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Mei JY, Platt LD. Reproductive genetic carrier screening in pregnancy: improving health outcomes and expanding access. J Perinat Med 2024; 0:jpm-2024-0059. [PMID: 38924780 DOI: 10.1515/jpm-2024-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
Reproductive genetic carrier screening (RGCS) serves to screen couples for their risk of having children affected by monogenic conditions. The included conditions are mostly autosomal recessive or X-linked with infantile or early-childhood onset. Cystic fibrosis, spinal muscular atrophy, and hemoglobinopathies are now recommended by the American College of Obstetricians and Gynecologists (ACOG) for universal screening. Recommendations for further RGCS remain ethnicity based. The American College of Medical Genetics and Genomics and the National Society of Genetic Counselors in recent years have recommended universal expanded-panel RGCS and moving towards a more equitable approach. ACOG guidelines state that offering RGCS is an acceptable option, however it has not provided clear guidance on standard of care. Positive results on RGCS can significantly impact reproductive plans for couples, including pursuing in vitro fertilization with preimplantation genetic testing, prenatal genetic testing, specific fetal or neonatal treatment, or adoption. RGCS is a superior approach compared to ethnicity-based carrier screening and moves away from single race-based medical practice. We urge the obstetrics and gynecology societies to adopt the guidelines for RGCS put forward by multiple societies and help reduce systemic inequalities in medicine in our new genetic age. Having national societies such as ACOG and the Society for Maternal-Fetal Medicine officially recommend and endorse RGCS would bolster insurance coverage and financial support by employers for RGCS. The future of comprehensive reproductive care in the age of genomic medicine entails expanding access so patients and families can make the reproductive options that best fit their needs.
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Affiliation(s)
- Jenny Y Mei
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, CA, USA
| | - Lawrence D Platt
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, CA, USA
- Center for Fetal Medicine and Women's Ultrasound, Los Angeles, CA, USA
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Capalbo A, de Wert G, Henneman L, Kakourou G, Mcheik S, Peterlin B, van El C, Vassena R, Vermeulen N, Viville S, Forzano F. An ESHG-ESHRE survey on the current practice of expanded carrier screening in medically assisted reproduction. Hum Reprod 2024:deae131. [PMID: 38872341 DOI: 10.1093/humrep/deae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
STUDY QUESTION What is the current practice and views on (expanded) carrier screening ((E)CS) among healthcare professionals in medically assisted reproductive (MAR) practices in Europe? SUMMARY ANSWER The findings show a limited support for ECS with less than half of the respondents affiliated to centres offering ECS, and substantial variation in practice between centres in Europe. WHAT IS KNOWN ALREADY The availability of next-generation sequencing, which enables testing for large groups of genes simultaneously, has facilitated the introduction and expansion of ECS strategies, currently offered particularly in the private sector in the context of assisted reproduction. STUDY DESIGN, SIZE, DURATION A cross-sectional survey evaluating practice and current views among professionals working in MAR practice in different European countries was designed using the online SurveyMonkey tool. The web-based questionnaire included questions on general information regarding the current practice of (E)CS in MAR and questions on what is offered, to whom the test is offered, and how it is offered. It consisted mostly of multiple-choice questions with comment boxes, but also included open questions on the respondents' attitudes/concerns relevant to (E)CS practice, and room to upload requested files (e.g. guidelines and gene panels). In total, 338 responses were collected from 8 February 2022 to 11 April 2022. PARTICIPANTS/MATERIALS, SETTING, METHODS The online survey was launched with an invitation email from the ESHRE central office (n = 4889 emails delivered) and the European Society of Human Genetics (ESHG) central office (n = 1790 emails delivered) sent to the ESHRE and ESHG members, and by social media posts. The survey was addressed to European MAR centres or gamete banks and to centres located in non-European countries participating in the European IVF-monitoring Consortium. Two reminder emails were sent. After exclusion of 39 incomplete responses received (e.g. only background information), 299 respondents from 40 different countries were included for analyses. MAIN RESULTS AND THE ROLE OF CHANCE Overall, 42.5% (127/299) of respondents were affiliated to centres offering ECS. The perceived responsibility to enable prospective parents to make informed reproductive decisions and preventing suffering/burden for parents were the main reasons to offer ECS. A single ECS panel is offered by nearly 45% (39/87 received answers) of the centres offering ECS, 25.3% (22/87) of those centres offer a selection of ECS panels, and 29.9% (26/87) offer whole exome sequencing and a large in silico panel. Different ranges of panel sizes and conditions were included in the ECS panel(s) offered. Most of the respondents (81.8%; 72/88 received answers) indicated that the panels they offer are universal and target the entire population. Pathogenic variants (89.7%; 70/78 received answers), and to a lesser extent, likely pathogenic variants (64.1%%; 50/78 received answers), were included in the ECS report for individuals and couples undergoing MAR with their own gametes. According to 87.9% (80/91 received answers) of the respondents, patients have to pay to undergo an ECS test. Most respondents (76.2%; 61/80 received answers) reported that counselling is provided before and after the ECS test. Preimplantation genetic testing, the use of donor gametes, and prenatal diagnostic testing were the three main reproductive options discussed with identified carrier couples. The main reason, according to the respondents, for not offering ECS in their centre, was the lack of professional recommendations supporting ECS (52.5%; 73/139 received answers) and the high cost for couples or reimbursement not being available (49.6%; 69/139). The challenges and moral dilemmas encountered by the respondents revolved mainly around the content of the offer, including the variants classification and the heterogeneity of the panels, the counselling, and the cost of the test. LIMITATIONS, REASONS FOR CAUTION Although the total number of respondents was acceptable, the completion rate of the survey was suboptimal. In addition, the heterogeneity of answers to open-ended questions and the ambiguity of some of the answers, along with incomplete responses, posed a challenge in interpreting survey results. It is also plausible that some questions were not easily understood by the respondents. For this reason, response and non-response bias are acknowledged as further limitations of the survey. WIDER IMPLICATIONS OF THE FINDINGS The results of this survey could aid in identifying potential challenges or areas for improvement in the current practice of ECS in the MAR field and contribute to the discussion on how to address them. The results underline the need to stimulate a more knowledge-based debate on the complexity and the pros and cons of a possible implementation of ECS in MAR. STUDY FUNDING/COMPETING INTEREST(S) All costs relating to the development process were covered from European Society of Human Reproduction and Embryology and European Society of Human Genetics funds. There was no external funding of the development process or manuscript production. A.C. is full-time employee of Juno Genetics. L.H. declared receiving a research grant during the past 36 months from the Netherlands Organisation for Health Research and Development. She has also participated in a Health Council report of the Netherlands on preconception carrier screening and collaborated with the VSOP Dutch Genetic Alliance (patient umbrella organization on rare and genetic disorders). L.H. and C.v.E. are affiliated with Amsterdam University Medical Centre, a hospital that offers ECS in a non-commercial setting. R.V. received honoraria for presentations from Merck Academy and is unpaid board member of the executive committee of the Spanish Fertility Society. The other authors had nothing to disclose. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Antonio Capalbo
- Department of Reproductive Genetics, Juno Genetics, Rome, Italy
- Unit of Medical Genetics, Centre for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Guido de Wert
- Department of Health, Ethics and Society, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Department of Health, Ethics and Society, CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Georgia Kakourou
- Laboratory of Medical Genetics, Choremio Research Laboratory, National and Kapodistrian University of Athens, "Agia Sophia" Children's Hospital, Athens, Greece
| | | | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Carla van El
- Department of Human Genetics, Amsterdam Public Health Research Institute, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | | | - Stéphane Viville
- Department of Developmental Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Strasbourg, France
- Department of Functional Genomics and Cancer, CNRS UMR 7104-INSERM U1258 Illkrich-Graffenstaden France
- Laboratory of Genetic Diagnostic, Genetics of Infertility Unit (UF3472), Strasbourg University Hospital, Strasbourg, France
| | - Francesca Forzano
- Department of Clinical Genetics, Guy's and St Thomas NHS Foundation Trust, London, UK
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Guha S, Reddi HV, Aarabi M, DiStefano M, Wakeling E, Dungan JS, Gregg AR. Laboratory testing for preconception/prenatal carrier screening: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024:101137. [PMID: 38814327 DOI: 10.1016/j.gim.2024.101137] [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: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 05/31/2024] Open
Abstract
Carrier screening has historically assessed a relatively small number of autosomal recessive and X-linked conditions selected based on frequency in a specific subpopulation and association with severe morbidity or mortality. Advances in genomic technologies enable simultaneous screening of individuals for several conditions. The American College of Medical Genetics and Genomics recently published a clinical practice resource that presents a framework when offering screening for autosomal recessive and X-linked conditions during pregnancy and preconception and recommends a tier-based approach when considering the number of conditions to screen for and their frequency within the US population in general. This laboratory technical standard aims to complement the practice resource and to put forth considerations for clinical laboratories and clinicians who offer preconception/prenatal carrier screening.
