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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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To-Mai XH, Nguyen HT, Nguyen-Thi TT, Nguyen TV, Nguyen-Thi MN, Thai KQ, Lai MT, Nguyen TA. Prevalence of common autosomal recessive mutation carriers in women in the Southern Vietnam following the application of expanded carrier screening. Sci Rep 2024; 14:7461. [PMID: 38553482 PMCID: PMC10980709 DOI: 10.1038/s41598-024-57513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
The common autosomal recessive (AR) mutation carrier is still unknown in Vietnam. This study aims to identify the most common AR gene mutation carriers in women of reproductive age to build a Vietnamese-specific carrier screening panel for AR and X-linked disorders in the preconception and prenatal healthcare program. A cross-sectional study was conducted at University Medical Center-Branch 2 in Ho Chi Minh City from December 1st, 2020, to June 30th, 2023. 338 women have consented to take a 5 mL blood test to identify 540 recessive genes. The carrier screening panel was designed based on the American College of Medical Genetics and Genomics (ACMG)-recommended genes and suggestions from 104 clinical experts in Vietnam. Obstetricians and genetic experts counseled all positive testing results to discuss the possibility of recessive diseases in their offspring. The most common recessive disorders were defined at a prevalence of 1 in 60 or greater, and those were added to a Vietnamese-specific carrier screening panel. 338 non-pregnant and pregnant women underwent the expanded carrier screening (ECS). The carrier frequency was 63.6%, in which 215 women carried at least one AR gene mutation. GJB2 hearing impairment was identified as the most common chronic condition (1 in 5). The second most common AR disorder was beta-thalassemia (1 in 16), followed by cystic fibrosis (1 in 23), G6PD deficiency (1 in 28), Wilson's disease (1 in 31), Usher's syndrome (1 in 31), and glycogen storage disease (1 in 56). Seven common recessive genes were added in ethnic-based carrier screening. Women in the South of Vietnam have been carried for many recessive conditions at high frequency, such as hearing impairment, genetic anemia, and cystic fibrosis. It is necessary to implement a preconception and prenatal screening program by using seven widely popular AR genes in a Vietnamese-specific carrier screening panel to reduce the burden related to AR and X-linked disorders.
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Affiliation(s)
- Xuan-Hong To-Mai
- University of Alberta, Edmonton, Canada
- University of Nam Can Tho, Can Tho, Vietnam
| | - Huu-Trung Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- University Medical Center-Branch 2, Ho Chi Minh City, Vietnam
| | | | - Thuy-Vy Nguyen
- University of Science, Vietnam National University Ho Chi Minh, Ho Chi Minh City, Vietnam
- Ktest Company, Ho Chi Minh City, Vietnam
| | - My-Nuong Nguyen-Thi
- University of Science, Vietnam National University Ho Chi Minh, Ho Chi Minh City, Vietnam
- Ktest Company, Ho Chi Minh City, Vietnam
| | | | | | - Tuan-Anh Nguyen
- University Medical Center-Branch 2, Ho Chi Minh City, Vietnam.
- Molecular Biomedical Center, University Medical Center, Ho Chí Minh City, Vietnam.
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Muthaffar OY, Abdulkareem AA, Ashi A, Naseer MI. A novel homozygous splice donor variant in the LRPPRC gene causing Leigh syndrome with epilepsy, a French-Canadian disorder in a Saudi family: case report. Front Pediatr 2023; 11:1288542. [PMID: 38046674 PMCID: PMC10690952 DOI: 10.3389/fped.2023.1288542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/24/2023] [Indexed: 12/05/2023] Open
Abstract
Background The mitochondria are a cellular power house. Tissues are involved in frequent energy consumption, and any failure or irregularity in the continuous energy production could lead to abnormalities. The leucine-rich pentatricopeptide repeat (LRPPRC) gene is one of the mitochondrial-related functions genes; variations in these genes are responsible for complex phenotypes that affect many organs such as the brain, liver, and muscles. Materials and methods This study enrolled a family with Leigh syndrome-like phenotype. The molecular diagnosis was conducted by first performing whole exome sequencing (WES), followed by Sanger sequencing. Results A novel splice-site variant (c.469 + 2T > A) at the exon-intron boundary in the LRPPRC gene was identified using the WES data analysis. Sanger validation confirmed the autosomal recessive inheritance of the identified variant. Based on the ACMG criteria for variant classification, PVS1 and PM2 suggest that the identified variant in the LRPPRC gene is likely to be pathogenic. Conclusion To the best of our knowledge, there have been no previous reports of this variant in the LRPPRC gene. Our research not only identifies a novel variant in the LRPPRC gene, but also confirms the unresolved molecular diagnosis of the family. WES can be used as a first-line diagnostic tool in familial cases, particularly in those cases when detailed clinical phenotyping is not possible. Once the molecular diagnosis is confirmed in a family, it is necessary to conduct a thorough re-evaluation of the patients' specific clinical phenotypes in order to establish a clear genotype-phenotype correlation.
