioles that lead to progressive pulmonary arterial pressures, right-sided heart failure, and a high mortality rate. Up to 30% of adult and 75% of pediatric PAH cases are associated with congenital heart disease (PAH-CHD), and the underlying etiology is largely unknown. There are no known major risk genes for PAH-CHD. Methods To identify novel genetic causes of PAH-CHD, we performed whole exome sequencing in 256 PAH-CHD patients. We performed a case-control gene-based association test of rare deleterious variants using 7509 gnomAD whole genome sequencing population controls. We then screened a separate cohort of 413 idiopathic and familial PAH patients without CHD for rare deleterious variants in the top association gene. Results We identified SOX17 as a novel candidate risk gene (p = 5.5e−7). SOX17 is highly constrained and encodes a transcription factor involved in Wnt/β-catenin and Notch signaling during development. We estimate that rare deleterious variants contribute to approximately 3.2% of PAH-CHD cases. The coding variants identified include likely gene-disrupting (LGD) and deleterious missense, with most of the missense variants occurring in a highly conserved HMG-box protein domain. We further observed an enrichment of rare deleterious variants in putative targets of SOX17, many of which are highly expressed in developing heart and pulmonary vasculature. In the cohort of PAH without CHD, rare deleterious variants of SOX17 were observed in 0.7% of cases. Conclusions These data strongly implicate SOX17 as a new risk gene contributing to PAH-CHD as well as idiopathic/familial PAH. Replication in other PAH cohorts and further characterization of the clinical phenotype will be important to confirm the precise role of SOX17 and better estimate the contribution of genes regulated by SOX17. Electronic supplementary material The online version of this article (10.1186/s13073-018-0566-x) contains supplementary material, which is available to authorized users.

Published
2018

40. 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

41. 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

42. 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

43. Sparse Project VCF: efficient encoding of population genotype matrices

Author

Jeffrey G. Reid, Xiaodong Bai, Michael F. Lin, and William J Salerno

Subjects
Statistics and Probability, Genotype, AcademicSubjects/SCI01060, Computer science, Population, Information loss, Computational biology, Biochemistry, 03 medical and health sciences, Encoding (memory), education, Molecular Biology, 030304 developmental biology, 0303 health sciences, education.field_of_study, Variant Call Format, Base Sequence, Size reduction, Genetics and Population Analysis, 030302 biochemistry & molecular biology, Genomics, Applications Notes, Biobank, Computer Science Applications, Computational Mathematics, Germ Cells, Computational Theory and Mathematics, Entropy reduction, Random access, Software
Abstract

Summary Variant Call Format (VCF), the prevailing representation for germline genotypes in population sequencing, suffers rapid size growth as larger cohorts are sequenced and more rare variants are discovered. We present Sparse Project VCF (spVCF), an evolution of VCF with judicious entropy reduction and run-length encoding, delivering >10× size reduction for modern studies with practically minimal information loss. spVCF interoperates with VCF efficiently, including tabix-based random access. We demonstrate its effectiveness with the DiscovEHR and UK Biobank whole-exome sequencing cohorts. Availability and implementation Apache-licensed reference implementation: github.com/mlin/spVCF. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2020

44. Genetic and Pharmacologic Inactivation of ANGPTL3 and Cardiovascular Disease

Author

Alex Lopez, Jerome I. Rotter, Yii-Der Ida Chen, Lukas Habegger, Anders Berg Wulff, Richard L Dunbar, John Penn, Anita M. van den Hoek, An Zhao, Omri Gottesman, Cristopher V. Van Hout, Scott M. Damrauer, Tanya M. Teslovich, Aurelie Bouzelmat, Daniel J. Rader, Poulabi Banerjee, David J. Carey, Viktoria Gusarova, Shane McCarthy, Frederick E. Dewey, Kae-Woei Liang, David H. Ledbetter, Gary Herman, Rick Zhang, Alan R. Shuldiner, Svati H. Shah, Claudia Schurmann, Neil Stahl, Marylyn D. Ritchie, Sara Hamon, Colm O'Dushlaine, Ingrid B. Borecki, Daniel A. Gipe, Jesper Gromada, Hans M.G. Princen, Børge G. Nordestgaard, H. Lester Kirchner, Michael F. Murray, Shannon Bruse, Aris Baras, Jeffrey G. Reid, Wayne H-H Sheu, William E. Kraus, Xiuqing Guo, Aeron Small, Brad Shumel, William J. Sasiela, Anne Tybjærg-Hansen, Andrew J. Murphy, Joseph B. Leader, John D. Overton, Robert Pordy, Scott Mellis, Weiping Shao, George D. Yancopoulos, Hayes Dansky, and I-Te Lee

