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van den Heuvel LM, Woudstra AJ, van der Hout S, Jans S, Wiersma T, Dondorp W, Birnie E, Lakeman P, Henneman L, Plantinga M, van Langen IM. Primary care professionals' views on population-based expanded carrier screening: an online focus group study. Fam Pract 2024; 41:571-578. [PMID: 36722294 PMCID: PMC11324326 DOI: 10.1093/fampra/cmad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Population-based expanded carrier screening (ECS) involves screening for multiple recessive diseases offered to all couples considering a pregnancy or during pregnancy. Previous research indicates that in some countries primary care professionals are perceived as suitable providers for ECS. However, little is known about their perspectives. We therefore aimed to explore primary care professionals' views on population-based ECS. METHODS Four online focus groups with 14 general practitioners (GPs) and 16 community midwives were conducted in the Netherlands. RESULTS Our findings highlight various perspectives on the desirability of population-based ECS. Participants agreed that ECS could enhance reproductive autonomy and thereby prevent suffering of the child and/or parents. However, they also raised several ethical, societal, and psychological concerns, including a tendency towards a perfect society, stigmatization, unequal access to screening and negative psychosocial consequences. Participants believed that provision of population-based ECS would be feasible if prerequisites regarding training and reimbursement for providers would be fulfilled. most GPs considered themselves less suitable or capable of providing ECS, in contrast to midwives who did consider themselves suitable. Nevertheless, participants believed that, if implemented, ECS should be offered in primary care or by public health services rather than as hospital-based specialized care, because they believed a primary care ECS offer increases access in terms of time and location. CONCLUSIONS While participants believed that an ECS offer would be feasible, they questioned its desirability and priority. Studies on the desirability and feasibility of population-based ECS offered in primary care or public health settings are needed.
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Affiliation(s)
- Lieke M van den Heuvel
- Department of Genetics, University Medical Centre Groningen/University of Groningen, Groningen, The Netherlands
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Anke J Woudstra
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Sanne van der Hout
- Department of Health, Ethics & Society, Maastricht University Medical Centre/Maastricht University, Maastricht, The Netherlands
| | - Suze Jans
- Department of Child Health, TNO, Leiden, The Netherlands
| | - Tjerk Wiersma
- Dutch College of General Practitioners, Utrecht, The Netherlands
| | - Wybo Dondorp
- Department of Health, Ethics & Society, Maastricht University Medical Centre/Maastricht University, Maastricht, The Netherlands
| | - Erwin Birnie
- Department of Genetics, University Medical Centre Groningen/University of Groningen, Groningen, The Netherlands
| | - Phillis Lakeman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Mirjam Plantinga
- Department of Genetics, University Medical Centre Groningen/University of Groningen, Groningen, The Netherlands
| | - Irene M van Langen
- Department of Genetics, University Medical Centre Groningen/University of Groningen, Groningen, The Netherlands
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Liu S, Huang S, Zhang VW, Cao L, Liu H, Wei X, Luo Y, Li Y, Zhou L, Li F, Zhu Q, Liu H. Customizing carrier screening in the Chinese population: Insights from a 334-gene panel. Prenat Diagn 2024. [PMID: 39030774 DOI: 10.1002/pd.6635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/22/2024]
Abstract
OBJECTIVE This study aimed to evaluate the yield and applicability of expanded carrier screening and propose carrier rate screening thresholds suitable for the Chinese population by comparing the current screening panel with the American College of Medical Genetics and Genomics recommended panel of 113 genes. METHODS Using targeted next-generation sequencing, a customized panel with 334 genes was performed on 2168 individuals without clinical phenotypes for expanded carrier screening purpose. Variant interpretation followed the American College of Medical Genetics and Genomics guidelines. Carrier rates were calculated for each identified variant and each gene. At-risk couple rates were also assessed. The yield of expanded carrier screening was evaluated through calculating cumulative carrier rate. RESULTS Overall, 65.87% of the individuals were found to be carriers of at least 1 disease causing variants. The overall at-risk couple rate was 11.76%, of which the GJB2:c.109G > A related at-risk couple rate was 5.78%. The cumulative carrier rate of 334-panel was 65.53%. When screened genes with gene carrier rate ≥1/1000, the expanded carrier screening can cover over 90% of the cumulative carrier rate and at-risk couples. A total of 86 genes overlapped with American College of Medical Genetics and Genomics Tier-3 genes and were attributed to the cumulative carrier rate of 47.33%. CONCLUSION Expanded carrier screening using the 334-gene panel showed high screening efficiency. A threshold of gene carrier rate ≥1/1000 is recommended for selecting carrier screening genes in the Chinese Han population. This study highlights the importance of customizing screening panels based on the ACMG Tier-3 genes in conjunction with population-specific carrier frequencies to improve the accuracy and effectiveness of expanded carrier screening.
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Affiliation(s)
- Sha Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Shuang Huang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | | | - Liyuan Cao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Haipeng Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiang Wei
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yuan Luo
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yue Li
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lin Zhou
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Fuping Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- Department of Reproductive Andrology/Human Sperm Bank, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qian Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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3
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Mei JY, Platt LD. Reproductive genetic carrier screening in pregnancy: improving health outcomes and expanding access. J Perinat Med 2024; 0:jpm-2024-0059. [PMID: 38924780 DOI: 10.1515/jpm-2024-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
Reproductive genetic carrier screening (RGCS) serves to screen couples for their risk of having children affected by monogenic conditions. The included conditions are mostly autosomal recessive or X-linked with infantile or early-childhood onset. Cystic fibrosis, spinal muscular atrophy, and hemoglobinopathies are now recommended by the American College of Obstetricians and Gynecologists (ACOG) for universal screening. Recommendations for further RGCS remain ethnicity based. The American College of Medical Genetics and Genomics and the National Society of Genetic Counselors in recent years have recommended universal expanded-panel RGCS and moving towards a more equitable approach. ACOG guidelines state that offering RGCS is an acceptable option, however it has not provided clear guidance on standard of care. Positive results on RGCS can significantly impact reproductive plans for couples, including pursuing in vitro fertilization with preimplantation genetic testing, prenatal genetic testing, specific fetal or neonatal treatment, or adoption. RGCS is a superior approach compared to ethnicity-based carrier screening and moves away from single race-based medical practice. We urge the obstetrics and gynecology societies to adopt the guidelines for RGCS put forward by multiple societies and help reduce systemic inequalities in medicine in our new genetic age. Having national societies such as ACOG and the Society for Maternal-Fetal Medicine officially recommend and endorse RGCS would bolster insurance coverage and financial support by employers for RGCS. The future of comprehensive reproductive care in the age of genomic medicine entails expanding access so patients and families can make the reproductive options that best fit their needs.
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Affiliation(s)
- Jenny Y Mei
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, CA, USA
| | - Lawrence D Platt
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, CA, USA
- Center for Fetal Medicine and Women's Ultrasound, Los Angeles, CA, USA
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4
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Wilson RD. Antenatal reproductive screening for pregnant people including preconception: Provides the best reproductive opportunity for informed consent, quality, and safety. Best Pract Res Clin Obstet Gynaecol 2024:102520. [PMID: 38991859 DOI: 10.1016/j.bpobgyn.2024.102520] [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: 11/09/2023] [Revised: 05/28/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024]
Abstract
INTRODUCTION This antenatal screening review will include reproductive screening evidence and approaches for pre-conception and post-conception, using first to third trimester screening opportunities. METHODS Focused antenatal screening peer-reviewed publications were evaluated and summarized. RESULTS Evidenced-based reproductive antenatal screening elements should be offered and discussed, with the pregnancy planning or pregnant person, during Preconception (genetic carrier screening for reproductive partners, personal and family (including reproductive partner) history review for increased genetic and pregnancy morbidity risks); First Trimester (fetal dating with ultrasound; fetal aneuploidy screening plus consideration for expanded fetal morbidity criteria, if appropriate; pregnant person preeclampsia screening; early fetal anatomy screening; early fetal cardiac screening); Second Trimester for standard fetal anatomy screening (18-22 weeks) including cardiac; pregnant person placental and cord pathology screening; pregnant person preterm birth screening with cervical length measurement); Third Trimester (fetal growth surveillance; continued preterm birth risk surveillance). CONCLUSION Antenatal reproductive screening has multiple elements, is complex, is time-consuming, and requires the use of pre- and post-testing counselling for most screening elements. The use of preconception and trimesters 'one to three' requires clear patient understanding and buy-in. Informed consent and knowledge transfer is a main goal for antenatal reproductive screening approaches.
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Affiliation(s)
- R Douglas Wilson
- Emeritus Department of Obstetrics and Gynecology Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
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5
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Go M, Shim SH. Genomic aspects in reproductive medicine. Clin Exp Reprod Med 2024; 51:91-101. [PMID: 38263590 PMCID: PMC11140259 DOI: 10.5653/cerm.2023.06303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 01/25/2024] Open
Abstract
Infertility is a complex disease characterized by extreme genetic heterogeneity, compounded by various environmental factors. While there are exceptions, individual genetic and genomic variations related to infertility are typically rare, often family-specific, and may serve as susceptibility factors rather than direct causes of the disease. Consequently, identifying the cause of infertility and developing prevention and treatment strategies based on these factors remain challenging tasks, even in the modern genomic era. In this review, we first examine the genetic and genomic variations associated with infertility, and subsequently summarize the concepts and methods of preimplantation genetic testing in light of advances in genome analysis technology.