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Affiliation(s)
| | - Honey V Reddi
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Mahmoud Aarabi
- UPMC Medical Genetics and Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA; Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | - Jeffrey S Dungan
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
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Wang Y, He Y, Shi Y, Qian DC, Gray KJ, Winn R, Martin AR. Aspiring toward equitable benefits from genomic advances to individuals of ancestrally diverse backgrounds. Am J Hum Genet 2024; 111:809-824. [PMID: 38642557 PMCID: PMC11080611 DOI: 10.1016/j.ajhg.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024] Open
Abstract
Advancements in genomic technologies have shown remarkable promise for improving health trajectories. The Human Genome Project has catalyzed the integration of genomic tools into clinical practice, such as disease risk assessment, prenatal testing and reproductive genomics, cancer diagnostics and prognostication, and therapeutic decision making. Despite the promise of genomic technologies, their full potential remains untapped without including individuals of diverse ancestries and integrating social determinants of health (SDOHs). The NHGRI launched the 2020 Strategic Vision with ten bold predictions by 2030, including "individuals from ancestrally diverse backgrounds will benefit equitably from advances in human genomics." Meeting this goal requires a holistic approach that brings together genomic advancements with careful consideration to healthcare access as well as SDOHs to ensure that translation of genetics research is inclusive, affordable, and accessible and ultimately narrows rather than widens health disparities. With this prediction in mind, this review delves into the two paramount applications of genetic testing-reproductive genomics and precision oncology. When discussing these applications of genomic advancements, we evaluate current accessibility limitations, highlight challenges in achieving representativeness, and propose paths forward to realize the ultimate goal of their equitable applications.
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Affiliation(s)
- Ying Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Yixuan He
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yue Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - David C Qian
- Department of Thoracic Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kathryn J Gray
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Robert Winn
- Virginia Commonwealth University Massey Cancer Center, Richmond, VA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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Wang Y, Sun Y, Meng L, He Q, Zhao J, Zhou R, Wang Z, Tan J, Ma D, Fan L, Chen Y, Wang Y, Jiang Z, Qiao Z, Wu X, Shao B, Xue Y, Song L, Wang T, Hu P, Xu Z. A new strategy for prenatal genetic screening of copy number variations in the DMD gene: A large cohort study based on NIPT analysis. Clin Transl Med 2024; 14:e1706. [PMID: 38797938 PMCID: PMC11128712 DOI: 10.1002/ctm2.1706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Affiliation(s)
- Yan Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | | | - Lulu Meng
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | - Quanze He
- Center for Reproduction and GeneticsThe Affiliated Suzhou Hospital of Nanjing Medical UniversitySuzhou Municipal Hospital, Gusu School, Nanjing Medical UniversitySuzhouChina
| | | | - Ran Zhou
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | | | - Jianxin Tan
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | - Dingyuan Ma
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | | | | | - Yuguo Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | - Zhu Jiang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | | | - Xiaojuan Wu
- Center for Reproduction and GeneticsThe Affiliated Suzhou Hospital of Nanjing Medical UniversitySuzhou Municipal Hospital, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Binbin Shao
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | - Ying Xue
- Center for Reproduction and GeneticsThe Affiliated Suzhou Hospital of Nanjing Medical UniversitySuzhou Municipal Hospital, Gusu School, Nanjing Medical UniversitySuzhouChina
| | | | - Ting Wang
- Center for Reproduction and GeneticsThe Affiliated Suzhou Hospital of Nanjing Medical UniversitySuzhou Municipal Hospital, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Ping Hu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
| | - Zhengfeng Xu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingChina
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Dioun SM, Perez LR, Prabhu M, Brewer JT, Ahsan MD, Hou JY, Sharaf RN, Wright JD, Frey MK. Cost-effectiveness of BRCA1 testing at time of obstetrical prenatal carrier screening for cancer prevention. Am J Obstet Gynecol 2024:S0002-9378(24)00520-9. [PMID: 38621481 DOI: 10.1016/j.ajog.2024.04.014] [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: 01/10/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Improved technologies paired with an increase in access to genetic testing have led to the availability of expanded carrier screening evaluating hundreds of disorders. Currently, most autosomal dominant mutations, such as BRCA1, are not included in expanded carrier assays. Screening pregnant or preconception reproductive-aged women for BRCA1 may present a unique opportunity to perform population-based screening for patients at a time when precancer screening, chemoprevention, and/or risk-reducing surgery may be beneficial. OBJECTIVE This study aimed to inform clinical decision-making as to whether the universal incorporation of BRCA1 testing at the time of obstetrical prenatal carrier screening is cost-effective. STUDY DESIGN A decision analysis and Markov model was created. The initial decision point in the model was BRCA1 testing at the time of expanded carrier screening. Model probabilities, cost, and utility values were derived from published literature. For BRCA1-positive patients, the model simulated breast cancer screening and risk-reducing surgical interventions. A cycle length of 1 year and a time horizon of 47 years were used to simulate the lifespan of patients. The setting was obstetrical clinics in the United States, and the participants were a theoretical cohort of 1,429,074 pregnant patients who annually underwent expanded carrier screening. RESULTS Among our cohort, BRCA1 testing resulted in the identification of an additional 3716 BRCA1-positive patients, the prevention of 1394 breast and ovarian cancer cases, and 1084 fewer deaths. BRCA1 testing was a cost-effective strategy compared with no BRCA1 testing with an incremental cost-effectiveness ratio of $86,001 per quality-adjusted life years. In a 1-way sensitivity analysis, we varied the prevalence of BRCA1 in the population from 0.00% to 20.00% and found that BRCA1 testing continued to be the cost-effective strategy until the prevalence rate was reduced to 0.16%. Multiple additional sensitivity analyses did not substantially affect the cost-effectiveness. CONCLUSION The addition of BRCA1 testing to obstetrical prenatal carrier screening is a cost-effective management strategy to identify at-risk women at a time when cancer screening and preventive strategies can be effective. Despite the burden of additional genetic counseling, prenatal care represents a unique opportunity to implement population-based genetic testing.