Subjects
0301 basic medicine, medicine.medical_specialty, Evinacumab, Population, 030204 cardiovascular system & hematology, Pharmacology, Coronary artery disease, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Internal medicine, ANGPTL3, Medicine, education, education.field_of_study, biology, business.industry, Cholesterol, General Medicine, medicine.disease, Human genetics, 030104 developmental biology, Endocrinology, chemistry, biology.protein, lipids (amino acids, peptides, and proteins), Antibody, business, Lipoprotein
Abstract

BackgroundLoss-of-function variants in the angiopoietin-like 3 gene (ANGPTL3) have been associated with decreased plasma levels of triglycerides, low-density lipoprotein (LDL) cholesterol, and high-density lipoprotein (HDL) cholesterol. It is not known whether such variants or therapeutic antagonism of ANGPTL3 are associated with a reduced risk of atherosclerotic cardiovascular disease. MethodsWe sequenced the exons of ANGPTL3 in 58,335 participants in the DiscovEHR human genetics study. We performed tests of association for loss-of-function variants in ANGPTL3 with lipid levels and with coronary artery disease in 13,102 case patients and 40,430 controls from the DiscovEHR study, with follow-up studies involving 23,317 case patients and 107,166 controls from four population studies. We also tested the effects of a human monoclonal antibody, evinacumab, against Angptl3 in dyslipidemic mice and against ANGPTL3 in healthy human volunteers with elevated levels of triglycerides or LDL cholesterol. ResultsIn th...

Published
2017

45. Familial Hypercholesterolemia and Type 2 Diabetes in the Old Order Amish

Author

Simeon I. Taylor, Thomas Jaworek, Eleftheria Zeggini, Kathleen A. Ryan, Lorraine Southam, Huichun Xu, Aris Baras, Braxton D. Mitchell, John D. Overton, Jeffrey G. Reid, Alan R. Shuldiner, and Marja Puurunen

Subjects
Blood Glucose, medicine.medical_specialty, Genotype, endocrine system diseases, Apolipoprotein B, Endocrinology, Diabetes and Metabolism, medicine.medical_treatment, Population, Type 2 diabetes, Familial hypercholesterolemia, 030204 cardiovascular system & hematology, Bioinformatics, Hyperlipoproteinemia Type II, 03 medical and health sciences, 0302 clinical medicine, Diabetes mellitus, Internal medicine, Internal Medicine, Humans, Insulin, Medicine, Genetic Predisposition to Disease, 030212 general & internal medicine, education, Apolipoproteins B, Glycated Hemoglobin, education.field_of_study, biology, business.industry, nutritional and metabolic diseases, Genetics/Genomes/Proteomics/Metabolomics, Cholesterol, LDL, medicine.disease, Impaired fasting glucose, Logistic Models, Endocrinology, Diabetes Mellitus, Type 2, Old Order Amish, biology.protein, lipids (amino acids, peptides, and proteins), Amish, business
Abstract

Alleles associated with lower levels of LDL cholesterol (LDL-C) have recently been associated with an increased risk of type 2 diabetes (T2D), highlighting the complex relationship between LDL-C and diabetes. This observation begs the question of whether LDL-C–raising alleles are associated with a decreased risk of T2D. This issue was recently addressed in a large familial hypercholesterolemia (FH) screening study, which reported a lower prevalence of self-reported diabetes in FH subjects than in age-matched relatives without FH. To extend this observation, we tested the association of FH with diabetes status and glycemia in a large Amish population enriched for the FH-associated APOB R3527Q variant that included 640 APOB R3527Q carriers and 4,683 noncarriers. Each copy of the R3527Q T allele was associated with a 74.9 mg/dL increase in LDL-C. There was little difference in T2D prevalence between subjects with (5.2%) and without (4.5%) the R3527Q allele (P = 0.23), and there was no association between R3527Q variant and impaired fasting glucose, fasting glucose or insulin, or oral glucose tolerance test–derived measures. Our data provide no evidence supporting an association between the APOB R3527Q variant and T2D or glycemia and highlight the asymmetry of the LDL-C–T2D relationship and/or the gene/variant-dependent specificity of the LDL-C–T2D association.

Published
2017

46. Epidemiology of DYT1 dystonia: Estimating prevalence via genetic ascertainment

Author

Pedro Gonzalez-Alegre, Jeffrey G. Reid, Aris Baras, Scott M. Damrauer, John D. Overton, and Joseph Park

Subjects
Genetics, Dystonia, education.field_of_study, medicine.medical_specialty, business.industry, Population, medicine.disease, Penetrance, Biobank, Article, Polymorphism (computer science), Mutation (genetic algorithm), Epidemiology, Medicine, Neurology (clinical), education, business, Genetics (clinical), Exome sequencing
Abstract

ObjectiveTo estimate the prevalence of TOR1A sequence variants associated with DYT1 dystonia.MethodsWe determined the frequency of the common trinucleotide deletion that causes DYT1 in the Genome Aggregation Database and the Penn Medicine Biobank, totaling exomes from over 135,000 individuals. We also evaluated the prevalence of other possible pathogenic variants in this gene and asked whether the D216H polymorphism is linked to a higher diagnostic rate for dystonia independent of the DYT1-causing mutation.ResultsThe estimated range of prevalence of the most common pathogenic variant that causes DYT1 is ∼17.6–26.1 carriers per 100,000 individuals. Based on the different data sets used, we predict that there are between 54,366 and 80,891 mutation carriers in the United States, which, due to the reduced penetrance of this variant, would translate into 16,475–24,513 DYT1 patients.ConclusionsOur data provide a prevalence estimate of the most common DYT1 mutation in the general population. This information is specifically important for those with interest in the development of precision therapeutics for dystonia.

