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Elfatih A, Saad C, Mifsud B, Mbarek H. Analysis of 14,392 whole genomes reveals 3.5% of Qataris carry medically actionable variants. Eur J Hum Genet 2024:10.1038/s41431-024-01656-1. [PMID: 39020067 DOI: 10.1038/s41431-024-01656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/19/2024] Open
Abstract
Arabic populations are underrepresented in large genome projects; therefore, the frequency of clinically actionable variants among Arabs is largely unknown. Here, we investigated genetic variation in 14,392 whole genomes from the Qatar Genome Program (QGP) across the list of 78 actionable genes (v3.1) determined by the American College of Medical Genetics and Genomics (ACMG). Variants were categorized into one of the following groups: (1) Pathogenic (P), (2) Likely pathogenic (LP), and (3) Rare variants of uncertain significance with evidence of pathogenicity. For the classification, we used variant databases, effect predictors, and the disease-relevant phenotypes available for the cohort. Data on cardiovascular disease, cancer, and hypercholesterolemia allowed us to assess the disease-relevant phenotype association of rare missense variants. We identified 248 distinct variants in 50 ACMG genes that fulfilled our criteria to be included in one of the three groups affecting 1036 genotype-positive participants of the QGP cohort. The most frequent variants were in TTN, followed by RYR1 and ATP7B. The prevalence of reportable secondary findings was 3.5%. A further 46 heterozygous variants in six genes with an autosomal recessive mode of inheritance were detected in 200 individuals, accounting for an additional 1.4%. Altogether, they affect 5% of the population. Due to the high consanguinity rate in the QGP cohort (28% in spouses and 60% in parents), P and LP variants both in genes with dominant and recessive inheritance are important for developing better treatment options and preventive strategies in Qatar and the Arabic population of the Middle East.
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Affiliation(s)
- Amal Elfatih
- Hamad Bin Khalifa University, College of Health and Life Science, Genomics and Precision Medicine, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation, Qatar Science and Technology Park, Innovation Center, Doha, Qatar
| | - Borbala Mifsud
- Hamad Bin Khalifa University, College of Health and Life Science, Genomics and Precision Medicine, Doha, Qatar.
- William Harvey Research Institute, Queen Mary University London, London, UK.
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation, Qatar Science and Technology Park, Innovation Center, Doha, Qatar.
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Wu J, Cui Y, Liu T, Gu C, Ma X, Yu C, Cai Y, Shu J, Wang W, Cai C. Whole exome sequencing approach for identification of the molecular etiology in pediatric patients with hematuria. Clin Chim Acta 2024; 554:117795. [PMID: 38262496 DOI: 10.1016/j.cca.2024.117795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/25/2023] [Accepted: 01/20/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Hematuria is a common condition in clinical practice of pediatric patients. It is related to a wide spectrum of disorders and has high heterogeneity both clinically and genetically, which contributes to challenges of diagnosis and lead many pediatric patients with hematuria not to receive accurate diagnosis and early management. METHODS In this single center study, 42 children with hematuria were included in Tianjin Children's Hospital between 2019 and 2020. We analyzed the clinical information and performed WES (Whole exome sequencing) for all cases. Then the classification of identified variants was performed according to the American College of Medical Genetics and Genomics (ACMG) guidelines for interpreting sequence variants. For the fragment deletion, qPCR was performed to validate and confirm the inherited pattern. RESULTS For the 42 patients, 16 cases had gross hematuria and 26 had microscopic hematuria. Molecular genetic causes were uncovered in 9 (21.4%) children, including 7 with Alport syndrome (AS), one with polycystic nephropathy and one with lipoprotein glomerulopathy. The genetic causes for other patients were not related with hematuria. CONCLUSIONS WES is a rapid and effective way to evaluate patients with hematuria. The analysis of genotype-phenotype correlations of patients with AS indicated that severe variants were associated with early kidney failure. Secondary findings were not rare in Chinese children, thus the clinician should pay more attention to the clinical interpretation of sequencing results and properly interaction with patients and their family.
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Affiliation(s)
- Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Yaqiong Cui
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Tao Liu
- The department of nephrology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China
| | - Chunyu Gu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Ximeng Ma
- Basic Medical College, Tianjin Medical University, Tianjin 30070, China
| | - Changshun Yu
- Tianjin KingMed Center for Clinical Laboratory Co. Ltd., Tianjin 300392, China
| | - Yingzi Cai
- Department of Medicine,Tianjin University, Tianjin 300110, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China.
| | - Wenhong Wang
- The department of nephrology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China.
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China.
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Rodríguez-Salgado LE, Silva-Aldana CT, Medina-Méndez E, Bareño-Silva J, Arcos-Burgos M, Silgado-Guzmán DF, Restrepo CM. Frequency of actionable Exomic secondary findings in 160 Colombian patients: Impact in the healthcare system. Gene 2022; 838:146699. [PMID: 35803546 DOI: 10.1016/j.gene.2022.146699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION By 2021, the American College of Medical Genetics and Genomics (ACMG) published the last version of their secondary findings (SF) reporting recommendations for cases in which a person receives a genetic test. OBJECTIVE To determine in a sample of the Colombian population the prevalence of SF for the 59 genes on the ACMG SF v2.0 list associated with 27 genetic diseases. MATERIALS AND METHODS An analytical cross-sectional study was developed by examining the sequences of 160 exomes. Based on the ACMG guidelines, a variant classification algorithm was designed to filter and select reportable SF. RESULTS Eleven pathogenic variants were identified in 13/160 (8.13%) patients in genes APOB, BRCA2, CACNA1S, COL3A1, LDLR, MYBPC3, PCSK9, PKP2, PMS2 and RYR2. No association was found between the sociodemographic variables and the SF to report (P > 0,05). CONCLUSION We reported the first approach of actionable pathogenic variants spectrum in the Colombian population. Given the frequency found in this study and the clinical impact of genomic variants on health, it is essential to actively search for SF having the opportunity to receive genetic counselling, prevention and clinical management.
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Affiliation(s)
| | | | | | - José Bareño-Silva
- School of Medicine, Mental Health Research Group, CES University, Medellin, Colombia
| | - Mauricio Arcos-Burgos
- Research Group on Psychiatric Disorders (GIPSI), Department of Psychiatry, Institute of Medical Research, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carlos M Restrepo
- Center for Research in Genetics and Genomics (CIGGUR), GeniURos Research Group, School of Medicine and Health Sciences, University of Rosario, Bogotá, Colombia.
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Kang HJ, Lee HY, Kim KT, Kim JW, Lee JY, Kim SW, Kim JC, Shin IS, Kim N, Kim JM. Genetic Differences between Physical Injury Patients With and Without Post-traumatic Syndrome: Focus on Secondary Findings and Potential Variants Revealed by Whole Exome Sequencing. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2021; 19:683-694. [PMID: 34690123 PMCID: PMC8553524 DOI: 10.9758/cpn.2021.19.4.683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
Objective Sudden traumatic physical injuries often cause psychological distress, which may be associated with chronic disability. Although considerable effort has been expended to identify genetic predictors of post-traumatic stress disorder (PTSD) after traumatic events, genetic predictors of psychological distress in response to severe physical injuries have been yet to be elucidated using whole exome sequencing (WES). Here, the genetic architecture of post-traumatic syndrome (PTS), which encompasses a broad range of psychiatric disorders after traumatic events including depression, anxiety disorder, acute stress disorder, and PTSD, was explored using WES in severely physically injured patients, focusing on secondary findings and potential PTS-related variants. Methods In total, 141 severely physically injured patients were consecutively recruited, and PTS was evaluated within 1 month of the injury. Secondary findings were analyzed according to PTS status. To identify PTS-related variants, genome-wide association analyses and the optimal sequencing kernel association test were performed. Results Of the 141 patients, 88 (62%) experienced PTS. There were 108 disease-causing variants in severely physically injured patients. As secondary findings, the stress- and inflammation-related signaling pathways were enriched in the PTS patients, while the glucose metabolism pathway was enriched in those without PTS. However, no significant PTS-related variants were identified. Conclusion Our findings suggest that genetic alterations in stress and inflammatory pathways might increase the likelihood of PTS immediately after severe physical injury. Future studies with larger samples and longitudinal designs are needed.