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Affiliation(s)
- Minyeon Go
- Department of Biomedical Science, College of Life Science, CHA University, Pocheon, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Pocheon, Republic of Korea
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Dive L, Laberge AM, Freeman L, Bunnik EM. Beyond severity: utility as a criterion for setting the scope of RGCS. Eur J Hum Genet 2024:10.1038/s41431-024-01640-9. [PMID: 38811715 DOI: 10.1038/s41431-024-01640-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/18/2024] [Accepted: 05/15/2024] [Indexed: 05/31/2024] Open
Abstract
Reproductive genetic carrier screening (RGCS) allows prospective parents to identify and act upon their chances of having a child with a genetic condition. In deciding which genetic conditions to include in RGCS, severity is often used as a criterion. However, the concept is inherently complex, subjective and multidimensional, and determinations of severity will remain intractably contested. We propose the concept of utility as a criterion for setting the scope of RGCS, and put forward two central arguments for doing so. First, utility is a more appropriate and effective concept as it responds to context and makes an explicit connection between the purpose of RGCS and the value of information obtained for that purpose: namely, to facilitate reproductive decision-making. Utility comprises both clinical and personal utility, and varies according to the availability and accessibility of reproductive options, including pre-implantation genetic testing, prenatal genetic diagnosis, and termination of pregnancy. Second, there are ethical reasons for preferring utility over severity. Utility is a property of the information gleaned from RGCS, while severity is a property of a genetic condition or of an instance of this condition in a person. While consideration of the severity of genetic conditions is not lost when focusing on utility, the need to rely on value judgements regarding the quality of life of people who live with genetic conditions is circumvented. Therefore, utility should replace severity as justification for the inclusion of genetic conditions in RGCS programmes.
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Affiliation(s)
- Lisa Dive
- Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia.
| | | | - Lucinda Freeman
- Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Eline M Bunnik
- Department of Medical Ethics, Philosophy and History of Medicine, Erasmus MC, Rotterdam, The Netherlands
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7
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Oyelese Y, Schioppo D, O'Brien B. Prenatal Screening and Diagnosis: Time for a Paradigm Shift. Am J Perinatol 2024. [PMID: 38657662 DOI: 10.1055/a-2312-8824] [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: 04/26/2024]
Abstract
Recent advances in genetics and imaging have ushered substantial breakthroughs in screening and diagnosis for chromosomal and structural abnormalities. Thus, it is imperative that health care providers caring for pregnant individuals should reexamine established practices in prenatal screening and diagnosis. In the past, screening for chromosomal abnormalities was based almost entirely on Down syndrome. Pregnant individuals aged > 35 years were considered at "high risk" or of "advanced maternal age" based on age alone; however, the advent of tests with high sensitivity for prenatal detection of chromosomal abnormalities should lead to abandoning that concept, at least from the perspective of chromosomal abnormalities. Given that first-trimester and second-trimester screenings will fail to detect between 5 and 20% of Down syndrome, in most situations, noninvasive testing with cell-free DNA should be the first-line screen for Down syndrome. The fact that over 99% of fetuses with Down syndrome will be detected prenatally with cell-free DNA gives other fetal chromosomal and structural abnormalities increasing prominence. Chromosomal microarray analysis (CMA) permits prenatal detection of several clinically important chromosomal aberrations that cannot be detected by karyotype and may exist in structurally normal fetuses with low-risk cell-free DNA screening. As such, CMA should be more readily conducted when invasive testing is performed, regardless of the presence of a structural abnormality. Isolated sonographic "soft markers" have no clinical significance in patients who have normal cell-free DNA screening, can cause unwarranted anxiety and a negative impact on pregnancy, and perhaps it is time to stop discussing them. Detailed first-trimester ultrasound allows early detection of several severe fetal anomalies and, therefore, in settings with adequately trained personnel and resources, should be used more frequently. This opinion traces the evolution of prenatal screening and diagnosis and advocates for a paradigm shift that aligns with recent developments in prenatal screening and diagnostic capabilities. KEY POINTS: · Noninvasive prenatal testing with cell-free DNA should be available to all pregnant individuals.. · Chromosomal microarray should be available to all pregnant individuals undergoing amniocentesis.. · Patients >35 years with low-risk screening are not at "high risk" for chromosomal abnormalities..
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Affiliation(s)
- Yinka Oyelese
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Maternal Fetal Care Center, Division of Fetal Medicine and Surgery, Department of Surgery, Boston Children's Hospital, Boston, Massachusetts
- Department of Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts
| | - Davia Schioppo
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Barbara O'Brien
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Maternal Fetal Care Center, Division of Fetal Medicine and Surgery, Department of Surgery, Boston Children's Hospital, Boston, Massachusetts
- Department of Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts
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8
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Rogers AP, Fitzgerald L, Liebelt J, Barnett C. Medicare-funded reproductive genetic carrier screening in Australia has arrived: are we ready? Med J Aust 2024; 220:394-397. [PMID: 38493786 DOI: 10.5694/mja2.52261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/11/2023] [Indexed: 03/19/2024]
Affiliation(s)
- Alice P Rogers
- SA Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA
- University of Adelaide, Adelaide, SA
| | - Lara Fitzgerald
- SA Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA
- Repromed (Adelaide Fertility Centre), Adelaide, SA
| | - Jan Liebelt
- SA Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA
- Repromed (Adelaide Fertility Centre), Adelaide, SA
| | - Christopher Barnett
- SA Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA
- University of Adelaide, Adelaide, SA
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Van Tongerloo AJAG, Verdin H, Steyaert W, Coucke PJ, Janssens S. Accepting or declining preconception expanded carrier screening: An exploratory study with 407 couples. J Genet Couns 2024. [PMID: 38610077 DOI: 10.1002/jgc4.1899] [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: 11/04/2021] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Rapidly evolving genomic technologies have made genetic expanded carrier screening (ECS) possible for couples considering a pregnancy. The aim of ECS is to identify couples at risk of having a child affected with a severe disorder and to facilitate their reproductive decision-making process. The ECS test we offer at our center, called BeGECS (Belgian Genetic ECS), consists of 1268 autosomal recessive (AR) and X-linked pathogenic genes, including severe childhood-onset disorders. However, thus far data are scarce regarding the actual uptake of preconception ECS in a clinical setting. Therefore, our aim was to describe the characteristics of 407 couples to whom ECS was offered at the Center for Medical Genetics of the University Hospital Ghent (CMGG). In addition, we aimed to identify their reasons for accepting or declining BeGECS. Between October 2019 and January 2023, 407 preconception couples were offered BeGECS and were asked to fill in a questionnaire after their decision. Of the 407 couples participating in the survey, 270 (66%) decided to take the test and 137 (34%) declined. We observed that age, highest education level as well as indication for consultation were statistically different between the group that accepted to take the test and the group that declined (p = 0.037). In particular, age and education level were substantially higher in the group that accepted the test. Major reasons for taking BeGECS include prevention, wishing to obtain all information possible, helping preparing their future reproductive decision and increasing their sense of control by being informed. However, couples that do not chose to take BeGECS stated that too much information would make them anxious, that the result would not change their decision to have children, that they do not want to spend money on something that will not happen and that they do not worry about their family history. These findings show that the majority of preconception couples that were offered ECS, accepted the test.
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Affiliation(s)
| | - Hannah Verdin
- Center for Medical Genetics Ghent, University Hospital Ghent, Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics Ghent, University Hospital Ghent, Ghent, Belgium
| | - Paul J Coucke
- Center for Medical Genetics Ghent, University Hospital Ghent, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics Ghent, University Hospital Ghent, Ghent, Belgium
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Tan L, Qi Y, Zhao P, Cheng L, Yu G, Zhao D, Song YX, Xiang YG. Clinical application value of pre-pregnancy carrier screening in Chinese Han childbearing population. Mol Genet Genomic Med 2024; 12:e2425. [PMID: 38562051 PMCID: PMC10985407 DOI: 10.1002/mgg3.2425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/29/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND To explore the clinical application value of pre-conception expanded carrier screening (PECS) in the Chinese Han ethnicity population of childbearing age. METHODS The results of genetic testing of infertile parents who underwent PECS in the Reproductive Medicine Center of the Second Affiliated Hospital of Zhengzhou University, China, from September 2019 to December 2021, were retrospectively analyzed. The carrier rate of single gene disease, the detection rate of high-risk parents, and the clinical outcome of high-risk parents were statistically analyzed. RESULTS A total of 1372 Chinese Han ethnicity patients underwent PECS, among which 458 patients underwent the extended 108-gene test, their overall carrier rate was 31.7%, and the detection rate of high-risk parents was 0.3%. The highest carrier rates were SLC22A (2.4%), ATP7B (2.4%), MMACHC (2.2%), PAH (1.8%), GALC (1.8%), MLC1 (1.3%), UNC13D (1.1%), CAPN3 (1.1%), and PKHD1 (1.1%). There were 488 women with fragile X syndrome-FMR1 gene detection, and 6 patients (1.2%) had FMR1 gene mutation. A total of 426 patients were screened for spinal muscular atrophy-SMN1, and the carrier rate was 3.5%, and the detection rate of parents' co-carrier was 0.5%. CONCLUSION Monogenic recessive hereditary diseases had a high carrier rate in the population. Pre-pregnancy screening could provide good prenatal and postnatal care guidance for patients and preimplantation genetic testing for monogenic/single gene disorders (PGT-M) and prenatal diagnosis could provide more precise reproductive choices for high-risk parents.