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Affiliation(s)
- Osama Y. Muthaffar
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Angham Abdulrhman Abdulkareem
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abrar Ashi
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Carrier Screening Programs for Cystic Fibrosis, Fragile X Syndrome, Hemoglobinopathies and Thalassemia, and Spinal Muscular Atrophy: A Health Technology Assessment. ONTARIO HEALTH TECHNOLOGY ASSESSMENT SERIES 2023; 23:1-398. [PMID: 37637488 PMCID: PMC10453298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Background We conducted a health technology assessment to evaluate the safety, effectiveness, and cost-effectiveness of carrier screening programs for cystic fibrosis (CF), fragile X syndrome (FXS), hemoglobinopathies and thalassemia, and spinal muscular atrophy (SMA) in people who are considering a pregnancy or who are pregnant. We also evaluated the budget impact of publicly funding carrier screening programs, and patient preferences and values. Methods We performed a systematic literature search of the clinical evidence. We assessed the risk of bias of each included study using the Cochrane Risk of Bias tool and the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS), and the quality of the body of evidence according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) Working Group criteria. We performed a systematic economic literature search and conducted cost-effectiveness analyses comparing preconception or prenatal carrier screening programs to no screening. We considered four carrier screening strategies: 1) universal screening with standard panels; 2) universal screening with a hypothetical expanded panel; 3) risk-based screening with standard panels; and 4) risk-based screening with a hypothetical expanded panel. We also estimated the 5-year budget impact of publicly funding preconception or prenatal carrier screening programs for the given conditions in Ontario. To contextualize the potential value of carrier screening, we spoke with 22 people who had sought out carrier screening. Results We included 107 studies in the clinical evidence review. Carrier screening for CF, hemoglobinopathies and thalassemia, FXS, and SMA likely results in the identification of couples with an increased chance of having an affected pregnancy (GRADE: Moderate). Screening likely impacts reproductive decision-making (GRADE: Moderate) and may result in lower anxiety among pregnant people, although the evidence is uncertain (GRADE: Very low).We included 21 studies in the economic evidence review, but none of the study findings were directly applicable to the Ontario context. Our cost-effectiveness analyses showed that in the short term, preconception or prenatal carrier screening programs identified more at-risk pregnancies (i.e., couples that tested positive) and provided more reproductive choice options compared with no screening, but were associated with higher costs. While all screening strategies had similar values for health outcomes, when comparing all strategies together, universal screening with standard panels was the most cost-effective strategy for both preconception and prenatal periods. The incremental cost-effectiveness ratios (ICERs) of universal screening with standard panels compared with no screening in the preconception period were $29,106 per additional at-risk pregnancy detected and $367,731 per affected birth averted; the corresponding ICERs in the prenatal period were about $29,759 per additional at-risk pregnancy detected and $431,807 per affected birth averted.We estimated that publicly funding a universal carrier screening program in the preconception period over the next 5 years would require between $208 million and $491 million. Publicly funding a risk-based screening program in the preconception period over the next 5 years would require between $1.3 million and $2.7 million. Publicly funding a universal carrier screening program in the prenatal period over the next 5 years would require between $128 million and $305 million. Publicly funding a risk-based screening program in the prenatal period over the next 5 years would require between $0.8 million and $1.7 million. Accounting for treatment costs of the screened health conditions resulted in a decrease in the budget impact of universally provided carrier screening programs or cost savings for risk-based programs.Participants value the perceived potential positive impact of carrier screening programs such as medical benefits from early detection and treatment, information for reproductive decision-making, and the social benefit of awareness and preparation. There was a strong preference expressed for thorough, timely, unbiased information to allow for informed reproductive decision-making. Conclusions Carrier screening for CF, FXS, hemoglobinopathies and thalassemia, and SMA is effective at identifying at-risk couples, and test results may impact preconception and reproductive decision-making.The cost-effectiveness and budget impact of carrier screening programs are uncertain for Ontario. Over the short term, carrier screening programs are associated with higher costs, and also higher chances of detecting at-risk pregnancies compared with no screening. The 5-year budget impact of publicly funding universal carrier screening programs is larger than that of risk-based programs. However, accounting for treatment costs of the screened health conditions results in a decrease in the total additional costs for universal carrier screening programs or in cost savings for risk-based programs.The people we spoke with who had sought out carrier screening valued the potential medical benefits of early detection and treatment, particularly the support and preparation for having a child with a potential genetic condition.
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Balciuniene J, Liu R, Bean L, Guo F, Nallamilli BRR, Guruju N, Chen-Deutsch X, Yousaf R, Fura K, Chin E, Mathur A, Ma Z, Carmichael J, da Silva C, Collins C, Hegde M. At-Risk Genomic Findings for Pediatric-Onset Disorders From Genome Sequencing vs Medically Actionable Gene Panel in Proactive Screening of Newborns and Children. JAMA Netw Open 2023; 6:e2326445. [PMID: 37523181 PMCID: PMC10391308 DOI: 10.1001/jamanetworkopen.2023.26445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
Importance Although the clinical utility of genome sequencing for critically ill children is well recognized, its utility for proactive pediatric screening is not well explored. Objective To evaluate molecular findings from screening ostensibly healthy children with genome sequencing compared with a gene panel for medically actionable pediatric conditions. Design, Setting, and Participants This case series study was conducted among consecutive, apparently healthy children undergoing proactive genetic screening for pediatric disorders by genome sequencing (n = 562) or an exome-based panel of 268 genes (n = 606) from March 1, 2018, through July 31, 2022. Exposures Genetic screening for pediatric-onset disorders using genome sequencing or an exome-based panel of 268 genes. Main Outcomes and Measures Molecular findings indicative of genetic disease risk. Results Of 562 apparently healthy children (286 girls [50.9%]; median age, 29 days [IQR, 9-117 days]) undergoing screening by genome sequencing, 46 (8.2%; 95% CI, 5.9%-10.5%) were found to be at risk for pediatric-onset disease, including 22 children (3.9%) at risk for high-penetrance disorders. Sequence analysis uncovered molecular diagnoses among 32 individuals (5.7%), while copy number variant analysis uncovered molecular diagnoses among 14 individuals (2.5%), including 4 individuals (0.7%) with chromosome scale abnormalities. Overall, there were 47 molecular diagnoses, with 1 individual receiving 2 diagnoses; of the 47 potential diagnoses, 22 (46.8%) were associated with high-penetrance conditions. Pathogenic variants in medically actionable pediatric genes were found in 6 individuals (1.1%), constituting 12.8% (6 of 47) of all diagnoses. At least 1 pharmacogenomic variant was reported for 89.0% (500 of 562) of the cohort. In contrast, of 606 children (293 girls [48.3%]; median age, 26 days [IQR, 10-67 days]) undergoing gene panel screening, only 13 (2.1%; 95% CI, 1.0%-3.3%) resulted in potential childhood-onset diagnoses, a significantly lower rate than those screened by genome sequencing (P < .001). Conclusions and Relevance In this case series study, genome sequencing as a proactive screening approach for children, due to its unrestrictive gene content and technical advantages in comparison with an exome-based gene panel for medically actionable childhood conditions, uncovered a wide range of heterogeneous high-penetrance pediatric conditions that could guide early interventions and medical management.