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Affiliation(s)
- Hee-Ju Kang
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Ho-Yeon Lee
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, University of Science and Technology (UST), Daejeon, Korea.,Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Ki-Tae Kim
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul, Korea
| | - Ju-Wan Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Ju-Yeon Lee
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Sung-Wan Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Jung-Chul Kim
- Trauma Center, Department of Surgery, Chonnam National University Medical School, Gwangju, Korea
| | - Il-Seon Shin
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Namshin Kim
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, University of Science and Technology (UST), Daejeon, Korea.,Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jae-Min Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
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Elfatih A, Mohammed I, Abdelrahman D, Mifsud B. Frequency and management of medically actionable incidental findings from genome and exome sequencing data; A systematic review. Physiol Genomics 2021; 53:373-384. [PMID: 34250816 DOI: 10.1152/physiolgenomics.00025.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The application of whole genome/exome sequencing technologies in clinical genetics and research has resulted in the discovery of incidental findings unrelated to the primary purpose of genetic testing. The American College of Medical Genetics and Genomics published guidelines for reporting pathogenic and likely pathogenic variants that are deemed to be medically actionable, which allowed us to learn about the epidemiology of incidental findings in different populations. However, consensus guidelines for variant reporting and classification are still lacking. We conducted a systematic literature review of incidental findings in whole genome/exome sequencing studies to obtain a comprehensive understanding of variable reporting and classification methods for variants that are deemed to be medically actionable across different populations. The review highlights the elements that demand further consideration or adjustment.
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Affiliation(s)
- Amal Elfatih
- College of Health and Life Sciences, Hamad bin Khalifa University, Doha, Qatar
| | - Idris Mohammed
- College of Health and Life Sciences, Hamad bin Khalifa University, Doha, Qatar
| | - Doua Abdelrahman
- Integrated Genomics Services, Translational Research, Research Branch, Sidra Medicine, Doha, Qatar
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad bin Khalifa University, Doha, Qatar.,William Harvey Research Institute, Queen Mary University London, London, UK
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Yogasundaram H, Alhumaid W, Dzwiniel T, Christian S, Oudit GY. Cardiomyopathies and Genetic Testing in Heart Failure: Role in Defining Phenotype-Targeted Approaches and Management. Can J Cardiol 2021; 37:547-559. [PMID: 33493662 DOI: 10.1016/j.cjca.2021.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/29/2022] Open
Abstract
Cardiomyopathies represent an important cause of heart failure, often affecting young individuals, and have important implications for relatives. Genetic testing for cardiomyopathies is an established care pathway in contemporary cardiology practice. The primary cardiomyopathies where genetic testing is indicated are hypertrophic, dilated, arrhythmogenic, and restrictive cardiomyopathies, with left ventricular noncompaction as a variant phenotype. Early identification and initiation of therapies in patients with inherited cardiomyopathies allow for targeting asymptomatic and presymptomatic patients in stages A and B of the American College of Cardiology/American Heart Association classification of heart failure. The current approach for genetic testing uses gene panel-based testing with the ability to extend to whole-exome and whole-genome sequencing in rare instances. The central components of genetic testing include defining the genetic basis of the diagnosis, providing prognostic information, and the ability to screen and risk-stratify relatives. Genetic testing for cardiomyopathies should be coordinated by a multidisciplinary team including adult and pediatric cardiologists, genetic counsellors, and geneticists, with access to expertise in cardiac imaging and electrophysiology. A pragmatic approach for addressing genetic variants of uncertain significance is important. In this review, we highlight the indications for genetic testing in the various cardiomyopathies, the value of early diagnosis and treatment, family screening, and the care process involved in genetic counselling and testing.
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Affiliation(s)
- Haran Yogasundaram
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Waleed Alhumaid
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Tara Dzwiniel
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Susan Christian
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Y Oudit
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada.
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7
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Ethical challenges of precision cancer medicine. Semin Cancer Biol 2020; 84:263-270. [PMID: 33045356 DOI: 10.1016/j.semcancer.2020.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/25/2020] [Accepted: 09/20/2020] [Indexed: 11/21/2022]
Abstract
Amongst common diseases, cancer is often both a leader in self-regulatory policy, or the field for contentious ethical issues such as the patenting of the BRCA1/2 genes. With the advent of genomic sequencing technologies, achieving precision cancer medicine requires prospective norms due to the large and varied sources of data involved. Here, we discuss the ethical and legal aspects of the policy debate around the relevant topics in precision cancer medicine: the return of incidental findings and sequencing raw data to patients, the communication of genetic results to patients' relatives, privacy and communication risks with concomitant oversight strategies, patient participation and consent models. We present the arguments and empirical data supporting specific policy solutions delineating still contested areas. What type of consent and oversight are required to acquire genomic data or to access it where desired, either by the participant/patient or third-party researchers? Most of the raw sequencing data is still uninterpretable and the variants revealed subject to reinterpretation over time. No doubt the ethical challenges of precision cancer medicine are a prototype of what's to come for other diseases. They are also paradigmatic for regulatory and ethical questions of the translational endeavors since the two worlds - basic science and patient care - are governed by different ethical and legal principles that need to be reconciled in precision cancer medicine.
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Horiuchi Y, Matsubayashi H, Kiyozumi Y, Nishimura S, Higashigawa S, Kado N, Nagashima T, Mizuguchi M, Ohnami S, Arai M, Urakami K, Kusuhara M, Yamaguchi K. Disclosure of secondary findings in exome sequencing of 2480 Japanese cancer patients. Hum Genet 2020; 140:321-331. [PMID: 32710294 DOI: 10.1007/s00439-020-02207-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/14/2020] [Indexed: 12/18/2022]
Abstract
High-throughput sequencing has greatly contributed to precision medicine. However, challenges remain in reporting secondary findings (SFs) of germline pathogenic variants and managing the affected patients. The aim of this study was to examine the incidence of SFs in Japanese cancer patients using whole exome sequencing (WES) and to understand patient preferences regarding SF disclosure. WES was conducted for 2480 cancer patients. Genomic data were screened and classified for variants of 59 genes listed by the American College of Medical Genetics and Genomics SF v2.0 and for an additional 13 hereditary cancer-related genes. Majority of the participants (68.9%; 1709/2480) opted for disclosure of their SFs. Thirty-two pathogenic or likely pathogenic variants, including BRCA1 (7 patients), BRCA2 (4), CHEK2 (4), PTEN (3), MLH1 (3), SDHB (2), MSH6 (1), NF1 (1), EXT2 (1), NF1 (1), NTRK1 (1), MYH7 (3), MYL2 (1), TNNT2 (1), LDLR (2), FBN1 (1), and KCNH2 (1) were recognized in 36 patients (1.5%). Twenty-eight (77.8%) patients underwent genetic counseling and received their SF results. Eighteen (64.3%) patients underwent clinical management for SFs. Genetic validation tests were administered significantly more frequently to patients with than without a SF-related personal history (P = 0.025). This was a first attempt at a large-scale systematic exome analysis in Japan; nevertheless, many cancer patients opted for disclosure of SFs and accepted or considered clinical management.
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Affiliation(s)
- Yasue Horiuchi
- Division of Genetic Counseling, Genetic Medicine Promotion, Shizuoka Cancer Center Hospital, Shizuoka, Japan.,Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiroyuki Matsubayashi
- Division of Genetic Counseling, Genetic Medicine Promotion, Shizuoka Cancer Center Hospital, Shizuoka, Japan.