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Affiliation(s)
- Li Tan
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yuefan Qi
- Department of Medical ImagingThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Peijuan Zhao
- Department of Reproductive GeneticsPingdingshan Maternal and Child Health HospitalPingdingshanChina
| | - LanLan Cheng
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Guo Yu
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Dongmei Zhao
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yu Xia Song
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yun Gai Xiang
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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11
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Vora NL, Langlois S, Chitty LS. Current controversy in prenatal diagnosis: The use of cfDNA to screen for monogenic conditions in low risk populations is ready for clinical use. Prenat Diagn 2024; 44:389-397. [PMID: 37991340 DOI: 10.1002/pd.6469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
Noninvasive cfDNA testing for monogenic disorders (sgNIPT) has become integrated into the care of pregnant women at increased risk based on carrier status, known family history, or ultrasound anomalies. The availability of commercial tests for common autosomal recessive and de novo autosomal dominant conditions has led to the use of these tests in low-risk pregnancies. However, is the technology ready for use in this low-risk population? This report is a summary of the debate on this topic at the 27th International Conference on Prenatal Diagnosis and Therapy. Both expert debaters provided strong arguments in favor and against the use of sgNIPT in low-risk pregnancies. The argument in favor of sgNIPT for autosomal recessive conditions is that it allows the identification of affected pregnancies without the need for involving the partner in testing. Arguments for sgNIPT for autosomal dominant conditions include identification of affected fetuses that would have either presented later in pregnancy with fetal anomalies or not been detected prenatally given normal ultrasounds, respect for patient autonomy and patient desire for information. Strong arguments were made against offering sgNIPT screening. Given that traditional carrier screening for recessive conditions can be carried out in many jurisdictions, the added value of sgNIPT has not been clearly demonstrated. Arguments against sgNIPT for autosomal dominant conditions included the total lack of clinical validation studies and the risk of false reassurance in cases of negative results and unnecessary invasive procedures in cases of false positive results. Although there is a desire to take advantage of new technologies to improve the detection of monogenic disorders in low-risk populations, based on the discussion and the audience vote, it appears premature to offer sgNIPT to all low risk pregnant women. Further clinical validation studies are needed prior to broad implementation.
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Affiliation(s)
- Neeta L Vora
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lyn S Chitty
- Genetics and Genomic Medicine, UCL Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, England
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Ricca J, Brandt JS, Jacob N, Ashkinadze E. Uptake rate of carrier screening among consanguineous couples. Prenat Diagn 2024. [PMID: 38497814 DOI: 10.1002/pd.6556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
OBJECTIVE To quantify the uptake rates of Carrier Screening (CS) in consanguineous couples and compare this rate to that of non-consanguineous couples. METHODS We performed a matched case control study of 82 consanguineous couples seen at Rutgers-Robert Wood Johnson Medical school who were offered carrier screening between January 1, 2012 and October 10, 2022. We then matched each consanguineous female patient to a non-consanguineous female control patient who was also offered CS at the time of their genetic counseling appointment. A 2 × 2 contingency table analysis was used to compare rates of acceptance and declination between the consanguineous and non-consanguineous groups. RESULTS The overall acceptance rate among consanguineous couples was 82.9%, whereas the overall acceptance rate among non-consanguineous couples was 56.1%. After statistical analysis, consanguineous couples were significantly more likely to accept CS as compared to non-consanguineous couples (OR = 3.801, 95% CI; p < 0.0001). We also report the carrier couple rates and individual carrier statistics between these two groups. CONCLUSION This study supports the idea that consanguineous couples are more likely to pursue CS and have a higher carrier couple yield.
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Affiliation(s)
- Julianne Ricca
- Department of Oncology Services, Rutgers Cancer Institute of New Jersey at University Hospital, Newark, New Jersey, USA
- Rutgers University Genetic Counseling Master's Program, Piscataway, New Jersey, USA
| | - Justin S Brandt
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | | | - Elena Ashkinadze
- Rutgers University Genetic Counseling Master's Program, Piscataway, New Jersey, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
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13
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Romdhane L, Kefi S, Mezzi N, Abassi N, Jmel H, Romdhane S, Shan J, Chouchane L, Abdelhak S. Ethnic and functional differentiation of copy number polymorphisms in Tunisian and HapMap population unveils insights on genome organizational plasticity. Sci Rep 2024; 14:4654. [PMID: 38409353 PMCID: PMC10897484 DOI: 10.1038/s41598-024-54749-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024] Open
Abstract
Admixture mapping has been useful in identifying genetic variations linked to phenotypes, adaptation and diseases. Copy number variations (CNVs) represents genomic structural variants spanning large regions of chromosomes reaching several megabases. In this investigation, the "Canary" algorithm was applied to 102 Tunisian samples and 991 individuals from eleven HapMap III populations to genotype 1279 copy number polymorphisms (CNPs). In this present work, we investigate the Tunisian population structure using the CNP makers previously identified among Tunisian. The study revealed that Sub-Saharan African populations exhibited the highest diversity with the highest proportions of allelic CNPs. Among all the African populations, Tunisia showed the least diversity. Individual ancestry proportions computed using STRUCTURE analysis revealed a major European component among Tunisians with lesser contribution from Sub-Saharan Africa and Asia. Population structure analysis indicated the genetic proximity with Europeans and noticeable distance from the Sub-Saharan African and East Asian clusters. Seven genes harbouring Tunisian high-frequent CNPs were identified known to be associated with 9 Mendelian diseases and/or phenotypes. Functional annotation of genes under selection highlighted a noteworthy enrichment of biological processes to receptor pathway and activity as well as glutathione metabolism. Additionally, pathways of potential concern for health such as drug metabolism, infectious diseases and cancers exhibited significant enrichment. The distinctive genetic makeup of the Tunisians might have been influenced by various factors including natural selection and genetic drift, resulting in the development of distinct genetic variations playing roles in specific biological processes. Our research provides a justification for focusing on the exclusive genome organization of this population and uncovers previously overlooked elements of the genome.
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Affiliation(s)
- Lilia Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
- Department of Biology, Faculty of Sciences of Bizerte, University of Carthage, Zarzouna, Tunisia.
| | - Sameh Kefi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nessrine Mezzi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najla Abassi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Haifa Jmel
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Safa Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Jingxuan Shan
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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14
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Isley L, Callum P, Luque J, Park J, Baldwin K. Management considerations for clinically relevant findings on expanded carrier screening in a sperm donor applicant population. F S Rep 2023; 4:384-389. [PMID: 38204949 PMCID: PMC10774867 DOI: 10.1016/j.xfre.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 01/12/2024] Open
Abstract
Objective To describe the clinical experience of managing expanded carrier screening (ECS) results in sperm donor applicants at a sperm bank in the United States, including considerations around suitability determination and appropriate education of prospective donors and recipients. Design A retrospective review of donor genetic screening records from July 2017 to December 2021. Setting A U.S.-based sperm bank. Patients Donor applicants at a sperm bank. Intervention Not applicable. Main Outcome Measures To examine the rate of potentially significant health risks on the basis of ECS results to inform donor management and donor/recipient counseling considerations. Results Nearly 2% of donor applicants were identified as having potentially significant health risks on the basis of their ECS results, and most individuals had no clinical manifestations related to these findings. Conclusion There are unique challenges related to ECS in third-party reproduction for gamete providers, recipients, and their healthcare providers. A collaborative, multidisciplinary approach is necessary to help mitigate risks to donor offspring and maximize patient experience. Informed consent and access to a trained genetics professional are paramount when facilitating ECS on donor applicants and disseminating results to recipients.
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15
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Souter V, Prigmore B, Becraft E, Repass E, Smart T, Sanapareddy N, Schweitzer M, Ortiz JB, Wang Y, Benn P. Reproductive Carrier Screening Results With Maternal Health Implications During Pregnancy. Obstet Gynecol 2023; 142:1208-1216. [PMID: 37562044 DOI: 10.1097/aog.0000000000005318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 08/12/2023]
Abstract
OBJECTIVE To identify conditions on a reproductive carrier screening panel with the potential for carrier manifestations during pregnancy and review the implications for obstetric care. METHODS This was a retrospective cross-sectional study of consecutive samples from female patients aged 18-55 years submitted to a commercial laboratory for a 274-gene carrier screening panel (January 2020 to September 2022). A literature review was performed to identify genes on the panel with potential for pregnancy complications in carriers. Carrier expression and published recommendations for clinical management were reviewed. RESULTS We identified 12 genes with potential for carrier manifestations during pregnancy based on reports in the literature: nine with manifestations irrespective of the fetal genetic status ( ABCB11 , COL4A3 , COL4A4 , COL4A5 , DMD , F9 , F11 , GLA , and OTC ) and three ( CPT1A , CYP19A1 , and HADHA ) with manifestations only if the fetus is affected by the condition. Manifestations included cardiomyopathy, hemorrhage, gestational hypertensive disorders, cholestasis of pregnancy, acute fatty liver, hyperammonemic crisis, and maternal virilization. Published recommendations for carrier management were identified for 11 of the 12 genes. Of 91,637 tests performed during the study period, a pathogenic or likely pathogenic variant was identified in 2,139 (2.3%), giving a carrier frequency for any of the 12 genes of 1 in 43 (95% CI 1/41-45) 1,826 (2.0%) of the study population were identified as carriers for one of the nine genes with the potential for carrier manifestations irrespective of an affected or unaffected fetus. CONCLUSION Approximately 1 in 40 female patients were identified as carriers for a condition with potential for maternal manifestations in pregnancy, including some serious or even life-threatening complications. Obstetric care professionals should be aware of the possibility of pregnancy complications among carriers and the available recommendations for management. FUNDING SOURCE This study was funded by Natera, Inc.
