484 results on '"Uncertain significance"'
Search Results
2. Systematic analysis of copy number variants of uncertain significance partially overlapping with the haploinsufficient or triplosensitive genes in clinical testing.
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Zhou, Ran, Jiao, Jiao, Wang, Yan, Meng, Lulu, Li, Yiming, Xu, Yiyun, Hu, Ping, and Xu, Zhengfeng
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DNA copy number variations ,CHROMOSOME analysis ,X chromosome ,GENETIC counseling ,MISCARRIAGE ,CHROMOSOME duplication ,Y chromosome - Abstract
Background: Copy number variants of uncertain significance (VUS) has brought much distress for patients and great counselling challenges for clinicians. Of these, a special type of VUS (HT-VUS), harbouring one or both breakpoints within the established haploinsufficient or triplosensitive genes, were considered to be more likely to cause clinical effects compared with other types of VUS. Methods: We retrospectively evaluated the properties and clinical significance of those HT-VUS samples in clinical testing for chromosome microarray analysis (CMA). Results: A total of 7150 samples were selected for HT-VUS screening, and 75 (1.05%) subjects with 75 HT-VUS were found. The majority of these HT-VUS were heterozygous duplications and chromosome X had the most HT-VUS. The prevalence of HT-VUS was 0.90% (28/3116) for prenatal low-risk samples, 1.18% (26/2196) for prenatal high-risk samples, 1.37% (10/728) for postnatal samples and 0.99% (11/1110) for early pregnancy loss samples. However, the incidence of HT-VUS was not statistically different between different groups. Conclusions: HT-VUS (deletions or duplications) involving introns and HT-VUS (duplications) including terminal coding exons (either the first or last exons) might be clinically neutral. Our study will be helpful for both interpretation and genetic counselling in the future. This study assessed the clinical impact and features of a special type of copy number variants of uncertain significance (HT-VUS) in samples from CMA retrospectively. Out of 7150 samples screened, 75 (1.05%) subjects had HT-VUS. Most HT-VUS were heterozygous duplications and chromosome X had the highest frequency of HT-VUS. HT-VUS (deletions or duplications) involving introns and HT-VUS (duplications) including terminal coding exons might be clinically neutral. This study would be helpful for future interpretation and genetic counselling. [ABSTRACT FROM AUTHOR]
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- 2023
- Full Text
- View/download PDF
3. Systematic analysis of copy number variants of uncertain significance partially overlapping with the haploinsufficient or triplosensitive genes in clinical testing
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Ran Zhou, Jiao Jiao, Yan Wang, Lulu Meng, Yiming Li, Yiyun Xu, Ping Hu, and Zhengfeng Xu
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Copy number variants ,uncertain significance ,haploinsufficient ,triplosensitive ,genetic counselling ,Medicine - Abstract
AbstractBackground: Copy number variants of uncertain significance (VUS) has brought much distress for patients and great counselling challenges for clinicians. Of these, a special type of VUS (HT-VUS), harbouring one or both breakpoints within the established haploinsufficient or triplosensitive genes, were considered to be more likely to cause clinical effects compared with other types of VUS.Methods: We retrospectively evaluated the properties and clinical significance of those HT-VUS samples in clinical testing for chromosome microarray analysis (CMA).Results: A total of 7150 samples were selected for HT-VUS screening, and 75 (1.05%) subjects with 75 HT-VUS were found. The majority of these HT-VUS were heterozygous duplications and chromosome X had the most HT-VUS. The prevalence of HT-VUS was 0.90% (28/3116) for prenatal low-risk samples, 1.18% (26/2196) for prenatal high-risk samples, 1.37% (10/728) for postnatal samples and 0.99% (11/1110) for early pregnancy loss samples. However, the incidence of HT-VUS was not statistically different between different groups.Conclusions: HT-VUS (deletions or duplications) involving introns and HT-VUS (duplications) including terminal coding exons (either the first or last exons) might be clinically neutral. Our study will be helpful for both interpretation and genetic counselling in the future.
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- 2023
- Full Text
- View/download PDF
4. Patterns of Uncertain Significance
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Saxena, Aneeta R., Hirsch, Lawrence J., Husain, Aatif M., editor, and Sinha, Saurabh R., editor
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- 2017
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5. Avoiding "toxic knowledge": the importance of framing personalized risk information in clinical decision-making.
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Kostick, Kristin M and Blumenthal-Barby, J S
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- 2021
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6. "It's probably nothing, but…" Couples' experiences of pregnancy following an uncertain prenatal genetic result.
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Lou, Stina, Lomborg, Kirsten, Lewis, Celine, Riedijk, Sam, Petersen, Olav Bjørn, and Vogel, Ida
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DNA copy number variations , *MEDICAL personnel , *PSYCHOLOGICAL adaptation , *PREGNANCY , *FETUS , *PRENATAL influences , *ADAPTABILITY (Personality) , *RESEARCH , *GENETICS , *PRENATAL diagnosis , *PSYCHOLOGY of parents , *RESEARCH methodology , *MICROARRAY technology , *UNCERTAINTY , *INTERVIEWING , *EVALUATION research , *MEDICAL cooperation , *COMPARATIVE studies , *CHROMOSOME abnormalities , *TERMS & phrases , *RESEARCH funding , *INFORMATION-seeking behavior , *GENETIC counseling , *FETAL ultrasonic imaging - Abstract
Introduction: A common concern regarding the introduction of chromosomal microarray in prenatal testing is the concomitant identification of an uncertain copy number variant (CNV) where significance and clinical implication for the unborn child can be difficult or impossible to predict. Following the identification of an uncertain CNV, prospective parents may decide to continue the pregnancy. The aim of this study was to explore how prospective parents manage uncertainty and experience pregnancy in light of an uncertain CNV result.Material and Methods: Qualitative interviews with 16 women and 10 partners who had received a prenatally diagnosed, uncertain CNV. Participants were recruited from the Aarhus University Hospital, Denmark and most were interviewed in their homes 1-14 weeks after birth. Data were analyzed using thematic analysis.Results: Following the CNV diagnosis, some couples focused on the severe syndromes ruled out by the result, whereas others were more concerned with the new potential risks, for example, learning disabilities. Most couples did not remember the actual diagnosis, but all described a number of attention points generated by the CNV result. During pregnancy, the couples used various strategies to limit worry and enjoy their pregnancy, such as limiting information seeking, reducing talk of the CNV, and deferring thoughts of potential consequences. Furthermore, ultrasound was considered a valuable resource for reducing worry as it provided reassurance about the development of the baby. Inherited CNVs caused relief on one hand, but also feelings of responsibility for the child's potential challenges. After birth, worry decreased considerably, but all couples paid some extra attention to the child's development, while also being alert to the risk of wrongfully interpreting the child's development in terms of the CNV. Eleven couples expressed satisfaction with knowing about the child's CNV, whereas five couples would rather not have known.Conclusions: The results indicate that health professionals should be mindful of terminology, remember to point out what has been ruled out by the CNV result, and discuss potential coping strategies with the couple. Furthermore, these couples may have a higher need for ultrasound during pregnancy to help reduce worry. More research is needed on the families' long-term coping. [ABSTRACT FROM AUTHOR]- Published
- 2020
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7. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification.
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Parsons, Michael T., Tudini, Emma, Li, Hongyan, Hahnen, Eric, Wappenschmidt, Barbara, Feliubadaló, Lidia, Aalfs, Cora M., Agata, Simona, Aittomäki, Kristiina, Alducci, Elisa, Alonso‐Cerezo, María Concepción, Arnold, Norbert, Auber, Bernd, Austin, Rachel, Azzollini, Jacopo, Balmaña, Judith, Barbieri, Elena, Bartram, Claus R., Blanco, Ana, and Blümcke, Britta
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The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co‐segregation, family cancer history profile, co‐occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case‐control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene‐specific calibration of evidence types used for variant classification. [ABSTRACT FROM AUTHOR]
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- 2019
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8. A phenotype-enhanced variant classification framework to decrease the burden of missense variants of uncertain significance in type 1 long QT syndrome
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Dan Ye, Hennie Bikker, Michael J. Ackerman, Sahej Bains, Ram K. Rohatgi, Steven M. Dotzler, Arthur A.M. Wilde, J. Martijn Bos, David J. Tester, John R. Giudicessi, Christian Krijger, Cardiology, Graduate School, ACS - Heart failure & arrhythmias, Human Genetics, ACS - Pulmonary hypertension & thrombosis, and ARD - Amsterdam Reproduction and Development
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medicine.medical_specialty ,Long QT syndrome ,Sudden cardiac death ,Physiology (medical) ,Internal medicine ,medicine ,Genetics ,Humans ,Missense mutation ,Genetic Testing ,Uncertain significance ,Retrospective Studies ,Genetic testing ,medicine.diagnostic_test ,business.industry ,medicine.disease ,Phenotype ,VUS ,Long QT Syndrome ,ACMG ,KCNQ1 Potassium Channel ,Mutation ,Cohort ,Medical genetics ,LQTS ,Cardiology and Cardiovascular Medicine ,business - Abstract
Background: Pathogenic/likely pathogenic (P/LP) variants in the KCNQ1-encoded Kv7.1 potassium channel cause type 1 long QT syndrome (LQT1). Despite the revamped 2015 American College of Medical Genetics (ACMG) variant interpretation guidelines, the burden of KCNQ1 variants of uncertain significance (VUS) in patients with LQTS remains ∼30%. Objective: The purpose of this study was to determine whether a phenotype-enhanced (PE) variant classification approach could reduce the VUS burden in LQTS genetic testing. Methods: Retrospective analysis was performed on 79 KCNQ1 missense variants in 356 patients from Mayo Clinic and an independent cohort of 42 variants in 225 patients from Amsterdam University Medical Center (UMC). Each variant was classified initially using the ACMG guidelines and then readjudicated using a PE-ACMG framework that incorporated the LQTS clinical diagnostic Schwartz score plus 4 “LQT1-defining features”: broad-based/slow upstroke T waves, syncope/seizure during exertion, swimming-associated events, and a maladaptive LQT1 treadmill stress test. Results: According to the ACMG guidelines, Mayo Clinic variants were classified as follows: 17 of 79 P variants (22%), 34 of 79 LP variants (43%), and 28 of 79 VUS (35%). Similarly, for Amsterdam UMC, the variant distribution was 9 of 42 P variants (22%), 14 of 42 LP variants (33%), and 19 of 42 variants VUS (45%). After PE-ACMG readjudication, the total VUS burden decreased significantly from 28 (35%) to 13 (16%) (P = .0007) for Mayo Clinic and from 19 (45%) to 12 (29%) (P = .02) for Amsterdam UMC. Conclusion: Phenotype-guided variant adjudication decreased significantly the VUS burden of LQT1 case–derived KCNQ1 missense variants in 2 independent cohorts. This study demonstrates the value of incorporating LQT1-specific phenotype/clinical data to aid in the interpretation of KCNQ1 missense variants identified during genetic testing for LQTS.
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- 2022
9. Deciphering pathogenicity of variants of uncertain significance with CRISPR-edited iPSCs
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Le Cong, Joseph C. Wu, Hongchao Guo, Masataka Nishiga, and Lichao Liu
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Gene Editing ,Virulence ,Induced Pluripotent Stem Cells ,Genetic variants ,Genome-wide association study ,Computational biology ,Biology ,Pathogenicity ,Article ,Genetics ,Humans ,CRISPR ,Clustered Regularly Interspaced Short Palindromic Repeats ,CRISPR-Cas Systems ,Induced pluripotent stem cell ,Uncertain significance ,Function (biology) ,Genome-Wide Association Study ,Genetic association - Abstract
Genetic variants play an important role in conferring risk for cardiovascular diseases (CVDs). With the rapid development of next-generation sequencing (NGS), thousands of genetic variants associated with CVDs have been identified by genome-wide association studies (GWAS), but the function of more than 40% of genetic variants is still unknown. This gap of knowledge is a barrier to the clinical application of the genetic information. However, determining the pathogenicity of a variant of uncertain significance (VUS) is challenging due to the lack of suitable model systems and accessible technologies. By combining clustered regularly interspaced short palindromic repeats (CRISPR) and human induced pluripotent stem cells (iPSCs), unprecedented advances are now possible in determining the pathogenicity of VUS in CVDs. Here, we summarize recent progress and new strategies in deciphering pathogenic variants for CVDs using CRISPR-edited human iPSCs.