| | - Yoshimi Kiyozumi
- Division of Genetic Counseling, Genetic Medicine Promotion, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Seiichiro Nishimura
- Division of Genetic Counseling, Genetic Medicine Promotion, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Satomi Higashigawa
- Division of Genetic Counseling, Genetic Medicine Promotion, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Nobuhiro Kado
- Division of Genetic Counseling, Genetic Medicine Promotion, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | | | - Maki Mizuguchi
- Research Institute of Shizuoka Cancer Center, Shizuoka, Japan
| | - Sumiko Ohnami
- Research Institute of Shizuoka Cancer Center, Shizuoka, Japan
| | - Makoto Arai
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kenichi Urakami
- Research Institute of Shizuoka Cancer Center, Shizuoka, Japan
| | | | - Ken Yamaguchi
- Research Institute of Shizuoka Cancer Center, Shizuoka, Japan
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Reduced penetrance of pathogenic ACMG variants in a deeply phenotyped cohort study and evaluation of ClinVar classification over time. Genet Med 2020; 22:1812-1820. [PMID: 32665702 PMCID: PMC7605437 DOI: 10.1038/s41436-020-0900-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 01/16/2023] Open
Abstract
PURPOSE We studied the penetrance of pathogenically classified variants in an elderly Dutch population from the Rotterdam Study, for which deep phenotyping is available. We screened the 59 actionable genes for which reporting of known pathogenic variants was recommended by the American College of Medical Genetics and Genomics (ACMG), and demonstrate that determining what constitutes a known pathogenic variant can be quite challenging. METHODS We defined "known pathogenic" as classified pathogenic by both ClinVar and the Human Gene Mutation Database (HGMD). In 2628 individuals, we performed exome sequencing and identified known pathogenic variants. We investigated the clinical records of carriers and evaluated clinical events during 25 years of follow-up for evidence of variant pathogenicity. RESULTS Of 3815 variants detected in the 59 ACMG genes, 17 variants were considered known pathogenic. For 14/17 variants the ClinVar classification had changed over time. Of 24 confirmed carriers of these variants, we observed at least one clinical event possibly caused by the variant in only three participants (13%). CONCLUSION We show that the definition of "known pathogenic" is often unclear and should be approached carefully. Additionally variants marked as known pathogenic do not always have clinical impact on their carriers. Definition and classification of true (individual) expected pathogenic impact should be defined carefully.
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Abstract
Autism spectrum disorder (ASD) is a heterogeneous condition affecting >1% of all children, characterized by impaired social interactions, repetitive behavior and a widely variable spectrum of comorbidities. These comorbidities may include developmental delay, gastrointestinal problems, cardiac disorders, immune and autoimmune dysregulation, neurological manifestations (e.g., epilepsy, intellectual disability), and other clinical features. This wide phenotypic heterogeneity is difficult to predict and manifests across a wide range of ages and with a high degree of difference in severity, making disease management and prediction of a successful intervention very difficult. Recently, advances in genomics and other molecular technologies have enabled the study of ASD on a molecular level, illuminating genes and pathways whose perturbations help explain the clinical variability among patients, and whose impairments provide possible opportunities for better treatment options. In fact, there are now >1000 genes that have been linked to ASD through genetic studies of more than 10,000 patients and their families. This chapter discusses these discoveries and in the context of recent developments in genomics and bioinformatics, while also examining the trajectory of gene discovery efforts over the past few decades, as both better ascertainment and global attention have been given to this highly vulnerable patient population.
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Clarke AJ, Wallgren-Pettersson C. Ethics in genetic counselling. J Community Genet 2019; 10:3-33. [PMID: 29949066 PMCID: PMC6325035 DOI: 10.1007/s12687-018-0371-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/15/2018] [Indexed: 12/22/2022] Open
Abstract
Difficult ethical issues arise for patients and professionals in medical genetics, and often relate to the patient's family or their social context. Tackling these issues requires sensitivity to nuances of communication and a commitment to clarity and consistency. It also benefits from an awareness of different approaches to ethical theory. Many of the ethical problems encountered in genetics relate to tensions between the wishes or interests of different people, sometimes even people who do not (yet) exist or exist as embryos, either in an established pregnancy or in vitro. Concern for the long-term welfare of a child or young person, or possible future children, or for other members of the family, may lead to tensions felt by the patient (client) in genetic counselling. Differences in perspective may also arise between the patient and professional when the latter recommends disclosure of information to relatives and the patient finds that too difficult, or when the professional considers the genetic testing of a child, sought by parents, to be inappropriate. The expectations of a patient's community may also lead to the differences in perspective between patient and counsellor. Recent developments of genetic technology permit genome-wide investigations. These have generated additional and more complex data that amplify and exacerbate some pre-existing ethical problems, including those presented by incidental (additional sought and secondary) findings and the recognition of variants currently of uncertain significance, so that reports of genomic investigations may often be provisional rather than definitive. Experience is being gained with these problems but substantial challenges are likely to persist in the long term.
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Affiliation(s)
- Angus J Clarke
- Institute of Medical Genetics, Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, CF14 4XN, UK.
| | - Carina Wallgren-Pettersson
- The Folkhaelsan Department of Medical Genetics, Topeliusgatan, 20 00250, Helsinki, Finland
- The Folkhaelsan Institute of Genetics and the Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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12
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Kim J, Luo W, Wang M, Wegman-Ostrosky T, Frone MN, Johnston JJ, Nickerson ML, Rotunno M, Li SA, Achatz MI, Brodie SA, Dean M, de Andrade KC, Fortes FP, Gianferante M, Khincha P, McMaster ML, McReynolds LJ, Pemov A, Pinheiro M, Santiago KM, Alter BP, Caporaso NE, Gadalla SM, Goldin LR, Greene MH, Loud J, Yang XR, Freedman ND, Gapstur SM, Gaudet MM, Calista D, Ghiorzo P, Fargnoli MC, Nagore E, Peris K, Puig S, Landi MT, Hicks B, Zhu B, Liu J, Sampson JN, Chanock SJ, Mirabello LJ, Morton LM, Biesecker LG, Tucker MA, Savage SA, Goldstein AM, Stewart DR. Prevalence of pathogenic/likely pathogenic variants in the 24 cancer genes of the ACMG Secondary Findings v2.0 list in a large cancer cohort and ethnicity-matched controls. Genome Med 2018; 10:99. [PMID: 30583724 PMCID: PMC6305568 DOI: 10.1186/s13073-018-0607-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Background Prior research has established that the prevalence of pathogenic/likely pathogenic (P/LP) variants across all of the American College of Medical Genetics (ACMG) Secondary Findings (SF) genes is approximately 0.8–5%. We investigated the prevalence of P/LP variants in the 24 ACMG SF v2.0 cancer genes in a family-based cancer research cohort (n = 1173) and in cancer-free ethnicity-matched controls (n = 982). Methods We used InterVar to classify variants and subsequently conducted a manual review to further examine variants of unknown significance (VUS). Results In the 24 genes on the ACMG SF v2.0 list associated with a cancer phenotype, we observed 8 P/LP unique variants (8 individuals; 0.8%) in controls and 11 P/LP unique variants (14 individuals; 1.2%) in cases, a non-significant difference. We reviewed 115 VUS. The median estimated per-variant review time required was 30 min; the first variant within a gene took significantly (p = 0.0009) longer to review (median = 60 min) compared with subsequent variants (median = 30 min). The concordance rate was 83.3% for the variants examined by two reviewers. Conclusion The 115 VUS required database and literature review, a time- and labor-intensive process hampered by the difficulty in interpreting conflicting P/LP determinations. By rigorously investigating the 24 ACMG SF v2.0 cancer genes, our work establishes a benchmark P/LP variant prevalence rate in a familial cancer cohort and controls. Electronic supplementary material The online version of this article (10.1186/s13073-018-0607-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,División de Investigación, Instituto Nacional de Cancerología, 14080, Mexico City, Mexico
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Jennifer J Johnston
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Michael L Nickerson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, 20877, USA
| | - Melissa Rotunno
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shengchao A Li
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Maria I Achatz
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,Centro de Oncologia, Hospital Sirio-Libanes, Sao Paulo, SP, 013050-050, Brazil
| | - Seth A Brodie
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, 20877, USA
| | - Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Fernanda P Fortes
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Matthew Gianferante
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Payal Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Mary L McMaster
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Maisa Pinheiro
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Karina M Santiago
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lynn R Goldin
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Jennifer Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Xiaohong R Yang
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Donato Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa and Genetics of Rare Cancers, IRCCS Ospedale Policinico San Martino, Genoa, Italy
| | | | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Ketty Peris
- Institute of Dermatology, Catholic University - Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clinic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain & Centro de Investigacion Biomedica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Maria Teresa Landi
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Joshua N Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Stephen J Chanock
- Office of the Director, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lisa J Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lindsay M Morton
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, Human Genetics Program National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Alisa M Goldstein
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.