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Affiliation(s)
- Vivienne Souter
- Natera, Inc., Austin, Texas; and the University of Connecticut Health Center, Farmington, Connecticut
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16
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Volovsky M, Frankfurter D. Gamete donors: to test, or how much to test? These are the questions. Fertil Steril 2023; 120:991-992. [PMID: 37709117 DOI: 10.1016/j.fertnstert.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Affiliation(s)
- Michelle Volovsky
- Division of Reproductive Endocrinology and Infertility, Yale Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut
| | - David Frankfurter
- Division of Reproductive Endocrinology and Infertility, Yale Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut
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17
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Tschirgi ML, Liaquat K, Mahey Kumar M, Wilson KL. Abandoning the word Caucasian. J Genet Couns 2023; 32:930-936. [PMID: 37237433 DOI: 10.1002/jgc4.1730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/21/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023]
Abstract
Traditionally, the field of genetics has used patient-reported genetic ancestry to assist in risk assessment, calculate detection rates, and understand residual risks for recessive or X-linked genetic diseases. Patient-reported genetic ancestry is useful for variant curation, based on practice guidelines from medical societies. Words used to describe a person's race, ethnicity, and genetic ancestry have changed over the last few centuries, especially in the last few decades. The origin and use of Caucasian to describe people of European ancestry have come into question. With recommendations from the Department of Health and Human Services (HHS) and the American College of Medical Genetics and Genomics (ACMG), among other organizations, the medical and genetics communities are moving away from using this term altogether. The purpose of this article is to review the history of the word Caucasian and to provide evidence that it should be avoided when documenting genetic ancestry in medical records, laboratory forms, and medical research.
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18
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Harper T, Kuohung W, Sayres L, Willis MD, Wise LA. Optimizing preconception care and interventions for improved population health. Fertil Steril 2023; 120:438-448. [PMID: 36516911 DOI: 10.1016/j.fertnstert.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
There is growing literature indicating that optimal preconception health is associated with improved reproductive, perinatal, and pediatric outcomes. Given that preconception care is recommended for all individuals planning a pregnancy, medical providers and public health practitioners have a unique opportunity to optimize care and improve health outcomes for reproductive-aged individuals. Knowledge of the determinants of preconception health is important for all types of health professionals, including policy makers. Although some evidence-based recommendations have already been implemented, additional research is needed to identify factors associated with favorable health outcomes and to ensure that effective interventions are made in a timely fashion. Given the largely clinical readership of this journal, this piece is primarily focused on clinical care. However, we acknowledge that optimizing preconception health for the entire population at risk of pregnancy requires broadening our strategies to include population-health interventions that consider the larger social systems, structures, and policies that shape individual health outcomes.
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Affiliation(s)
- Teresa Harper
- Division of Maternal and Fetal Medicine, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, Colorado.
| | - Wendy Kuohung
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Boston University School of Medicine, Boston, Massachusetts
| | - Lauren Sayres
- Division of Maternal and Fetal Medicine, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, Colorado
| | - Mary D Willis
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Lauren A Wise
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
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19
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Chen SC, Zhou XY, Li SY, Zhao MM, Huang HF, Jia J, Xu CM. Carrier burden of over 300 diseases in Han Chinese identified by expanded carrier testing of 300 couples using assisted reproductive technology. J Assist Reprod Genet 2023; 40:2157-2173. [PMID: 37450097 PMCID: PMC10440320 DOI: 10.1007/s10815-023-02876-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Expanded carrier screening (ECS) has become a common practice for identifying carriers of monogenic diseases. However, existing large gene panels are not well-tailored to Chinese populations. In this study, ECS testing for pathogenic variants of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in 330 genes implicated in 342 autosomal recessive (AR) or X-linked diseases was carried out. We assessed the differences in allele frequencies specific to the Chinese population who have used assisted reproductive technology (ART) and the important genes to screen for in this population. METHODOLOGY A total of 300 heterosexual couples were screened by our ECS panel using next-generation sequencing. A customed bioinformatic algorithm was used to analyze SNVs and CNVs. Guidelines from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology were adapted for variant interpretation. Pathogenic or likely pathogenic (P/LP) SNVs located in high homology regions/deletions and duplications of one or more exons in length were independently verified with other methods. RESULTS 64.83% of the patients were identified to be carriers of at least one of 342 hereditary conditions. We identified 622 P/LP variants, 4.18% of which were flagged as CNVs. The rate of at-risk couples was 3%. A total of 149 AR diseases accounted for 64.05% of the cumulative carrier rate, and 48 diseases had a carrier rate above 1/200 in the test. CONCLUSION An expanded screening of inherited diseases by incorporating different variant types, especially CNVs, has the potential to reduce the occurrence of severe monogenic diseases in the offspring of patients using ART in China.
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Affiliation(s)
- Song-Chang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xuan-You Zhou
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shu-Yuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ming-Min Zhao
- Fujungenetics Biotechnology Co., Ltd., No. 70 of Tongchuan Road, Putuo District, Shanghai, 200333, China
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Jia Jia
- Fujungenetics Biotechnology Co., Ltd., No. 70 of Tongchuan Road, Putuo District, Shanghai, 200333, China.
| | - Chen-Ming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, 566 Fangxie Road, Huangpu District, Shanghai, 200001, China.
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.
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20
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Dunn TM, Subramaniam A. Updates in Genetic Screening for the General Obstetrician. Obstet Gynecol Clin North Am 2023; 50:493-507. [PMID: 37500212 DOI: 10.1016/j.ogc.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The number of prenatal genetic screening options, including aneuploidy screening and carrier screening, has drastically increased with rapid advancements in DNA sequencing technologies. Noninvasive prenatal screening analyzing cell-free DNA has quickly been integrated into routine prenatal care as it is the most sensitive and specific screening method for pregnancies at increased and average risk of fetal aneuploidy. The aim of this article is to outline current recommendations for cell-free DNA screening and carrier screening, important aspects of pretest and posttest counseling for obstetric providers, and which patients should be referred to a genetic specialist.
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Affiliation(s)
- Taylor M Dunn
- Department of Genetics, University of Alabama at Birmingham, 1720 2nd Avenue South, VH1L108B, Birmingham, AL 35294-0019, USA.
| | - Akila Subramaniam
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of Alabama at Birmingham, 1700 6th Avenue South, Women and Infants Center, 10270, Birmingham, AL 35249, USA
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21
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Veneruso I, Ranieri A, Falcone N, Tripodi L, Scarano C, La Monica I, Pastore L, Lombardo B, D’Argenio V. The Potential Usefulness of the Expanded Carrier Screening to Identify Hereditary Genetic Diseases: A Case Report from Real-World Data. Genes (Basel) 2023; 14:1651. [PMID: 37628702 PMCID: PMC10454493 DOI: 10.3390/genes14081651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Expanded carrier screening (ECS) means a comprehensive genetic analysis to evaluate an individual's carrier status. ECS is becoming more frequently used, thanks to the availability of techniques such as next generation sequencing (NGS) and array comparative genomic hybridization (aCGH), allowing for extensive genome-scale analyses. Here, we report the case of a couple who underwent ECS for a case of autism spectrum disorder in the male partner family. aCGH and whole-exome sequencing (WES) were performed in the couple. aCGH analysis identified in the female partner two deletions involving genes associated to behavioral and neurodevelopment disorders. No clinically relevant alterations were identified in the husband. Interestingly, WES analysis identified in the male partner a pathogenic variant in the LPL gene that is emerging as a novel candidate gene for autism. This case shows that ECS may be useful in clinical contexts, especially when both the partners are analyzed before conception, thus allowing the estimation of their risk to transmit an inherited condition. On the other side, there are several concerns related to possible incidental findings and difficult-to-interpret results. Once these limits are defined by the establishment of specific guidelines, ECS may have a greater diffusion.
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Affiliation(s)
- Iolanda Veneruso
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Annaluisa Ranieri
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
| | - Noemi Falcone
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lorella Tripodi
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Carmela Scarano
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Ilaria La Monica
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Barbara Lombardo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, via di Val Cannuta 247, 00166 Rome, Italy
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22
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Buckley LE, Hopkins MK, Kuller JA. The Evolving Landscape of Genetic Carrier Screening: Clinical Considerations and Challenges. Obstet Gynecol Surv 2023; 78:483-489. [PMID: 37594438 DOI: 10.1097/ogx.0000000000001168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Importance Genetic carrier screening is performed to identify carriers of rare genetic diseases. Identification of carriers allows patients to make informed reproductive health choices and can decrease the incidence of genetic disorders with serious medical implications. Objective This review aims to provide an overview of the history of prenatal genetic screening and the various forms of carrier screening, a synopsis of recent changes in society recommendations and current practice guidelines, and discussion of clinical challenges associated with carrier screening. Evidence Acquisition Published practice guidelines from relevant professional societies were reviewed and synthesized. PubMed search was performed for relevant history and clinical considerations of carrier screening. Results Information and evidence summarized in this review include professional society practice guidelines, review articles, and peer-reviewed research articles. Conclusions and Relevance Current practice guidelines differ between stakeholder professional organizations. Expanded carrier screening offers increased identification of rare disease carriers allowing for more informed reproductive choices. However, there are several barriers to the implementation of expanded carrier screening for all patients.
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Affiliation(s)
| | - Maeve K Hopkins
- Associate Staff, Section of Maternal-Fetal Medicine, Women's Health Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - Jeffrey A Kuller
- Professor, Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC
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23
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Rice SM, McLaren RA, Mustafa HJ, Dugoff L, Al-Kouatly HB. Connecting the dots: Carrier screening and the Genetic Information Nondiscrimination Act in the United States. Prenat Diagn 2023; 43:1142-1149. [PMID: 37392371 DOI: 10.1002/pd.6405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/17/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023]
Abstract
OBJECTIVE To highlight the possibility of genetic discrimination in the United States with respect to carrier screening under limitations of the Genetic Information Nondiscrimination Act (GINA) and to encourage providers to educate patients about this possibility during pretest counseling. METHODS Review of current professional guidelines and practice resources regarding the necessary components of pretest counseling for carrier screening in the context of GINA's limitations and the potential impact of carrier screening results on life, long-term care and disability insurance. RESULTS Current practice resources advise that patients in the United States should be informed that their employer or health insurance company generally cannot use their genetic information during the underwriting process. However, these resources do not elaborate on GINA's limitations or explain why there may be adverse consequences to patients regarding these limitations. Studies have demonstrated significant gaps in provider knowledge of GINA, especially for those without formal genetic training. CONCLUSION Enhanced education and provision of GINA educational resources for providers and patients will help ensure that patients have the opportunity to prioritize their insurance needs prior to undergoing carrier screening.