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Affiliation(s)
| | - Ruby Liu
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Lora Bean
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Fen Guo
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | | | - Naga Guruju
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | | | - Rizwan Yousaf
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Kristina Fura
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Ephrem Chin
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Abhinav Mathur
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | - Zeqiang Ma
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
| | | | | | | | - Madhuri Hegde
- PerkinElmer Genomics, PerkinElmer Inc, Pittsburgh, Pennsylvania
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Sagaser KG, Malinowski J, Westerfield L, Proffitt J, Hicks MA, Toler TL, Blakemore KJ, Stevens BK, Oakes LM. Expanded carrier screening for reproductive risk assessment: An evidence-based practice guideline from the National Society of Genetic Counselors. J Genet Couns 2023. [PMID: 36756860 DOI: 10.1002/jgc4.1676] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 02/10/2023]
Abstract
Expanded carrier screening (ECS) intends to broadly screen healthy individuals to determine their reproductive chance for autosomal recessive (AR) and X-linked (XL) conditions with infantile or early-childhood onset, which may impact reproductive management (Committee Opinion 690, Obstetrics and Gynecology, 2017, 129, e35). Compared to ethnicity-based screening, which requires accurate knowledge of ancestry for optimal test selection and appropriate risk assessment, ECS panels consist of tens to hundreds of AR and XL conditions that may be individually rare in various ancestries but offer a comprehensive approach to inherited disease screening. As such, the term "equitable carrier screening" may be preferable. This practice guideline provides evidence-based recommendations for ECS using the GRADE Evidence to Decision framework (Guyatt et al., BMJ, 2008, 336, 995; Guyatt et al., BMJ, 2008, 336, 924). We used evidence from a recent systematic evidence review (Ramdaney et al., Genetics in Medicine, 2022, 20, 374) and compiled data from peer-reviewed literature, scientific meetings, and clinical experience. We defined and prioritized the outcomes of informed consent, change in reproductive plans, yield in identification of at-risk carrier pairs/pregnancies, perceived barriers to ECS, amount of provider time spent, healthcare costs, frequency of severely/profoundly affected offspring, incidental findings, uncertain findings, patient satisfaction, and provider attitudes. Despite the recognized barriers to implementation and change in management strategies, this analysis supported implementation of ECS for these outcomes. Based upon the current level of evidence, we recommend ECS be made available for all individuals considering reproduction and all pregnant reproductive pairs, as ECS presents an ethnicity-based carrier screening alternative which does not rely on race-based medicine. The final decision to pursue carrier screening should be directed by shared decision-making, which takes into account specific features of patients as well as their preferences and values. As a periconceptional reproductive risk assessment tool, ECS is superior compared to ethnicity-based carrier screening in that it both identifies more carriers of AR and XL conditions as well as eliminates a single race-based medical practice. ECS should be offered to all who are currently pregnant, considering pregnancy, or might otherwise biologically contribute to pregnancy. Barriers to the broad implementation of and access to ECS should be identified and addressed so that test performance for carrier screening will not depend on social constructs such as race.
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Affiliation(s)
- Katelynn G Sagaser
- Division of Maternal Fetal Medicine, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Lauren Westerfield
- Department of Human and Molecular Genetics, Baylor College of Medicine, Texas Children's Pavilion for Women at Texas Children's Hospital, Houston, Texas, USA
| | | | | | - Tomi L Toler
- Division of Genetics & Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Karin J Blakemore
- Division of Maternal Fetal Medicine, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Blair K Stevens
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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A robust pipeline for ranking carrier frequencies of autosomal recessive and X-linked Mendelian disorders. NPJ Genom Med 2022; 7:72. [PMID: 36535936 PMCID: PMC9763236 DOI: 10.1038/s41525-022-00344-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Single gene disorders are individually rare but collectively common leading causes of neonatal and pediatric morbidity and mortality. Both parents or the mothers of affected individuals with autosomal recessive or X-linked recessive diseases, respectively, are carrier(s). Carrier frequencies of recessive diseases can vary drastically among different ethnicities. This study established a robust pipeline for estimating and ranking carrier frequencies of all known 2699 recessive genes based on genome-wide sequencing data in healthy individuals. The discovery gnomAD cohort contained sequencing data on 76,156 genomes and 125,748 exomes from individuals with seven ethnicity backgrounds. The three validation cohorts composed of the SG10K Project with 4810 genomes on East Asian and South Asian, the ChinaMAP project with 10,588 Chinese genomes, and the WBBC pilot project with 4480 Chinese genomes. Within each cohort, comprehensive selection criteria for various kinds of deleterious variants were instituted, including known pathogenic variants (Type 1), presumably loss-of-function changes (Type 2), predicted deleterious missense variants (Type 3), and potentially harmful in-frame INDELs (Type 4). Subsequently, carrier frequencies of the 2699 genes were calculated and ranked based on ethnicity-specific carrier rates of Type 1 to Type 4 variants. Comparison of results from different cohorts with similar ethnicity background exhibited high degree of correlation, particularly between the ChinaMAP and the WBBC cohorts (Pearson correlation coefficient R = 0.92), confirming the validity of our variant selection criteria and the overall analysis pipeline.
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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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Tong K, He W, He Y, Li X, Hu L, Hu H, Lu G, Lin G, Dong C, Zhang VW, Du J, Liu D. Clinical Utility of Medical Exome Sequencing: Expanded Carrier Screening for Patients Seeking Assisted Reproductive Technology in China. Front Genet 2022; 13:943058. [PMID: 36072675 PMCID: PMC9441495 DOI: 10.3389/fgene.2022.943058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: Expanded carrier screening (ECS) is an effective method to identify at-risk couples (ARCs) and avoid birth defects. This study aimed to reveal the carrier spectrum in the Chinese population and to delineate an expanded carrier gene panel suitable in China.Methods: Medical exome sequencing (MES), including 4,158 disease-causing genes, was offered to couples at two reproductive centers. It was initially used as a diagnostic yield for potential patients and then used for ECS. Clinical information and ECS results were retrospectively collected.Results: A total of 2,234 couples, representing 4,468 individuals, underwent MES. In total, 254 individuals showed genetic disease symptoms, and 56 of them were diagnosed with genetic diseases by MES. Overall, 94.5% of them were carriers of at least one disease-causing variant. The most prevalent genes were GJB2 for autosomal recessive disorders and G6PD for X-linked diseases. The ARC rate was 9.80%, and couples were inclined to undergo preimplantation genetic testing when diseases were classified as “profound” or “severe.”Conclusion: This study provided insight to establish a suitable ECS gene panel for the Chinese population. Disease severity significantly influenced reproductive decision-making. The results highlighted the importance of conducting ECS for couples before undergoing assisted reproductive technology.
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Affiliation(s)
- Keya Tong
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Wenbin He
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yao He
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Xiurong Li
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Liang Hu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Hao Hu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Guangxiu Lu
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Ge Lin
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | | | | | - Juan Du
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- Genetics Centre, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- *Correspondence: Juan Du, ; Dongyun Liu,
| | - Dongyun Liu
- Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Human Embryo Engineering, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Juan Du, ; Dongyun Liu,
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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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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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12
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Molina Romero M, Yoldi Chaure A, Gañán Parra M, Navas Bastida P, del Pico Sánchez JL, Vaquero Argüelles Á, de la Fuente Vaquero P, Ramírez López JP, Castilla Alcalá JA. Probability of high-risk genetic matching with oocyte and semen donors: complete gene analysis or genotyping test? J Assist Reprod Genet 2022; 39:341-355. [PMID: 35091964 PMCID: PMC8956772 DOI: 10.1007/s10815-021-02381-0] [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: 03/29/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To estimate the probability of high-risk genetic matching when assisted reproductive techniques (ART) are applied with double gamete donation, following an NGS carrier test based on a complete study of the genes concerned. We then determine the results that would have been obtained if the genotyping tests most widely used in Spanish gamete banks had been applied. METHODS In this descriptive observational study, 1818 gamete donors were characterised by NGS. The pathogenic variants detected were analysed to estimate the probability of high-risk genetic matching and to determine the results that would have been obtained if the three most commonly used genotyping tests in ART had been applied. RESULTS The probability of high-risk genetic matching with gamete donation, screened by NGS and complete gene analysis, was 5.5%, versus the 0.6-2.7% that would have been obtained with the genotyping test. A total of 1741 variants were detected, including 607 different variants, of which only 22.6% would have been detected by all three genotyping tests considered and 44.7% of which would not have been detected by any of these tests. CONCLUSION Our study highlights the considerable heterogeneity of the genotyping tests, which present significant differences in their ability to detect pathogenic variants. The complete study of the genes by NGS considerably reduces reproductive risks when genetic matching is performed with gamete donors. Accordingly, we recommend that carrier screening in gamete donors be carried out using NGS and a complete study with nontargeted analysis of the variants of the screened genes.