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13
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Rego S, Dagan-Rosenfeld O, Zhou W, Sailani MR, Limcaoco P, Colbert E, Avina M, Wheeler J, Craig C, Salins D, Röst HL, Dunn J, McLaughlin T, Steinmetz LM, Bernstein JA, Snyder MP. High-frequency actionable pathogenic exome variants in an average-risk cohort. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003178. [PMID: 30487145 PMCID: PMC6318774 DOI: 10.1101/mcs.a003178] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 09/10/2018] [Indexed: 12/19/2022] Open
Abstract
Exome sequencing is increasingly utilized in both clinical and nonclinical settings, but little is known about its utility in healthy individuals. Most previous studies on this topic have examined a small subset of genes known to be implicated in human disease and/or have used automated pipelines to assess pathogenicity of known variants. To determine the frequency of both medically actionable and nonactionable but medically relevant exome findings in the general population we assessed the exomes of 70 participants who have been extensively characterized over the past several years as part of a longitudinal integrated multiomics profiling study. We analyzed exomes by identifying rare likely pathogenic and pathogenic variants in genes associated with Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. We then used American College of Medical Genetics (ACMG) guidelines for the classification of rare sequence variants. Additionally, we assessed pharmacogenetic variants. Twelve out of 70 (17%) participants had medically actionable findings in Mendelian disease genes. Five had phenotypes or family histories associated with their genetic variants. The frequency of actionable variants is higher than that reported in most previous studies and suggests added benefit from utilizing expanded gene lists and manual curation to assess actionable findings. A total of 63 participants (90%) had additional nonactionable findings, including 60 who were found to be carriers for recessive diseases and 21 who have increased Alzheimer's disease risk because of heterozygous or homozygous APOE e4 alleles (18 participants had both). Our results suggest that exome sequencing may have considerably more utility for health management in the general population than previously thought.
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Affiliation(s)
- Shannon Rego
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Orit Dagan-Rosenfeld
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - M Reza Sailani
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Patricia Limcaoco
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Elizabeth Colbert
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Monika Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jessica Wheeler
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Colleen Craig
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Denis Salins
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Hannes L Röst
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jessilyn Dunn
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Mobilize Center, Stanford University, Stanford, California 94305, USA
| | - Tracey McLaughlin
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lars M Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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14
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D’Angelo A, Farrelly E, Stevenson D. Neurofibromatosis Type 1 and Polydactyly. CASE REPORTS IN ORTHOPEDIC RESEARCH 2018. [DOI: 10.1159/000494214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a neurocutaneous disorder that can impact the musculoskeletal system. Polydactyly is not a commonly reported skeletal feature in NF1, but the presence of several case reports in the literature raises the question of an association. We report an individual with bilateral postaxial polydactyly of the feet diagnosed with NF1. To investigate whether these findings are coincidental or nonrandom, the prevalence of polydactyly in an NF1 research database and in other reported NF1 cohorts were compared to the prevalence of polydactyly in the general population. The previously documented cases of individuals with NF1 and polydactyly certainly provoke the question of a nonrandom association between these two findings. However, there are conflicting data from the previous reports that looked at the frequency of polydactyly in NF1 populations, and the data from our database point to a coincidental association rather than a nonrandom association. While several reports have suggested a potential mechanism for the co-occurrence of polydactyly and NF1, a concrete association is still not yet well supported and caution should be used in attributing polydactyly to NF1.
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15
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Chen W, Li W, Ma Y, Zhang Y, Han B, Liu X, Zhao K, Zhang M, Mi J, Fu Y, Zhou Z. Secondary findings in 421 whole exome-sequenced Chinese children. Hum Genomics 2018; 12:42. [PMID: 30217213 PMCID: PMC6137878 DOI: 10.1186/s40246-018-0174-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/23/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Variants with known or possible pathogenicity located in genes that are unrelated to primary disease conditions are defined as secondary findings. Secondary findings are not the primary targets of whole exome and genome sequencing (WES/WGS) assay but can be of great practical value in early disease prevention and intervention. The driving force for this study was to investigate the impact of racial difference and disease background on secondary findings. Here, we analyzed secondary findings frequencies in 421 whole exome-sequenced Chinese children who are phenotypically normal or bear congenital heart diseases/juvenile obesity. In total, 421 WES datasets were processed for potential deleterious variant screening. A reference gene list was defined according to the American College of Medical Genetics and Genomics (ACMG) recommendations for reporting secondary findings v2.0 (ACMG SF v2.0). The variant classification was performed according to the evidence-based guidelines recommended by the joint consensus of the ACMG and the Association for Molecular Pathology (AMP). RESULTS Among the 421 WES datasets, we identified 11 known/expected pathogenic variants in 12 individuals, accounting for 2.85% of our samples, which is much higher than the reported frequency in a Caucasian population. In conclusion, secondary findings are not so rare in Chinese children, which means that we should pay more attention to the clinical interpretation of sequencing results.
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Affiliation(s)
- Wen Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wenke Li
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yi Ma
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yujing Zhang
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Bianmei Han
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuewen Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Kun Zhao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Meixian Zhang
- Department of Epidemiology, Capital Institute of Paediatrics, Beijing, China
| | - Jie Mi
- Department of Epidemiology, Capital Institute of Paediatrics, Beijing, China
| | - Yuanyuan Fu
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhou Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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16
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Jain A, Gandhi S, Koshy R, Scaria V. Incidental and clinically actionable genetic variants in 1005 whole exomes and genomes from Qatar. Mol Genet Genomics 2018; 293:919-929. [PMID: 29557500 DOI: 10.1007/s00438-018-1431-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022]
Abstract
Incidental findings in genomic data have been studied in great detail in the recent years, especially from population-scale data sets. However, little is known about the frequency of such findings in ethnic groups, specifically the Middle East, which were not previously covered in global sequencing studies. The availability of whole exome and genome data sets for a highly consanguineous Arab population from Qatar motivated us to explore the incidental findings in this population-scale data. The sequence data of 1005 Qatari individuals were systematically analyzed for incidental genetic variants in the 59 genes suggested by the American College of Medical Genetics and Genomics. We identified four genetic variants which were pathogenic or likely pathogenic. These variants occurred in six individuals, suggesting a frequency of 0.59% in the population, much lesser than that previously reported from European and African populations. Our analysis identified a variant in RYR1 gene associated with Malignant Hyperthermia that has significantly higher frequency in the population compared to global frequencies. Evaluation of the allele frequencies of these variants suggested enrichment in sub-populations, especially in individuals of Sub-Saharan African ancestry. The present study thereby provides the information on pathogenicity and frequency, which could aid in genomic medicine. To the best of our knowledge, this is the first comprehensive analysis of incidental genetic findings in any Arab population and suggests ethnic differences in incidental findings.
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Affiliation(s)
- Abhinav Jain
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology(CSIR-IGIB), Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi, 110025, India
| | - Shrey Gandhi
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology(CSIR-IGIB), Mathura Road, Delhi, 110025, India
| | - Remya Koshy
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology(CSIR-IGIB), Mathura Road, Delhi, 110025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology(CSIR-IGIB), Mathura Road, Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi, 110025, India.
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17
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Natarajan P, Gold NB, Bick AG, McLaughlin H, Kraft P, Rehm HL, Peloso GM, Wilson JG, Correa A, Seidman JG, Seidman CE, Kathiresan S, Green RC. Aggregate penetrance of genomic variants for actionable disorders in European and African Americans. Sci Transl Med 2017; 8:364ra151. [PMID: 27831900 DOI: 10.1126/scitranslmed.aag2367] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/30/2016] [Indexed: 12/21/2022]
Abstract
In populations that have not been selected for family history of disease, it is unclear how commonly pathogenic variants (PVs) in disease-associated genes for rare Mendelian conditions are found and how often they are associated with clinical features of these conditions. We conducted independent, prospective analyses of participants in two community-based epidemiological studies to test the hypothesis that persons carrying PVs in any of 56 genes that lead to 24 dominantly inherited, actionable conditions are more likely to exhibit the clinical features of the corresponding diseases than those without PVs. Among 462 European American Framingham Heart Study (FHS) and 3223 African-American Jackson Heart Study (JHS) participants who were exome-sequenced, we identified and classified 642 and 4429 unique variants, respectively, in these 56 genes while blinded to clinical data. In the same participants, we ascertained related clinical features from the participants' clinical history of cancer and most recent echocardiograms, electrocardiograms, and lipid measurements, without knowledge of variant classification. PVs were found in 5 FHS (1.1%) and 31 JHS (1.0%) participants. Carriers of PVs were more likely than expected, on the basis of incidence in noncarriers, to have related clinical features in both FHS (80.0% versus 12.4%) and JHS (26.9% versus 5.4%), yielding standardized incidence ratios of 6.4 [95% confidence interval (CI), 1.7 to 16.5; P = 7 × 10-4) in FHS and 4.7 (95% CI, 1.9 to 9.7; P = 3 × 10-4) in JHS. Individuals unselected for family history who carry PVs in 56 genes for actionable conditions have an increased aggregated risk of developing clinical features associated with the corresponding diseases.