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Affiliation(s)
- Stephanie M Rice
- Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Rodney A McLaren
- Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Hiba J Mustafa
- Division of Maternal-Fetal Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Fetal Center, Riley Children's Health, Indiana University Health, Indianapolis, Indiana, USA
| | - Lorraine Dugoff
- Division of Reproductive Genetics, Division of Maternal-Fetal Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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24
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McGlynn J, DeCelie-Germana JK, Kier C, Langfelder-Schwind E. Reproductive Counseling and Care in Cystic Fibrosis: A Multidisciplinary Approach for a New Therapeutic Era. Life (Basel) 2023; 13:1545. [PMID: 37511919 PMCID: PMC10381247 DOI: 10.3390/life13071545] [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: 05/19/2023] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023] Open
Abstract
With the advent of highly effective modulator therapies, many people with cystic fibrosis (CF) are living longer, healthier lives. Pregnancy rates for women with CF more than doubled between 2019 and 2021, reflecting increases in both planned and unplanned pregnancies. For men with CF, CF-associated infertility can be mitigated with assistive reproductive technology, yet patient knowledge of these challenges and options is variable. Preconception and prenatal counseling for individuals with CF and for parents of children with CF who wish to expand their families requires nuanced discussions to promote informed reproductive decisions, drawing from a combination of standard practice recommendations and CF-specific assessments. This review article synthesizes the current literature and practice recommendations regarding reproductive counseling and care in CF, outlining the role of genetic counseling, carrier screening, teratogen counseling, in vitro fertilization and pre-implantation genetic diagnosis, and careful assessment and management of cystic fibrosis-related diabetes when present. Via a multidisciplinary, patient-centered approach, clinicians can support adults with CF and parents of children with CF as they make informed reproductive decisions and embark on family planning.
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Affiliation(s)
- Julie McGlynn
- Gynecology and Reproductive Sciences, Department of Obstetrics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Joan K DeCelie-Germana
- Zucker School of Medicine at Northwell Division of Pediatric Pulmonary, and Cystic Fibrosis Center, Cohen Children's Medical Center, New Hyde Park, NY 11040, USA
| | - Catherine Kier
- Renaissance School of Medicine at Stony Brook, Department of Pediatrics, Stony Brook, NY 11794, USA
| | - Elinor Langfelder-Schwind
- The Cystic Fibrosis Center, Department of Pulmonary Medicine, Lenox Hill Hospital, Northwell Health, New York, NY 10075, USA
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Jämterud SM, Snoek A. Preconception Expanded Carrier Screening: A Discourse Analysis of Dutch Webpages. Healthcare (Basel) 2023; 11:healthcare11101511. [PMID: 37239797 DOI: 10.3390/healthcare11101511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Preconception expanded carrier screening (PECS) informs prospective parents about the risk of conceiving a child with a heritable genetic condition. PECS will also, for many, become an important screening test, and websites will likely play a vital role in providing information on this practice. The aim of this article is to examine rationalities in the information on PECS on Dutch websites. The method used is multimodal critical discourse analysis. This method allows an examination of norms and assumptions in the descriptions, as well as of the positions that are discursively made available. The data consist of publicly available material on websites from two genetics departments in the Netherlands. In the results, we present the three main discourses and subject positions that were identified: risk and the couple as possible mediators of severe conditions; the focus on scientific facts and rational conceivers; and severity of the conditions and the responsible couple. In this study, we highlight the importance of acknowledging the interrelation between epistemology and ethics in the discourse on PECS. Finally, it is claimed that the focus on scientific facts in information on PECS risks making existential and ethical dilemmas and choices invisible.
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Affiliation(s)
- Sofia Morberg Jämterud
- Department of Thematic Studies, Technology and Social Change, Linköping University, 581 85 Linköping, Sweden
| | - Anke Snoek
- Department of Ethics, Law and Medical Humanities, Amsterdam University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
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Fang Y, Li J, Zhang M, Cheng Y, Wang C, Zhu J. Clinical application value of expanded carrier screening in the population of childbearing age. Eur J Med Res 2023; 28:151. [PMID: 37031186 PMCID: PMC10082524 DOI: 10.1186/s40001-023-01112-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
OBJECTIVE The objective of this study was to explore the clinical utility of the implementation of expanded carrier screening (ECS) in Chinese population of childbearing age. MATERIALS AND METHODS Based on capillary electrophoresis, a first-generation sequencing technology, a prospective screening study of carriers of 15 single-gene diseases was carried out in 327 subjects in Anhui Province, including 84 couples and 159 women of childbearing age, the disease carrier rate, types of screened pathogenic genes, and incidence of both partners carrying the same pathogenic genes were summarized and analyzed. RESULTS In 320 people with normal phenotypes who underwent ECS for 15 genetic diseases and 7 spouses who underwent targeted gene sequencing, 65 carriers of at least one disease were detected, with a total carrier rate of 20.31% (65/320). Among the 65 carriers, 81.54% (53/65) carried one genetic variant, 16.92% (11/65) carried two genetic variants, and 1.54% (1/65) carried three genetic variants. In this study, the three diseases with the highest carrier rates were hereditary deafness (8.13%, 26/320), Wilson's disease (4.06%, 13/320), and phenylketonuria (3.13%, 10/320). One high-risk couple (1.19%, 1/84) was detected. CONCLUSIONS It has certain clinical application value to implement ECS in the population of childbearing age in China.
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Affiliation(s)
- Yuqin Fang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jingran Li
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Miaomiao Zhang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Yuan Cheng
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Chaohong Wang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China.
- Maternity and Child Health Hospital of Anhui Province, Hefei, China.
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27
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Pasquier L, Reyneke M, Beeckman L, Siermann M, Van Steijvoort E, Borry P. Attitudes of professional stakeholders towards implementation of reproductive genetic carrier screening: a systematic review. Eur J Hum Genet 2023; 31:395-408. [PMID: 36631542 PMCID: PMC10133284 DOI: 10.1038/s41431-022-01274-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/27/2022] [Accepted: 12/15/2022] [Indexed: 01/13/2023] Open
Abstract
Reproductive genetic carrier screening (RGCS) for hundreds of different genetic conditions is technically available for prospective parents, but these tests have not been integrated in a public health policy except for specific sub-groups. We aimed to provide an overview of the perspectives of multiple professional stakeholder groups in order to enhance a responsible implementation of population-based reproductive genetic carrier screening. We conducted a systematic literature search using eight online databases focussing on studies that were published from January 2009 to January 2021. We selected articles dealing with attitudes and opinions from different professional stakeholders, in particular healthcare professionals and policymakers, on how to implement a policy about carrier screening for a reproductive purpose. We identified 18 studies that met our inclusion criteria. Based on our inductive analysis, we identified ten themes categorized in both clinical and program management challenges: ensuring availability of RGCS to all couples who request the test, embedding RGCS as a test offer before pregnancy, providing clear and reliable information, ensuring voluntary participation, developing genetic counselling pre- and post-testing (after positive or negative result), avoiding psychological harm, ensuring equal access, avoiding social pressure, educating and involving a broad spectrum of non-genetic health care professionals, and promoting an independent non-commercial organisational structure. We highlight one major stumbling block on how to responsibly inform couples about hundreds different genetic conditions within constraints regarding time and ability of non-genetic professionals. We promote further research to tackle the issues brought up by this systematic review through pilot studies. Trial Registration: PROSPERO International Prospective Register of Systematic Reviews PROSPERO 2021 # CRD42021233762; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=233762 .
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Affiliation(s)
- Laurent Pasquier
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium.
- Clinical genetics, Reference Center for Rares Diseases "Intellectual Disabilities", Rennes University Hospital, 35203, Rennes, France.
| | - Maryn Reyneke
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
- Faculty of Health, Medicine and Life Sciences, Department of Health, Ethics and Society GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Lauranne Beeckman
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Maria Siermann
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Eva Van Steijvoort
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Pascal Borry
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
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Abstract
Thalassemia syndromes are common monogenic disorders and represent a significant health issue worldwide. In this review, the authors elaborate on fundamental genetic knowledge about thalassemias, including the structure and location of globin genes, the production of hemoglobin during development, the molecular lesions causing α-, β-, and other thalassemia syndromes, the genotype-phenotype correlation, and the genetic modifiers of these conditions. In addition, they briefly discuss the molecular techniques applied for diagnosis and innovative cell and gene therapy strategies to cure these conditions.
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Affiliation(s)
- Nicolò Tesio
- Department of Clinical and Biological Sciences, San Luigi Gonzaga University Hospital, University of Torino, Regione Gonzole, 10, 10043 Orbassano, Turin, Italy. https://twitter.com/nicolotesio
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA.