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Affiliation(s)
- Marta Molina Romero
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain
| | | | | | | | | | | | | | | | - José Antonio Castilla Alcalá
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain ,U. Reproducción, UGC Obstetricia y Ginecología, HU Virgen de Las Nieves, Granada, Spain ,Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
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13
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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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14
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Rothwell E, Cheek-O'Donnell S, Johnson E, Wilson A, Anderson RA, Botkin J. Exploring the use of a Comic for Education about Expanded Carrier Screening among a Diverse Group of Mothers. ACTA ACUST UNITED AC 2021; 14:252-258. [PMID: 34721662 DOI: 10.1080/17538068.2021.1909398] [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] [Indexed: 10/21/2022]
Abstract
Purpose Expanded carrier screening (ECS) during prenatal care is an important test for identifying prospective parents' risk of inherited genetic diseases. However, barriers remain for effectively educating patients about ECS. Graphic medicine (i.e. comics) has grown as a mechanism for patient education. The purpose of this study was to explore attitudes and opinions of a comic to educate about ECS during prental care. Methods Focus groups were conducted with pregnant women or women who recently gave birth (6 groups, n=54). The participants were all female, 44.4% Latino/Hispanic, 16.7% Bi-Racial/Other, and 43.3% reporting some college education or high school degree. Results Most participants reported high enjoyment with the comic due to their relatability to the characters, simplicity of the story, description of medical outcomes in everyday terms and the exploration of multiple outcomes possible with ECS. In addition, participants reported that during pregnancy their reading habits increase as well as emotional reactions to the content and some participants stated they avoided reading information that may cause stress or anxiety. Conclusion More research is needed to assess what features of the comic promote understanding and how that influences decisions and pre-test patient education for ECS. The use of graphic narratives may enable individuals to better understand medical information in general.
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15
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Hussein N, Henneman L, Kai J, Qureshi N. Preconception risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease. Cochrane Database Syst Rev 2021; 10:CD010849. [PMID: 34634131 PMCID: PMC8504980 DOI: 10.1002/14651858.cd010849.pub4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Globally, about 6% of children are born with a serious birth defect of genetic or partially genetic origin. Carrier screening or testing is one way to identify couples at increased risk of having a child with an autosomal recessive condition. The most common autosomal recessive conditions are thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease, with higher carrier rates in high-risk populations of specific ancestral backgrounds. Identifying and counselling couples at genetic risk of the conditions before pregnancy enables them to make fully informed reproductive decisions, with some of these choices not being available if testing is only offered in an antenatal setting. This is an update of a previously published review. OBJECTIVES To assess the effectiveness of systematic preconception genetic risk assessment to enable autonomous reproductive choice and to improve reproductive outcomes in women and their partners who are both identified as carriers of thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease in healthcare settings when compared to usual care. SEARCH METHODS We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group's Trials Registers. Date of latest search of the registers: 04 August 2021. In addition, we searched for all relevant trials from 1970 (or the date at which the database was first available if after 1970) to date using electronic databases (MEDLINE, Embase, CINAHL, PsycINFO), clinical trial databases (National Institutes of Health, Clinical Trials Search portal of the World Health Organization, metaRegister of controlled clinical trials), and hand searching of key journals and conference abstract books from 1998 to date (European Journal of Human Genetics, Genetics in Medicine, Journal of Community Genetics). We also searched the reference lists of relevant articles, reviews and guidelines and also contacted subject experts in the field to request any unpublished or other published trials. Date of latest search of all these sources: 25 June 2021. SELECTION CRITERIA: Any randomised controlled trials (RCTs) or quasi-RCTs (published or unpublished) comparing reproductive outcomes of systematic preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease when compared to usual care. DATA COLLECTION AND ANALYSIS We identified 37 papers, describing 22 unique trials which were potentially eligible for inclusion in the review. However, after assessment, we found no RCTs of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease. MAIN RESULTS No RCTs of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease are included. A trial identified earlier has published its results and has subsequently been listed as excluded in this review. AUTHORS' CONCLUSIONS As there are no RCTs of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis, or Tay-Sachs disease included in either the earlier or current versions of this review, we recommend considering potential non-RCTs studies (for example prospective cohorts or before-and-after studies) for future reviews. While RCTs are desirable to inform evidence-based practice and robust recommendations, the ethical, legal and social implications associated with using this trial design to evaluate the implementation of preconception genetic risk assessment involving carrier testing and reproductive autonomy must also be considered. In addition, rather than focusing on single gene-by-gene carrier testing for specific autosomal-recessive conditions as the intervention being evaluated, preconception expanded genetic screening should also be included in future searches as this has received much attention in recent years as a more pragmatic strategy. The research evidence for current international policy recommendations is limited to non-randomised studies.