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Affiliation(s)
- Pradeep Natarajan
- Center for Human Genetic Research, Cardiovascular Research Center, and Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nina B Gold
- Harvard Medical School, Boston, MA 02115, USA.,Boston Children's Hospital, Boston, MA 02115, USA
| | - Alexander G Bick
- Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Heather McLaughlin
- Harvard Medical School, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.,Partners HealthCare Personalized Medicine, Boston, MA 02115, USA
| | - Peter Kraft
- Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Heidi L Rehm
- Harvard Medical School, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.,Partners HealthCare Personalized Medicine, Boston, MA 02115, USA
| | - Gina M Peloso
- Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Adolfo Correa
- Departments of Pediatrics and Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jonathan G Seidman
- Harvard Medical School, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christine E Seidman
- Harvard Medical School, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sekar Kathiresan
- Center for Human Genetic Research, Cardiovascular Research Center, and Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA 02115, USA. .,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Partners HealthCare Personalized Medicine, Boston, MA 02115, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
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18
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Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals. J Hum Genet 2017; 63:213-230. [PMID: 29192238 DOI: 10.1038/s10038-017-0347-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 01/07/2023]
Abstract
Clarifying allele frequencies of disease-related genetic variants in a population is important in genomic medicine; however, such data is not yet available for the Japanese population. To estimate frequencies of actionable pathogenic variants in the Japanese population, we examined the reported pathological variants in genes recommended by the American College of Medical Genetics and Genomics (ACMG) in our reference panel of genomic variations, 2KJPN, which was created by whole-genome sequencing of 2049 individuals of the resident cohort of the Tohoku Medical Megabank Project. We searched for pathogenic variants in 2KJPN for 57 autosomal ACMG-recommended genes responsible for 26 diseases and then examined their frequencies. By referring to public databases of pathogenic variations, we identified 143 reported pathogenic variants in 2KJPN for the 57 ACMG recommended genes based on a classification system. At the individual level, 21% of the individuals were found to have at least one reported pathogenic allele. We then conducted a literature survey to review the variants and to check for evidence of pathogenicity. Our results suggest that a substantial number of people have reported pathogenic alleles for the ACMG genes, and reviewing variants is indispensable for constructing the information infrastructure of genomic medicine for the Japanese population.
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19
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Adam S, Friedman JM. Controversy and debate on clinical genomics sequencing-paper 2: clinical genome-wide sequencing: don't throw out the baby with the bathwater! J Clin Epidemiol 2017; 92:7-10. [PMID: 28916491 DOI: 10.1016/j.jclinepi.2017.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 08/30/2016] [Accepted: 08/24/2017] [Indexed: 09/30/2022]
Abstract
Genome-wide (exome or whole genome) sequencing with appropriate genetic counseling should be considered for any patient with a suspected Mendelian disease that has not been identified by conventional testing. Clinical genome-wide sequencing provides a powerful and effective means of identifying specific genetic causes of serious disease and improving clinical care.
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Affiliation(s)
- Shelin Adam
- Department of Medical Genetics, Children and Women's Hospital, University of British Columbia, 4500 Oak Street, Vancouver, British Columbia V6H 3V4, Canada.
| | - Jan M Friedman
- Department of Medical Genetics, Children and Women's Hospital, University of British Columbia, 4500 Oak Street, Vancouver, British Columbia V6H 3V4, Canada
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20
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Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017. [PMID: 28349240 DOI: 10.1007/s00439‐017‐1779‐6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD ( http://www.hgmd.org ) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.
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Affiliation(s)
- Peter D Stenson
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Hayden
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michelle Hussain
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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21
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Gerhard GS, Bann DV, Broach J, Goldenberg D. Pitfalls of exome sequencing: a case study of the attribution of HABP2 rs7080536 in familial non-medullary thyroid cancer. NPJ Genom Med 2017; 2:8. [PMID: 28884020 PMCID: PMC5584869 DOI: 10.1038/s41525-017-0011-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing using exome capture is a common approach used for analysis of familial cancer syndromes. Despite the development of robust computational algorithms, the accrued experience of analyzing exome data sets and published guidelines, the analytical process remains an ad hoc series of important decisions and interpretations that require significant oversight. Processes and tools used for sequence data generation have matured and are standardized to a significant degree. For the remainder of the analytical pipeline, however, the results can be highly dependent on the choices made and careful review of results. We used primary exome sequence data, generously provided by the corresponding author, from a family with highly penetrant familial non-medullary thyroid cancer reported to be caused by HABP2 rs7080536 to review the importance of several key steps in the application of exome sequencing for discovery of new familial cancer genes. Differences in allele frequencies across populations, probabilities of familial segregation, functional impact predictions, corroborating biological support, and inconsistent replication studies can play major roles in influencing interpretation of results. In the case of HABP2 rs7080536 and familial non-medullary thyroid cancer, these factors led to the conclusion of an association that most data and our re-analysis fail to support, although larger studies from diverse populations will be needed to definitively determine its role.
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Affiliation(s)
- Glenn S. Gerhard
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140 USA
| | | | - James Broach
- Penn State College of Medicine, Hershey, PA 17033 USA
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Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017; 136:665-677. [PMID: 28349240 PMCID: PMC5429360 DOI: 10.1007/s00439-017-1779-6] [Citation(s) in RCA: 912] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.
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Affiliation(s)
- Peter D Stenson
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Hayden
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michelle Hussain
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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23
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Fiallos K, Applegate C, Mathews DJ, Bollinger J, Bergner AL, James CA. Choices for return of primary and secondary genomic research results of 790 members of families with Mendelian disease. Eur J Hum Genet 2017; 25:530-537. [PMID: 28272539 DOI: 10.1038/ejhg.2017.21] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 01/26/2017] [Accepted: 02/01/2017] [Indexed: 01/12/2023] Open
Abstract
Although consensus is building that primary (PR) and secondary findings (SF) from genomic research should be offered to participants under some circumstances, data describing (1) actual choices of study participants and (2) factors associated with these choices are limited, hampering study planning. We conducted a cross-sectional analysis of choices made for return of PR and SF during informed consent by members of the first 247 families (790 individuals) enrolled in the Baylor-Hopkins Center for Mendelian Genomics, a genome sequencing study. Most (619; 78.3%) chose to receive SF and PR, 66 (8.4%) chose PR only, 65 (8.2%) wanted no results, and 40 (5.1%) chose SF only. Choosing SF was associated with an established clinical diagnosis in the proband (87.8 vs 79%, P=0.009) and European ancestry (EA) (87.7 vs 73%, P<0.008). Participants of non-European ancestry (NEA) were as likely as those of EA to choose SF when consented by a genetic counselor (GC) (82% NEA vs 88.3% EA, P=0.09) but significantly less likely when consented by a physician (67.4% NEA vs 85.4% EA, P=0.001). Controlling for proband diagnosis, individuals of NEA were 2.13-fold (95% CI: 1.11-4.08) more likely to choose SF when consented by a GC rather than a physician. Participants of NEA were 3-fold more likely than those of EA to decline all study results (14.7% NEA vs 5.4% EA, P<0.008). In this ethnically diverse population, whereas most participants desired PR and SF, more than 20% declined some or all results, highlighting the importance of research participant choice.
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Affiliation(s)
- Katie Fiallos
- National Human Genome Research Institute, NIH, Bethesda, MD, USA.,Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Carolyn Applegate
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Debra Jh Mathews
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD, USA
| | - Juli Bollinger
- Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD, USA
| | - Amanda L Bergner
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Ambry Genetics, Inc., Aliso Viejo, CA, USA
| | - Cynthia A James
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, USA
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24
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Deep brain stimulation for dystonia: a novel perspective on the value of genetic testing. J Neural Transm (Vienna) 2017; 124:417-430. [PMID: 28160152 DOI: 10.1007/s00702-016-1656-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/16/2016] [Indexed: 10/20/2022]
Abstract
The dystonias are a group of disorders characterized by excessive muscle contractions leading to abnormal movements and postures. There are many different clinical manifestations and underlying causes. Deep brain stimulation (DBS) provides an effect treatment, but outcomes can vary considerably among the different subtypes of dystonia. Several variables are thought to contribute to this variation including age of onset and duration of dystonia, specific characteristics of the dystonic movements, location of stimulation and stimulator settings, and others. The potential contributions of genetic factors have received little attention. In this review, we summarize evidence that some of the variation in DBS outcomes for dystonia is due to genetic factors. The evidence suggests that more methodical genetic testing may provide useful information in the assessment of potential surgical candidates, and in advancing our understanding of the biological mechanisms that influence DBS outcomes.