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Affiliation(s)
- Shayan M Dioun
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, NY; NewYork-Presbyterian Hospital, New York, NY.
| | | | - Malavika Prabhu
- Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | | | | | - June Y Hou
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, NY; NewYork-Presbyterian Hospital, New York, NY
| | | | - Jason D Wright
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, NY; NewYork-Presbyterian Hospital, New York, NY
| | - Melissa K Frey
- NewYork-Presbyterian Hospital, New York, NY; Weill Cornell Medicine, New York, NY
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Kandolin M, Pöyhönen M, Jakkula E. Estimation of carrier frequencies utilizing the gnomAD database for ACMG recommended carrier screening and Finnish disease heritage conditions in non-Finnish European, Finnish, and Ashkenazi Jewish populations. Am J Med Genet A 2024:e63588. [PMID: 38459613 DOI: 10.1002/ajmg.a.63588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/24/2024] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
American College of Medical Genetics and Genomics (ACMG) recommends offering Tier 3 carrier screening to pregnant patients and those planning a pregnancy for conditions with a carrier frequency of ≥1/200 (96 genes for autosomal recessive [AR] conditions). Certain AR conditions referred to as Finnish disease heritage (FINDIS) have a higher prevalence in Finland than elsewhere. Data from gnomAD v2.1 were extracted to assess carrier frequencies for ACMG-recommended AR and FINDIS AR and X-linked genes in Finnish, non-Finnish European, and Ashkenazi Jewish populations. Following variants were considered: ClinVar pathogenic or likely pathogenic, loss-of-function, and Finnish founder variants. Gene carrier (GCR), cumulative carrier (CCR), and at-risk couple rates (ACR) were estimated. In Finnish population, 47 genes had a GCR of ≥0.5%. CCRs were 52.7% (Finnish), 48.9% (non-Finnish European), and 58.3% (Ashkenazi Jewish), whereas ACRs were 1.4%, 0.93%, and 2.3% respectively. Approximately 141 affected children with analyzed AR conditions are estimated to be born in Finland annually. Eighteen genes causing FINDIS conditions had a GCR of ≥0.5% in the Finnish population but were absent in the ACMG Tier 3 gene list. Two genes (RECQL4 and RMRP) had GCR of ≥0.5% either in non-Finnish Europeans or Ashkenazi Jewish populations. Results highlight the need for careful curation of carrier screening panels.
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Affiliation(s)
- Miska Kandolin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, Diagnostic Center, HUH, Helsinki, Finland
| | - Minna Pöyhönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, Diagnostic Center, HUH, Helsinki, Finland
| | - Eveliina Jakkula
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, Diagnostic Center, HUH, Helsinki, Finland
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Hsu JS, Wu DC, Shih SH, Liu JF, Tsai YC, Lee TL, Chen WA, Tseng YH, Lo YC, Lin HY, Chen YC, Chen JY, Chou TH, Chang DTH, Su MW, Guo WH, Mao HH, Chen CY, Chen PL. Complete genomic profiles of 1496 Taiwanese reveal curated medical insights. J Adv Res 2023:S2090-1232(23)00405-8. [PMID: 38159844 DOI: 10.1016/j.jare.2023.12.018] [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: 08/14/2023] [Revised: 12/03/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
INTRODUCTION The population of Taiwan has a long history of ethno-cultural evolution. The Taiwanese population was isolated from other large populations such as the European, Han Chinese, and Japanese population. The Taiwan Biobank (TWB) project has built a nationwide database, particularly for personal whole-genome sequence (WGS) to facilitate basic and clinical collaboration nationally and internationally, making it one of the most valuable public datasets of the East Asian population. OBJECTIVES This study provides comprehensive medical genomic findings from TWB WGS data, for better characterization of disease susceptibility and the choice of ideal treatment regimens in Taiwanese population. METHODS We reanalyzed 1496 WGS using a PrecisionFDA Truth challenge winner method Sentieon DNAscope. Single nucleotide variants (SNV) and small insertions/deletions (INDEL) were benchmarked. We also analyzed pharmacogenomic (PGx) drug-associated alleles, and copy number variants (CNV). Multiple practicing clinicians reviewed and curated the clinically significant variants. Variant annotations can be browsed at TaiwanGenomes (https://genomes.tw). RESULTS We found that each participant had an average of 6,870.7 globally novel variants and 75.3% (831/1103) of the participants harbored at least one PharmGKB-selected high evidence level human leukocyte antigen (HLA) risk allele. 54 PharmGKB-reported high-level instances of evidence of Cytochrome P450 variant-drug pairs, with a population frequency of over 13.2%. We also identified 23 variants in the ACMG secondary finding V3 gene list from 25 participants, suggesting that 1.67% (25/1496) of the population is harboring at least one medical actionable variant. Our carrier status analyses suggest that one in 25 couples (3.94%) would risk having offspring with at least one pathogenic variant, which is in line with rates found in Japan and Singapore. For pathogenic CNV, we detected 6.88% and 2.02% carrier rates for alpha thalassemia and spinal muscular atrophy, respectively. CONCLUSION Our study highlights the overall medical insights of a complete Taiwanese genomic profile.
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Affiliation(s)
- Jacob Shujui Hsu
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Dung-Chi Wu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Shang-Hung Shih
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Jen-Feng Liu
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Ya-Chen Tsai
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Tung-Lin Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan
| | - Wei-An Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan
| | - Yi-Hsuan Tseng
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Yi-Chung Lo
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan
| | - Hong-Ye Lin
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Chieh Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Jing-Yi Chen
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan
| | - Ting-Hsuan Chou
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Darby Tien-Hao Chang
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan; Digital Technology Division, SinoPac Holdings, Taiwan
| | - Ming Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Wei-Hong Guo
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Hsiang Mao
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Yu Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan.
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Singer A, Aartsma-Rus A, Grinshpun-Cohen J, Sagi-Dain L. Lessons learned from the first national population-based genetic carrier-screening program for Duchenne muscular dystrophy. Genet Med 2023; 25:100981. [PMID: 37712502 DOI: 10.1016/j.gim.2023.100981] [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: 01/20/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
PURPOSE To summarize the results of first year implementation of pan-ethnic screening testing for Duchenne muscular dystrophy (DMD) and present the ensuing challenges. METHODS Data acquisition for this study was performed by retrospective search of Ministry of Health registry for reports of all laboratories performing genetic screening tests. DMD testing was performed by multiplex ligation-dependent probe amplification technology. In case of single-exon deletion, sequencing of the specific exon was performed to rule out underlying single-nucleotide variant. RESULTS Of overall 85,737 DMD tests, 82 clinically significant findings were noted (0.095%, or 1:1,046 women). In addition, 80 findings with uncertain clinical significance were detected (0.093%, or 1:1072), as well as 373 cases (0.4%, or 1:230) of single-exon deletions subsequently identified as false positives because of underlying single-nucleotide variant, mostly variants in exon 8 in North African Jewish population, and in exon 48 in Arab Muslim population. CONCLUSION Interpretation of population-based DMD carrier screening is complex, occasionally requiring additional genetic testing methods and ethical considerations. Multicenter data registry, including ethnic origin and familial segregation in selected cases, is crucial for optimal definition of the results during genetic counseling and informed decisions regarding prenatal testing.
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Affiliation(s)
- Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Lena Sagi-Dain
- Genetics Institute, Carmel Medical Center, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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10
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Souter V, Prigmore B, Becraft E, Repass E, Smart T, Sanapareddy N, Schweitzer M, Ortiz JB, Wang Y, Benn P. Reproductive Carrier Screening Results With Maternal Health Implications During Pregnancy. Obstet Gynecol 2023; 142:1208-1216. [PMID: 37562044 DOI: 10.1097/aog.0000000000005318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 08/12/2023]
Abstract
OBJECTIVE To identify conditions on a reproductive carrier screening panel with the potential for carrier manifestations during pregnancy and review the implications for obstetric care. METHODS This was a retrospective cross-sectional study of consecutive samples from female patients aged 18-55 years submitted to a commercial laboratory for a 274-gene carrier screening panel (January 2020 to September 2022). A literature review was performed to identify genes on the panel with potential for pregnancy complications in carriers. Carrier expression and published recommendations for clinical management were reviewed. RESULTS We identified 12 genes with potential for carrier manifestations during pregnancy based on reports in the literature: nine with manifestations irrespective of the fetal genetic status ( ABCB11 , COL4A3 , COL4A4 , COL4A5 , DMD , F9 , F11 , GLA , and OTC ) and three ( CPT1A , CYP19A1 , and HADHA ) with manifestations only if the fetus is affected by the condition. Manifestations included cardiomyopathy, hemorrhage, gestational hypertensive disorders, cholestasis of pregnancy, acute fatty liver, hyperammonemic crisis, and maternal virilization. Published recommendations for carrier management were identified for 11 of the 12 genes. Of 91,637 tests performed during the study period, a pathogenic or likely pathogenic variant was identified in 2,139 (2.3%), giving a carrier frequency for any of the 12 genes of 1 in 43 (95% CI 1/41-45) 1,826 (2.0%) of the study population were identified as carriers for one of the nine genes with the potential for carrier manifestations irrespective of an affected or unaffected fetus. CONCLUSION Approximately 1 in 40 female patients were identified as carriers for a condition with potential for maternal manifestations in pregnancy, including some serious or even life-threatening complications. Obstetric care professionals should be aware of the possibility of pregnancy complications among carriers and the available recommendations for management. FUNDING SOURCE This study was funded by Natera, Inc.