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Affiliation(s)
- Norita Hussein
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Lidewij Henneman
- Director Amsterdam Reproduction & Development research institute (AR&D), Amsterdam University Medical Centers, Amsterdam, Netherlands
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16
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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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17
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Capalbo A, Poli M, Riera-Escamilla A, Shukla V, Kudo Høffding M, Krausz C, Hoffmann ER, Simon C. Preconception genome medicine: current state and future perspectives to improve infertility diagnosis and reproductive and health outcomes based on individual genomic data. Hum Reprod Update 2020; 27:254-279. [PMID: 33197264 DOI: 10.1093/humupd/dmaa044] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/13/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Our genetic code is now readable, writable and hackable. The recent escalation of genome-wide sequencing (GS) applications in population diagnostics will not only enable the assessment of risks of transmitting well-defined monogenic disorders at preconceptional stages (i.e. carrier screening), but also facilitate identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting reproductive fitness. Through GS, the acquisition and curation of reproductive-related findings will warrant the expansion of genetic assessment to new areas of genomic prediction of reproductive phenotypes, pharmacogenomics and molecular embryology, further boosting our knowledge and therapeutic tools for treating infertility and improving women's health. OBJECTIVE AND RATIONALE In this article, we review current knowledge and potential development of preconception genome analysis aimed at detecting reproductive and individual health risks (recessive genetic disease and medically actionable secondary findings) as well as anticipating specific reproductive outcomes, particularly in the context of IVF. The extension of reproductive genetic risk assessment to the general population and IVF couples will lead to the identification of couples who carry recessive mutations, as well as sub-lethal conditions prior to conception. This approach will provide increased reproductive autonomy to couples, particularly in those cases where preimplantation genetic testing is an available option to avoid the transmission of undesirable conditions. In addition, GS on prospective infertility patients will enable genome-wide association studies specific for infertility phenotypes such as predisposition to premature ovarian failure, increased risk of aneuploidies, complete oocyte immaturity or blastocyst development failure, thus empowering the development of true reproductive precision medicine. SEARCH METHODS Searches of the literature on PubMed Central included combinations of the following MeSH terms: human, genetics, genomics, variants, male, female, fertility, next generation sequencing, genome exome sequencing, expanded carrier screening, secondary findings, pharmacogenomics, controlled ovarian stimulation, preconception, genetics, genome-wide association studies, GWAS. OUTCOMES Through PubMed Central queries, we identified a total of 1409 articles. The full list of articles was assessed for date of publication, limiting the search to studies published within the last 15 years (2004 onwards due to escalating research output of next-generation sequencing studies from that date). The remaining articles' titles were assessed for pertinence to the topic, leaving a total of 644 articles. The use of preconception GS has the potential to identify inheritable genetic conditions concealed in the genome of around 4% of couples looking to conceive. Genomic information during reproductive age will also be useful to anticipate late-onset medically actionable conditions with strong genetic background in around 2-4% of all individuals. Genetic variants correlated with differential response to pharmaceutical treatment in IVF, and clear genotype-phenotype associations are found for aberrant sperm types, oocyte maturation, fertilization or pre- and post-implantation embryonic development. All currently known capabilities of GS at the preconception stage are reviewed along with persisting and forthcoming barriers for the implementation of precise reproductive medicine. WIDER IMPLICATIONS The expansion of sequencing analysis to additional monogenic and polygenic traits may enable the development of cost-effective preconception tests capable of identifying underlying genetic causes of infertility, which have been defined as 'unexplained' until now, thus leading to the development of a true personalized genomic medicine framework in reproductive health.
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Affiliation(s)
- Antonio Capalbo
- Igenomix Italy, Marostica, Italy.,Igenomix Foundation, INCLIVA, Valencia, Spain
| | | | - Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Vallari Shukla
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Miya Kudo Høffding
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Krausz
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain.,Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Eva R Hoffmann
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Carlos Simon
- Igenomix Foundation, INCLIVA, Valencia, Spain.,Department of Obstetrics and Gynecology, University of Valencia, Valencia, Spain.,Department of Obstetrics and Gynecology BIDMC, Harvard University, Cambridge, MA, USA
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18
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Roman TS, Crowley SB, Roche MI, Foreman AKM, O'Daniel JM, Seifert BA, Lee K, Brandt A, Gustafson C, DeCristo DM, Strande NT, Ramkissoon L, Milko LV, Owen P, Roy S, Xiong M, Paquin RS, Butterfield RM, Lewis MA, Souris KJ, Bailey DB, Rini C, Booker JK, Powell BC, Weck KE, Powell CM, Berg JS. Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project. Am J Hum Genet 2020; 107:596-611. [PMID: 32853555 PMCID: PMC7536575 DOI: 10.1016/j.ajhg.2020.08.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Newborn screening (NBS) was established as a public health program in the 1960s and is crucial for facilitating detection of certain medical conditions in which early intervention can prevent serious, life-threatening health problems. Genomic sequencing can potentially expand the screening for rare hereditary disorders, but many questions surround its possible use for this purpose. We examined the use of exome sequencing (ES) for NBS in the North Carolina Newborn Exome Sequencing for Universal Screening (NC NEXUS) project, comparing the yield from ES used in a screening versus a diagnostic context. We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant's underlying diagnosis in 15 out of 17 (88%) children with metabolic disorders and in 5 out of 28 (∼18%) children with hearing loss. We discovered actionable findings in four participants that would not have been detected by standard NBS. A subset of parents was eligible to receive additional information for their child about childhood-onset conditions with low or no clinical actionability, clinically actionable adult-onset conditions, and carrier status for autosomal-recessive conditions. We found pathogenic variants associated with hereditary breast and/or ovarian cancer in two children, a likely pathogenic variant in the gene associated with Lowe syndrome in one child, and an average of 1.8 reportable variants per child for carrier results. These results highlight the benefits and limitations of using genomic sequencing for NBS and the challenges of using such technology in future precision medicine approaches.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie B Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myra I Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryce A Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chelsea Gustafson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natasha T Strande
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Phillips Owen
- Renaissance Computing Institute, Chapel Hill, NC 27517, USA
| | - Sayanty Roy
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mai Xiong
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan S Paquin
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Rita M Butterfield
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC 27705, USA
| | - Megan A Lewis
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Katherine J Souris
- Department of Health Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald B Bailey
- Genomics, Bioinformatics and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Christine Rini
- Feinberg School of Medicine, Department of Medical Social Sciences, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Jessica K Booker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen E Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Hernandez-Nieto C, Alkon-Meadows T, Lee J, Cacchione T, Iyune-Cojab E, Garza-Galvan M, Luna-Rojas M, Copperman AB, Sandler B. Expanded carrier screening for preconception reproductive risk assessment: Prevalence of carrier status in a Mexican population. Prenat Diagn 2020; 40:635-643. [PMID: 32003480 DOI: 10.1002/pd.5656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/30/2019] [Accepted: 01/21/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Genetic carrier screening has the potential to identify couples at risk of having a child affected with an autosomal recessive or X-linked disorder. However, the current prevalence of carrier status for these conditions in developing countries is not well defined. This study assesses the prevalence of carrier status of selected genetic conditions utilizing an expanded, pan-ethnic genetic carrier screening panel (ECS) in a large population of Mexican patients. METHODS Retrospective chart review of all patients tested with a single ECS panel at an international infertility center from 2012 to 2018 were included, and the prevalence of positive carrier status in a Mexican population was evaluated. RESULTS Eight hundred five individuals were analyzed with ECS testing for 283 genetic conditions. Three hundred fifty-two carriers (43.7%) were identified with 503 pathogenic variants in 145 different genes. Seventeen of the 391 participating couples (4.34%) were identified as being at-risk couples. The most prevalent alleles found were associated with alpha thalassemia, cystic fibrosis, GJB2 nonsyndromic hearing loss, biotinidase deficiency, and familial Mediterranean fever. CONCLUSION Based on the prevalence and severity of Mendelian disorders, we recommend that couples who wish to conceive regardless of their ethnicity background explore carrier screening and genetic counseling prior to reproductive medical treatment.