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- 2021
10. Multiple myeloma screening within a fracture liaison service (FLS)
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R Eckert, Muhammad Javaid, Ross Sadler, S Mahoney, C Milan, P Osborne, G Agarwal, G White, P Stevens, S Connacher, K Ramasamy, and Z Mohsin
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medicine.medical_specialty ,Hematology ,business.industry ,Endocrinology, Diabetes and Metabolism ,Osteoporosis ,Urine electrophoresis ,Newly diagnosed ,medicine.disease ,Monoclonal gammopathy ,Serum free ,Internal medicine ,medicine ,medicine.symptom ,business ,Uncertain significance ,Multiple myeloma - Abstract
Multiple myeloma (MM) remains incurable. Although early diagnosis improves outcomes, it has been unclear which populations to target for screening with serum electrophoresis, serum free light chains and urine electrophoresis. Here, we assessed the value of MM screening in a Fracture Liaison Service, finding that 1 per 195 fragility fractures has undiagnosed MM, which can be expedited to Haematology Services. Purpose A key role of the Fracture Liaison Service (FLS) is screening for secondary causes of osteoporosis. In 2019, the Royal Osteoporosis Society recommended that all patients attending FLS who are recommended anti-osteoporosis therapy have universal screening for myeloma based on serum electrophoresis, serum free light chains and urine electrophoresis. Here, we examined the impact of universal myeloma screening within an FLS. Methods We sampled all patients seen by the Oxfordshire FLS between January and April 2018. The completion rates and outcomes of screening were checked using the hospital and FLS databases. Results Of 950 patients identified by the FLS, 628 were eligible for MM screening; 473 (75%) of these were female, and the average age was 78.4 years. Overall, 584 had some form of myeloma screening, of which 577 (92%) had serum electrophoresis, 525 (84%) had serum free light chains and 407 (65%) had urine electrophoresis measured. A total of 327 (59%) patients had complete screening. Three patients (0.5%) had newly diagnosed myeloma and were urgently referred to Haematology Services. Furthermore, 46 (8%) patients had a detectable serum paraprotein with a likely diagnosis of monoclonal gammopathy of uncertain significance (MGUS) and referred for community annual surveillance according to local guidelines. Conclusion Addition of universal myeloma screening to laboratory testing identified myeloma in 1 per 195 patients, and its precursor state MGUS in 1 per 13 patients, which may have otherwise been missed. Further analysis with long-term follow-up is needed to clearly define the value of diagnosing MGUS within the FLS setting and establish the benefits vs. costs and methods to improve screening completion rates.
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- 2021
11. Primary care providers’ responses to unsolicited Lynch syndrome secondary findings of varying clinical significance
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Kurt D. Christensen, Robert C. Green, Catherine Hajek, Charlene L. Preys, Lauren N. Galbraith, Heidi L. Rehm, and Maren T. Scheuner
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medicine.medical_specialty ,Primary Health Care ,business.industry ,Medical laboratory ,Genomics ,Primary care ,medicine.disease ,Colorectal Neoplasms, Hereditary Nonpolyposis ,United States ,Article ,Human genetics ,Lynch syndrome ,Family medicine ,Humans ,Medicine ,Clinical significance ,business ,Uncertain significance ,Genetics (clinical) - Abstract
Purpose: How primary care providers (PCPs) respond to genomic secondary findings (SFs) of varying clinical significance (pathogenic, uncertain significance (VUS), or benign) is unknown. Methods: We randomized 148 American Academy of Family Physicians members to review three reports with varying significance for Lynch syndrome. Participants provided open-ended responses about the follow-up they would address and organized the SF reports and five other topics in the order they would prioritize responding to them (1=highest priority, 6=lowest priority). Results: PCPs suggested referrals more often for pathogenic variants or VUSs than benign variants (72% vs 16%, p0.46). SF reports were prioritized highest for pathogenic variants (2.7 for pathogenic variants, 3.6 for VUSs, 4.3 for benign variants, all p≤0.014). Conclusions: Results suggest that while PCPs appreciated the differences in clinical significance, disclosure of VUSs as SFs would substantially increase downstream health care utilization.
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- 2021
12. Beneficial effects of the ketogenic diet on drug-resistant epileptic encephalopathy associated with a de novo NBEA pathogenic variant
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Carlotta Spagnoli, Daniele Frattini, Susanna Rizzi, Carlo Fusco, Francesco Pisani, Grazia Gabriella Salerno, and Silvia Schiavoni
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Male ,medicine.medical_treatment ,Nerve Tissue Proteins ,Drug resistance ,Bioinformatics ,Epilepsy ,drug-resistant epilepsy ,Neurodevelopmental disorder ,medicine ,Humans ,Child ,Beneficial effects ,Uncertain significance ,business.industry ,Epileptic encephalopathy ,General Medicine ,Drug Resistant Epilepsy ,medicine.disease ,neurodevelopmental disorder ,NBEA ,epileptic encephalopathy ,Pharmaceutical Preparations ,Neurology ,ketogenic diet ,Neurodevelopmental Disorders ,Epilepsy, Generalized ,Neurology (clinical) ,Carrier Proteins ,Diet, Ketogenic ,business ,Ketogenic diet - Abstract
Although neurobeachin (NBEA) de novo genetic variants have been mainly reported in patients with neurodevelopmental disorders (NDD), they have also been recently associated with early childhood epilepsy. We report an 11-year-old boy who was first evaluated at 34 months of age because of drug-resistant epileptic encephalopathy. He also had developmental delay and prominent autistic features. Whole-exome sequencing (WES) disclosed a pathogenic NBEA c.5258_5279del, p.(Ala1753Valfs*13) variant, occurring de novo and a paternally-inherited heterozygous NBEA c.416T>C p.(Met139Thr) variant of uncertain significance (VUS). The patient showed good response to the ketogenic diet, suggesting that this therapy may be an effective option for patients with seizures who carry NBEA variants.
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- 2021
13. Comparison of flow cytometry and next‐generation sequencing in minimal residual disease monitoring of acute myeloid leukemia: One institute’s practical clinical experience
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Da Zhang, Wei Cui, Andrew K. Godwin, Paul F McGowan, Regina M. Plummer, and Stephen Hyter
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Oncology ,medicine.medical_specialty ,Neoplasm, Residual ,Clinical Biochemistry ,Sensitivity and Specificity ,DNA sequencing ,Immunophenotyping ,Flow cytometry ,Internal medicine ,Biomarkers, Tumor ,Humans ,Medicine ,Multiparameter flow cytometry ,Uncertain significance ,Retrospective Studies ,medicine.diagnostic_test ,business.industry ,Biochemistry (medical) ,Disease progression ,Disease Management ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Myeloid leukemia ,Hematology ,General Medicine ,Flow Cytometry ,Minimal residual disease ,Leukemia, Myeloid, Acute ,Real-time polymerase chain reaction ,Mutation ,business - Abstract
Introduction Monitoring patients with acute myeloid leukemia can be implemented through various techniques such as multiparameter flow cytometry, real-time quantitative polymerase chain reaction, and next-generation sequencing. However, there is scarce studies when comparing the data of next-generation sequencing and flow cytometry for monitoring disease progression, particularly how they might supplement one another when used in tandem. Methods We investigated 107 patients via retrospective analysis using follow-up MFC and NGS data with a total of 717 MFC and 247 NGS studies to compare these methods in monitoring minimal/measurable residual disease. Results 197 instances were MFC+ /NGS+ , 3 were MFC- /NGS- , 44 were MFC- /NGS+ , and 3 are MFC+ /NGS- . The majority of the MFC- /NGS+ cases occurred within 6 months during the post-treatment phase (64%). Among 44 MFC- /NGS+ instances, 13 had similar NGS profiles to their original day 0 diagnosis. The remaining cases showed preleukemic clonal hematopoiesis mutations, "likely pathogenic mutations," or "variants of uncertain significance." Conclusion Our findings show that flow cytometry has its advantages with comparable sensitivity in detecting minimal/measurable residual disease. Next-generation sequencing could be used in an increased and more regular capacity in conjunction with flow cytometry to achieve a more comprehensive surveillance of these patients, resulting in improved outcomes.
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- 2021
14. To offer or request? Disclosing variants of uncertain significance in prenatal testing
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Gabriel Watts and Ainsley J Newson
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Health (social science) ,business.industry ,Health Personnel ,Health Policy ,Presumption ,Genetic counseling ,Internet privacy ,Uncertainty ,Genetic Counseling ,Bioethics ,Solidarity ,Philosophy ,Pregnancy ,Prenatal Diagnosis ,Humans ,Position (finance) ,Normative ,Female ,Genetic Testing ,Personalized medicine ,business ,Psychology ,Uncertain significance - Abstract
The use of genomic testing in pregnancy is increasing, giving rise to questions over how the information that is generated should be offered and returned in clinical practice. While these tests provide important information for prenatal decision-making, they can also generate information of uncertain significance. This paper critically examines three models for approaching the disclosure of variants of uncertain significance (VUS), which can arise from forms of genomic testing such as prenatal chromosomal microarray analysis (CMA). Contrary to prevailing arguments, we argue that respect for reproductive autonomy does not justify adopting a model on which an offer to disclose VUS is a routine part of genetic counselling. Instead, we contend that a commitment both to solidarity between healthcare providers and pregnant women and to the acceptance of a novel principle of caution under normative uncertainty means that we should instead adopt a model of VUS disclosure that imposes a strong presumption against offering to disclose VUS. The upshot of this is that it should be standard practice to only offer to disclose VUS when this is requested by the woman undergoing CMA. We defend our position against claims that arise from an alleged right to such information and that a presumption against an offer will lead to inequity.
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- 2021
15. Gaseous and Particulate Content of Laser Tattoo Removal Plume
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Eric Glassford, Yakir S Levin, Brett J. Green, Michael P. Grant, Mathew M. Avram, and Angela R. Lemons
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Air sampling ,Swine ,Hydrogen sulfide ,Lasers, Solid-State ,Dermatology ,Article ,law.invention ,Pig skin ,chemistry.chemical_compound ,law ,Occupational Exposure ,Animals ,Humans ,Particle Size ,Uncertain significance ,Skin ,Tattooing ,Chemistry ,Air ,Tattoo removal ,General Medicine ,Particulates ,Laser ,Plume ,Environmental chemistry ,Models, Animal ,Ink ,Particulate Matter ,Surgery ,Gases - Abstract
Background There is increasing awareness of the potential hazards of surgical plumes. The plume associated with laser tattoo removal remains uncharacterized. Objective To determine the gaseous, particulate, and microbiological content of the laser tattoo removal plume. Materials and methods Air sampling was performed during laser tattoo removal from pig skin and from patients. Measurement of metals, volatile organic compounds (VOCs), carbon monoxide (CO), hydrogen sulfide (HS), and ultrafine particulates (UPs) as well as bacterial 16S ribosomal DNA sequencing were performed. Results Metals were identified in the plume from both pig and human skin. Volatile organic compounds were found at similar levels within and outside the treatment room. Several bacterial phyla were detected in the treatment room, but not outside. High levels of UPs were measured throughout the treatment room during tattoo removal from pig skin. Ultrafine particulates were detected at low levels in the room periphery during tattoo removal from human skin, but at higher levels in the immediate treatment zone. HS and CO were not detected. Conclusion Metals, VOCs, HS, and CO were found at levels below applicable occupational exposure limits. The presence of bacteria is of uncertain significance, but may be hazardous. High levels of UPs require further investigation.
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- 2021
16. The First Korean Case of SLC12A3 Aberrant Skipping of Two Exons Detected by RNA Splicing Analysis
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Kiwoong Ko and Jong-Won Kim
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Genetics ,medicine.diagnostic_test ,business.industry ,In silico ,Genetic counseling ,Gitelman syndrome ,medicine.disease ,Autosomal recessive trait ,Exon ,Nephrology ,RNA splicing ,medicine ,business ,Uncertain significance ,Genetic testing - Abstract
Gitelman syndrome is a salt-losing tubular disorder that is transmitted as an autosomal recessive trait. Variants in the SLC12A3 gene are found in the majority of Gitelman syndrome patients. A 26-year-old woman visited the genetic counseling clinic. Her fiancé was a known Gitelman syndrome patient who was previously diagnosed with 2 pathogenic variants in SLC12A3. In advance of marriage and future family planning, she wanted to perform genetic testing of SLC12A3. A silent exonic variant c.1050G>A was found, and multiple splice site in silico algorithms predicted this variant to have potential alteration of splicing. This variant was classified as “variant of uncertain significance,” and RNA splicing analysis was additionally performed. RNA splicing analysis showed aberrant splicing of exon 7–8 skipping. The result points out the potential pathogenicity of this variant, which should be considered a candidate of variant reclassification in the future. We highly recommend the performance of additional RNA splicing analysis, especially for silent variants predicted to have potential alteration of splicing.