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Affiliation(s)
- Vivienne Souter
- Natera, Inc., Austin, Texas; and the University of Connecticut Health Center, Farmington, Connecticut
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11
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Benn P. Correspondence on "Maternal carrier screening with single-gene NIPS provides accurate fetal risk assessments for recessive conditions" by Hoskovec et al. Genet Med 2023; 25:100902. [PMID: 37522893 DOI: 10.1016/j.gim.2023.100902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 08/01/2023] Open
Affiliation(s)
- Peter Benn
- Professor Emeritus, Department of Obstetrics and Gynecology, UCONN Health, Farmington, CT.
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12
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Khan A, Petukhova L. Advances Toward the Clinical Translation of Hidradenitis Suppurativa Genetic Studies. JAMA Dermatol 2023; 159:913-915. [PMID: 37494029 DOI: 10.1001/jamadermatol.2023.2205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Affiliation(s)
- Atlas Khan
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York
| | - Lynn Petukhova
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
- Department of Dermatology, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York
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13
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Hoskovec J, Hardisty EE, Talati AN, Carozza JA, Wynn J, Riku S, Ten Bosch JR, Vora NL. Maternal carrier screening with single-gene NIPS provides accurate fetal risk assessments for recessive conditions. Genet Med 2023; 25:100334. [PMID: 36454238 DOI: 10.1016/j.gim.2022.10.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 12/02/2022] Open
Abstract
PURPOSE The purpose of this study was to evaluate the clinical performance of carrier screening for cystic fibrosis, hemoglobinopathies, and spinal muscular atrophy with reflex single-gene noninvasive prenatal screening (sgNIPS), which does not require paternal carrier screening. METHODS An unselected sample of 9151 pregnant individuals from the general US pregnant population was screened for carrier status, of which 1669 (18.2%) were identified as heterozygous for one or more pathogenic variants and reflexed to sgNIPS. sgNIPS results were compared with newborn outcomes obtained from parent survey responses or provider reports for a cohort of 201 pregnancies. RESULTS Overall, 98.7% of pregnant individuals received an informative result (no-call rate = 1.3%), either a negative carrier report or, if identified as heterozygous for a pathogenic variant, a reflex sgNIPS report. In the outcomes cohort, the negative predictive value of sgNIPS was 99.4% (95% CI = 96.0%-99.9%) and average positive predictive value (PPV) of sgNIPS was 48.3% (95% CI = 36.1%-60.1%). Importantly, personalized PPVs accurately reflected the percentage of affected pregnancies in each PPV range, and all pregnancies with a sgNIPS fetal risk of >9 in 10 (90% PPV) were affected. CONCLUSION Although traditional carrier screening is most effective when used to assess reproductive risk before pregnancy, more than 95% of the time it is pursued during a pregnancy and is complicated by incomplete uptake of paternal carrier screening (<50%) and misattributed paternity (∼10%). Even in an idealized setting, when both partners have carrier screening, the maximum risk for having an affected pregnancy is 1 in 4 (equivalent of a 25% PPV). Carrier screening with sgNIPS during pregnancy is an alternative that does not require a paternal sample and provides accurate fetal risk in a timely manner that can be used for prenatal counseling and pregnancy management.
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Affiliation(s)
| | - Emily E Hardisty
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Asha N Talati
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | | | | | | | | | - Neeta L Vora
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
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14
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Reiner J, Rosenblum LS, Xin W, Zhou Z, Zhu H, Leach N. Incidental molecular diagnoses and heterozygous risk alleles in a carrier screening cohort. Genet Med 2023; 25:100317. [PMID: 36459106 DOI: 10.1016/j.gim.2022.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 12/05/2022] Open
Abstract
PURPOSE Expanded pan-ethnic carrier screening is an effective tool for the management of reproductive risk. However, growth in the number of conditions screened, in combination with increasingly more comprehensive test methodologies, can lead to the detection of genetic findings that may affect the health of the tested individual. The objective of this study was to investigate the frequency of pathogenic genotypes in a presumed healthy carrier screening cohort to facilitate broader discussions regarding disclosure of genetic information from carrier screening. METHODS A retrospective analysis of 73,755 targeted carrier screens was performed to identify individuals with pathogenic genotypes and heterozygous risk alleles. RESULTS In this study, we identified 79 individuals (0.11%) with pathogenic genotypes associated with moderate to profound autosomal recessive or X-linked conditions. In addition, 10 cases had chromosome X dosage abnormalities suggestive of a sex chromosome abnormality. Heterozygote risk alleles represented the majority of ancillary findings in this cohort, including 280 female carriers of FMR1 premutation alleles, 15 heterozygous females with pathogenic DMD variants, and 174 heterozygotes with pathogenic variants in genes that may confer increased risk for somatic malignancies in the heterozygous state. CONCLUSION These data suggest that nearly 1% of individuals undergoing carrier screening will have a finding that may require clinical evaluation or surveillance.
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15
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Vintschger E, Kraemer D, Joset P, Horn AHC, Rauch A, Sticht H, Bachmann-Gagescu R. Challenges for the implementation of next generation sequencing-based expanded carrier screening: Lessons learned from the ciliopathies. Eur J Hum Genet 2022:10.1038/s41431-022-01267-8. [PMID: 36550190 PMCID: PMC10400553 DOI: 10.1038/s41431-022-01267-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) can detect carrier status for rare recessive disorders, informing couples about their reproductive risk. The recent ACMG recommendations support offering NGS-based carrier screening (NGS-CS) in an ethnic and population-neutral manner for all genes that have a carrier frequency >1/200 (based on GnomAD). To evaluate current challenges for NGS-CS, we focused on the ciliopathies, a well-studied group of rare recessive disorders. We analyzed 118 ciliopathy genes by whole exome sequencing in ~400 healthy local individuals and ~1000 individuals from the UK1958-birth cohort. We found 20% of healthy individuals (1% of couples) to be carriers of reportable variants in a ciliopathy gene, while 50% (4% of couples) carry variants of uncertain significance (VUS). This large proportion of VUS is partly explained by the limited utility of the ACMG/AMP variant-interpretation criteria in healthy individuals, where phenotypic match or segregation criteria cannot be used. Most missense variants are thus classified as VUS and not reported, which reduces the negative predictive value of the screening test. We show how gene-specific variation patterns and structural protein information can help prioritize variants most likely to be disease-causing, for (future) functional assays. Even when considering only strictly pathogenic variants, the observed carrier frequency is substantially higher than expected based on estimated disease prevalence, challenging the 1/200 carrier frequency cut-off proposed for choice of genes to screen. Given the challenges linked to variant interpretation in healthy individuals and the uncertainties about true carrier frequencies, genetic counseling must clearly disclose these limitations of NGS-CS.