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Raymond MB, Barbera JP, Boudova S, Vinekar K, Horgan R, McLaren R, Al-Kouatly HB. Implications for Prenatal Genetic Testing in the United States After the Reversal of Roe v Wade. Obstet Gynecol 2023; 141:445-454. [PMID: 36649348 DOI: 10.1097/aog.0000000000005094] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/15/2022] [Indexed: 01/18/2023]
Abstract
Prenatal genetic screening and diagnostic testing should be offered to every pregnant individual, with methods varying based on gestational age. Since Roe v Wade was overturned in June 2022, many states have implemented gestational age-based abortion restrictions. It is critical that reproductive health care professionals be aware of the interaction between the timing of genetic screening and diagnostic testing and the availability of legal abortion services in their state. We examined individual state abortion restrictions per publicly available data from The New York Times and the Guttmacher Institute and reviewed which genetic screening and diagnostic tests could be performed to provide results in time for individuals to decide whether to terminate their pregnancies legally in each state. As of December 11, 2022, 14 states have restrictions in which no diagnostic testing could be completed before gestational age-based cutoffs. Gestational age-based abortion restrictions may also influence a patient to favor chorionic villous sampling (CVS) over amniocentesis. There are two states, Florida and Arizona, where CVS would be feasible before the state's gestational age limit on abortion but amniocentesis would not. Both CVS and amniocentesis are feasible in 35 states, with legal challenges pending in 8 of the 35. Seven states specifically prohibit abortion for fetuses with genetic abnormalities. Clinicians may be placed in the suboptimal position of counseling patients with screening results alone before the gestational age-based ban in their state. There are several potential downstream consequences of gestational age-based termination restrictions for current genetic screening and testing paradigms, from adjustments to counseling options to potentially higher CVS procedure rates. Clinicians should be prepared for practice patterns to change to best serve patients in this evolving legal context.
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Affiliation(s)
- Megan B Raymond
- Department of Obstetrics and Gynecology, the Sidney Kimmel Medical College, and the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, Pennsylvania; and the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, Virginia
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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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Yang H, Li M, Zou L, Zou H, Zhao Y, Cui Y, Han J. A regionally adapted HRM-based technique to screen MMACHC carriers for methylmalonic acidemia with homocystinuria in Shandong Province, China. Intractable Rare Dis Res 2023; 12:29-34. [PMID: 36873673 PMCID: PMC9976096 DOI: 10.5582/irdr.2023.01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 02/27/2023] Open
Abstract
Methylmalonic acidemia with homocystinuria (MMA-cblC) is an autosomal recessive genetic disorder of organic acid metabolism. Shandong, a northern province of China, has a significantly high incidence of about 1/4,000, suggesting a high carrying rate among the local population. The current study established a PCR technique involving high-resolution melting (HRM) to screen for carriers based on hotspot mutation analysis to further develop a preventive strategy to reduce the local incidence of this rare disease. Whole-exome sequencing of 22 families with MMA-cblC and a comprehensive literature review were used to identify MMACHC hotspot mutations in Shandong Province. Subsequently, a PCR-HRM assay based on the selected mutations was established and optimized for large-scale hotspot mutation screening. The accuracy and efficiency of the screening technique was validated using samples from 69 individuals with MMA-cblC and 1,000 healthy volunteers. Six hotspot mutations in the MMACHC gene (c.609G>A, c.658_660delAAG, c.80A>G, c.217C>T, c.567dupT and c.482G>A), which account for 74% of the alleles associated with MMA-cblC, were used to establish a screening technique. The established PCR-HRM assay detected 88 MMACHC mutation alleles in a validation study with 100% accuracy. In the general population in Shandong, the carrying rate of 6 MMACHC hotspot mutations was 3.4%. In conclusion, the 6 hotspots identified cover the majority of the MMACHC mutation spectrum, and the Shandong population has a particularly high carrying rate of MMACHC mutations. The PCR-HRM assay is highly accurate, cost-effective, and easy to use, making it an ideal choice for mass carrier screening.
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Affiliation(s)
- Haining Yang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, Shandong, China
- Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, Shandong, China
| | - Mian Li
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, Shandong, China
- Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, Shandong, China
| | - Liang Zou
- Bone Biomechanics Engineering Laboratory of Shandong Province, Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Hui Zou
- Ji'nan Maternity and Child Care Hospital, Ji'nan 250000, Shandong, China
| | - Yan Zhao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, Shandong, China
- Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, Shandong, China
- Address correspondence to:Jinxiang Han, Yazhou Cui, and Yan Zhao, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences; NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences); Key Lab for Rare & Uncommon Diseases of Shandong Province, 6699 Qingdao Road, Ji'nan 250117, Shandong, China. E-mail: (JH); (YC); (YZ)
| | - Yazhou Cui
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, Shandong, China
- Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, Shandong, China
- Address correspondence to:Jinxiang Han, Yazhou Cui, and Yan Zhao, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences; NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences); Key Lab for Rare & Uncommon Diseases of Shandong Province, 6699 Qingdao Road, Ji'nan 250117, Shandong, China. E-mail: (JH); (YC); (YZ)
| | - Jinxiang Han
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, Shandong, China
- Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, Shandong, China
- Address correspondence to:Jinxiang Han, Yazhou Cui, and Yan Zhao, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences; NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences); Key Lab for Rare & Uncommon Diseases of Shandong Province, 6699 Qingdao Road, Ji'nan 250117, Shandong, China. E-mail: (JH); (YC); (YZ)
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Rink BD. Informed consent for expanded carrier screening: Past, present, and future. Prenat Diagn 2023; 43:489-495. [PMID: 36636969 DOI: 10.1002/pd.6310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/01/2022] [Accepted: 01/08/2023] [Indexed: 01/14/2023]
Abstract
History, law, bioethics, and geocultural influences all have impacted the modern application of informed consent. It is a complex, multilayered process to communicate information and obtain voluntary patient permission before a health care intervention. Lack of provider education about genetic disorders, complexities of advanced genomic technologies, limited time during patient encounters, and low health literacy within a population all represent challenges to effective communication. There is no consensus on how informed consent in reproductive genetics is optimally obtained. Expanded carrier screening (ECS) is purposed to simultaneously test for a large list of diseases in a pan-ethnic manner. The increased use of ECS is driven by advances in genomic technologies, decreased cost, an improved understanding of single gene disorders, and in support of reproductive autonomy. Academic organizations recommend pretest counseling when patients consider ECS, yet best practice is not established. Ongoing research is needed to determine how optimally implement informed consent given the increased complexity of ECS.
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Affiliation(s)
- Britton D Rink
- Director Clinical Genetics Mount Carmel Health Systems, Division of Genetic and Genomic Medicine Nationwide Children's Hospital, Columbus, Ohio, USA
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Goldberg JD, Pierson S, Johansen Taber K. Expanded carrier screening: What conditions should we screen for? Prenat Diagn 2023; 43:496-505. [PMID: 36624552 DOI: 10.1002/pd.6306] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/15/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Carrier screening tests reproductive couples for their risk of having children affected by serious monogenic conditions. Carrier screening has historically been offered for certain conditions in high-risk populations. However, more recent evidence has shown that offering carrier screening to all patients, regardless of their ethnicity, more effectively and equitably identifies at-risk couples. Coupled with technology that enables screening for a nearly unlimited number of conditions, this expanded carrier screening (ECS) approach is now supported by professional society guidelines. Despite recent recommendations by the American College of Medical Genetics and Genomics to screen all patients who are pregnant or considering pregnancy for 113 conditions, questions remain about what conditions should be included on a core ECS panel. Here, we briefly review the history of carrier screening and guidelines on criteria for panel design. We then suggest which of these criteria are most critical, as well as thresholds to identify which conditions meet these criteria. Based on these interpretations, we recommend a core panel of 64 conditions that would identify the vast majority of at-risk couples. Widespread adoption of a core panel such as this would result in a marked improvement in the number of patients currently receiving comprehensive carrier screening.
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Heil BJ, Greene CS. The Field-Dependent Nature of PageRank Values in Citation Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522943. [PMID: 36711900 PMCID: PMC9881996 DOI: 10.1101/2023.01.05.522943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The value of scientific research can be easier to assess at the collective level than at the level of individual contributions. Several journal-level and article-level metrics aim to measure the importance of journals or individual manuscripts. However, many are citation-based and citation practices vary between fields. To account for these differences, scientists have devised normalization schemes to make metrics more comparable across fields. We use PageRank as an example metric and examine the extent to which field-specific citation norms drive estimated importance differences. In doing so, we recapitulate differences in journal and article PageRanks between fields. We also find that manuscripts shared between fields have different PageRanks depending on which field's citation network the metric is calculated in. We implement a degree-preserving graph shuffling algorithm to generate a null distribution of similar networks and find differences more likely attributed to field-specific preferences than citation norms. Our results suggest that while differences exist between fields' metric distributions, applying metrics in a field-aware manner rather than using normalized global metrics avoids losing important information about article preferences. They also imply that assigning a single importance value to a manuscript may not be a useful construct, as the importance of each manuscript varies by the reader's field.
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Affiliation(s)
- Benjamin J. Heil
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania
| | - Casey S. Greene
- Department of Pharmacology, University of Colorado School of Medicine; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine
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Abstract
PURPOSE OF REVIEW Prenatal genetic testing can be divided into two categories: screening and diagnostic. This article will focus on reviewing prenatal genetic screening tests. RECENT FINDINGS Cell-free DNA (cfDNA) is a new prenatal genetic screening test with a high degree of accuracy for identifying certain genetic conditions like trisomy 21, 18, and 13. However, cfDNA has also been applied in the screening of other genetic conditions without similar research support. SUMMARY Prenatal genetic screening evaluates at risk pregnancies - including both carrier screening, which can be done at any point in a person's life, and aneuploidy screening, which is done during pregnancy. Within screening, there is a new noninvasive technology that has revolutionized prenatal screening called cfDNA testing. Compared to previous methods, this technology is easier to administer and more accurate for certain genetic conditions. However, cfDNA has also been applied to test for less common genetic conditions without efficacious research support. In this time of expansion in genetic testing, it is important that providers educate themselves on the research support behind each type of genetic test. It is vital that professional organizations continuously update their testing approach to match these rapidly evolving technologies and the patient population they serve.