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- 2021
17. Pathogenic Intronic Splice-Affecting Variants in MYBPC3 in Three Patients with Hypertrophic Cardiomyopathy
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Katherine A. Wood, C Hopton, O Raymond, J Ellingford, Huw B. Thomas, E James, and William G. Newman
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0301 basic medicine ,Genetics ,splice variants ,Mutant allele ,Hypertrophic cardiomyopathy ,Wild type ,RNA ,030204 cardiovascular system & hematology ,Biology ,hypertrophic cardiomyopathy ,medicine.disease ,MYBPC3 ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,minigene assays ,RC666-701 ,RNA splicing ,medicine ,Diseases of the circulatory (Cardiovascular) system ,General Earth and Planetary Sciences ,splice ,Uncertain significance ,General Environmental Science ,Minigene - Abstract
Genetic variants in MYBPC3 are one of the most common causes of hypertrophic cardiomyopathy (HCM). While variants in MYBPC3 affecting canonical splice site dinucleotides are a well-characterised cause of HCM, only recently has work begun to investigate the pathogenicity of more deeply intronic variants. Here, we present three patients with HCM and intronic splice-affecting MYBPC3 variants and analyse the impact of variants on splicing using in vitro minigene assays. We show that the three variants, a novel c.927-8G>A variant and the previously reported c.1624+4A>T and c.3815-10T>G variants, result in MYBPC3 splicing errors. Analysis of blood-derived patient RNA for the c.3815-10T>G variant revealed only wild type spliced product, indicating that mis-spliced transcripts from the mutant allele are degraded. These data indicate that the c.927-8G>A variant of uncertain significance and likely benign c.3815-10T>G should be reclassified as likely pathogenic. Furthermore, we find shortcomings in commonly applied bioinformatics strategies to prioritise variants impacting MYBPC3 splicing and re-emphasise the need for functional assessment of variants of uncertain significance in diagnostic testing.
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- 2021
18. Three Patient Kindred with a Novel Phenotype of Osteogenesis Imperfecta due to a COL1A1 Variant
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Seth W. Gregory, Nidhi Gupta, Peter J. Tebben, and David R. Deyle
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Pediatrics ,medicine.medical_specialty ,Bone density ,business.industry ,Endocrinology, Diabetes and Metabolism ,Long bone ,medicine.disease ,Phenotype ,Osteopenia ,Endocrinology ,medicine.anatomical_structure ,Osteogenesis imperfecta ,Pediatrics, Perinatology and Child Health ,medicine ,In patient ,Toddler ,business ,Uncertain significance - Abstract
Osteogenesis imperfecta (OI) is characterized by fractures and progressive bone deformities. Fracture rates peak during the toddler and adolescent years and decline during adulthood but do not stop entirely. We describe a kindred, the affected members of which were the mother and two sons, who presented with an apparently unique phenotype of OI. Our patients demonstrated a pattern of prenatal bone deformities followed by multiple, nontraumatic long bone fractures within the first two years of life and then an absence of nontraumatic fractures thereafter. No extra-skeletal manifestations have been noted to date. The mother did not receive bisphosphonate therapy but had no nontraumatic fractures after the age of five months. Intravenous bisphosphonate therapy was started for both sons within two months of birth, with the most recent infusions at age 18 months and 28 months in Patients 2 and 3, respectively. Two patients harbored a variant of uncertain significance in the COL1A1 gene. This heterozygous variant, c.3548C>T; p.(Pro1183Leu), is listed in the OI Variant Database as affecting only one other individual with osteopenia. We describe three family members with a unique presenting phenotype of OI, characterized by cessation of nontraumatic fractures after the first two years of life.
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- 2021
19. E70 A new mutation of uncertain significance in Farber disease.
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Kenza, Bouayed, Yousra, Bellarhrib, Asmaa, Sakhi, Kathleen, Crosby, and Thierry, Levade
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GENETIC mutation , *UNCERTAINTY , *GENETIC testing , *CONFERENCES & conventions , *LYSOSOMAL storage diseases , *CERAMIDASES - Abstract
Introduction Farber disease is a rare autosomal recessive lysosomal storage disorder. It is caused by a mutation in the ASAH1 gene, which results in a deficiency of acid ceramidase and subsequently an accumulation of ceramide in various tissues. The manifestations are diverse and the cardinal symptoms of the Farber disease triad include subcutaneous nodules, joint pain and hoarseness. Aims To recall the clinical features of this rare disease in order to avoid a late diagnosis and to inform about the identification of a novel mutation in a Moroccan patient known until now as a mutation of uncertain significance in the acid ceramidase gene. Method About a clinical case reported retrospectively with a prospective follow-up. Results We report the case of a fourteen-year-old boy born from healthy, consanguineous Moroccan parents after an uneventful pregnancy and delivery. He had normal development until the age of 9 months. The first symptoms appeared at the end of the first year of life with joint stiffness, hoarseness, subcutaneous nodules, blepharitis resulting in amblyopia, dental enamel defect, gingival hyperplasia, and severe failure to thrive, without any visceral manifestations. Routine laboratory investigations revealed normal hydroelectolytic, glycemic, hepatic, renal, and thyroid status. Standard radiography revealed diffuse bone demineralization, laryngoscopy showed laryngeal dyskinesia, echocardiography and abdominal ultrasound were normal. Biopsy of a nodule revealed hyalinosis deposition leading initially to the hypothesis of systemic hyalinosis. The diagnosis of Farber disease was suspected at the age of eight and definitively confirmed at the age of fourteen after a genetic study of ASAH1 revealing a novel compound homozygous mutation in exon 3 c.194T>G (p.Leu65Trp) whose significance was considered uncertain to date with an acid ceramidase enzyme assay that showed a markedly reduced leucocyte acid ceramidase activity, consistent with a homozygous status for acid ceramidase deficiency. Treatment with analgesics based on paracetamol and nonsteroidal anti-inflammatory drugs, with iron, calcium and vitamin D supplements was prescribed. Physiotherapy was recommended but was very difficult as the child is so painful. Discussion and Conclusion Farber disease is a rare condition with only about 200 cases identified worldwide. It is caused by mutations in the ASAH1 gene. The disease has a wide range of clinical presentations, and this case report highlights the challenge of diagnosis, with a long delay due to lack of awareness of the disease among clinicians. Furthermore, this case describes a novel homozygous mutation in the ASAH1 gene: c.194T>G (p.Leu65Trp) of the ASAH1 gene in a Moroccan patient, expanding the phenotypic spectrum of the disease. Genetic testing should be considered in patients with a clinical presentation consistent with the disease, supplemented by an acid ceramidase enzyme assay in case of doubt as was done in our patient. To date, there is no cure for Farber disease, and treatment is symptomatic and supportive. However, early diagnosis and appropriate management can help improve the quality of life for patients and their families. This case highlights the importance of further research in order to develop more effective treatments for this rare condition. Clinical trials are planned in the close future. Ethics The patient and his family members provided informed consent for publication of indirectly identifiable data. [ABSTRACT FROM AUTHOR]
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- 2023
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20. To develop cytology procedure as a routine and to get familiar with cytological appearances of the commonly encountered cervical and vaginal lesions
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Dupinder Kaur and Pooja Agarwal
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0301 basic medicine ,medicine.medical_specialty ,Clinical pathology ,Low-Grade Squamous Intraepithelial Lesions ,business.industry ,Obstetrics ,Cytology procedure ,Surgical pathology ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,medicine ,Vaginal smear ,Observational study ,business ,Uncertain significance ,Cervix - Abstract
Background & Method: The material for the current investigation contained assessment of 1542 cervical/vaginal smear, taken from patients going to the out-tolerant Department of Obstretric and Gynecology and further shipped off Department of Pathology for cytomorphological examination. The legitimate example assortment is perhaps the main strides in pap smear screening. At any rate one half to 66% of bogus negatives are the aftereffect of patient conditions present at the hour of test assortment and accommodation and the expertise and information on the person who acquires the example. Sufficient cervical cytology tests ought to be gathered and submitted to the lab with proper clinical data. Study Designed: Cross sectional observational study. Result: 27 cases of epithelial cell abnormality, out of which 17 cases show Atypical squamous cells of uncertain significance, 1 case show Atypical glandular cells of uncertain significance. 2 cases shows low grade squamous intraepithelial lesions, 2 cases shows high grade squamous intra epithelial lesions. A total of 5 smears show invasive carcinoma cervix. Maximum cases of LSIL were detected in 41-50 years of age group and maximum cases of HSIL were detected in 31-60 years of age group whereas maximum cases of carcinoma cervix were detected in 51-60 years of age group. Conclusion: In the developing countries like India, cervical cytology, due to its low cost and easy availability, is the most important diagnostic tool for the screening of females of reproductive age group. The patient attending the Gynecology Out Patient Department were targeted in this study, so as to screening all the females, even with minor symptoms like discharge per vaginum. Keywords: Cytological, Cervical and vaginal lesions.
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- 2021
21. Data sharing to improve concordance in variant interpretation across laboratories: results from the Canadian Open Genetics Repository
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Michelle M. Axford, Ron Agatep, Marcos Clavier, Stacey Hume, Elizabeth Spriggs, Andrea K Vaags, George S. Charames, Harriet Feilotter, Nicholas A. Watkins, Amanda C. Smith, Tracy Tucker, Matthew S. Lebo, Vanessa Di Gioacchino, Jordan Lerner-Ellis, Ian Bosdet, Mohammad R. Akbari, William D. Foulkes, Chloe Mighton, Sean S. Young, Lorena Lazo de la Vega, Talia Silver, Ryan E. Lamont, Laura Semenuk, Robert Tomaszewski, Christian R. Marshall, Nancy Hamel, Justin Mayers, Henry K. Wong, Jillian S. Parboosingh, Marsha Speevak, Aly Karsan, George Chong, and Sherryl Taylor
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Canada ,Concordance ,Article ,03 medical and health sciences ,Likely benign ,Genetics ,medicine ,Humans ,Genetic Predisposition to Disease ,Genetic Testing ,Clinical care ,Uncertain significance ,Genetics (clinical) ,Likely pathogenic ,030304 developmental biology ,Genetic testing ,0303 health sciences ,medicine.diagnostic_test ,Information Dissemination ,business.industry ,030305 genetics & heredity ,Genetic Variation ,Human genetics ,Data sharing ,Laboratories ,business - Abstract
BackgroundThis study aimed to identify and resolve discordant variant interpretations across clinical molecular genetic laboratories through the Canadian Open Genetics Repository (COGR), an online collaborative effort for variant sharing and interpretation.MethodsLaboratories uploaded variant data to the Franklin Genoox platform. Reports were issued to each laboratory, summarising variants where conflicting classifications with another laboratory were noted. Laboratories could then reassess variants to resolve discordances. Discordance was calculated using a five-tier model (pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB), benign (B)), a three-tier model (LP/P are positive, VUS are inconclusive, LB/B are negative) and a two-tier model (LP/P are clinically actionable, VUS/LB/B are not). We compared the COGR classifications to automated classifications generated by Franklin.ResultsTwelve laboratories submitted classifications for 44 510 unique variants. 2419 variants (5.4%) were classified by two or more laboratories. From baseline to after reassessment, the number of discordant variants decreased from 833 (34.4% of variants reported by two or more laboratories) to 723 (29.9%) based on the five-tier model, 403 (16.7%) to 279 (11.5%) based on the three-tier model and 77 (3.2%) to 37 (1.5%) based on the two-tier model. Compared with the COGR classification, the automated Franklin classifications had 94.5% sensitivity and 96.6% specificity for identifying actionable (P or LP) variants.ConclusionsThe COGR provides a standardised mechanism for laboratories to identify discordant variant interpretations and reduce discordance in genetic test result delivery. Such quality assurance programmes are important as genetic testing is implemented more widely in clinical care.