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Affiliation(s)
- Ella Vintschger
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland
| | - Dennis Kraemer
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Anselm H C Horn
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany.,Praeclare Clinical Research Priority Program of the Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland.,Praeclare Clinical Research Priority Program of the Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, 8952, Schlieren, Switzerland. .,Praeclare Clinical Research Priority Program of the Medical Faculty, University of Zurich, Zurich, Switzerland. .,Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
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16
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Abstract
PURPOSE OF REVIEW Prenatal genetic testing can be divided into two categories: screening and diagnostic. This article will focus on reviewing prenatal genetic screening tests. RECENT FINDINGS Cell-free DNA (cfDNA) is a new prenatal genetic screening test with a high degree of accuracy for identifying certain genetic conditions like trisomy 21, 18, and 13. However, cfDNA has also been applied in the screening of other genetic conditions without similar research support. SUMMARY Prenatal genetic screening evaluates at risk pregnancies - including both carrier screening, which can be done at any point in a person's life, and aneuploidy screening, which is done during pregnancy. Within screening, there is a new noninvasive technology that has revolutionized prenatal screening called cfDNA testing. Compared to previous methods, this technology is easier to administer and more accurate for certain genetic conditions. However, cfDNA has also been applied to test for less common genetic conditions without efficacious research support. In this time of expansion in genetic testing, it is important that providers educate themselves on the research support behind each type of genetic test. It is vital that professional organizations continuously update their testing approach to match these rapidly evolving technologies and the patient population they serve.
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17
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The Australian Reproductive Genetic Carrier Screening Project (Mackenzie's Mission): Design and Implementation. J Pers Med 2022; 12:jpm12111781. [PMID: 36579509 PMCID: PMC9698511 DOI: 10.3390/jpm12111781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 01/01/2023] Open
Abstract
Reproductive genetic carrier screening (RGCS) provides people with information about their chance of having children with autosomal recessive or X-linked genetic conditions, enabling informed reproductive decision-making. RGCS is recommended to be offered to all couples during preconception or in early pregnancy. However, cost and a lack of awareness may prevent access. To address this, the Australian Government funded Mackenzie’s Mission—the Australian Reproductive Genetic Carrier Screening Project. Mackenzie’s Mission aims to assess the acceptability and feasibility of an easily accessible RGCS program, provided free of charge to the participant. In study Phase 1, implementation needs were mapped, and key study elements were developed. In Phase 2, RGCS is being offered by healthcare providers educated by the study team. Reproductive couples who provide consent are screened for over 1200 genes associated with >750 serious, childhood-onset genetic conditions. Those with an increased chance result are provided comprehensive genetic counseling support. Reproductive couples, recruiting healthcare providers, and study team members are also invited to complete surveys and/or interviews. In Phase 3, a mixed-methods analysis will be undertaken to assess the program outcomes, psychosocial implications and implementation considerations alongside an ongoing bioethical analysis and a health economic evaluation. Findings will inform the implementation of an ethically robust RGCS program.
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18
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Zhang K, Lin G, Li J. Carrier screening: An update. Clin Chim Acta 2022; 535:92-98. [PMID: 35973610 DOI: 10.1016/j.cca.2022.08.015] [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: 06/01/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022]
Abstract
Genetic carrier screening (CS) for reproductive decision making was introduced 50 years ago. Technological advances and improvements in knowledge of the human genome makes multi-disease, pan-ethnic CS possible. Such screening will identify most individuals as carriers of at least one autosomal recessive or X-linked recessive disorder. Past experiences and best practices have provided a framework for CS. Although its clinical utilization is increasing, some challenges remain. In this study, several aspects of CS panel implementation have been addressed including how to evaluate the quantitative gene inclusion criteria, how to classify the severity of genetic conditions, how to understand clinical validity at the level of gene-disease association and variant classification, and how to minimize residual risks.
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Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China.
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19
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Guidelines for Cystic Fibrosis Carrier Screening in the Prenatal/Preconception Period. Obstet Gynecol Surv 2022; 77:606-610. [DOI: 10.1097/ogx.0000000000001062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Vaidyanathan S, Trumbull AM, Bar L, Rao M, Yu Y, Sellers ZM. CFTR genotype analysis of Asians in international registries highlights disparities in the diagnosis and treatment of Asian patients with cystic fibrosis. Genet Med 2022; 24:2180-2186. [PMID: 35857025 DOI: 10.1016/j.gim.2022.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022] Open
Abstract
PURPOSE Cystic fibrosis (CF) is not well-characterized in Asians, potentially resulting in delayed diagnosis and poor prognosis. We characterized CF in Asian subgroups to address these disparities. METHODS De-identified ethnicity and CFTR variant data were obtained from the United States, United Kingdom, and Canadian CF registries. We measured the prevalence of CF, CFTR variant allele frequencies, effectiveness of screening panels, and eligibility for modulator therapies. RESULTS The prevalence of CF was 1 in 74,982 people (Canada) to 1 in 13,340 people (United Kingdom) for South Asians and 1 in 256,541 (Canada) to 1 in 52,563 (United Kingdom) for other Asians, suggesting 26,000 to 146,000 patients with CF in South Asia. p.(F508del) variant was markedly less frequent in Asians than in non-Hispanic Whites. Splicing and nonsense variants occurred at high allelic frequencies in Asians, resulting in 41% to 49% of South Asians and 21% to 39% of other Asians being ineligible for CFTR modulator therapies. Hologic/EU2v1 panels failed to identify 37% to 47% of South Asian and 23% to 46% of other Asian patients with CF. CONCLUSIONS Among Asians, CF appears to be more common in South Asians. A significant CF population may exist in South Asia. CFTR variants in South and other Asians markedly differ from non-Hispanic Whites causing inequities in newborn screening, diagnosis, and treatment. New strategies are necessary to mitigate these health care disparities.
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Affiliation(s)
| | | | - Lilly Bar
- Center for Asian Health Research and Education, Stanford University, Stanford, CA
| | - Manaeha Rao
- Center for Asian Health Research and Education, Stanford University, Stanford, CA
| | - Yunnan Yu
- Center for Asian Health Research and Education, Stanford University, Stanford, CA
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21
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Goddard KAB, Lee K, Buchanan AH, Powell BC, Hunter JE. Establishing the Medical Actionability of Genomic Variants. Annu Rev Genomics Hum Genet 2022; 23:173-192. [PMID: 35363504 PMCID: PMC10184682 DOI: 10.1146/annurev-genom-111021-032401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Actionability is an important concept in medicine that does not have a well-accepted standard definition, nor is there a general consensus on how to establish it. Medical actionability is often conflated with clinical utility, a related but distinct concept. This lack of clarity contributes to practice variation and inconsistent coverage decisions in genomic medicine, leading to the potential for systematic bias in the use of evidence-based interventions. We clarify how medical actionability and clinical utility are distinct and then discuss the spectrum of actionability, including benefits for the person, the family, and society. We also describe applications across the life course, including prediction, diagnosis, and treatment. Current challenges in assessing the medical actionability of identified genomic variants include gaps in the evidence, limited contexts with practice guidelines, and subjective aspects of medical actionability. A standardized and authoritative assessment of medical actionability is critical to implementing genomic medicine in a fashion that improves population health outcomes and reduces health disparities. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Kristy Lee
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Adam H Buchanan
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Bradford C Powell
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
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22
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Current Updates on Expanded Carrier Screening: New Insights in the Omics Era. Medicina (B Aires) 2022; 58:medicina58030455. [PMID: 35334631 PMCID: PMC8951681 DOI: 10.3390/medicina58030455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic carrier screening has been successfully used over the last decades to identify individuals at risk of transmitting specific DNA variants to their newborns, thus having an affected child. Traditional testing has been offered based on familial and/or ethnic backgrounds. The development of high-throughput technologies, such as next-generations sequencing, able to allow the study of large genomic regions in a time and cost-affordable way, has moved carrier screening toward a more comprehensive and extensive approach, i.e., expanded carrier screening (ECS). ECS simultaneously analyses several disease-related genes and better estimates individuals’ carrier status. Indeed, it is not influenced by ethnicity and is not limited to a subset of mutations that may arise from poor information in some populations. Moreover, if couples carry out ECS before conceiving a baby, it allows them to obtain a complete estimation of their genetic risk and the possibility to make an informed decision regarding their reproductive life. Despite these advantages, some weakness still exists regarding, for example, the number of genes and the kind of diseases to be analyzed and the interpretation and communication of the obtained results. Once these points are fixed, it is expectable that ECS will become an ever more frequent practice in clinical settings.