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Affiliation(s)
- Carlos Hernandez-Nieto
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Tamar Alkon-Meadows
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Joseph Lee
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA
| | - Teresa Cacchione
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA
| | - Esther Iyune-Cojab
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Maria Garza-Galvan
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Martha Luna-Rojas
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Alan B Copperman
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Sema4, A Mount Sinai Venture, Stamford CT, USA
| | - Benjamin Sandler
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
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20
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Rowe CA, Wright CF. Expanded universal carrier screening and its implementation within a publicly funded healthcare service. J Community Genet 2019; 11:21-38. [PMID: 31828606 PMCID: PMC6962405 DOI: 10.1007/s12687-019-00443-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/28/2019] [Indexed: 11/25/2022] Open
Abstract
Carrier screening, a well-established clinical initiative, has been slow to take advantage of the new possibilities offered by high-throughput next generation sequencing technologies. There is evidence of significant benefit in expanding carrier screening to include multiple autosomal recessive conditions and offering a ‘universal’ carrier screen that could be used for a pan-ethnic population. However, the challenges of implementing such a programme and the difficulties of demonstrating efficacy worthy of public health investment are significant barriers. In order for such a programme to be successful, it would need to be applicable and acceptable to the population, which may be ethnically and culturally diverse. There are significant practical and ethical implications associated with determining which variants, genes and conditions to include whilst maintaining adequate sensitivity and accuracy. Although preconception screening would maximise the potential benefits from universal carrier screening, the resource implications of different modes of delivery need to be carefully evaluated and balanced against maximising reproductive autonomy and ensuring equity of access. Currently, although a number of existing initiatives are increasing access to carrier screening, there is insufficient evidence to inform the development of a publicly funded, expanded, universal carrier screening programme that would justify investment over other healthcare interventions.
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Affiliation(s)
- Charlotte A Rowe
- University of Exeter, St Luke's Campus, 79 Heavitree Rd, Exeter, EX1 1TX, UK. .,Post Graduate Centre, Royal Cornwall Hospitals NHS Trust, Treliske, Truro, Cornwall, TR1 3LQ, UK.
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, RILD Building, RD&E, Barrack Road, Exeter, EX2 5DW, UK.
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21
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Capalbo A, Valero RA, Jimenez-Almazan J, Pardo PM, Fabiani M, Jiménez D, Simon C, Rodriguez JM. Optimizing clinical exome design and parallel gene-testing for recessive genetic conditions in preconception carrier screening: Translational research genomic data from 14,125 exomes. PLoS Genet 2019; 15:e1008409. [PMID: 31589614 PMCID: PMC6797235 DOI: 10.1371/journal.pgen.1008409] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/17/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022] Open
Abstract
Limited translational genomic research data have been reported on the application of exome sequencing and parallel gene testing for preconception carrier screening (PCS). Here, we present individual-level data from a large PCS program in which exome sequencing was routinely performed on either gamete donors (5,845) or infertile patients (8,280) undergoing in vitro fertilization (IVF) treatment without any known family history of inheritable genetic conditions. Individual-level data on pathogenic variants were used to define conditions for PCS based on criteria for severity, penetrance, inheritance pattern, and age of onset. Fetal risk was defined based on actual carrier frequency data accounting for the specific inheritance pattern (fetal disease risk, FDR). In addition, large-scale application of exome sequencing for PCS allowed a deep investigation of the incidence of medically actionable secondary findings in this population. Exome sequencing achieved remarkable clinical sensitivity for reproductive risk of highly penetrant childhood-onset disorders (1/337 conceptions) through analysis of 114 selected gene-condition pairs. A significant contribution to fetal disease risk was observed for rare (carrier rate < 1:100) and X-linked conditions (16.7% and 41.2% of total FDR, respectively). Subgroup analysis of 776 IVF couples identified 37 at increased reproductive risk (4.8%; 95% CI = 3.4–6.5). Further, two additional couples had increased risk for very rare conditions when both members of a parental pair were treated as a unit and the search was extended to the entire exome. About 2.3% of participants showed at least one pathogenic variant for genes included in the updated American College of Medical Genetics and Genomics v2.0 list of secondary findings. Gamete donors and IVF couples showed similar carrier burden for both carrier screening and secondary findings, indicating no causal relationship to fertility. These translational research data will facilitate development of more effective PCS strategies that maximize clinical sensitivity with minimal counterproductive effects. We provide here crucial information for optimizing the gene-panel design for preconception carrier screening based on the analysis of a large exome sequencing dataset from infertile individuals and gamete donors. Sequencing the entire coding portion of the human genome combined with separate analysis for few relevant genes offers the possibility to detect most of the pathogenetic variants associated with recessive Mendelian diseases and to develop preconception screening strategies that maximise clinical sensitivity with minimal counterproductive effects. Using a large dataset of individual-level exome sequencing data, we have defined gene specific and aggregate fetal risk detectable for conditions selected on discrete criteria of severity, penetrance, inheritance pattern, and age of onset. About 1 out of 300 affected pregnancies can be detected based on a gene-panel of 114 conditions and ~5% of the couples analysed showed an increased risk that warrant consideration from a reproductive viewpoint. These results suggest the use of exome sequencing and parallel gene testing is clinically effective and feasible for preconception carrier screening after proper validation and translational research has been carried out. However, further studies are necessary to define the best framework for clinical implementation and the actual detection rate of at risk couples.