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25
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Safarova MS, Klee EW, Baudhuin LM, Winkler EM, Kluge ML, Bielinski SJ, Olson JE, Kullo IJ. Variability in assigning pathogenicity to incidental findings: insights from LDLR sequence linked to the electronic health record in 1013 individuals. Eur J Hum Genet 2017; 25:410-415. [PMID: 28145427 DOI: 10.1038/ejhg.2016.193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/14/2016] [Accepted: 11/01/2016] [Indexed: 11/09/2022] Open
Abstract
Knowledge of variant pathogenicity is key to implementing genomic medicine. We describe variability between expert reviewers in assigning pathogenicity to sequence variants in LDLR, the causal gene in the majority of cases of familial hypercholesterolemia. LDLR was sequenced on the Illumina HiSeq platform (average read depth >200 × ) in 1013 Mayo Biobank participants recruited from 2012 to 2013. Variants with a minor allele frequency (MAF) <5% predicted to be functional or referenced in HGMD (Human Gene Mutation Database) or NCBI-ClinVar databases were reviewed. To assign pathogenicity, variant frequency in population data sets, computational predictions, reported observations and patient-level data including electronic health record-based post hoc phenotyping were leveraged. Of 178 LDLR variants passing quality control, 25 were selected for independent review using either an in-house protocol or a disease/gene-specific semi-quantitative framework based on the American College of Medical Genetics and Genomics-recommended lines of evidence. NCBI-ClinVar included interpretations for all queried variants with 74% (14/19) of variants with >1 submitter showing inconsistency in classification and 26% (5/19) appearing with conflicting clinical actionability. The discordance rate (one-step level of disagreement out of five classes in variant interpretation) between the reviewers was 40% (10/25). Two LDLR variants were independently deemed clinically actionable and returnable. Interpretation of LDLR variants was often discordant among ClinVar submitters and between expert reviewers. A quantitative approach based on strength of each predefined criterion in the context of specific genes and phenotypes may yield greater consistency between different reviewers.
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Affiliation(s)
- Maya S Safarova
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Linnea M Baudhuin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erin M Winkler
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michelle L Kluge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
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26
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Ku CS, Cooper DN, Patrinos GP. The Rise and Rise of Exome Sequencing. Public Health Genomics 2016; 19:315-324. [DOI: 10.1159/000450991] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/23/2016] [Indexed: 12/19/2022] Open
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27
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Preuss C, Capredon M, Wünnemann F, Chetaille P, Prince A, Godard B, Leclerc S, Sobreira N, Ling H, Awadalla P, Thibeault M, Khairy P, Samuels ME, Andelfinger G. Family Based Whole Exome Sequencing Reveals the Multifaceted Role of Notch Signaling in Congenital Heart Disease. PLoS Genet 2016; 12:e1006335. [PMID: 27760138 PMCID: PMC5070860 DOI: 10.1371/journal.pgen.1006335] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/31/2016] [Indexed: 11/23/2022] Open
Abstract
Left-ventricular outflow tract obstructions (LVOTO) encompass a wide spectrum of phenotypically heterogeneous heart malformations which frequently cluster in families. We performed family based whole-exome and targeted re-sequencing on 182 individuals from 51 families with multiple affected members. Central to our approach is the family unit which serves as a reference to identify causal genotype-phenotype correlations. Screening a multitude of 10 overlapping phenotypes revealed disease associated and co-segregating variants in 12 families. These rare or novel protein altering mutations cluster predominantly in genes (NOTCH1, ARHGAP31, MAML1, SMARCA4, JARID2, JAG1) along the Notch signaling cascade. This is in line with a significant enrichment (Wilcoxon, p< 0.05) of variants with a higher pathogenicity in the Notch signaling pathway in patients compared to controls. The significant enrichment of novel protein truncating and missense mutations in NOTCH1 highlights the allelic and phenotypic heterogeneity in our pediatric cohort. We identified novel co-segregating pathogenic mutations in NOTCH1 associated with left and right-sided cardiac malformations in three independent families with a total of 15 affected individuals. In summary, our results suggest that a small but highly pathogenic fraction of family specific mutations along the Notch cascade are a common cause of LVOTO. Left-ventricular outflow tract obstructions comprise a group of developmental heart disorders that are genetically and phenotypically heterogeneous, with no single gene accounting for the majority of cases. In order to identify mutations contributing to disease, we selected patients from 51 families with a history of congenital cardiac malformations. We interrogated the entire coding sequences of 106 patients and identified a small but highly pathogenic fraction of mutations that are likely to contribute to disease in 12 families (23.5%). Furthermore, we present a strategy for identifying candidate mutations based on familial segregation in a genetically heterogeneous disorder.
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Affiliation(s)
- Christoph Preuss
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Melanie Capredon
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Florian Wünnemann
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Faculty of Biology, University of Muenster, Muenster, Germany
| | - Philippe Chetaille
- Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l'Université (CHU) de Québec, Quebec City, Québec, Canada
| | - Andrea Prince
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Beatrice Godard
- Omics-Ethics Research Group, Research Institute of Public Health, Université de Montréal, Montréal Québec, Canada
| | - Severine Leclerc
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Nara Sobreira
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Hua Ling
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Maryse Thibeault
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Paul Khairy
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | | | - Mark E. Samuels
- Centre de Recherche CHU Sainte Justine, Université de Montreal, Montréal, Québec, Canada
- Department of Medicine, Université de Montreal, Montréal, Québec, Canada
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- * E-mail:
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28
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Balmaña J, Digiovanni L, Gaddam P, Walsh MF, Joseph V, Stadler ZK, Nathanson KL, Garber JE, Couch FJ, Offit K, Robson ME, Domchek SM. Conflicting Interpretation of Genetic Variants and Cancer Risk by Commercial Laboratories as Assessed by the Prospective Registry of Multiplex Testing. J Clin Oncol 2016; 34:4071-4078. [PMID: 27621404 PMCID: PMC5562435 DOI: 10.1200/jco.2016.68.4316] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose Massively parallel sequencing allows simultaneous testing of multiple genes associated with cancer susceptibility. Guidelines are available for variant classification; however, interpretation of these guidelines by laboratories and providers may differ and lead to conflicting reporting and, potentially, to inappropriate medical management. We describe conflicting variant interpretations between Clinical Laboratory Improvement Amendments-approved commercial clinical laboratories, as reported to the Prospective Registry of Multiplex Testing (PROMPT), an online genetic registry. Methods Clinical data and genetic testing results were gathered from 1,191 individuals tested for inherited cancer susceptibility and self-enrolled in PROMPT between September 2014 and October 2015. Overall, 518 participants (603 genetic variants) had a result interpreted by more than one laboratory, including at least one submitted to ClinVar, and these were used as the final cohort for the current analysis. Results Of the 603 variants, 221 (37%) were classified as a variant of uncertain significance (VUS), 191 (32%) as pathogenic, and 34 (6%) as benign. The interpretation differed among reporting laboratories for 155 (26%). Conflicting interpretations were most frequently reported for CHEK2 and ATM, followed by RAD51C, PALB2, BARD1, NBN, and BRIP1. Among all participants, 56 of 518 (11%) had a variant with conflicting interpretations ranging from pathogenic/likely pathogenic to VUS, a discrepancy that may alter medical management. Conclusions Conflicting interpretation of genetic findings from multiplex panel testing used in clinical practice is frequent and may have implications for medical management decisions.