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Aderoba AK, Adu-Bonsaffoh K. Antenatal and Postnatal Care. Obstet Gynecol Clin North Am 2022; 49:665-692. [DOI: 10.1016/j.ogc.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Beck NM, Sagaser KG, Lawson CS, Hertenstein C, Jachens A, Forster KR, Miller KA, Jelin AC, Blakemore KJ, Hoover‐Fong J. Not just a carrier: Clinical presentation and management of patients with heterozygous disease-causing alkaline phosphatase (ALPL) variants identified through expanded carrier screening. Mol Genet Genomic Med 2022; 11:e2056. [PMID: 36444396 PMCID: PMC9834184 DOI: 10.1002/mgg3.2056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/05/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
Hypophosphatasia (HPP) is an underrecognized, complex bone mineralization disorder with variable manifestations caused by one or two deleterious variants in the alkaline phosphatase (ALPL) gene. Expanded carrier screening (ECS), inclusive of ALPL, intends to inform reproductive risk but may incidentally reveal an HPP diagnosis with 50% familial risks. We sought to investigate at-risk individuals and develop a multidisciplinary referral and evaluation protocol for ECS-identified ALPL heterozygosity. A retrospective database query of ECS results from 8 years to 1 month for heterozygous pathogenic/likely pathogenic ALPL variants was completed. We implemented a clinical protocol for diagnostic testing and imaging, counseling, and interdisciplinary care management for identified patients, and outcomes were documented. Heterozygous ALPL variants were identified in 12/2248 unrelated patients undergoing ECS (0.53%; heterozygote frequency 1/187). Of 10 individuals successfully contacted, all demonstrated symptomatology and/or alkaline phosphatase values consistent with HPP. ECS may reveal incidental health risks, including recognition of missed HPP diagnoses in ALPL heterozygotes. In our cohort, all ECS-identified ALPL heterozygotes with clinical and/or biochemical data available demonstrated features of HPP. Referral to a genetics professional familiar with HPP is indicated for family history assessment, genetic counseling, cascade testing, and long-term bone health management.
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Affiliation(s)
- Natalie M. Beck
- Greenberg Center for Skeletal Dysplasias, Department Genetic of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA,Genome Medical ServicesSan FranciscoCaliforniaUSA
| | - Katelynn G. Sagaser
- Division of Maternal Fetal Medicine, Department of Gynecology and ObstetricsJohns Hopkins University School of MedicineBaltimoreMarylandUSA,JunoDxSan DiegoCaliforniaUSA
| | - Cathleen S. Lawson
- Division of Maternal Fetal Medicine, Department of Gynecology and ObstetricsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Christine Hertenstein
- Division of Maternal Fetal Medicine, Department of Gynecology and ObstetricsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Ashley Jachens
- Center for Maternal and Fetal MedicineHoward County General Hospital, Johns Hopkins HospitalBaltimoreMarylandUSA
| | - Katherine R. Forster
- Center for Fetal TherapyJohns Hopkins University School of MedicineBaltimoreMarylandUSA,Sibley Memorial Hospital Maternal Fetal MedicineWashingtonDistrict of ColumbiaUSA
| | - Kristen A. Miller
- Division of Maternal Fetal Medicine, Department of Gynecology and ObstetricsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Angie C. Jelin
- Division of Maternal Fetal Medicine, Department of Gynecology and ObstetricsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Karin J. Blakemore
- Division of Maternal Fetal Medicine, Department of Gynecology and ObstetricsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Julie Hoover‐Fong
- Greenberg Center for Skeletal Dysplasias, Department Genetic of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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Capalbo A, Gabbiato I, Caroselli S, Picchetta L, Cavalli P, Lonardo F, Bianca S, Giardina E, Zuccarello D. Considerations on the use of carrier screening testing in human reproduction: comparison between recommendations from the Italian Society of Human Genetics and other international societies. J Assist Reprod Genet 2022; 39:2581-2593. [PMID: 36370240 PMCID: PMC9722986 DOI: 10.1007/s10815-022-02653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/31/2022] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Carrier screening (CS) is a term used to describe a genetic test performed on individuals without family history of genetic disorders, to investigate the carrier status for pathogenic variants associated with multiple recessive conditions. The advent of next-generation sequencing enabled simultaneous CS for an increasing number of conditions; however, a consensus on which diseases to include in gene panels and how to best develop the provision of CS is far to be reached. Therefore, the provision of CS is jeopardized and inconsistent and requires solving several important issues. METHODS In 2020, the Italian Society of Human Genetics (SIGU) established a working group composed of clinical and laboratory geneticists from public and private fields to elaborate a document to define indications and best practice of CS provision for couples planning a pregnancy. RESULTS Hereby, we present the outcome of the Italian working group's activity and compare it with previously published international recommendations (American College of Medical Genetics and Genomics (ACMG), American College of Obstetricians and Gynecologists (ACOG), and Royal Australian and New Zealand College of Obstetricians and Gynaecologists (RANZCOG)). We determine a core message on genetic counseling and nine main subject categories to explore, spanning from goals and execution to technical scientific, ethical, and socio-economic topics. Moreover, a level of agreement on the most critical points is discussed using a 5-point agreement scale, demonstrating a high level of consensus among the four societies. CONCLUSIONS This document is intended to provide genetic and healthcare professionals involved in human reproduction with guidance regarding the clinical implementation of CS.
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Affiliation(s)
| | - Ilaria Gabbiato
- Department of Lab Medicine, Unit of Clinical Genetics and Epidemiology University Hospital of Padova, Padua, Italy
| | | | | | | | - Fortunato Lonardo
- UOSD Genetica Medica, AORN "San Pio" - P.O. "G. Rummo", Benevento, Italy
| | | | - Emiliano Giardina
- Laboratorio Di Medicina Genomica - UILDM Università Degli Studi Di Roma "Tor Vergata", Fondazione Santa Lucia-IRCCS, Rome, Italy
| | - Daniela Zuccarello
- Department of Lab Medicine, Unit of Clinical Genetics and Epidemiology University Hospital of Padova, Padua, Italy
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Edwards S, Laing N. Genetic Counselling Needs for Reproductive Genetic Carrier Screening: A Scoping Review. J Pers Med 2022; 12:1699. [PMID: 36294838 PMCID: PMC9605645 DOI: 10.3390/jpm12101699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/17/2022] Open
Abstract
Reproductive genetic carrier screening provides individuals and couples with information regarding their risk of having a child affected by an autosomal recessive or X-linked recessive genetic condition. This information allows them the opportunity to make reproductive decisions in line with their own beliefs and values. Traditionally, carrier screening has been accessed by family members of affected individuals. In recent years, improvements to accessibility and updates to recommendations suggest that all women planning or in early pregnancy should be offered reproductive genetic carrier screening. As uptake moves towards the population scale, how can the genetic counselling needs of such large-scale screening be met? A scoping review of the literature was performed to ascertain what the genetic counselling needs of reproductive genetic carrier screening are, and what future research is needed. Four broad themes were identified in the existing literature: (1) The offer-when and in what context to offer screening; (2) Information-the importance of and what to include in education, and pre- and post-test counselling; (3) Who and how-who the genetic counselling is performed by and how; (4) Personalization-how do we find the balance between standardized and individualized approaches? Based on the existing literature, we present a set of recommendations for consideration in implementing population-scale reproductive genetic carrier screening as well as suggested areas for future research.
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Affiliation(s)
- Samantha Edwards
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia
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40
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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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Xiao M, Shi H, Rao J, Xi Y, Zhang S, Wu J, Zhu S, Zhou J, Xu H, Lei C, Sun X. Combined Preimplantation Genetic Testing for Genetic Kidney Disease: Genetic Risk Identification, Assisted Reproductive Cycle, and Pregnancy Outcome Analysis. Front Med (Lausanne) 2022; 9:936578. [PMID: 35783601 PMCID: PMC9247246 DOI: 10.3389/fmed.2022.936578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundGenetic kidney disease is a major cause of morbidity and mortality in neonates and end-stage renal disease (ESRD) in children and adolescents. Genetic diagnosis provides key information for early identification of congenital kidney disease and reproductive risk counseling. Preimplantation genetic testing for monogenic disease (PGT-M) as a reproductive technology helps prospective parents to prevent passing on disease-causing mutations to their offspring.Materials and MethodsA retrospective cohort of couples counseled on PGT who had a risk to given birth to a child with genetic kidney disease or had a history of prenatal fetal kidney and urinary system development abnormalities from 2011 to 2021. Through a combination of simultaneously screening for aneuploidy and monogenic kidney disease, we achieved reproductive genetic intervention.ResultsA total of 64 couples counseled on PGT for monogenic kidney disease in a single reproductive center during the past 10 years, of whom 38 different genetic kidney diseases were identified. The most frequent indications for referral were autosomal recessive disease (54.7%), then autosomal dominant disease (29.7%), and X-linked disease (15.6%). Polycystic kidney disease was the most common diseases counted for 34.4%. After oocyte-retrieval in all of 64 females, a total of 339 embryos were diagnosed and 63 embryos were transferred in succession. Among 61 cycles of frozen-embryo transfer (FET), ongoing pregnancy/live birth rate (OP/LBR) reached 57.38%. The cumulative OP/LBR in our cohort for the 64 couples was 54.69%. In addition, we have carried out expanded carrier screening (ECS) in all the in vitro fertilization (IVF) couples performed PGT covering 7,311 individuals. The carrier frequency of the candidate genes for monogenic kidney diseases accounted for 12.19%.ConclusionOverall, the customization PGT-M plan in our IVF center is pivotal to decreasing the morbidity and implementing reproductive genetic intervention of genetic kidney disease.