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Affiliation(s)
- Antonio Capalbo
- Igenomix Reproductive Genetic Laboratory, Marostica, Italy
- DAHFMO Unit of Histology and Medical Embryology, Sapienza University of Rome, Italy
- Igenomix, Valencia, Spain
- * E-mail: (AC); (JM)
| | | | | | | | - Marco Fabiani
- Igenomix Reproductive Genetic Laboratory, Marostica, Italy
| | | | - Carlos Simon
- Igenomix, Valencia, Spain
- Department of Obstetrics and Gynecology, Valencia University; and INCLIVA, Valencia, Spain
- Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, California, United States of America
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22
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Ghidini A, Bianchi DW, Levy B, Van Mieghem T, Deprest J, Chitty LS. In case you missed it: The prenatal diagnosis editors bring you the most significant advances of 2018. Prenat Diagn 2019; 39:61-69. [PMID: 30593668 DOI: 10.1002/pd.5407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Alessandro Ghidini
- Antenatal Testing Center Alexandria Hospital, Alexandria, VA, USA.,Department of Obstetrics and Gynecology, Georgetown University Hospital, Washington, D.C., USA
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Brynn Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Tim Van Mieghem
- Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Canada
| | - Jan Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Lyn S Chitty
- North East Thames Regional Genetics Service, Great Ormond Street NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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23
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24
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25
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Fiévet A, Bellanger D, Rieunier G, Dubois d'Enghien C, Sophie J, Calvas P, Carriere JP, Anheim M, Castrioto A, Flabeau O, Degos B, Ewenczyk C, Mahlaoui N, Touzot F, Suarez F, Hully M, Roubertie A, Aladjidi N, Tison F, Antoine-Poirel H, Dahan K, Doummar D, Nougues MC, Ioos C, Rougeot C, Masurel A, Bourjault C, Ginglinger E, Prieur F, Siri A, Bordigoni P, Nguyen K, Philippe N, Bellesme C, Demeocq F, Altuzarra C, Mathieu-Dramard M, Couderc F, Dörk T, Auger N, Parfait B, Abidallah K, Moncoutier V, Collet A, Stoppa-Lyonnet D, Stern MH. Functional classification of ATM variants in ataxia-telangiectasia patients. Hum Mutat 2019; 40:1713-1730. [PMID: 31050087 DOI: 10.1002/humu.23778] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022]
Abstract
Ataxia-telangiectasia (A-T) is a recessive disorder caused by biallelic pathogenic variants of ataxia-telangiectasia mutated (ATM). This disease is characterized by progressive ataxia, telangiectasia, immune deficiency, predisposition to malignancies, and radiosensitivity. However, hypomorphic variants may be discovered associated with very atypical phenotypes, raising the importance of evaluating their pathogenic effects. In this study, multiple functional analyses were performed on lymphoblastoid cell lines from 36 patients, comprising 49 ATM variants, 24 being of uncertain significance. Thirteen patients with atypical phenotype and presumably hypomorphic variants were of particular interest to test strength of functional analyses and to highlight discrepancies with typical patients. Western-blot combined with transcript analyses allowed the identification of one missing variant, confirmed suspected splice defects and revealed unsuspected minor transcripts. Subcellular localization analyses confirmed the low level and abnormal cytoplasmic localization of ATM for most A-T cell lines. Interestingly, atypical patients had lower kinase defect and less altered cell-cycle distribution after genotoxic stress than typical patients. In conclusion, this study demonstrated the pathogenic effects of the 49 variants, highlighted the strength of KAP1 phosphorylation test for pathogenicity assessment and allowed the establishment of the Ataxia-TeLangiectasia Atypical Score to predict atypical phenotype. Altogether, we propose strategies for ATM variant detection and classification.
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Affiliation(s)
- Alice Fiévet
- Institut Curie, PSL Research University, INSERM U830, Paris, France.,Institut Curie, Hôpital, Service de Génétique, Paris, France
| | - Dorine Bellanger
- Institut Curie, PSL Research University, INSERM U830, Paris, France
| | | | | | - Julia Sophie
- CHU de Toulouse, Service de Génétique Médicale, Toulouse, France
| | - Patrick Calvas
- CHU de Toulouse, Service de Génétique Médicale, Toulouse, France
| | - Jean-Paul Carriere
- Hopital des enfants de Toulouse, Unité de Neuropédiatrie, Toulouse, France
| | - Mathieu Anheim
- CHU de Strasbourg, Service de Neurologie, Strasbourg, France
| | - Anna Castrioto
- CHU de Grenoble, Pole de Psychiatrie et de Neurologie, Grenoble, France
| | - Olivier Flabeau
- CH de la côte Basque, Service de Neurologie, Bayonne, France
| | - Bertrand Degos
- Département des Maladies du Système Nerveux, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Paris, France
| | - Claire Ewenczyk
- Hôpitaux universitaires Pitié Salpêtrière - Charles Foix, Service de Génétique, Paris, France
| | - Nizar Mahlaoui
- Hôpital Necker Enfants Malades, Service d'Immunologie, d'Hématologie et de Rhumatologie Pédiatriques, Paris, France
| | - Fabien Touzot
- Hôpital Necker Enfants Malades, Service d'Immunologie, d'Hématologie et de Rhumatologie Pédiatriques, Paris, France
| | - Felipe Suarez
- Hôpital Necker Enfants Malades, Service d'Hématologie Adulte, Paris, France
| | - Marie Hully
- Hôpital Necker Enfants Malades, Service de Neurologie Pédiatrique, Paris, France
| | - Agathe Roubertie
- CHU de Montpellier, Service de Neuropédiatrie, Montpellier, France
| | | | - François Tison
- CHU de Bordeaux, Département de Neurologie, Bordeaux, France
| | - Hélène Antoine-Poirel
- Centre de Génétique Humaine, Cliniques Universitaires Saint-Luc & Université Catholique de Louvain, Brussels, Belgium
| | - Karine Dahan
- Centre de Génétique Humaine, Cliniques Universitaires Saint-Luc & Université Catholique de Louvain, Brussels, Belgium
| | - Diane Doummar
- Hopital Armand Trousseau, Service de Neurologie Pédiatrique, Paris, France
| | | | - Christine Ioos
- Hôpital Raymond Poincaré, Pôle de Pédiatrie, Garches, France
| | | | - Alice Masurel
- Hopital d'Enfants de Dijon, Service de Génétique, Dijon, France
| | - Caroline Bourjault
- CH de Bretagne sud, Site du Scorff, Service de Pédiatrie, Lorient, France
| | | | - Fabienne Prieur
- CHU de St Etienne, Hôpital Nord, Service de Génétique Médicale, Saint Etienne, France
| | - Aurélie Siri
- CHU de Nancy, Service de Neurologie, Nancy, France
| | - Pierre Bordigoni
- CHU Nancy, Hôpitaux de Brabois, Service de Pédiatrie II, Vandoeuvre, France
| | - Karine Nguyen
- Département de Génétique Médicale, Hopital de la Timone, Marseille, France
| | - Noel Philippe
- Hopital Debrousse, Service d'Hématologie Pédiatrique, Lyon, France
| | - Céline Bellesme
- GH Cochin-saint-Vincent de Paul, Service d'Endocrinologie et de Neurologie Pédiatrique, Paris, France
| | - François Demeocq
- CHU de Clermont-Ferrand, Hôtel Dieu, Service de Pédiatrie B, Clermont-Ferrand, France
| | | | | | - Fanny Couderc
- CH d'Aix en Provence - du Pays d'Aix, Service de Pédiatrie, Aix en Provence, France
| | - Thilo Dörk
- Gynecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Nathalie Auger
- Gustave Roussy, Service Génétique des Tumeurs, Villejuif, France
| | - Béatrice Parfait
- Centre de ressources Biologiques, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | | | - Agnès Collet
- Institut Curie, Hôpital, Service de Génétique, Paris, France
| | - Dominique Stoppa-Lyonnet
- Institut Curie, PSL Research University, INSERM U830, Paris, France.,Institut Curie, Hôpital, Service de Génétique, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, INSERM U830, Paris, France.,Institut Curie, Hôpital, Service de Génétique, Paris, France
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26
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Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals. Hum Genet 2019; 138:389-409. [PMID: 30887117 DOI: 10.1007/s00439-019-01998-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/06/2019] [Indexed: 12/19/2022]
Abstract
Incidence rates of Mendelian diseases vary among ethnic groups, and frequencies of variant types of causative genes also vary among human populations. In this study, we examined to what extent we can predict population frequencies of recessive disorders from genomic data, and explored better strategies for variant interpretation and classification. We used a whole-genome reference panel from 3552 general Japanese individuals constructed by the Tohoku Medical Megabank Organization (ToMMo). Focusing on 32 genes for 17 congenital metabolic disorders included in newborn screening (NBS) in Japan, we identified reported and predicted pathogenic variants through variant annotation, interpretation, and multiple ways of classifications. The estimated carrier frequencies were compared with those from the Japanese NBS data based on 1,949,987 newborns from a previous study. The estimated carrier frequency based on genomic data with a recent guideline of variant interpretation for the PAH gene, in which defects cause hyperphenylalaninemia (HPA) and phenylketonuria (PKU), provided a closer estimate to that by the observed incidence than the other methods. In contrast, the estimated carrier frequencies for SLC25A13, which causes citrin deficiency, were much higher compared with the incidence rate. The results varied greatly among the 11 NBS diseases with single responsible genes; the possible reasons for departures from the carrier frequencies by reported incidence rates were discussed. Of note, (1) the number of pathogenic variants increases by including additional lines of evidence, (2) common variants with mild effects also contribute to the actual frequency of patients, and (3) penetrance of each variant remains unclear.