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Affiliation(s)
- Judith Balmaña
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Laura Digiovanni
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Pragna Gaddam
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Michael F Walsh
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Vijai Joseph
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Zsofia K Stadler
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Katherine L Nathanson
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Judy E Garber
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Fergus J Couch
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Kenneth Offit
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Mark E Robson
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
| | - Susan M Domchek
- Judith Balmaña, Hospital Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Laura Digiovanni, Susan M. Domchek, and Katherine L. Nathanson, University of Pennsylvania, Philadelphia, PA; Pragna Gaddam, Michael F. Walsh, Vijai Joseph, Zsofia K. Stadler, Kenneth Offit, and Mark E. Robson, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Judy E. Garber, Dana-Farber Cancer Institute, Boston, MA; and Fergus J. Couch, Mayo Clinic, Rochester, MN
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29
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Posey JE, Rosenfeld JA, James RA, Bainbridge M, Niu Z, Wang X, Dhar S, Wiszniewski W, Akdemir ZH, Gambin T, Xia F, Person RE, Walkiewicz M, Shaw CA, Sutton VR, Beaudet AL, Muzny D, Eng CM, Yang Y, Gibbs RA, Lupski JR, Boerwinkle E, Plon SE. Molecular diagnostic experience of whole-exome sequencing in adult patients. Genet Med 2016; 18:678-85. [PMID: 26633545 PMCID: PMC4892996 DOI: 10.1038/gim.2015.142] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 08/31/2015] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Whole-exome sequencing (WES) is increasingly used as a diagnostic tool in medicine, but prior reports focus on predominantly pediatric cohorts with neurologic or developmental disorders. We describe the diagnostic yield and characteristics of WES in adults. METHODS We performed a retrospective analysis of consecutive WES reports for adults from a diagnostic laboratory. Phenotype composition was determined using Human Phenotype Ontology terms. RESULTS Molecular diagnoses were reported for 17.5% (85/486) of adults, which is lower than that for a primarily pediatric population (25.2%; P = 0.0003); the diagnostic rate was higher (23.9%) for those 18-30 years of age compared to patients older than 30 years (10.4%; P = 0.0001). Dual Mendelian diagnoses contributed to 7% of diagnoses, revealing blended phenotypes. Diagnoses were more frequent among individuals with abnormalities of the nervous system, skeletal system, head/neck, and growth. Diagnostic rate was independent of family history information, and de novo mutations contributed to 61.4% of autosomal dominant diagnoses. CONCLUSION Early WES experience in adults demonstrates molecular diagnoses in a substantial proportion of patients, informing clinical management, recurrence risk, and recommendations for relatives. A positive family history was not predictive, consistent with molecular diagnoses often revealed by de novo events, informing the Mendelian basis of genetic disease in adults.Genet Med 18 7, 678-685.
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Affiliation(s)
- Jennifer E. Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Jill A. Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Regis A. James
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX
| | - Matthew Bainbridge
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Zhiyv Niu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Xia Wang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Shweta Dhar
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Wojciech Wiszniewski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Zeynep H.C. Akdemir
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Fan Xia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Richard E. Person
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Magdalena Walkiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Chad A. Shaw
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - V. Reid Sutton
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Arthur L. Beaudet
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Donna Muzny
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Christine M. Eng
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Yaping Yang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - James R. Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children’s Hospital, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Human Genetics Center, University of Texas Health Science Center, Houston, TX
| | - Sharon E. Plon
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children’s Hospital, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX
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30
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Recommendations for the integration of genomics into clinical practice. Genet Med 2016; 18:1075-1084. [PMID: 27171546 DOI: 10.1038/gim.2016.17] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/19/2016] [Indexed: 12/21/2022] Open
Abstract
The introduction of diagnostic clinical genome and exome sequencing (CGES) is changing the scope of practice for clinical geneticists. Many large institutions are making a significant investment in infrastructure and technology, allowing clinicians to access CGES, especially as health-care coverage begins to extend to clinically indicated genomic sequencing-based tests. Translating and realizing the comprehensive clinical benefits of genomic medicine remain a key challenge for the current and future care of patients. With the increasing application of CGES, it is necessary for geneticists and other health-care providers to understand its benefits and limitations in order to interpret the clinical relevance of genomic variants identified in the context of health and disease. New, collaborative working relationships with specialists across diverse disciplines (e.g., clinicians, laboratorians, bioinformaticians) will undoubtedly be key attributes of the future practice of clinical genetics and may serve as an example for other specialties in medicine. These new skills and relationships will also inform the development of the future model of clinical genetics training curricula. To address the evolving role of the clinical geneticist in the rapidly changing climate of genomic medicine, two Clinical Genetics Think Tank meetings were held that brought together physicians, laboratorians, scientists, genetic counselors, trainees, and patients with experience in clinical genetics, genetic diagnostics, and genetics education. This article provides recommendations that will guide the integration of genomics into clinical practice.Genet Med 18 11, 1075-1084.
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31
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Maxwell K, Hart S, Vijai J, Schrader K, Slavin T, Thomas T, Wubbenhorst B, Ravichandran V, Moore R, Hu C, Guidugli L, Wenz B, Domchek S, Robson M, Szabo C, Neuhausen S, Weitzel J, Offit K, Couch F, Nathanson K. Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer. Am J Hum Genet 2016; 98:801-817. [PMID: 27153395 DOI: 10.1016/j.ajhg.2016.02.024] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/26/2016] [Indexed: 01/24/2023] Open
Abstract
Sequencing tests assaying panels of genes or whole exomes are widely available for cancer risk evaluation. However, methods for classification of variants resulting from this testing are not well studied. We evaluated the ability of a variant-classification methodology based on American College of Medical Genetics and Genomics (ACMG) guidelines to define the rate of mutations and variants of uncertain significance (VUS) in 180 medically relevant genes, including all ACMG-designated reportable cancer and non-cancer-associated genes, in individuals who met guidelines for hereditary cancer risk evaluation. We performed whole-exome sequencing in 404 individuals in 253 families and classified 1,640 variants. Potentially clinically actionable (likely pathogenic [LP] or pathogenic [P]) versus nonactionable (VUS, likely benign, or benign) calls were 95% concordant with locus-specific databases and Clinvar. LP or P mutations were identified in 12 of 25 breast cancer susceptibility genes in 26 families without identified BRCA1/2 mutations (11%). Evaluation of 84 additional genes associated with autosomal-dominant cancer susceptibility identified LP or P mutations in only two additional families (0.8%). However, individuals from 10 of 253 families (3.9%) had incidental LP or P mutations in 32 non-cancer-associated genes, and 9% of individuals were monoallelic carriers of a rare LP or P mutation in 39 genes associated with autosomal-recessive cancer susceptibility. Furthermore, 95% of individuals had at least one VUS. In summary, these data support the clinical utility of ACMG variant-classification guidelines. Additionally, evaluation of extended panels of cancer-associated genes in breast/ovarian cancer families leads to only an incremental clinical benefit but substantially increases the complexity of the results.
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32
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A Clinician's perspective on clinical exome sequencing. Hum Genet 2016; 135:643-54. [PMID: 27126233 DOI: 10.1007/s00439-016-1662-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/23/2016] [Indexed: 12/22/2022]
Abstract
Clinical exome sequencing has clearly improved our ability as clinicians to identify the cause of a wide variety of disorders. Prior to exome sequencing, a majority of patients with apparent syndromes never received a specific molecular genetic diagnosis despite extensive diagnostic odysseys. Even for those receiving an answer to the question of what caused their disorder, the diagnostic odyssey often spanned years to decades. Determining the particular genetic cause in an individual patient can be challenging due to inherent phenotypic and genetic heterogeneity of disease, technical limitations of testing or both. Blended phenotypes, due to multiple monogenic disorders in the same patient, are true dilemmas for traditional genetic evaluations, but are increasingly being diagnosed through clinical exome sequencing. New sequencing technologies have increased the proportion of patients receiving molecular diagnoses, while significantly shortening the time scale, providing multiple benefits for the health-care team, patient and family.
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Jamuar SS, Kuan JL, Brett M, Tiang Z, Tan WLW, Lim JY, Liew WKM, Javed A, Liew WK, Law HY, Tan ES, Lai A, Ng I, Teo YY, Venkatesh B, Reversade B, Tan EC, Foo R. Incidentalome from Genomic Sequencing: A Barrier to Personalized Medicine? EBioMedicine 2016; 5:211-6. [PMID: 27077130 PMCID: PMC4816806 DOI: 10.1016/j.ebiom.2016.01.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/16/2016] [Accepted: 01/25/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In Western cohorts, the prevalence of incidental findings (IFs) or incidentalome, referring to variants in genes that are unrelated to the patient's primary condition, is between 0.86% and 8.8%. However, data on prevalence and type of IFs in Asian population is lacking. METHODS In 2 cohorts of individuals with genomic sequencing performed in Singapore (total n = 377), we extracted and annotated variants in the 56 ACMG-recommended genes and filtered these variants based on the level of pathogenicity. We then analyzed the precise distribution of IFs, class of genes, related medical conditions, and potential clinical impact. RESULTS We found a total of 41,607 variants in the 56 genes in our cohort of 377 individuals. After filtering for rare and coding variants, we identified 14 potential variants. After reviewing primary literature, only 4 out of the 14 variants were classified to be pathogenic, while an additional two variants were classified as likely pathogenic. Overall, the cumulative prevalence of IFs (pathogenic and likely pathogenic variants) in our cohort was 1.6%. CONCLUSION The cumulative prevalence of IFs through genomic sequencing is low and the incidentalome may not be a significant barrier to implementation of genomics for personalized medicine.