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- 2021
22. Dealing with uncertain results from chromosomal microarray and exome sequencing in the prenatal setting: An international cross‐sectional study with healthcare professionals
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Kelly E. Ormond, Mahesh Choolani, Melissa Hill, Celine Lewis, Jennifer Hammond, Ida Vogel, Stina Lou, Sam Riedijk, Charlotta Ingvoldstad-Malmgren, Lisa Hui, Jasmijn E. Klapwijk, Emma Jane Szepe, Eleanor Harding, Maria Johansson Soller, Human genetics, and Clinical Genetics
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Adult ,0301 basic medicine ,medicine.medical_specialty ,Cross-sectional study ,Denmark ,Health Personnel ,030105 genetics & heredity ,Interviews as Topic ,03 medical and health sciences ,0302 clinical medicine ,Pregnancy ,Exome Sequencing ,medicine ,Humans ,Lack of knowledge ,Uncertain significance ,Genetics (clinical) ,Exome sequencing ,Netherlands ,Sweden ,Singapore ,030219 obstetrics & reproductive medicine ,Health professionals ,Qualitative interviews ,Australia ,Uncertainty ,Obstetrics and Gynecology ,Prenatal Care ,Original Articles ,Microarray Analysis ,United Kingdom ,3. Good health ,Cross-Sectional Studies ,Family medicine ,Original Article ,Female ,Psychology ,Healthcare providers ,Healthcare system - Abstract
Objectives To conduct qualitative interviews with healthcare providers working in different countries to understand their experiences of dealing with uncertain results from prenatal chromosome microarray analysis (CMA) and exome sequencing (ES). Methods Semi‐structured interviews with 31 healthcare providers who report or return prenatal CMA and/or ES results (clinicians, genetic counsellors and clinical scientists) in six countries with differing healthcare systems; Australia (4), Denmark (5), Netherlands (6), Singapore (4), Sweden (6) and United Kingdom (6). The topic guide explored the main sources of uncertainty and their management. Results There was variation in reporting practices both between and across countries for variants of uncertain significance, however, there was broad agreement on reporting practices for incidental findings. There was also variation in who decides what results are reported (clinical scientists or clinicians). Technical limitations and lack of knowledge (to classify variants and of prenatal phenotypes) were significant challenges, as were turnaround times and lack of guidelines. Conclusion Health professionals around the globe are dealing with similar sources of uncertainty, but managing them in different ways, Continued dialogue with international colleagues on ways of managing uncertain results is important to compare and contrast the benefits and limitations of the different approaches., Key points What's already known about this topic? Chromosome microarray analysis and exome sequencing have increased diagnostic yield over karyotyping but have increased the incidence of uncertain results. What does this study add? Our findings highlight variation in reporting practices both between and across countries for variants of uncertain significance, although there is broad agreement on reporting practices for incidental findings.International guidelines may help to standardise how we define and categorise variants, however, global uniformity on the management of uncertain results may not be a realistic or desirable goal.
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- 2021
23. Technical factors to consider when developing an Expanded Carrier Screening platform
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Francesco Cogo, Marco Fabiani, Antonio Capalbo, and Maurizio Poli
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medicine.medical_specialty ,education.field_of_study ,030219 obstetrics & reproductive medicine ,business.industry ,Genetic Carrier Screening ,Best practice ,Population ,MEDLINE ,Obstetrics and Gynecology ,Disease Association ,03 medical and health sciences ,0302 clinical medicine ,030220 oncology & carcinogenesis ,medicine ,Humans ,Genetic Testing ,Intensive care medicine ,Carrier screening ,education ,business ,Uncertain significance - Abstract
Purpose of review Expanded Carrier Screening (ECS) is a genetic test able to detect carriers for a large number of autosomal recessive and X-linked diseases. Its clinical utilization is increasing but some technical aspects for its implementation are still controversial. Recent findings In the current literature, several aspects of ECS panel implementation have been addressed. One of the most relevant topics involves which genes/pathologies should be included in an optimized ECS panel and which variants should be reported. Summary Here, we review the best practice criteria to refine and improve clinical utility and validity of an ECS panel. The criteria for optimal ECS panel implementation include the severity of pathologies, the prevalence of diseases in general population and a definitive or strong gene/disease association. Moreover, we discuss the main complications associated with the reporting of Variant of Uncertain Significance and the need for periodic reassessment.
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- 2021
24. Strong functional data for pathogenicity or neutrality classify BRCA2 DNA-binding-domain variants of uncertain significance
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Kelly Fulk, David E. Goldgar, Steven N. Hart, Tina Pesaran, Marcy E. Richardson, Chunling Hu, Kun Y. Lee, Fergus J. Couch, Elizabeth C. Chao, Ashley Deckman, Alvaro N.A. Monteiro, Kate Durda, Rohan Gnanaolivu, Eric C. Polley, and Holly LaDuca
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0301 basic medicine ,Functional assay ,DNA repair ,Mutation, Missense ,Breast Neoplasms ,Computational biology ,Biology ,Article ,Germline ,Structure-Activity Relationship ,03 medical and health sciences ,breast cancer ,0302 clinical medicine ,predisposition gene ,Genetics ,Humans ,Missense mutation ,ACMG/AMP ,Genetic Predisposition to Disease ,Clinical significance ,Uncertain significance ,Gene ,Genetics (clinical) ,BRCA2 Protein ,variant of uncertain significance ,Genetic Variation ,Recombinational DNA Repair ,DNA-binding domain ,BRCA2 ,030104 developmental biology ,030220 oncology & carcinogenesis ,Female ,functional assay - Abstract
Summary Determination of the clinical relevance of rare germline variants of uncertain significance (VUSs) in the BRCA2 cancer predisposition gene remains a challenge as a result of limited availability of data for use in classification models. However, laboratory-based functional data derived from validated functional assays of known sensitivity and specificity may influence the interpretation of VUSs. We evaluated 252 missense VUSs from the BRCA2 DNA-binding domain by using a homology-directed DNA repair (HDR) assay and identified 90 as non-functional and 162 as functional. The functional assay results were integrated with other available data sources into an ACMG/AMP rules-based classification framework used by a hereditary cancer testing laboratory. Of the 186 missense variants observed by the testing laboratory, 154 were classified as VUSs without functional data. However, after applying protein functional data, 86% (132/154) of the VUSs were reclassified as either likely pathogenic/pathogenic (39/132) or likely benign/benign (93/132), which impacted testing results for 1,900 individuals. These results indicate that validated functional assay data can have a substantial impact on VUS classification and associated clinical management for many individuals with inherited alterations in BRCA2.
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- 2021
25. Abstract PS8-19: High rates of BRCA1 and BRCA2 variants of uncertain significance (VUS) among Jordanian breast cancer patients
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Faris Tamimi, Hikmat Abdel-Razeq, Lama Abujamous, and Razan Abu Khashabeh
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Oncology ,High rate ,Cancer Research ,medicine.medical_specialty ,Breast cancer ,business.industry ,Internal medicine ,medicine ,business ,medicine.disease ,Uncertain significance - Abstract
Background: Contrary to pathogenic BRCA mutations, recommendations for management of Variants of Uncertain Significance (VUS) is not clear and focus more on clinical factors, personal and family history of cancer; breast and ovarian in particular. Genetic variants that may or may not have clinical consequence can be confusing and anxiety-provoking to patients and physicians, alike. No data exist on Arab patients with VUS mutations. In this study we search for the frequency of VUS among high risk breast cancer patients tested for BRCA mutations and study risk-reduction interventions related to such findings. Methods: We utilized an institutional database started January 2015 for all patients with breast cancer tested for BRCA mutations as per the National Comprehensive Cancer Network (NCCN) guidelines, including those with early onset cancers, triple-negative disease and positive family history. We also reviewed surgical interventions patients had in relation to their breast cancer and VUS mutation identification. RESULTS: Between January 2015 and May 2020, a total of 1181 patients were tested for BRCA1 and BRCA2 mutations as per the NCCN guidelines. Pathogenic mutations were detected in 134 (11.3%) patients, while 109 (9.2%) others had VUS; 79 (72.5%) were in BRCA2. At time of testing, all VUS patients had breast cancer; 7 (6.4%) with metastatic disease. Median age (range) was 39 (25-66) years with 63 (57.8%) were 40 years or younger at diagnosis. Twelve (11.0%) had triple negative disease while 14 (13.1%) others had bilateral or two or more unilateral primary breast cancers. Family history of breast, ovarian or pancreatic cancers, in at least one close relative, was identified in 52 (47.7 %) patients. Among 101 patients with nonmetastatic disease, 48 (48.0%) had breast conserving surgery (BCS) while only 5 (5.0%) had bilateral mastectomies, all were due to bilateral disease and not prophylactic. VUS diagnosis was known prior to initial surgery in 33 (32.7%) patients; 11 (33.3%) of them had lumpectomy only. Since we started genetic testing 5 years ago, there is a slight decline in VUS rate but none of the VUS reported mutations so far were reclassified. Conclusions: Despite significant decline in VUS rates reported in the western societies, our rate continues to be high and alarming. Our knowledge of VUS had not significantly impacted on therapeutic or prophylactic surgical decisions. Given the relatively high rate of second breast cancers among such patients, management should be dictated by their personal or family history. A regional (Arab) VUS registry and comprehensive genetic counseling to ensure appropriate follow up and understanding by affected patients, are highly needed. Citation Format: Hikmat Abdel-Razeq, Faris Tamimi, Lama Abujamous, Razan Abu Khashabeh. High rates of BRCA1 and BRCA2 variants of uncertain significance (VUS) among Jordanian breast cancer patients [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-19.
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- 2021
26. Exploring Interrater Disagreement on Essential Tremor Using a Standardized Tremor Elements Assessment
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Bettina Balint, Christian Schlenstedt, Kailash P. Bhatia, Günther Deuschl, Jos Steffen Becktepe, Rodger J. Elble, and Felix Gövert
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0301 basic medicine ,Neurological signs ,medicine.medical_specialty ,Future studies ,Ataxia ,030105 genetics & heredity ,03 medical and health sciences ,0302 clinical medicine ,Physical medicine and rehabilitation ,dystonic tremor ,medicine ,tremor classification ,essential tremor ,Uncertain significance ,Research Articles ,Dystonia ,Essential tremor ,business.industry ,Parkinsonism ,medicine.disease ,tremor ,nervous system diseases ,Inter-rater reliability ,Neurology ,Neurology (clinical) ,medicine.symptom ,business ,030217 neurology & neurosurgery ,Research Article - Abstract
Background: Patients with upper limb action tremor frequently exhibit additional neurological signs of uncertain significance. Clinicians vary in their interpretation, and interrater agreement on the final diagnosis is poor. Objectives: A new clinical tool for assessing the presence or absence of clinical signs that are important in axis-1 classification of tremor patients is introduced: the Standardized Tremor Elements Assessment (STEA). Interrater agreement is determined, and signs leading to disagreement in the final diagnosis are identified. Methods: Three tremor-focussed and one dystonia-focussed movement disorder specialists rated 59 videos of patients with upper limb action tremor syndromes using STEA. Interrater agreements for final diagnosis and STEA items were calculated. Results: Interrater agreement regarding the final diagnosis was higher within the group of tremor specialists and poor between dystonia and tremor specialists. Greater agreement was found for items characterizing tremor than for signs of dystonia. Conclusions: Clinical signs leading to diagnostic disagreement were identified with STEA, and STEA should therefore be useful in future studies of diagnostic disagreement. The thresholds for considering neurological signs as soft versus significant for ataxia, parkinsonism, dystonia, etc. are critically important in tremor classification and must be studied across movement disorder subspecialties, not simply within a pool of tremor specialists.
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- 2021
27. The St George's Classification Algorithm of Primary Lymphatic Anomalies
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Malou van Zanten, Kristiana Gordon, Sahar Mansour, Pia Ostergaard, Steve Jeffery, and Peter S. Mortimer
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Lymphatic Abnormalities ,medicine.diagnostic_test ,business.industry ,030204 cardiovascular system & hematology ,medicine.disease ,University hospital ,humanities ,Clinical Practice ,03 medical and health sciences ,0302 clinical medicine ,Lymphatic system ,GEORGE (programming language) ,030220 oncology & carcinogenesis ,medicine ,Humans ,Primary lymphedema ,Lymphedema ,Cardiology and Cardiovascular Medicine ,business ,Algorithm ,Uncertain significance ,Algorithms ,Genetic testing - Abstract
Clinicians and scientists at St George's University Hospital have collaborated to develop a classification algorithm for primary lymphatic anomalies. Instruction is offered on how to apply the algorithm in clinical practice to refine the diagnosis of primary lymphedema and guide on genetic testing and management. It can also be used to interpret mutation testing results of uncertain significance. The algorithm has evolved as more genes have been discovered, and it remains a "work in progress" as further discoveries are made. This transformational approach has revolutionized the understanding and classification of primary lymphatic anomalies.