Published
2019

47. 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

48. Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank

Author

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

Subjects
education.field_of_study, Genotype, Population, Disease, Computational biology, Biology, education, Exome, Gene, Biobank, Exome sequencing, Loss function
Abstract

SUMMARYThe UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world. Here we describe the first tranche of large-scale exome sequence data for 49,960 study participants, revealing approximately 4 million coding variants (of which ~98.4% have frequency < 1%). The data includes 231,631 predicted loss of function variants, a >10-fold increase compared to imputed sequence for the same participants. Nearly all genes (>97%) had ≥1 predicted loss of function carrier, and most genes (>69%) had ≥10 loss of function carriers. We illustrate the power of characterizing loss of function variation in this large population through association analyses across 1,741 phenotypes. In addition to replicating a range of established associations, we discover novel loss of function 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 significance in this population, finding that 2% of the population has a medically actionable variant. Additionally, we leverage the phenotypic data to characterize the relationship between rare BRCA1 and BRCA2 pathogenic variants and cancer risk. Exomes from the first 49,960 participants are now made accessible to the scientific community and highlight the promise offered by genomic sequencing in large-scale population-based studies.

Published
2019

49. Identification of Neuropsychiatric Copy Number Variants in a Health Care System Population

Author

Lukas Habegger, Evan Maxwell, David H. Ledbetter, Matthew T. Oetjens, Christa Lese Martin, Karen E. Wain, Abby Hare-Harris, Kasia Tolwinski, Scott M. Myers, Emily Palen, Jeffrey G. Reid, and Lauren Kasparson Walsh

Subjects
medicine.medical_specialty, education.field_of_study, business.industry, Genetic counseling, Population, Odds ratio, Penetrance, 030227 psychiatry, 03 medical and health sciences, Psychiatry and Mental health, 0302 clinical medicine, Family medicine, Cohort, Health care, Community health, medicine, business, education, 030217 neurology & neurosurgery, Cohort study
Abstract

Importance Population screening for medically relevant genomic variants that cause diseases such as hereditary cancer and cardiovascular disorders is increasing to facilitate early disease detection or prevention. Neuropsychiatric disorders (NPDs) are common, complex disorders with clear genetic causes; yet, access to genetic diagnosis is limited. We explored whether inclusion of NPD in population-based genomic screening programs is warranted by assessing 3 key factors: prevalence, penetrance, and personal utility. Objective To evaluate the suitability of including pathogenic copy number variants (CNVs) associated with NPD in population screening by determining their prevalence and penetrance and exploring the personal utility of disclosing results. Design, Setting, and Participants In this cohort study, the frequency of 31 NPD CNVs was determined in patient-participants via exome data. Associated clinical phenotypes were assessed using linked electronic health records. Nine CNVs were selected for disclosure by licensed genetic counselors, and participants’ psychosocial reactions were evaluated using a mixed-methods approach. A primarily adult population receiving medical care at Geisinger, a large integrated health care system in the United States with the only population-based genomic screening program approved for medically relevant results disclosure, was included. The cohort was identified from the Geisinger MyCode Community Health Initiative. Exome and linked electronic health record data were available for this cohort, which was recruited from February 2007 to April 2017. Data were collected for the qualitative analysis April 2017 through February 2018. Analysis began February 2018 and ended December 2019. Main Outcomes and Measures The planned outcomes of this study include (1) prevalence estimate of NPD-associated CNVs in an unselected health care system population; (2) penetrance estimate of NPD diagnoses in CNV-positive individuals; and (3) qualitative themes that describe participants’ responses to receiving NPD-associated genomic results. Results Of 90 595 participants with CNV data, a pathogenic CNV was identified in 708 (0.8%; 436 women [61.6%]; mean [SD] age, 50.04 [18.74] years). Seventy percent (n = 494) had at least 1 associated clinical symptom. Of these, 28.8% (204) of CNV-positive individuals had an NPD code in their electronic health record, compared with 13.3% (11 835 of 89 887) of CNV-negative individuals (odds ratio, 2.21; 95% CI, 1.86-2.61;P Conclusions and Relevance This study informs critical factors central to the development of population-based genomic screening programs and supports the inclusion of NPD in future designs to promote equitable access to clinically useful genomic information.

Published
2020

50. 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

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