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Affiliation(s)
- Saumya Shekhar Jamuar
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatric Academic Clinical Programme, Singhealth Duke-NUS Graduate Medical School, Singapore
| | - Jyn Ling Kuan
- Genome Institute of Singapore, ASTAR, Singapore; Cardiovascular Research Institute, National University of Singapore, National University Health System, Singapore
| | - Maggie Brett
- KK Research Center, KK Women's and Children's Hospital, Singapore
| | - Zenia Tiang
- Genome Institute of Singapore, ASTAR, Singapore; Cardiovascular Research Institute, National University of Singapore, National University Health System, Singapore
| | - Wilson Lek Wen Tan
- Genome Institute of Singapore, ASTAR, Singapore; Cardiovascular Research Institute, National University of Singapore, National University Health System, Singapore
| | - Jiin Ying Lim
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Wendy Kein Meng Liew
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatric Academic Clinical Programme, Singhealth Duke-NUS Graduate Medical School, Singapore
| | - Asif Javed
- Genome Institute of Singapore, ASTAR, Singapore
| | - Woei Kang Liew
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Hai Yang Law
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatric Academic Clinical Programme, Singhealth Duke-NUS Graduate Medical School, Singapore
| | - Ee Shien Tan
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatric Academic Clinical Programme, Singhealth Duke-NUS Graduate Medical School, Singapore
| | - Angeline Lai
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatric Academic Clinical Programme, Singhealth Duke-NUS Graduate Medical School, Singapore
| | - Ivy Ng
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatric Academic Clinical Programme, Singhealth Duke-NUS Graduate Medical School, Singapore
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | | | | | - Ene Choo Tan
- KK Research Center, KK Women's and Children's Hospital, Singapore
| | - Roger Foo
- Genome Institute of Singapore, ASTAR, Singapore; Cardiovascular Research Institute, National University of Singapore, National University Health System, Singapore
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34
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Souzeau E, Burdon KP, Mackey DA, Hewitt AW, Savarirayan R, Otlowski M, Craig JE. Ethical Considerations for the Return of Incidental Findings in Ophthalmic Genomic Research. Transl Vis Sci Technol 2016; 5:3. [PMID: 26929883 PMCID: PMC4757467 DOI: 10.1167/tvst.5.1.3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 12/25/2022] Open
Abstract
Whole genome and whole exome sequencing technologies are being increasingly used in research. However, they have the potential to identify incidental findings (IF), findings not related to the indication of the test, raising questions regarding researchers' responsibilities toward the return of this information to participants. In this study we discuss the ethical considerations related to the return of IF to research participants, emphasizing that the type of the study matters and describing the current practice standards. There are currently no legal obligations for researchers to return IF to participants, but some viewpoints consider that researchers might have an ethical one to return IF of clinical validity and clinical utility and that are actionable. The reality is that most IF are complex to interpret, especially since they were not the indication of the test. The clinical utility often depends on the participants' preferences, which can be challenging to conciliate and relies on participants' understanding. In summary, in the context of a lack of clear guidance, researchers need to have a clear plan for the disclosure or nondisclosure of IF from genomic research, balancing their research goals and resources with the participants' rights and their duty not to harm.
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Affiliation(s)
- Emmanuelle Souzeau
- Department of Ophthalmology Flinders University, Flinders Medical Centre, Adelaide, Australia
| | - Kathryn P. Burdon
- Department of Ophthalmology Flinders University, Flinders Medical Centre, Adelaide, Australia
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
| | - David A. Mackey
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Alex W. Hewitt
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Australia
| | | | - Jamie E. Craig
- Department of Ophthalmology Flinders University, Flinders Medical Centre, Adelaide, Australia
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35
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Krier JB, Green RC. Management of Incidental Findings in Clinical Genomic Sequencing. ACTA ACUST UNITED AC 2015; 87:9.23.1-9.23.16. [PMID: 26439717 DOI: 10.1002/0471142905.hg0923s87] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genomic sequencing is becoming accurate, fast, and increasingly inexpensive, and is rapidly being incorporated into clinical practice. Incidental or secondary findings, which can occur in large numbers from genomic sequencing, are a potential barrier to the utility of this new technology due to their relatively high prevalence and the lack of evidence or guidelines available to guide their clinical interpretation. This unit reviews the definition, classification, and management of incidental findings from genomic sequencing. The unit focuses on the clinical aspects of handling incidental findings, with an emphasis on the key role of clinical context in defining incidental findings and determining their clinical relevance and utility.
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Affiliation(s)
- Joel B Krier
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Robert C Green
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Broad Institute, Boston, Massachusetts
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36
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Abstract
Incidental findings are the subject of intense ethical debate in medical genomic research. Every human genome contains a number of potentially disease-causing alterations that may be detected during comprehensive genetic analyses to investigate a specific condition. Yet available evidence shows that the frequency of incidental findings in research is much lower than expected. In this Opinion, we argue that the reason for the low level of incidental findings is that the filtering techniques and methods that are applied during the routine handling of genomic data remove these alterations. As incidental findings are systematically filtered out, it is now time to evaluate whether the ethical debate is focused on the right issues. We conclude that the key question is whether to deliberately target and search for disease-causing variations outside the indication that has originally led to the genetic analysis, for instance by using positive lists and algorithms.
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37
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Romdhane L, Messaoud O, Bouyacoub Y, Kerkeni E, Naouali C, Cherif Ben Abdallah L, Tiar A, Charfeddine C, Monastiri K, Chabchoub I, Hachicha M, Tadmouri GO, Romeo G, Abdelhak S. Comorbidity in the Tunisian population. Clin Genet 2015; 89:312-9. [PMID: 26010040 DOI: 10.1111/cge.12616] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/19/2015] [Accepted: 05/17/2015] [Indexed: 12/18/2022]
Abstract
Genetic diseases in the Tunisian population represent a real problem of public health as their spectrum encompasses more than 400 disorders. Their frequency and distribution in the country have been influenced by demographic, economic and social features especially consanguinity. In this article, we report on genetic disease association referred to as comorbidity and discuss factors influencing their expressivity. Seventy-five disease associations have been reported among Tunisian families. This comorbidity could be individual or familial. In 39 comorbid associations, consanguinity was noted. Twenty-one founder and 11 private mutations are the cause of 34 primary diseases and 13 of associated diseases. As the information dealing with this phenomenon is fragmented, we proposed to centralize it in this report in order to draw both clinicians' and researcher's attention on the occurrence of such disease associations in inbred populations as it makes genetic counseling and prenatal diagnosis challenging even when mutations are known.
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Affiliation(s)
- L Romdhane
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Department of Biology, Faculty of Science of Bizerte, Université Tunis Carthage, Zarzouna, Tunisia
| | - O Messaoud
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Y Bouyacoub
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - E Kerkeni
- Laboratoire de Pharmacologie, Faculté de Médecine de Monastir, Université de Monastir, Monastir, Tunisia
| | - C Naouali
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - L Cherif Ben Abdallah
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - A Tiar
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - C Charfeddine
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - K Monastiri
- EPS Fattouma Bourguiba, Centre de Maternité & de Néonatologie de Monastir, Service de Réanimation et de Médecine Néonatale, Monastir, Tunisia
| | - I Chabchoub
- Service de Pédiatrie, CHU Hédi Chaker, Sfax, Tunisia
| | - M Hachicha
- Service de Pédiatrie, CHU Hédi Chaker, Sfax, Tunisia
| | - G O Tadmouri
- Faculty of Public Health, Jinan University, Tripoli, Lebanon
| | - G Romeo
- Dipartimento di Scienze Mediche e Chirurgiche Policlinico Sant'Orsola-Malpighi, Unità Operativa di Genetica Medica, Bologna, Italy
| | - S Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
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