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- 2021
28. Economic impact of multigene panel testing for hereditary breast and ovarian cancer
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Stacey DaCosta Byfield, Mary DuCharme, Helen Wei, and Johnathan M. Lancaster
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Oncology ,medicine.medical_specialty ,Breast Neoplasms ,Carcinoma, Ovarian Epithelial ,03 medical and health sciences ,0302 clinical medicine ,Breast cancer ,Internal medicine ,medicine ,Humans ,Genetic Predisposition to Disease ,Genetic Testing ,030212 general & internal medicine ,Uncertain significance ,health care economics and organizations ,Retrospective Studies ,Ovarian Neoplasms ,business.industry ,Health Policy ,Cancer ,Retrospective cohort study ,medicine.disease ,Healthcare utilization ,030220 oncology & carcinogenesis ,Female ,Ovarian cancer ,business ,Medical costs - Abstract
Aim: Healthcare utilization and costs were compared following 25-gene panel (panel) or single syndrome (SS) testing for hereditary breast and ovarian cancer. Materials & methods: Retrospective cohort study of patients unaffected by cancer with panel (n = 6359) or SS (n = 4681) testing for hereditary breast and ovarian cancer (01 January 2014 to 31 December 2016). Groups were determined by test type and result (positive, negative, variant of uncertain significance [VUS]). Results: There were no differences in total unadjusted healthcare costs between the panel (US$14,425) and SS (US$14,384) groups (p = 0.942). Among VUS patients in the panel and SS groups, mean all-cause costs were US$14,404 versus US$20,607 (p = 0.361) and mean risk-reduction/early detection-specific costs were US$718 versus US$679 (p = 0.890), respectively. Adjusted medical costs were not significantly different between panel and SS cohorts. Conclusion: Healthcare utilization and costs were comparable between the SS and panel tests overall and for patients with VUS.
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- 2021
29. Usefulness of copy number variant detection following monogenic disease exclusion in prenatal diagnosis
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Panlai Shi, Yanjie Xia, Qianqian Li, and Xiangdong Kong
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Pediatrics ,medicine.medical_specialty ,DNA Copy Number Variations ,3q29 microdeletion syndrome ,Duchenne muscular dystrophy ,Chromosome Disorders ,Prenatal diagnosis ,Monogenic disease ,03 medical and health sciences ,0302 clinical medicine ,Pregnancy ,medicine ,Humans ,copy number variant ,Copy-number variation ,Uncertain significance ,Retrospective Studies ,Chromosome Aberrations ,Fetus ,prenatal diagnosis ,030219 obstetrics & reproductive medicine ,business.industry ,Obstetrics and Gynecology ,Original Articles ,copy number variant sequencing ,medicine.disease ,030220 oncology & carcinogenesis ,monogenic disease ,Original Article ,Female ,business - Abstract
Aim Families with an adverse history of monogenic disease focus on single‐gene diagnosis instead of low‐depth whole‐genome sequence, during subsequent pregnancies. The aim of this study was to assess the potential usefulness of low‐depth whole‐genome sequencing (copy number variant sequencing [CNV‐seq]) detection following monogenic disease exclusion in prenatal diagnosis. Methods A total of 285 families with a history of monogenic disease (of 41 different types; eliminated during the current pregnancy) were recruited and retrospectively analyzed. Low‐depth whole‐genome sequencing (CNV‐Seq, Next‐Seq CN500 platform) was performed for all fetuses. Results The CNV detection results of the 285 samples were as follows: one case of 18‐trisomy chimera (0.35%), one case of pathogenic 3q29 microdeletion syndrome CNV (0.35%), four cases of variant of uncertain significance (VUS) CNVs (1.40%), and four cases of Duchenne muscular dystrophy (DMD) carriers (1.40%); and the remaining samples were normal (96.15%). Of note, 2/285 (0.70%) samples still exhibited pathogenic abnormalities. All positive samples were followed up where the two cases of pathogenic abnormalities elected the pregnancy termination, while the four VUS cases and four DMD‐carrier cases were born healthy. Conclusion In cases where prenatal fetal monogenic disease has been ruled out, CNV detection is still beneficial and should be performed to prevent missed pathogenic CNVs. However, the costs need to be balanced against benefits, and the research will need to assess other types of testing.
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- 2021
30. Clinical Application of Easychip 8x15K Platform in 4106 Pregnancies Without Ultrasound Anomalies
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Ester Sallicandro, Maria Teresa Liambo, Antonio Novelli, Maria Grazia Di Gregorio, Valeria Orlando, Michela Canestrelli, Marcello Niceta, Francesco Corrado, Gianluca Di Giacomo, Anna Maria Nardone, Bruno Dallapiccola, Silvia Di Tommaso, Viola Alesi, Giusy Calvieri, Giuseppe Barrano, and Chiara Calacci
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0301 basic medicine ,Amniotic fluid ,DNA Copy Number Variations ,Genetic counseling ,Chromosome Disorders ,Genetic Counseling ,Context (language use) ,Prenatal diagnosis ,Bioinformatics ,Ultrasonography, Prenatal ,Cytogenetics ,03 medical and health sciences ,0302 clinical medicine ,Pregnancy ,Prenatal Diagnosis ,Humans ,Medicine ,Genetic Testing ,Copy-number variation ,Uncertain significance ,030219 obstetrics & reproductive medicine ,business.industry ,Ultrasound ,Obstetrics and Gynecology ,030104 developmental biology ,medicine.anatomical_structure ,Karyotyping ,Chorionic villi ,Female ,business - Abstract
Clinical utility of Array-CGH Easychip 8x15K platform can be assessed by testing its ability to detect the occurrence of pathogenic copy number variants (CNVs), and occurrence of variants of uncertain significance (VoUS) in pregnancies without structural fetal malformations. The demand of chromosomal microarray analysis in prenatal diagnosis is progressively increasing in uneventful pregnancies. However, depending on such platform resolution, a genome-wide approach also provides a high risk of detecting VoUS and incidental finding (IF) also defined as "toxic findings." In this context, novel alternative strategies in probe design and data filtering are required to balance the detection of disease causing CNVs and the occurrence of unwanted findings. In a cohort of consecutive pregnancies without ultrasound anomalies, a total of 4106 DNA samples from cultured and uncultured amniotic fluid or chorionic villi were collected and analyzed by a previously designed Array-CGH mixed-resolution custom platform, which is able to detect pathogenic CNVs and structural imbalanced rearrangements limiting the identification of VoUS and IF. Pathogenic CNVs were identified in 88 samples (2.1%), 19 of which (0.5%) were undetectable by standard karyotype. VoUS accounted for 0.6% of cases. Our data confirm that a mixed-resolution and targeted array CGH platform, as Easychip 8x15K, yields a similar detection rate of higher resolution CMA platforms and reduces the occurrence of "toxic findings," hence making it eligible for a first-tier genetic test in pregnancies without ultrasound anomalies.
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- 2021
31. Disease-specific ACMG/AMP guidelines improve sequence variant interpretation for hearing loss
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Mayher J. Patel, Marina T. DiStefano, Andrea M. Oza, Madeline Y. Hughes, Emma H. Wilcox, Sarah E. Hemphill, Brandon J. Cushman, Andrew R. Grant, Rebecca K. Siegert, Jun Shen, Alex Chapin, Nicole J. Boczek, Lisa A. Schimmenti, Kiyomitsu Nara, Margaret Kenna, Hela Azaiez, Kevin T. Booth, Karen B. Avraham, Hannie Kremer, Andrew J. Griffith, Heidi L. Rehm, Sami S. Amr, Ahmad N. Abou Tayoun, Sonia Abdelhak, John Alexander, Zippora Brownstein, Rachel Burt, Byung Yoon Choi, Lilian Downie, Thomas Friedman, Anne Giersch, John Greinwald, Jeffrey Holt, Makoto Hosoya, Un-Kyung Kim, Ian Krantz, Suzanne Leal, Saber Masmoudi, Tatsuo Matsunaga, Matías Morín, Cynthia Morton, Hideki Mutai, Arti Pandya, Richard Smith, Mustafa Tekin, Shin-Ichi Usami, Guy Van Camp, Kazuki Yamazawa, Hui-Jun Yuan, Elizabeth Black-Zeigelbein, and Kejian Zhang
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Disease specific ,medicine.medical_specialty ,Hearing loss ,Molecular pathology ,business.industry ,Genome, Human ,Genetic Variation ,Computational biology ,Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12] ,Human genetics ,Article ,medicine ,Medical genetics ,Humans ,Genetic Testing ,medicine.symptom ,business ,Hearing Loss ,Uncertain significance ,Genetics (clinical) ,Likely pathogenic ,Sequence (medicine) - Abstract
Contains fulltext : 243959.pdf (Publisher’s version ) (Closed access) PURPOSE: The ClinGen Variant Curation Expert Panels (VCEPs) provide disease-specific rules for accurate variant interpretation. Using the hearing loss-specific American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines, the Hearing Loss VCEP (HL VCEP) illustrates the utility of expert specifications in variant interpretation. METHODS: A total of 157 variants across nine HL genes, previously submitted to ClinVar, were curated by the HL VCEP. The curation process involved collecting published and unpublished data for each variant by biocurators, followed by bimonthly meetings of an expert curation subgroup that reviewed all evidence and applied the HL-specific ACMG/AMP guidelines to reach a final classification. RESULTS: Before expert curation, 75% (117/157) of variants had single or multiple variants of uncertain significance (VUS) submissions (17/157) or had conflicting interpretations in ClinVar (100/157). After applying the HL-specific ACMG/AMP guidelines, 24% (4/17) of VUS and 69% (69/100) of discordant variants were resolved into benign (B), likely benign (LB), likely pathogenic (LP), or pathogenic (P). Overall, 70% (109/157) variants had unambiguous classifications (B, LB, LP, P). We quantify the contribution of the HL-specified ACMG/AMP codes to variant classification. CONCLUSION: Expert specification and application of the HL-specific ACMG/AMP guidelines effectively resolved discordant interpretations in ClinVar. This study highlights the utility of ClinGen VCEPs in supporting more consistent clinical variant interpretation.
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- 2021
32. The Diagnostic Yield of Prenatal Genetic Technologies in Congenital Heart Disease: A Prospective Cohort Study
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Matthew E. Hurles, Eamonn R. Maher, Bethany K. Stott, Stephanie Allen, Dominic J. McMullan, E Quinlan-Jones, Susan Hamilton, Fionnuala Mone, Mark D. Kilby, and Anna N. Seale
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Embryology ,medicine.medical_specialty ,030219 obstetrics & reproductive medicine ,Heart disease ,business.industry ,Obstetrics and Gynecology ,Aneuploidy ,Prenatal diagnosis ,General Medicine ,medicine.disease ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Pediatrics, Perinatology and Child Health ,Medicine ,Radiology, Nuclear Medicine and imaging ,030212 general & internal medicine ,Genetic diagnosis ,business ,Prospective cohort study ,Uncertain significance ,Exome sequencing - Abstract
Introduction: The objective was to evaluate: (i) the proportion of prenatally diagnosed congenital heart disease (CHD) associated with an abnormal quantitative fluorescence-PCR (QF-PCR), chromosome microarray (CMA), and exome sequencing (ES) result; and (ii) the diagnostic yield of these technologies based on CHD category and presence of extra-cardiac anomalies (ECAs). Methods: This prospective cohort study was set across 12 UK foetal medicine centres. All cases underwent QF-PCR, CMA, and ES, and the diagnostic yield in n = 147 cases of prenatally diagnosed CHD was assessed. Results: In 34.7% (n = 51/147), a genetic diagnosis was obtained. Using a stepwise testing strategy, the diagnostic yield for QF-PCR, CMA, and ES was 15.6% (n = 23/147), 13.7% (n = 17/124), and 10.2% (n = 11/107), respectively. Abnormal QF-PCR/shunt (septal) defects 31.4% (n = 11/35), p = 0.046, and abnormal CMA/conotruncal anomalies 22.7% (n = 10/44), p = 0.04, had significant associations. Monogenic variants were commonest in complex CHD 36.4% (n = 4/11). Multisystem CHD had a greater diagnostic yield overall compared to isolated OR 2.41 (95% CI, 1.1–5.1), particularly in association with brain and gastrointestinal tract anomalies. The proportion of variants of uncertain significance was 4.7% (n = 5/107) with ES, with none in the CMA group. Conclusion: In the era of prenatal ES, there remains an important role for QF-PCR and CMA. Identification of monogenic pathologic variants further allows delineation of prognosis in CHD.