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Affiliation(s)
- Min Xiao
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Hua Shi
- Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
| | - Jia Rao
- Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
| | - Yanping Xi
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Shuo Zhang
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Junping Wu
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
- *Correspondence: Hong Xu,
| | - Caixia Lei
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Caixia Lei,
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Xiaoxi Sun,
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Schmitz MJ, Aarabi M, Bashar A, Rajkovic A, Gregg AR, Yatsenko SA. Carrier frequency of autosomal recessive genetic conditions in diverse populations: lessons learned from the Genome Aggregation Database. Clin Genet 2022; 102:87-97. [PMID: 35532184 DOI: 10.1111/cge.14148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/15/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
Abstract
An equitable approach by the American College of Medical Genetics and Genomics (ACMG) has recently recommended carrier screening for genes associated with moderate to severe autosomal recessive conditions with a carrier frequency of ≥1/200 in the Genome Aggregation Database exomes (gnomADv2.0.2). We analyzed carrier frequencies in gnomADv3.1.1 genomes representing diverse populations. ClinVar data on 35,996 pathogenic/likely pathogenic variants in 419 genes were used to estimate the gnomAD frequency of heterozygous carriers. We found that ninety-two genes had a carrier frequency of ≥1/200, of which 63 were shared between v3.1.1 and v2.0.2 and 29 were new in v3.1.1. Addition of new populations (Amish, Finnish and Middle Eastern) increased the number of new genes with a carrier frequency of ≥1/200 to 71. Changes in carrier frequencies were attributed to new gnomAD populations, different sample sizes, new ClinVar data, and technical differences between exomes and genomes. This study highlights the dynamic changes in carrier frequencies due to new datasets from diverse populations and provides updated carrier frequencies based on the combined data from 184,352 genomes and exomes in gnomAD. We recommend a periodic review for inclusion of new population data to update carrier screening panels in the future. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Matthew J Schmitz
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mahmoud Aarabi
- UPMC Medical Genetics & Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA, USA.,Departments of Pathology, and Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Ali Bashar
- Faculty of Science, York University, Toronto, ON, Canada
| | - Aleksandar Rajkovic
- Departments of Pathology and Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC, USA
| | - Svetlana A Yatsenko
- UPMC Medical Genetics & Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA, USA.,Departments of Pathology, and Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.,Magee-Womens Research Institute, Pittsburgh, PA, USA
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Goddard KAB, Lee K, Buchanan AH, Powell BC, Hunter JE. Establishing the Medical Actionability of Genomic Variants. Annu Rev Genomics Hum Genet 2022; 23:173-192. [PMID: 35363504 PMCID: PMC10184682 DOI: 10.1146/annurev-genom-111021-032401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Actionability is an important concept in medicine that does not have a well-accepted standard definition, nor is there a general consensus on how to establish it. Medical actionability is often conflated with clinical utility, a related but distinct concept. This lack of clarity contributes to practice variation and inconsistent coverage decisions in genomic medicine, leading to the potential for systematic bias in the use of evidence-based interventions. We clarify how medical actionability and clinical utility are distinct and then discuss the spectrum of actionability, including benefits for the person, the family, and society. We also describe applications across the life course, including prediction, diagnosis, and treatment. Current challenges in assessing the medical actionability of identified genomic variants include gaps in the evidence, limited contexts with practice guidelines, and subjective aspects of medical actionability. A standardized and authoritative assessment of medical actionability is critical to implementing genomic medicine in a fashion that improves population health outcomes and reduces health disparities. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Kristy Lee
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Adam H Buchanan
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Bradford C Powell
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
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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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Addressing Reproductive Healthcare Disparities through Equitable Carrier Screening: Medical Racism and Genetic Discrimination in United States’ History Highlights the Needs for Change in Obstetrical Genetics Care. SOCIETIES 2022. [DOI: 10.3390/soc12020033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Carrier screening, a nearly half-century old practice, aims to provide individuals and couples with information about their risk of having children with serious genetic conditions. Traditionally, the conditions for which individuals were offered screening depended on their self-reported race or ethnicity and which conditions were seen commonly in that population. This process has led to disparities and inequities in care as the multi-racial population in the U.S. has grown exponentially, yet databases used to determine clinical practice guidelines are made up of primarily White cohorts. Technological advancements now allow for pan-ethnic expanded carrier screening (ECS), which screens for many conditions regardless of self-reported race or ethnicity. ECS presents a unique opportunity to promote equitable genetic testing practices in reproductive medicine. However, this goal can only be achieved if we acknowledge and appreciate the innumerable inequities evidenced in reproductive medicine and other socio-legal practices in the United States, and if we intentionally work in concert with healthcare providers, policy makers, advocates, and community health champions to reduce current and future reproductive health disparities. Herein, we provide a brief review of the way that US medical racism and genetic discrimination has shaped the current landscape of carrier screening.
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Owens KM, Terhaar C, Zdrodowski J, Johnson LR, Eveleigh D. Refining reproductive risk for FMR1 premutation carriers in the general obstetric population. Am J Med Genet A 2022; 188:1476-1481. [PMID: 35129870 DOI: 10.1002/ajmg.a.62666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/31/2021] [Accepted: 01/06/2022] [Indexed: 11/08/2022]
Abstract
Female FMR1 premutation (FMR1 PM) carriers for fragile X syndrome (FXS) are at risk to have a child with FXS based on their CGG repeat size and AGG interruption number. Studies examining this risk in unselected populations of female PM carriers are lacking. This retrospective cohort study analyzed carrier status, CGG repeat length, AGG interruption result, and reproductive risk refinement in a population of female patients who underwent routine carrier screening for FXS. A total of 1536 PM carriers (0.43%) were identified, 95% of whom had between 55 and 90 CGG repeats. A number of 1334 carriers underwent AGG interruption testing. The majority had at least one AGG interruption and received a lower reproductive risk for FXS following AGG interruption testing (89% and 85%, respectively) as compared to their risk calculated based on CGG repeat size alone. The average change in risk across the population following AGG interruption testing was -3.4%, with a range from -50.8% to 48.9%. This article describes the range of CGG repeats and AGG interruptions in an unselected population of female PM carriers and suggests that most carriers would benefit from AGG interruption testing to refine their reproductive risk of having a child with FXS.
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Fei H, Wu Y, Wang Y, Zhang J. Exome sequencing and RNA analysis identify two novel CPLANE1 variants causing Joubert syndrome. Mol Genet Genomic Med 2022; 10:e1877. [PMID: 35092359 PMCID: PMC8922956 DOI: 10.1002/mgg3.1877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/26/2021] [Accepted: 01/06/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Joubert syndrome (JS) is a genetically heterogeneous disorder; its genetic etiology involves more than 35 genes, and a limited number of studies have investigated the pathogenic mechanism of variants in patients with JS. RNA splicing analysis is critical to determine the functional significance for noncanonical splicing variants. METHODS Whole exome sequencing was performed to screen the causative gene variants in a JS family. Sanger sequencing was used to verify the variants. cDNA PCR products were analyzed and functional experiments were performed to determine the pathogenicity of the variants. RESULTS The clinical phenotypes and CPLANE1 variants in the JS patient were analyzed and proved consistent. We identified two novel heterozygous variants of CPLANE1 in the proband first, including c.4459del (frameshift variant) and c.7534-14G > A (intronic variant). We analyzed the pathogenic consequences of the 2 variants and classified the c.4459del as likely pathogenic according to the ACMG/AMP guidelines; however, the pathogenic significance of c.7534-14G > A was uncertain. Furthermore, we performed RNA splicing analysis and revealed that the noncanonical splicing variant (c.7534-14G > A) caused aberrant exon 37 skipping. It produced an aberrant transcript that was predicted to encode a C-terminal truncated protein. CONCLUSIONS The genetic variation spectrum of JS caused by CPLANE1 was updated. Two novel variants further deepened our insight into the disease's molecular mechanism and confirmed the significance of diagnostic whole-exome sequencing.
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Affiliation(s)
- Hongjun Fei
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Wu
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanlin Wang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junyu Zhang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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A capillary electrophoresis-based multiplex PCR assay for expanded carrier screening in the eastern Han Chinese population. NPJ Genom Med 2022; 7:6. [PMID: 35079019 PMCID: PMC8789796 DOI: 10.1038/s41525-021-00280-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/20/2021] [Indexed: 12/05/2022] Open
Abstract
Expanded carrier screening, a type of reproductive genetic testing for couples, has gained tremendous popularity for assessing the risk of passing on certain genetic conditions to offspring. Here, a carrier screening assay for 448 pathogenic variants was developed using capillary electrophoresis-based multiplex PCR technology. The capillary electrophoresis-based multiplex PCR assay achieved a sensitivity, specificity, and accuracy of 97.4%, 100%, and 99.6%, respectively, in detecting the specific variants. Among the 1915 couples (3830 individuals), 708 individuals (18.5%) were identified as carriers for at least one condition. Of the 708 carriers, 633 (89.4%) were heterozygous for one condition, 71 (10.0%) for two disorders, 3 (0.4%) for three disorders, and 1 (0.1%) for four disorders. Meanwhile, 30 (1.57%) couples were identified as at‐risk couples. This study describes an inexpensive and effective method for expanded carrier screening. The simplicity and accuracy of this approach will facilitate the clinical implementation of expanded carrier screening.
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