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23
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Ramdaney A, Lichten L, Propst L, Mann C, Lazarin GA, Jones M, Taylor A, Malinowski J. Expanded carrier screening in the United States: A systematic evidence review exploring client and provider experiences. J Genet Couns 2022; 31:937-948. [PMID: 35212439 DOI: 10.1002/jgc4.1566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 11/08/2022]
Abstract
The aim of carrier screening is to identify prospective parents at risk of having a pregnancy affected with an autosomal recessive or X-linked disorder. Though minimal guideline-based screening is available, expanded carrier screening (ECS) is quickly becoming a feasible option for the general population due to its growing availability and affordability. However, the impact of ECS on clients and providers remains relatively unexplored. We performed a systematic evidence review to identify publications describing client-, provider-, and test-related outcomes. We searched several biomedical databases for articles published between January 1, 2003 and May 31, 2021. Studies were eligible for inclusion if they described genetic counseling and/or genetic testing for carrier screening (minimal guideline-based or ECS) in a prenatal or preconception setting in the United States. Title and abstract screening were performed using the Raayan web application or customized Google Forms. Full-text review and data extraction of included articles were performed using custom Google Forms. Two researchers performed a multistep selection process independently for validation purposes. Of 5413 unique articles screened, 36 studies were included with several studies contributing to multiple outcomes. Twenty described outcomes relating to patients/clients, 10 described provider-based outcomes, and 16 described test-based outcomes. Findings suggest that client and provider perceptions of ECS and minimal guideline-based carrier screening are multifaceted. Though clients have expressed desire for ECS, clinical uptake and impact on reproductive decision-making varies. Additionally, though genetic counselors seem to be comfortable with ECS, most other reproductive care providers seem to prefer minimal guideline or ancestry-based screening due to perceived barriers, such as time needed for ECS results disclosure and follow-up, as well as the desire to have panels set by professional societies/recommendations. There are limitations within the gathered literature, leading to potential uncertainty in the generalizability of our review. We outline several recommendations for future studies, including the need to examine variant interpretation and use of next-generation sequencing.
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Affiliation(s)
- Aarti Ramdaney
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lauren Lichten
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Caitlin Mann
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Malorie Jones
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Amy Taylor
- Houston Methodist Hospital, Houston, Texas, USA
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24
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Addressing Reproductive Healthcare Disparities through Equitable Carrier Screening: Medical Racism and Genetic Discrimination in United States’ History Highlights the Needs for Change in Obstetrical Genetics Care. SOCIETIES 2022. [DOI: 10.3390/soc12020033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Carrier screening, a nearly half-century old practice, aims to provide individuals and couples with information about their risk of having children with serious genetic conditions. Traditionally, the conditions for which individuals were offered screening depended on their self-reported race or ethnicity and which conditions were seen commonly in that population. This process has led to disparities and inequities in care as the multi-racial population in the U.S. has grown exponentially, yet databases used to determine clinical practice guidelines are made up of primarily White cohorts. Technological advancements now allow for pan-ethnic expanded carrier screening (ECS), which screens for many conditions regardless of self-reported race or ethnicity. ECS presents a unique opportunity to promote equitable genetic testing practices in reproductive medicine. However, this goal can only be achieved if we acknowledge and appreciate the innumerable inequities evidenced in reproductive medicine and other socio-legal practices in the United States, and if we intentionally work in concert with healthcare providers, policy makers, advocates, and community health champions to reduce current and future reproductive health disparities. Herein, we provide a brief review of the way that US medical racism and genetic discrimination has shaped the current landscape of carrier screening.
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Owens KM, Terhaar C, Zdrodowski J, Johnson LR, Eveleigh D. Refining reproductive risk for FMR1 premutation carriers in the general obstetric population. Am J Med Genet A 2022; 188:1476-1481. [PMID: 35129870 DOI: 10.1002/ajmg.a.62666] [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: 03/08/2021] [Revised: 08/31/2021] [Accepted: 01/06/2022] [Indexed: 11/08/2022]
Abstract
Female FMR1 premutation (FMR1 PM) carriers for fragile X syndrome (FXS) are at risk to have a child with FXS based on their CGG repeat size and AGG interruption number. Studies examining this risk in unselected populations of female PM carriers are lacking. This retrospective cohort study analyzed carrier status, CGG repeat length, AGG interruption result, and reproductive risk refinement in a population of female patients who underwent routine carrier screening for FXS. A total of 1536 PM carriers (0.43%) were identified, 95% of whom had between 55 and 90 CGG repeats. A number of 1334 carriers underwent AGG interruption testing. The majority had at least one AGG interruption and received a lower reproductive risk for FXS following AGG interruption testing (89% and 85%, respectively) as compared to their risk calculated based on CGG repeat size alone. The average change in risk across the population following AGG interruption testing was -3.4%, with a range from -50.8% to 48.9%. This article describes the range of CGG repeats and AGG interruptions in an unselected population of female PM carriers and suggests that most carriers would benefit from AGG interruption testing to refine their reproductive risk of having a child with FXS.
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Next generation sequencing is a highly reliable method to analyze exon 7 deletion of survival motor neuron 1 (SMN1) gene. Sci Rep 2022; 12:223. [PMID: 34997153 PMCID: PMC8741787 DOI: 10.1038/s41598-021-04325-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common and severe genetic diseases. SMA carrier screening is an effective way to identify couples at risk of having affected children. Next-generation sequencing (NGS)-based expanded carrier screening could detect SMN1 gene copy number without extra experiment and with high cost performance. However, its performance has not been fully evaluated. Here we conducted a systematic comparative study to evaluate the performance of three common methods. 478 samples were analyzed with multiplex ligation probe amplification (MLPA), real-time quantitative polymerase chain reaction (qPCR) and NGS, simultaneously. Taking MLPA-based results as the reference, for 0 copy, 1 copy and ≥ 2 copy SMN1 analysis with NGS, the sensitivity, specificity and precision were all 100%. Using qPCR method, the sensitivity was 100%, 97.52% and 94.30%, respectively; 98.63%, 95.48% and 100% for specificity; and 72.72%, 88.72% and 100% for precision. NGS repeatability was higher than that of qPCR. Moreover, among three methods, NGS had the lowest retest rate. Thus, NGS is a relatively more reliable method for SMN1 gene copy number detection. In expanded carrier screening, compared with the combination of multiple methods, NGS method could reduce the test cost and simplify the screening process.
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Morgenstern-Kaplan D, Raijman-Policar J, Majzner-Aronovich S, Aradhya S, Pineda-Alvarez DE, Aguinaga M, García-Vences EE. Carrier screening in the Mexican Jewish community using a pan-ethnic expanded carrier screening NGS panel. Genet Med 2021; 24:821-830. [PMID: 34961661 DOI: 10.1016/j.gim.2021.11.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE The Mexican Jewish community (MJC) is a previously uncharacterized, genetically isolated group composed of Ashkenazi and Sephardi-Mizrahi Jews who migrated in the early 1900s. We aimed to determine the heterozygote frequency of disease-causing variants in 302 genes in this population. METHODS We conducted a cross-sectional study of the MJC involving individuals representing Ashkenazi Jews, Sephardi-Mizrahi Jews, or mixed-ancestry Jews. We offered saliva-based preconception pan-ethnic expanded carrier screening, which examined 302 genes. We analyzed heterozygote frequencies of pathogenic/likely pathogenic variants and compared them with those in the Genome Aggregation Database (gnomAD). RESULTS We recruited 208 participants. The carrier screening results showed that 72.1% were heterozygous for at least 1 severe disease-causing variant in 1 of the genes analyzed. The most common genes with severe disease-causing variants were CFTR (16.8% of participants), MEFV (11.5%), WNT10A (6.7%), and GBA (6.7%). The allele frequencies were compared with those in the gnomAD; 85% of variant frequencies were statistically different from those found in gnomAD (P <.05). Finally, 6% of couples were at risk of having a child with a severe disorder. CONCLUSION The heterozygote frequency of at least 1 severe disease-causing variant in the MJC was 72.1%. The use of carrier screening in the MJC and other understudied populations could help parents make more informed decisions.