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- 2021
33. Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk
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Rosemary M. Lemons, Jacob O. Kitzman, Xiaoyan Jia, Victor J. Chen, Mariam Maksutova, Sajini Jayakody, and Bala Bharathi Burugula
- Subjects
variants of uncertain significance ,DNA mismatch repair ,Functional testing ,Mutation, Missense ,Computational biology ,Biology ,Article ,deep mutational scanning ,Genetics ,medicine ,Humans ,cancer ,Missense mutation ,Genetic Predisposition to Disease ,Uncertain significance ,Massively parallel ,Genetics (clinical) ,medicine.disease ,Colorectal Neoplasms, Hereditary Nonpolyposis ,Lynch syndrome ,MSH2 ,genotype-phenotype ,HEK293 Cells ,MutS Homolog 2 Protein ,Functional status - Abstract
Summary The lack of functional evidence for the majority of missense variants limits their clinical interpretability and poses a key barrier to the broad utility of carrier screening. In Lynch syndrome (LS), one of the most highly prevalent cancer syndromes, nearly 90% of clinically observed missense variants are deemed “variants of uncertain significance” (VUS). To systematically resolve their functional status, we performed a massively parallel screen in human cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2. The resulting functional effect map is substantially complete, covering 94% of the 17,746 possible variants, and is highly concordant (96%) with existing functional data and expert clinicians’ interpretations. The large majority (89%) of missense variants were functionally neutral, perhaps unexpectedly in light of its evolutionary conservation. These data provide ready-to-use functional evidence to resolve the ∼1,300 extant missense VUSs in MSH2 and may facilitate the prospective classification of newly discovered variants in the clinic.
- Published
- 2021
34. A survey of aortic disease biorepository participants’ preferences for return of research genetic results
- Author
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J. Scott Roberts, Wendy R. Uhlmann, Whitney E. Hornsby, Jamie Love-Nichols, Patricia Arscott, and Cristen J. Willer
- Subjects
Male ,medicine.medical_specialty ,business.industry ,Genetic counseling ,Aortic Diseases ,Infant, Newborn ,Patient portal ,Genetic Counseling ,Genomics ,Primary care ,Aortic disease ,Biobank ,Article ,Biorepository ,Informed consent ,Neoplasms ,Surveys and Questionnaires ,Family medicine ,Humans ,Medicine ,Female ,business ,Uncertain significance ,Genetics (clinical) - Abstract
There is ongoing debate on whether and what research genetic results to return to study participants. To date, no study in this area has focused on aortopathy populations despite known genes that are clinically actionable. Participants (n = 225, 79% male, mean age = 61 years) with an aortopathy were surveyed to assess preferences for receiving research genetic results. Participants were 'very' or 'extremely likely' to want results for pathogenic variants in aortopathy genes with implications for family members (81%) or that would change medical management (76%). Similarly, participants were 'very' or 'extremely likely' to want actionable secondary findings related to cancer (75%) or other cardiac diseases (70%). Significantly lower interest was observed for non-actionable findings-pathogenic variants in aortopathy genes that would not change medical management (51%) and variants of uncertain significance (38%) (p .0001). Higher health and genomic literacy were positively associated with interest in actionable findings. Most participants (63%) were accepting of any means of return; however, a substantial minority (18%-38%) deemed certain technological means unacceptable (e.g., patient portal). Over 90% of participants reported that a range of health professionals, including cardiovascular specialists, genetics specialists, and primary care providers, were acceptable to return results. Participants with aortopathies are highly interested in research genetic results perceived to be medically actionable for themselves or family members. Participants are accepting of a variety of means for returning results. Findings suggest that research participants should be asked what results are preferred at time of informed consent and that genetic counseling may clarify implications of results that are not personally medically actionable.
- Published
- 2020
35. Limited diagnostic impact of duplications <1 Mb of uncertain clinical significance: a 10-year retrospective analysis of reporting practices at the Mayo Clinic
- Author
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Hutton M. Kearney, Beth A. Pitel, Nicole L. Hoppman, Erik C. Thorland, Clinton E. Hagen, Linda B. Baughn, Nicole J. Boczek, Cherisse A. Marcou, and Ross A. Rowsey
- Subjects
0301 basic medicine ,Microarray ,business.industry ,030105 genetics & heredity ,Bioinformatics ,03 medical and health sciences ,030104 developmental biology ,Gene duplication ,Retrospective analysis ,RefSeq ,Medicine ,Clinical significance ,Copy-number variation ,business ,Uncertain significance ,Exome ,Genetics (clinical) - Abstract
PURPOSE Copy-number variants (CNVs) of uncertain clinical significance are routinely reported in a clinical setting only when exceeding predetermined reporting thresholds, typically based on CNV size. Given that very few genes are associated with triplosensitive phenotypes, it is not surprising that many interstitial duplications
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- 2020
36. Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations
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Raul Urrutia, Nikita R. Dsouza, Michael T. Zimmermann, and Swarnendu Tripathi
- Subjects
Statistics and Probability ,Adult ,medicine.medical_specialty ,AcademicSubjects/SCI01060 ,Mutation, Missense ,GTPase ,Computational biology ,Biology ,Biochemistry ,DNA sequencing ,Correlation ,03 medical and health sciences ,Structural bioinformatics ,0302 clinical medicine ,Neoplasms ,medicine ,Missense mutation ,Humans ,Molecular Biology ,Uncertain significance ,Gene ,030304 developmental biology ,0303 health sciences ,Computational Biology ,Genomics ,Original Papers ,Structural Bioinformatics ,Computer Science Applications ,Computational Mathematics ,Computational Theory and Mathematics ,030220 oncology & carcinogenesis ,ras Proteins ,Medical genetics - Abstract
Motivation Protein-coding genetic alterations are frequently observed in Clinical Genetics, but the high yield of variants of uncertain significance remains a limitation in decision making. RAS-family GTPases are cancer drivers, but only 54 variants, across all family members, fall within well-known hotspots. However, extensive sequencing has identified 881 non-hotspot variants for which significance remains to be investigated. Results Here, we evaluate 935 missense variants from seven RAS genes, observed in cancer, RASopathies and the healthy adult population. We characterized hotspot variants, previously studied experimentally, using 63 sequence- and 3D structure-based scores, chosen by their breadth of biophysical properties. Applying scores that display best correlation with experimental measures, we report new valuable mechanistic inferences for both hot-spot and non-hotspot variants. Moreover, we demonstrate that 3D scores have little-to-no correlation with those based on DNA sequence, which are commonly used in Clinical Genetics. Thus, combined, these new knowledge bear significant relevance. Availability and implementation All genomic and 3D scores, and markdown for generating figures, are provided in our supplemental data. Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2020
37. A Novel, Recurrent, 3.6-kb Deletion in the PYGL Gene Contributes to Glycogen Storage Disease Type VI
- Author
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Yulan Lu, Bo Liu, Yi Lu, Feifan Xiao, Wenhao Zhou, Yu-Chuan Li, Jian-She Wang, Huijun Wang, Xin-Bao Xie, Bingbing Wu, Ping Zhang, Renchao Liu, Xinran Dong, and Gang Li
- Subjects
Male ,0301 basic medicine ,China ,Heterozygote ,Glycogen storage disease type VI ,Population ,Hypoglycemia ,Biology ,Real-Time Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Glycogen Phosphorylase, Liver Form ,Pathology and Forensic Medicine ,03 medical and health sciences ,Exon ,0302 clinical medicine ,Gene Frequency ,Exome Sequencing ,medicine ,Humans ,Exome ,Glycogen Storage Disease Type VI ,Child ,education ,Uncertain significance ,Allele frequency ,Gene ,Exome sequencing ,Retrospective Studies ,Genetics ,education.field_of_study ,Infant, Newborn ,Infant ,Exons ,medicine.disease ,030104 developmental biology ,Child, Preschool ,030220 oncology & carcinogenesis ,Molecular Medicine ,Female ,Gene Deletion - Abstract
The PYGL gene is the only established gene known to cause glycogen storage disease type VI (GSD6), which is a rare autosomal recessive disorder associated with hepatomegaly, elevated levels of hepatic transaminases, and hypoglycemia. Extended bioinformatics analysis was performed on the exome sequencing data of 5 patients who were clinically diagnosed as having or highly suspected of having GSD, and a single heterozygous pathogenic or likely pathogenic or rare variant of uncertain significance single-nucleotide variant was identified on the PYGL gene. A recurrent, novel, 3.6-kb deletion involving exons 14 to 17 of PYGL was identified in three of the five patients. Together with the two novel and one established stop-gain SNVs, they were diagnosed as compounds heterozygous of PYGL variants and confirmed as GSD6. The detected 3.6-kb deletion was further screened in a Chinese cohort of 31,317 individuals without hepatic abnormalities, and 10 carriers were identified, showing an allele frequency of 0.016%. Compared with the previously established 47 PYGL pathogenic or likely pathogenic SNVs, the novel pathogenic deletion had the second highest allele frequency among the population. This recurrent, novel, 3.6-kb deletion improved the molecular diagnostic rate of the GSD6. The relatively high frequency of the variant suggests that it is a potential mutation hotspot in patients with GSD6.
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- 2020
38. Prioritizing genes for systematic variant effect mapping
- Author
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Frederick P. Roth, Rebecca Truty, Robert L. Nussbaum, Britt Johnson, Carlos L. Araya, Da Kuang, Jochen Weile, and Keith Nykamp
- Subjects
Statistics and Probability ,Supplementary data ,0303 health sciences ,Protein function ,AcademicSubjects/SCI01060 ,Systems Biology ,Functional testing ,Mutation, Missense ,Proteins ,Computational biology ,Biology ,Pathogenicity ,Original Papers ,Biochemistry ,Computer Science Applications ,03 medical and health sciences ,Computational Mathematics ,0302 clinical medicine ,Computational Theory and Mathematics ,030220 oncology & carcinogenesis ,Missense mutation ,Molecular Biology ,Gene ,Uncertain significance ,030304 developmental biology - Abstract
Motivation When rare missense variants are clinically interpreted as to their pathogenicity, most are classified as variants of uncertain significance (VUS). Although functional assays can provide strong evidence for variant classification, such results are generally unavailable. Multiplexed assays of variant effect can generate experimental ‘variant effect maps’ that score nearly all possible missense variants in selected protein targets for their impact on protein function. However, these efforts have not always prioritized proteins for which variant effect maps would have the greatest impact on clinical variant interpretation. Results Here, we mined databases of clinically interpreted variants and applied three strategies, each building on the previous, to prioritize genes for systematic functional testing of missense variation. The strategies ranked genes (i) by the number of unique missense VUS that had been reported to ClinVar; (ii) by movability- and reappearance-weighted impact scores, to give extra weight to reappearing, movable VUS and (iii) by difficulty-adjusted impact scores, to account for the more resource-intensive nature of generating variant effect maps for longer genes. Our results could be used to guide systematic functional testing of missense variation toward greater impact on clinical variant interpretation. Availability and implementation Source code available at: https://github.com/rothlab/mave-gene-prioritization Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2020
39. Leukocyte Phosphomannomutase and Phosphomannose Isomerase Activity in an Indian Cohort
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Mihika B. Dave, Vrajesh Udani, Tester F. Ashavaid, and Alpa J. Dherai
- Subjects
0301 basic medicine ,chemistry.chemical_classification ,biology ,Short Communication ,Clinical Biochemistry ,medicine.disease ,Molecular biology ,Enzyme assay ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Enzyme ,chemistry ,030220 oncology & carcinogenesis ,Cohort ,medicine ,biology.protein ,Population study ,Phosphomannose isomerase activity ,Uncertain significance ,Congenital disorder of glycosylation ,Phosphomannomutase - Abstract
Advances in molecular sequencing technology has increased the diagnostic yield for Congenital disorder of glycosylation (CDG). However, novel variants or those of uncertain significance (vus) often pose a challenge and in such cases confirmed diagnosis can be warranted through enzyme analysis of these defects. We thus, aimed to optimize leukocyte-based enzyme assays for first two enzymes involved in N-glycosylation pathway i.e. Phosphomannomutase (PMM) and Phosphomannose isomerase (MPI). Study population comprised of 50 healthy non-alcoholic adults and 20 pediatric controls. Leukocyte enzyme activity was measured by monitoring the conversion of NADP to NADPH at 340 nm. The conditions were optimized and precision was assessed for both low and normal activity leukocyte controls. Enzyme activities for PMM and MPI in healthy individuals were measured in the range 1.6–3.9 and 7–20 nmol/min/mg protein respectively and did not vary with age and gender. The precision for both PMM and MPI showed %CV of 19.9 and 19.8 respectively. The enzyme activity in leukocyte pellet was found to be stable for up to 9 months when stored at -80 °C. The enzyme assays are optimized for PMM and MPI and can be used for evaluation of CDG patients in India.