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27
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Capalbo A, Chokoshvili D, Dugoff L, Franasiak J, Gleicher N, Pennings G, Simon C. Should the reproductive risk of a couple aiming to conceive be tested in the contemporary clinical context? Fertil Steril 2019; 111:229-238. [PMID: 30642571 DOI: 10.1016/j.fertnstert.2018.11.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/27/2022]
Affiliation(s)
| | - Davit Chokoshvili
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Lorraine Dugoff
- Maternal Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Jason Franasiak
- IVI-RMA America, Reproductive Medicine Associates of New Jersey, Basking Ridge, New Jersey; Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Norbert Gleicher
- Center for Human Reproduction, New York, New York; Foundation for Reproductive Medicine, New York, New York; Stem Cell Biology and Molecular Embryology Laboratory, Rockefeller University, New York, New York; Department of Obstetrics and Gynecology, Vienna University of Medicine, Vienna, Austria
| | - Guido Pennings
- Bioethics Institute Ghent (BIG), Department of Philosophy and Moral Science, Ghent University, Ghent, Belgium
| | - Carlos Simon
- Department of Obstetrics and Gynecology, Valencia University, and INCLIVA, Valencia, Spain; Department of Obstetrics and Gynecology, Stanford University, Stanford, California; Igenomix, Valencia, Spain.
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28
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Rope AF, Kauffman TL, Himes P, Amendola LM, Punj S, Akkari Y, Potter A, Davis JV, Schneider JL, Reiss JA, Gilmore MJ, McMullen CK, Nickerson DA, Richards CS, Jarvik GP, Wilfond BS, Goddard KAB. A case for expanding carrier testing to include actionable X-linked disorders. Clin Case Rep 2018; 6:2092-2095. [PMID: 30455898 PMCID: PMC6230667 DOI: 10.1002/ccr3.1806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/27/2018] [Accepted: 08/20/2018] [Indexed: 11/10/2022] Open
Abstract
A research study utilizing whole-genome sequence analysis for preconception carrier screening provided a genome-first detection of a severe de novo Factor VIII mutation in a woman with implications for pregnancy management and life-saving interventions of her newborn son, and a challenge to the existing paradigm regarding carrier testing.
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Affiliation(s)
- Alan F. Rope
- Department of GeneticsKaiser Permanente NorthwestPortlandOregon
| | - Tia L. Kauffman
- Center for Health ResearchKaiser Permanente NorthwestPortlandOregon
| | - Pat Himes
- Department of GeneticsKaiser Permanente NorthwestPortlandOregon
| | - Laura M. Amendola
- Department of MedicineDivision of Medical GeneticsUniversity of WashingtonSeattleWashington
| | - Sumit Punj
- Department of Molecular and Medical GeneticsOregon Health & Science UniversityPortlandOregon
| | - Yassmine Akkari
- Department of Molecular and Medical GeneticsOregon Health & Science UniversityPortlandOregon
| | - Amiee Potter
- Department of Molecular and Medical GeneticsOregon Health & Science UniversityPortlandOregon
| | - James V. Davis
- Center for Health ResearchKaiser Permanente NorthwestPortlandOregon
| | | | - Jacob A. Reiss
- Center for Health ResearchKaiser Permanente NorthwestPortlandOregon
| | - Mari J. Gilmore
- Department of GeneticsKaiser Permanente NorthwestPortlandOregon
| | | | | | - C. Sue Richards
- Department of Molecular and Medical GeneticsOregon Health & Science UniversityPortlandOregon
| | - Gail P. Jarvik
- Department of MedicineDivision of Medical GeneticsUniversity of WashingtonSeattleWashington
- Department of Genome SciencesUniversity of WashingtonSeattleWashington
| | - Benjamin S. Wilfond
- Treuman Katz Center for Pediatric BioethicsSeattle Children's Hospital and Research InstituteSeattleWashington
- Divison of BioethicsDepartment of PediatricsUniversity of Washington School of MedicineSeattleWashington
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29
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Kraft SA, Duenas D, Wilfond BS, Goddard KAB. The evolving landscape of expanded carrier screening: challenges and opportunities. Genet Med 2018; 21:790-797. [PMID: 30245516 PMCID: PMC6752283 DOI: 10.1038/s41436-018-0273-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/06/2018] [Indexed: 12/27/2022] Open
Abstract
Carrier screening allows individuals to learn their chance of passing on an autosomal or X-linked condition to their offspring. Initially introduced as single-disease, ancestry-based screening, technological advances now allow for the possibility of multi-disease, pan-ethnic carrier screening, which we refer to as “expanded carrier screening.” There are numerous potential benefits to expanded carrier screening, including maximizing the opportunity for couples to make autonomous reproductive decisions, and efficiency and marginal additional costs of including more conditions if the test is already being offered. While numerous laboratories currently offer expanded carrier screening services, it is not yet commonly used in clinical practice, and there is a lack of consensus among experts about the service, including whether this should be offered to individuals and couples, whether this should be offered preconception or prenatally, and what conditions to include in screening programs. Challenges for expanded carrier screening programs include a lack of demand from the public, low prioritization by health systems, the potential for pressure to undergo screening, the possibility of disability-based discrimination, needed adaptations to pre- and post-test counseling, technical limitations, and the evolving technological and socio-political landscape.
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Affiliation(s)
- Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA, USA.,Division of Bioethics and Palliative Care, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Devan Duenas
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA, USA.,Division of Bioethics and Palliative Care, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
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