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Affiliation(s)
- Dan Morgenstern-Kaplan
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico.
| | - Jaime Raijman-Policar
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico
| | - Sore Majzner-Aronovich
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico
| | | | | | - Mónica Aguinaga
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico; Sexual and Reproductive Health Department, National Institute of Perinatology, Mexico City, Mexico
| | - Edna Elisa García-Vences
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico
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Systematic review of outcomes in studies of reproductive genetic carrier screening: Towards development of a core outcome set. Genet Med 2021; 24:1-14. [PMID: 34906455 DOI: 10.1016/j.gim.2021.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/09/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Current practice recommendations support the widespread implementation of reproductive genetic carrier screening (RGCS). These consensus-based recommendations highlight a research gap, with findings from current studies being insufficient to meet the standard required for more rigorous evidence-based recommendations. This systematic review assessed methodological aspects of studies on RGCS to inform the need for a core outcome set. METHODS We conducted a systematic search to identify peer-reviewed published studies offering population-based RGCS. Study designs, outcomes, and measurement methods were extracted. A narrative synthesis was conducting using an existing outcome taxonomy and criteria used in the evaluation of genetic screening programs as frameworks. RESULTS Sixty-five publications were included. We extracted 120 outcomes representing 24 outcome domains. Heterogeneity in outcome selection, measurement methods and time points of assessment was extensive. Quality appraisal raised concerns for bias. We found that reported outcomes had limited applicability to criteria used to evaluate genetic screening programs. CONCLUSION Despite a large body of literature, diverse approaches to research have limited the conclusions that can be cumulatively drawn from this body of evidence. Consensus regarding meaningful outcomes for evaluation of RGCS would be a valuable first step in working towards evidence-based practice recommendations, supporting the development of a core outcome set.
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Johansen Taber K, Ben-Shachar R, Torres R, Arjunan A, Muzzey D, Kaseniit KE, Goldberg J, Brown H. A guidelines-consistent carrier screening panel that supports equity across diverse populations. Genet Med 2021; 24:201-213. [PMID: 34906503 DOI: 10.1016/j.gim.2021.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/25/2021] [Accepted: 09/13/2021] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The American College of Obstetricians and Gynecologists (ACOG) and the American College of Medical Genetics and Genomics (ACMG) suggest carrier screening panel design criteria intended to ensure meaningful results. This study used a data-driven approach to interpret the criteria to identify guidelines-consistent panels. METHODS Carrier frequencies in >460,000 individuals across 11 races/ethnicities were used to assess carrier frequency. Other criteria were interpreted on the basis of published data. A total of 176 conditions were then evaluated. Stringency thresholds were set as suggested by ACOG and/or ACMG or by evaluating conditions already recommended by ACOG and ACMG. RESULTS Forty and 75 conditions had carrier frequencies of ≥1 in 100 and ≥1 in 200, respectively; 175 had a well-defined phenotype; and 165 met at least 1 severity criterion and had an onset early in life. Thirty-seven conditions met conservative thresholds, including a carrier frequency of ≥1 in 100, and 74 conditions met permissive thresholds, including a carrier frequency of ≥1 in 200; thus, both were identified as guidelines-consistent panels. CONCLUSION Clear panel design criteria are needed to ensure quality and consistency among carrier screening panels. Evidence-based analyses of criteria resulted in the identification of guidelines-consistent panels of 37 and 74 conditions.
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Affiliation(s)
| | - Rotem Ben-Shachar
- Department of Clinical Development, Myriad Genetics, Inc, Salt Lake City, UT
| | - Raul Torres
- Department of Clinical Development, Myriad Genetics, Inc, Salt Lake City, UT
| | - Aishwarya Arjunan
- Department of Medical Affairs, Myriad Women's Health, Inc, South San Francisco, CA
| | - Dale Muzzey
- Department of Research and Development, Myriad Genetics, Inc, Salt Lake City, UT
| | - Kristjan E Kaseniit
- Department of Clinical Development, Myriad Genetics, Inc, Salt Lake City, UT
| | - James Goldberg
- Department of Medical Affairs, Myriad Women's Health, Inc, South San Francisco, CA
| | - Haywood Brown
- Department of Obstetrics & Gynecology, Morsani College of Medicine, University of South Florida, Tampa, FL
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Leonard SJ. Reproductive genetic screening for information: evolving paradigms? J Perinat Med 2021; 49:998-1002. [PMID: 34448384 DOI: 10.1515/jpm-2021-0353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 12/26/2022]
Abstract
Reproductive genetic screening has introduced the possibility for pregnant women to learn, during the pregnancy or sometimes earlier, about the likelihood of their baby being affected with certain genetic conditions. As medicine progresses, the options afforded by this early information have expanded. This has led to a shifting paradigm in prenatal screening, wherein the early knowledge is seen as useful not solely for its inherent value to the pregnant woman, but also as enabling an expansion of conditions whose identification may allow early intervention and clinical impact. This article discusses this paradigm against the backdrop of prenatal genetic screening that is available today.
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Bennett RL, Malleda NR, Byers PH, Steiner RD, Barr KM. Genetic counseling and screening of consanguineous couples and their offspring practice resource: Focused Revision. J Genet Couns 2021; 30:1354-1357. [PMID: 34309119 DOI: 10.1002/jgc4.1477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/08/2022]
Abstract
There are no evidence-based guidelines to inform genetic counseling for consanguineous couples and their offspring. This focused revision builds on the expert opinions from the original publication of "Genetic Counseling and Screening of Consanguineous Couples and Their Offspring," based on a review of literature published since 2002.
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Affiliation(s)
- Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Peter H Byers
- Department of Laboratory Medicine and Pathology, Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington, USA
| | - Robert D Steiner
- Marshfield Clinic Health System, Prevention Genetics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Kimberly M Barr
- Department of Genetics, Kaiser Permanente Medical Center, San Francisco, California, USA
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Clarke JL. Impact of Pan-Ethnic Expanded Carrier Screening in Improving Population Health Outcomes: Proceedings from a Multi-Stakeholder Virtual Roundtable Summit, June 25, 2020. Popul Health Manag 2021; 24:622-630. [PMID: 34142856 DOI: 10.1089/pop.2021.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Janice L Clarke
- Jefferson College of Population Health, Philadelphia, Pennsylvania, USA
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Guo Q, Chang YY, Huang CH, Hsiao YS, Hsiao YC, Chiu IF, Zhou Y, Zhang H, Ko TM. Population-based carrier screening and prenatal diagnosis of fragile X syndrome in East Asian populations. J Genet Genomics 2021; 48:1104-1110. [PMID: 34412977 DOI: 10.1016/j.jgg.2021.04.012] [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: 01/21/2021] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
Identification of carriers of fragile X syndrome (FXS) with the subsequent prenatal diagnosis and knowledge of FXS-associated genetic profiles are essential for intervention in specific populations. We report the results of carrier screening of 39,458 East Asian adult women and prenatal diagnosis from 87 FXS carriers. The prevalence of FXS carriers and full mutation fetuses was estimated to be 1/581 and 1/3124 in East Asian populations, respectively. We confirmed the validity of the current threshold of CGG trinucleotide repeats for FMR1 categorization; the integral risks of full mutation expansion were approximately 6.0%, 43.8%, and 100% for premutation alleles with 55-74, 75-89, and ≥90 CGG repeats, respectively. The protective effect of AGG (adenine-guanine-guanine nucleotides) interruption in East Asian populations was validated, which is important in protecting premutation alleles with 75-89 CGG repeats from full mutation expansion. Finally, family history was shown not an effective indicator for FXS carrier screening in East Asian populations, and population-based screening was more cost-effective. This study provides an insight into the largest carrier screening and prenatal diagnosis for FXS in East Asian populations to date. The FXS-associated genetic profiles of East Asian populations are delineated, and population-based carrier screening is shown to be promising for FXS intervention.