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- 2020
40. Utility of RNA Sequencing Analysis in the Context of Genetic Testing
- Author
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Jackie Tahiliani, Karen Ouyang, Swaroop Aradhya, Jeanne Leisk, Keith Nykamp, and Kerry W. Aradhya
- Subjects
0301 basic medicine ,Standardization ,medicine.diagnostic_test ,Computer science ,Genetic counseling ,RNA ,Genomics ,Context (language use) ,General Medicine ,Computational biology ,030105 genetics & heredity ,03 medical and health sciences ,030104 developmental biology ,RNA splicing ,medicine ,Uncertain significance ,Genetic testing - Abstract
Purpose of Review RNA analysis is beginning to be integrated into clinical laboratory genomics, and a review of its current uses and limitations is warranted. Here, we summarize the scope and utility of RNA analysis in the context of clinical genetic testing, including considerations for genetic counseling. Recent Findings RNA analysis is a powerful approach for interpreting some variants of uncertain significance, for analyzing splicing alterations, for providing additional functional evidence for sequence and structural variants, and for discovering novel variants. However, a review of RNA sequencing methods has noted variability in both laboratory processes and findings. Genetic counseling related to RNA analysis has to take into account nonstandardized laboratory processes, sample-type limitations, and differences in variant-interpretation outcomes. Summary RNA analysis is an important complement to DNA testing, although limitations still exist. Maximizing the utility of RNA analysis will require appropriate patient referrals and standardization of laboratory processes as the practice continues to expand the ability to identify and resolve molecular diagnoses.
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- 2020
41. Raman Spectroscopic Stratification of Multiple Myeloma Patients Based on Exosome Profiling
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Caterina Riillo, Gerardo Perozziello, Mario Vincenzo Russo, Natalia Malara, Pierosandro Tagliaferri, Francesca Scionti, Marco Rossi, Vincenzo Mollace, Maria Laura Coluccio, Patrizio Candeloro, Pierfrancesco Tassone, Luca Tirinato, Maria Teresa Di Martino, Santo Gratteri, and Giuseppe Viglietto
- Subjects
General Chemical Engineering ,Plasma cell ,Exosome ,Article ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,medicine ,Uncertain significance ,QD1-999 ,Multiple myeloma ,030304 developmental biology ,0303 health sciences ,business.industry ,Bone marrow failure ,General Chemistry ,medicine.disease ,3. Good health ,Monoclonal gammopathy ,Chemistry ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Cancer research ,symbols ,Bone marrow ,medicine.symptom ,business ,Raman spectroscopy - Abstract
Multiple myeloma (MM) is a hematological malignancy characterized by abnormal plasma cell proliferation within the bone marrow which leads to progressive bone marrow failure, skeletal osteolytic lesions, and renal insufficiency, thus severely affecting the quality of life. MM is always preceded by monoclonal gammopathy of uncertain significance (MGUS), which progresses to asymptomatic-MM (aMM) or symptomatic-MM (sMM) at a rate of 1% per year. Despite impressive progress in the therapy of the disease, MM remains incurable. Based on these premises, the identification of biomarkers of MGUS progression to MM is a crucial issue in disease management. In this regard, exosomes (EXs) and their precious biomolecular cargo could play a pivotal role in MM detection, stratification, and follow-up. Raman spectroscopy, a label- and manipulation-free technique, and its enhanced version, surface-enhanced Raman spectroscopy (SERS), have been used for characterizing MGUS, aMM, and sMM patient-derived EXs. Here, we have demonstrated the capability of Raman spectroscopy for discriminating EXs along the progression from MGUS to aMM and sMM, thus providing useful clinical indications for patient care. The used SERS devices, based on random nanostructures, have shown good potential in terms of sensitivity, but further developments are needed for achieving reproducible and quantitative SERS results.
- Published
- 2020
42. The odyssey of complex neurogenetic disorders: From undetermined to positive
- Author
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Betiana G Comas, Sergio Alejandro Rodríguez-Quiroga, Luca Marsili, Josefina Perez-Maturo, Walter Silva, Valeria Salinas, Nerina Martínez, Hernán Amartino, Patricia Vega, Clarisa Maxit, Marcelo Andrés Kauffman, Kevin R Duque, Nancy Medina, Lucia Zavala, Ignacio Sfaello, Alberto J. Espay, Damián Consalvo, Andrea Sturchio, Barbara Grimberg, and Dolores González-Morón
- Subjects
Genetics ,Genetic heterogeneity ,High-Throughput Nucleotide Sequencing ,Biology ,Pathogenicity ,DNA sequencing ,Germline ,Clinical neurology ,Gene panel ,Exome Sequencing ,Humans ,Uncertain significance ,Genetics (clinical) ,Exome sequencing - Abstract
The genetic and phenotypic heterogeneity of neurogenetic diseases forces patients and their families into a "diagnostic odyssey." An increase in the variability of genetic disorders and the corresponding gene-disease associations suggest the need to periodically re-evaluate the significance of variants of undetermined pathogenicity. Here, we report the diagnostic and clinical utility of Targeted Gene Panel Sequencing (TGPS) and Whole Exome Sequencing (WES) in 341 patients with suspected neurogenetic disorders from centers in Buenos Aires and Cincinnati over the last 4 years, focusing on the usefulness of reinterpreting variants previously classified as of uncertain significance. After a mean of ±2years (IC 95:0.73-3.27), approximately 30% of the variants of uncertain significance were reclassified as pathogenic. The use of next generation sequencing methods has facilitated the identification of both germline and mosaic pathogenic variants, expanding the diagnostic yield. These results demonstrate the high clinical impact of periodic reanalysis of undetermined variants in clinical neurology.
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- 2020
43. Perceptions of provider’s epistemic authority in response to variant of uncertain significance‐related recommendations
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Banu Arun, Maureen E. Mork, Susan K. Peterson, Robert J. Volk, and Sukh Makhnoon
- Subjects
medicine.diagnostic_test ,business.industry ,media_common.quotation_subject ,Best practice ,Genetic counseling ,Context (language use) ,Article ,Mean difference ,Perception ,medicine ,Epistemic authority ,business ,Uncertain significance ,Genetics (clinical) ,Clinical psychology ,Genetic testing ,media_common - Abstract
Uncertain genetic information such as variants of uncertain significance (VUS) is often encountered by patients in clinical cancer genetic testing. Although healthcare providers facilitate patient's understanding of VUS-associated empirical risk and its medical implications, patients' understanding and perceptions of risk often differ and may be based on subjective evaluations such as their perception of provider's epistemic authority (EA). This study examines the hypothesis that individuals attribute greater EA to genetic counselors (GCs) (compared to gastrointestinal oncologists) and to providers who recommend more active VUS-related recommendations (compared to inactive). In a factorial experiment, 652 adult participants recruited on Amazon Mechanical Turk were block-randomized to read one of 10 different types of VUS-related scenarios in the context of colon cancer (5 recommendation types × 2 provider types). GCs were attributed higher EA than gastrointestinal oncologists (p =
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- 2020
44. The articularis genu muscle and its relevance in oncological surgical margins
- Author
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H. Thomas Temple, Nicholas A. Athanasou, Catherine L. McCarthy, Thomas D A Cosker, M Gibbons, Jessica Caterson, and Matthew Williams
- Subjects
General Orthopaedics ,quadriceps ,business.industry ,bone tumour ,General Engineering ,Articularis genus ,Anatomy ,Thigh ,articularis genu ,lcsh:RD701-811 ,medicine.anatomical_structure ,lcsh:Orthopedic surgery ,oncology ,femoral resection ,Medicine ,Compartment (pharmacokinetics) ,business ,Uncertain significance ,mri - Abstract
Aims The aticularis genu (AG) is the least substantial and deepest muscle of the anterior compartment of the thigh and of uncertain significance. The aim of the study was to describe the anatomy of AG in cadaveric specimens, to characterize the relevance of AG in pathological distal femur specimens, and to correlate the anatomy and pathology with preoperative magnetic resonance imaging (MRI) of AG. Methods In 24 cadaveric specimens, AG was identified, photographed, measured, and dissected including neurovascular supply. In all, 35 resected distal femur specimens were examined. AG was photographed and measured and its utility as a surgical margin examined. Preoperative MRIs of these cases were retrospectively analyzed and assessed and its utility assessed as an anterior soft tissue margin in surgery. In all cadaveric specimens, AG was identified as a substantial structure, deep and separate to vastus itermedius (VI) and separated by a clear fascial plane with a discrete neurovascular supply. Mean length of AG was 16.1 cm ( ± 1.6 cm) origin anterior aspect distal third femur and insertion into suprapatellar bursa. In 32 of 35 pathological specimens, AG was identified (mean length 12.8 cm ( ± 0.6 cm)). Where AG was used as anterior cover in pathological specimens all surgical margins were clear of disease. Of these cases, preoperative MRI identified AG in 34 of 35 cases (mean length 8.8 cm ( ± 0.4 cm)). Results AG was best visualized with T1-weighted axial images providing sufficient cover in 25 cases confirmed by pathological findings.These results demonstrate AG as a discrete and substantial muscle of the anterior compartment of the thigh, deep to VI and useful in providing anterior soft tissue margin in distal femoral resection in bone tumours. Conclusion Preoperative assessment of cover by AG may be useful in predicting cases where AG can be dissected, sparing the remaining quadriceps muscle, and therefore function. Cite this article: Bone Joint Open 2020;1-9:585–593.
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- 2020
45. Implementation of exome sequencing in fetal diagnostics—Data and experiences from a tertiary center in Denmark
- Author
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Puk Sandager, Ida Vogel, Stina Lou, Rikke Christensen, Lotte Andreasen, Naja Becher, and Olav Bjørn Petersen
- Subjects
medicine.medical_specialty ,Microarray ,Denmark ,Prenatal diagnosis ,Ultrasonography, Prenatal ,Congenital Abnormalities ,Fetal Development ,03 medical and health sciences ,Fetus ,0302 clinical medicine ,Pregnancy ,Prenatal Diagnosis ,Exome Sequencing ,medicine ,Humans ,030212 general & internal medicine ,Uncertain significance ,Exome ,Exome sequencing ,Retrospective Studies ,030219 obstetrics & reproductive medicine ,Obstetrics ,business.industry ,High-Throughput Nucleotide Sequencing ,Obstetrics and Gynecology ,General Medicine ,medicine.disease ,Female ,business ,Genetic diagnosis - Abstract
INTRODUCTION Applying whole-exome sequencing (WES) for the diagnosis of diseases in children has shown significant diagnostic strength compared with chromosomal microarray. WES may also have the potential of adding clinically relevant prenatal information in cases where a fetus is found to have structural anomalies. We present results from the first fetal exomes performed in a tertiary center in Denmark. MATERIAL AND METHODS Couples/expectant parents were included in Central Denmark Region from July 2016 to March 2019. Inclusion was not systematic, but where one or more fetal malformations or severe fetal hydrops were detected, and a specific diagnosis had not been obtained by chromosomal microarray. WES was performed in ongoing pregnancies (N = 11), after intrauterine demise (N = 5), or after termination of pregnancy based on ultrasound findings (N = 19). In most cases, a trio format was applied comprising fetal and parental DNA. RESULTS WES was performed in 35 highly selected fetal cases. Pathogenic variants, or variants likely to explain the phenotype, were detected in 9/35 (26%). Variants of uncertain significance were detected in 7/35 (20%) and there was one secondary finding (3%). Out of the 11 ongoing pregnancies, four reached a genetic diagnosis (36%). Detection rate was highest in cases of multisystem anomalies (7/13, 54%). WES was completed in all three trimesters and both autosomal dominant, autosomal recessive and X-linked inheritance were revealed. CONCLUSIONS We present data from 35 cases of exome sequencing applied in a setting of fetal malformations. Importantly, though, we wish to share our personal experiences with implementing WES into a prenatal setting. As a medical society, we must continue to share what we do not understand, what went wrong, what is difficult, and what we do not agree upon. A common understanding and language are warranted. We also advocate that more research is needed concerning the clinical value, as well as costs and patient perspectives, of using WES in pregnancy. We believe that WES will lead to improved prenatal and perinatal care.