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Affiliation(s)
- Qiwei Guo
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361102, China.
| | - Yih-Yuan Chang
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei 100, Taiwan, China
| | - Chien-Hao Huang
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei 100, Taiwan, China
| | - Yu-Shan Hsiao
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei 100, Taiwan, China
| | - Yu-Chiao Hsiao
- Biofast Biotechnology Co., Ltd., Xiamen, Fujian 361102, China
| | - I-Fan Chiu
- Biofast Biotechnology Co., Ltd., Xiamen, Fujian 361102, China
| | - Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361102, China
| | - Haixia Zhang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361102, China
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei 100, Taiwan, China.
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Milligan JN, Larson JL, Filipovic-Sadic S, Laosinchai-Wolf W, Huang YW, Ko TM, Abbott KM, Lemmink HH, Toivonen M, Schleutker J, Gentile C, Van Deerlin VM, Zhu H, Latham GJ. Multisite Evaluation and Validation of a Sensitive Diagnostic and Screening System for Spinal Muscular Atrophy that Reports SMN1 and SMN2 Copy Number, along with Disease Modifier and Gene Duplication Variants. J Mol Diagn 2021; 23:753-764. [PMID: 33798739 DOI: 10.1016/j.jmoldx.2021.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 11/24/2022] Open
Abstract
Spinal muscular atrophy is a severe autosomal recessive disease caused by disruptions in the SMN1 gene. The nearly identical SMN2 gene copy number is associated with disease severity. SMN1 duplication markers, such as c.∗3+80T>G and c.∗211_∗212del, can assess residual carrier risk. An SMN2 disease modifier (c.859G>C) can help inform prognostic outcomes. The emergence of multiple precision gene therapies for spinal muscular atrophy requires accurate and rapid detection of SMN1 and SMN2 copy numbers to enable early treatment and optimal patient outcomes. We developed and evaluated a single-tube PCR/capillary electrophoresis assay system that quantifies SMN1/2 copy numbers and genotypes three additional clinically relevant variants. Analytical validation was performed with human cell lines and whole blood representing varying SMN1/2 copies on four capillary electrophoresis instrument models. In addition, four independent laboratories used the assay to test 468 residual clinical genomic DNA samples. The results were ≥98.3% concordant with consensus SMN1/2 exon 7 copy numbers, determined using multiplex ligation-dependent probe amplification and droplet digital PCR, and were 100% concordant with Sanger sequencing for the three variants. Furthermore, copy number values were 98.6% (SMN1) and 97.1% (SMN2) concordant to each laboratory's own reference results.
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Affiliation(s)
| | | | | | | | - Ya-Wen Huang
- GenePhile Bioscience Laboratory, Ko's Obstetrics and Gynecology Clinic, Taipei City, Taiwan
| | - Tsang-Ming Ko
- GenePhile Bioscience Laboratory, Ko's Obstetrics and Gynecology Clinic, Taipei City, Taiwan
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Henny H Lemmink
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Minna Toivonen
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | - Johanna Schleutker
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland; Institute of Biomedicine, University of Turku, Turun yliopisto, Finland
| | - Caren Gentile
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Huiping Zhu
- Research and Development, Asuragen Inc., Austin, Texas
| | - Gary J Latham
- Research and Development, Asuragen Inc., Austin, Texas
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Arjunan A, Torres R, Gardiner A, Kaseniit KE, Wootton J, Ben-Shachar R, Johansen Taber K. Evaluating the efficacy of three carrier screening workflows designed to identify at-risk carrier couples. Prenat Diagn 2021; 41:896-904. [PMID: 33450092 PMCID: PMC8248057 DOI: 10.1002/pd.5900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/21/2020] [Accepted: 12/31/2020] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To evaluate the efficacy of three different carrier screening workflows designed to identify couples at risk for having offspring with autosomal recessive conditions. METHODS Partner testing compliance, unnecessary testing, turnaround time, and ability to identify at-risk couples (ARCs) were measured across all three screening strategies (sequential, tandem, or tandem reflex). RESULTS A total of 314,100 individuals who underwent carrier screening were analyzed. Sequential, tandem, and tandem reflex screening yielded compliance frequencies of 25.8%, 100%, and 95.9%, respectively. Among 14,595 couples tested in tandem, 42.2% of females were screen-negative, resulting in unnecessary testing of the male partner. In contrast, less than 1% of tandem reflex couples included unnecessary male testing. The median turnaround times were 29.2 days (sequential), 8 days (tandem), and 13.3 days (tandem reflex). The proportion of ARCs detected per total number of individual screens were 0.5% for sequential testing and 1.3% for both tandem and tandem reflex testing. CONCLUSION The tandem reflex strategy simplifies a potentially complex clinical scenario by providing a mechanism by which providers can maximize partner compliance and the detection of at-risk couples while minimizing workflow burden and unnecessary testing and is more efficacious than both sequential and tandem screening strategies.
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Affiliation(s)
| | - Raul Torres
- Myriad Genetics, Inc., Salt Lake City, Utah, USA
| | | | | | - Jeff Wootton
- Myriad Women's Health, South San Francisco, California, USA
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Dugger C, Anderson HS, Miller CE, Wong B, Johnson EP, Rothwell E. Assessing clinical education tools for expanded carrier screening. J Genet Couns 2020; 30:606-615. [PMID: 33135283 DOI: 10.1002/jgc4.1349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 01/06/2023]
Abstract
Expanded carrier screening (ECS) is increasingly offered to a broader population and raises challenges of how to best educate and counsel the volume of screened individuals. For this study, we compared three educational tools (brochure, video and comic) about ECS on knowledge and decision making. A convenience online sample of 151 pregnant women was randomized to one of three groups (Video, n = 42; Comic n = 54; Brochure n = 55). Knowledge scores were significantly higher for the comic group compared to the video or the brochure groups (p < .001). No significant differences in preparation for decision making, decisional conflict, or perceptions of shared decision making were identified between the study groups. This study suggests that a comic about ECS may improve patient attention and retention of information. The use of graphic narratives may enable individuals to better understand medical information in general.
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Affiliation(s)
- Chloe Dugger
- Graduate Program in Genetic Counseling, University of Utah, Salt Lake City, UT, USA
| | | | | | - Bob Wong
- College of Nursing, University of Utah, Salt Lake City, UT, USA
| | - Erin P Johnson
- Department of Ob/Gyn, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Erin Rothwell
- Department of Ob/Gyn, School of Medicine, University of Utah, Salt Lake City, UT, USA
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Genetic ancestry analysis on >93,000 individuals undergoing expanded carrier screening reveals limitations of ethnicity-based medical guidelines. Genet Med 2020; 22:1694-1702. [PMID: 32595206 PMCID: PMC7521993 DOI: 10.1038/s41436-020-0869-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 11/14/2022] Open
Abstract
Purpose Carrier status associates strongly with genetic ancestry, yet current carrier screening guidelines recommend testing for a limited set of conditions based on a patient’s self-reported ethnicity. Ethnicity, which can reflect both genetic ancestry and cultural factors (e.g., religion), may be imperfectly known or communicated by patients. We sought to quantitatively assess the efficacy and equity with which ethnicity-based carrier screening captures recessive disease risk. Methods For 93,419 individuals undergoing a 96-gene expanded carrier screen (ECS), correspondence was assessed among carrier status, self-reported ethnicity, and a dual-component genetic ancestry (e.g., 75% African/25% European) calculated from sequencing data. Results Self-reported ethnicity was an imperfect indicator of genetic ancestry, with 9% of individuals having >50% genetic ancestry from a lineage inconsistent with self-reported ethnicity. Limitations of self-reported ethnicity led to missed carriers in at-risk populations: for 10 ECS conditions, patients with intermediate genetic ancestry backgrounds—who did not self-report the associated ethnicity—had significantly elevated carrier risk. Finally, for 7 of the 16 conditions included in current screening guidelines, most carriers were not from the population the guideline aimed to serve. Conclusion Substantial and disproportionate risk for recessive disease is not detected when carrier screening is based on ethnicity, leading to inequitable reproductive care.
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