- Published
- 2020
46. Genetic panel screening in patients with clinically unclassified systemic autoinflammatory diseases
- Author
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Ferhat Demir, Nuray Aktay Ayaz, Yasemin Kendir Demirkol, Hamdi Levent Doganay, Betül Sözeri, Şerife Gül Karadağ, Hafize Emine Sönmez, Kubra Ermis Tekkus, Ozlem Akgun Dogan, and Sezin Canbek
- Subjects
myalgia ,Oral aphthae ,Abdominal pain ,medicine.medical_specialty ,Fever ,Genotype ,Monogenic disease ,03 medical and health sciences ,0302 clinical medicine ,Rheumatology ,medicine ,Humans ,In patient ,Genetic Testing ,030212 general & internal medicine ,Uncertain significance ,030203 arthritis & rheumatology ,business.industry ,Hereditary Autoinflammatory Diseases ,High-Throughput Nucleotide Sequencing ,General Medicine ,medicine.disease ,Dermatology ,medicine.symptom ,Periodic fever syndrome ,business - Abstract
Systemic autoinflammatory diseases (SAIDs) may not always present with typical clinical findings of a monogenic disease. We aimed to genetically screen and diagnose these clinically unclassified patients by next-generation sequencing (NGS) analysis.A total of 64 patients who had clinical findings of a periodic fever syndrome but did not meet the clinical diagnostic criteria for any SAID or had clinical findings for more than one monogenic SAID were identified as "clinically unclassified SAIDs." NGS panel analysis, including 16 genes, was performed in these patients. Patients, who could not be classified as one of the defined SAID after the result of the NGS gene analysis, were identified as "undefined SAID."The most common autoinflammatory symptoms in unclassified SAID patients were abdominal pain (60.9%), arthralgia (48.4%), urticarial rash (43.8%), myalgia (40.6%), oral aphthae (28.1%), and conjunctivitis (20.3%), respectively. In the result of the NGS gene panel screening, pathogenic, likely pathogenic variants, or VUS (variants of uncertain significance) were detected in 36 of 64 patients in at least one gene in the NGS panel. A total of 15 patients were diagnosed with a monogenic SAID according to both phenotypic and genotypic data; 12 patients as FMF, two patients as FCAS, and one patient as TRAPS, respectively. A total of 49 patients who did not meet the classification criteria including genetic results for a monogenic SAID were followed as undefined SAID.The classification criteria described for SAIDs so far unfortunately do not cover all patients with signs of periodic fevers. The NGS gene panel appears to be a useful diagnostic tool for some of the patients with clinically unclassified SAID findings. Key Points • The classification criteria described for SAIDs do not cover all patients with signs of periodic fevers • The use of the undefined SAID nomenclature will benefit clinicians for diagnosis and initiating early treatment • The NGS panel appears to be a useful diagnostic tool in patients with clinically unclassified SAIDs.
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- 2020
47. Interpretation of mitochondrial tRNA variants
- Author
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Sha Tang, Victor Wei Zhang, Megan L. Landsverk, William J. Craigen, Shulin Zhang, Fangyuan Li, Eric S. Schmitt, Yue Wang, Lee-Jun C. Wong, Jing Wang, and Ting Chen
- Subjects
0301 basic medicine ,Genetics ,Genetic counseling ,030105 genetics & heredity ,Biology ,Phenotype ,Mitochondrial trna ,Heteroplasmy ,03 medical and health sciences ,030104 developmental biology ,Clinical diagnosis ,Transfer RNA ,Clinical significance ,Uncertain significance ,Genetics (clinical) - Abstract
To develop criteria to interpret mitochondrial transfer RNA (mt-tRNA) variants based on unique characteristics of mitochondrial genetics and conserved structural/functional properties of tRNA. We developed rules on a set of established pathogenic/benign variants by examining heteroplasmy correlations with phenotype, tissue distribution, family members, and among unrelated families from published literature. We validated these deduced rules using our new cases and applied them to classify novel variants. Evaluation of previously reported pathogenic variants found that 80.6% had sufficient evidence to support phenotypic correlation with heteroplasmy levels among and within families. The remaining variants were downgraded due to the lack of similar evidence. Application of the verified criteria resulted in rescoring 80.8% of reported variants of uncertain significance (VUS) to benign and likely benign. Among 97 novel variants, none met pathogenic criteria. A large proportion of novel variants (84.5%) remained as VUS, while only 10.3% were likely pathogenic. Detection of these novel variants in additional individuals would facilitate their classification. Proper interpretation of mt-tRNA variants is crucial for accurate clinical diagnosis and genetic counseling. Correlations with tissue distribution, heteroplasmy levels, predicted perturbations to tRNA structure, and phenotypes provide important evidence for determining the clinical significance of mt-tRNA variants.
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- 2020
48. A Middle-Aged Man Presenting With Progressive Heart Failure, Myopathy, and Monoclonal Gammopathy of Uncertain Significance
- Author
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Kaspar Broch, Christoffer Jonsrud, Einar Gude, Silje Skaara, Ellen-Ann Antal, Gerhard Bosse, Ahmed Elsais, Yngvar Fløisand, Terje Hegard, and Trine Haug Popperud
- Subjects
0301 basic medicine ,Cardiac function curve ,medicine.medical_specialty ,Cardiomyopathy ,Case Report ,SLONM, sporadic late-onset nemaline myopathy ,030105 genetics & heredity ,MGUS, monoclonal gammopathy of uncertain significance ,Endomyocardial biopsy ,03 medical and health sciences ,0302 clinical medicine ,Clinical Case ,Internal medicine ,medicine ,echocardiography ,Diseases of the circulatory (Cardiovascular) system ,Myopathy ,Uncertain significance ,business.industry ,imaging ,medicine.disease ,Skeletal myopathy ,chronic heart failure ,Monoclonal gammopathy ,Heart failure ,RC666-701 ,Cardiology ,right-sided catheterization ,medicine.symptom ,Cardiology and Cardiovascular Medicine ,business ,cardiomyopathy ,030217 neurology & neurosurgery - Abstract
A 48-year-old man presented with rapidly progressive heart failure and monoclonal gammopathy of uncertain significance. No specific cause was detected on endomyocardial biopsy. As the heart failure worsened, he also developed progressive skeletal myopathy. This provided the clue to the diagnosis, and cardiac function recovered rapidly with cause-directed therapy. (Level of Difficulty: Intermediate.), Graphical abstract, A 48-year-old man presented with rapidly progressive heart failure and monoclonal gammopathy of uncertain significance. No specific cause was…
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- 2020
49. Maternity health care professionals' views and experiences of fetal genomic uncertainty: A review
- Author
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Celine Lewis, Jane Halliday, Lisa Hui, and Emma Jane Szepe
- Subjects
0301 basic medicine ,medicine.medical_specialty ,Attitude of Health Personnel ,Genetic counseling ,education ,Prenatal diagnosis ,030105 genetics & heredity ,Midwifery ,03 medical and health sciences ,0302 clinical medicine ,Pregnancy ,Physicians ,Prenatal Diagnosis ,Health care ,medicine ,Humans ,Uncertain significance ,Genetics (clinical) ,030219 obstetrics & reproductive medicine ,Whole Genome Sequencing ,business.industry ,Uncertainty ,High-Throughput Nucleotide Sequencing ,Physicians, Family ,Obstetrics and Gynecology ,Genomics ,Microarray Analysis ,medicine.disease ,Obstetrics ,Family medicine ,Medical genetics ,Female ,business ,Psychosocial ,Postpartum period - Abstract
The field of prenatal screening and diagnosis for fetal anomalies has been marked by a rapid succession of technological advances, including most notably, chromosomal microarray analysis and next generation sequencing. Despite the diagnostic advantages of these technologies, their incorporation into prenatal testing has created additional challenges of revealing genomic variants of unknown or uncertain significance, and secondary findings. While detailed post-test counselling about uncertain variants is best performed by medical geneticists, many of the screening and diagnostic tests that lead to this information are actually ordered by general maternity health care professionals (HCPs), such as obstetricians, midwives and family physicians. Maternity HCPs support pregnant women through to the conclusion of their pregnancy and the postpartum period, and thus are close observers of the psychosocial impart of fetal genomic uncertainty on women and their families. Whilst there have been many studies exploring the handling of genomic uncertainty by genetics HCPs there has been relatively less attention paid to maternity HCPs without speciality training in genetics. This review explores the current literature surrounding non-genetic maternity HCPs' views and experiences of genomic uncertainty and returning uncertain results in the prenatal setting. This article is protected by copyright. All rights reserved.
- Published
- 2020
50. 'It's probably nothing, but…' Couples' experiences of pregnancy following an uncertain prenatal genetic result
- Author
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Stina Lou, Olav Bjørn Petersen, Samantha Riedijk, Ida Vogel, Kirsten Lomborg, Celine Lewis, and Clinical Genetics
- Subjects
Male ,Parents ,Coping (psychology) ,INFORMATION ,Denmark ,Terminology ,0302 clinical medicine ,CHROMOSOMAL MICROARRAY ,Pregnancy ,Prenatal Diagnosis ,Adaptation, Psychological ,Medicine ,030212 general & internal medicine ,media_common ,030219 obstetrics & reproductive medicine ,Uncertainty ,parents ,prenatal testing ,Obstetrics and Gynecology ,General Medicine ,uncertain significance ,Feeling ,Learning disability ,Female ,pregnancy ,Thematic analysis ,Worry ,medicine.symptom ,Clinical psychology ,Adult ,DNA Copy Number Variations ,media_common.quotation_subject ,Information Seeking Behavior ,Genetic Counseling ,DIAGNOSIS ,Ultrasonography, Prenatal ,Interviews as Topic ,Young Adult ,03 medical and health sciences ,Terminology as Topic ,Humans ,penetrance ,Chromosome Aberrations ,business.industry ,Information seeking ,Microarray Analysis ,medicine.disease ,chromosomal microarray analysis ,experiences ,business ,copy number variants - Abstract
INTRODUCTION: A common concern regarding the introduction of Chromosomal Micro-Array in prenatal testing is the concomitant identification of an uncertain copy number variant (CNV) where significance and clinical implication for the unborn child can be difficult or impossible to predict. Following the identification of an uncertain CNV, prospective parents may decide to continue the pregnancy. The aim of this study was to explore how prospective parents manage uncertainty and experience pregnancy in light of an uncertain CNV result.MATERIAL AND METHODS: Qualitative interviews with 16 women and 10 partners who had received a prenatally diagnosed, uncertain CNV. Participants were recruited from the Aarhus University Hospital, Denmark and most were interviewed in their homes 1-14 weeks after birth. Data were analyzed using thematic analysis.RESULTS: Following the CNV diagnosis, some couples focused on the severe syndromes ruled out by the result, while others were more concerned with the new potential risks, e.g. learning disabilities. Most couples did not remember the actual diagnosis, but all described a number of attention points generated by the CNV result. During pregnancy, the couples used various strategies to limit worry and enjoy their pregnancy such as limiting information seeking, reducing talk of the CNV and deferring thoughts of potential consequences. Furthermore, ultrasound was considered a valuable resource for reducing worry as it provided reassurance about the development of the baby. Inherited CNVs caused relief on one hand, but also feelings of responsibility for the child's potential challenges. After birth, worry decreased considerably, but all couples paid some extra attention to the child's development, while also being alert to the risk wrongfully interpreting the child's development in terms of the CNV. Eleven couples expressed satisfaction with knowing about the child's CNV, whereas five couples would rather not have known.CONCLUSIONS: The results indicate that health professionals should be mindful of terminology, remember to point out what has been ruled out by the CNV result, and discuss potential coping strategies with the couple. Furthermore, these couples may have a higher need for ultrasound during pregnancy to help reduce worry. More research is needed on the families' long-term coping.
- Published
- 2020
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