51
|
Guo W, Lai Y, Yan Z, Wang Y, Nie Y, Guan S, Kuo Y, Zhang W, Zhu X, Peng M, Zhi X, Wei Y, Yan L, Qiao J. Trio-whole-exome sequencing and preimplantation genetic diagnosis for unexplained recurrent fetal malformations. Hum Mutat 2019; 41:432-448. [PMID: 31680349 DOI: 10.1002/humu.23935] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/19/2019] [Accepted: 10/16/2019] [Indexed: 01/18/2023]
Abstract
Whole-exome sequencing (WES) is widely used to detect genetic mutations that cause Mendelian diseases, and has been successfully applied in combination with preimplantation genetic diagnosis (PGD) to avoid the transmission of genetic defects. We investigated 40 nonconsanguineous families with unexplained, recurrent fetal malformations (two or more malformed fetuses) from May 2016 to December 2018. Using Trio-WES, we identified 32 disease-associated variants in 40 families (80% positive rate), which were subsequently verified. Known Mendelian diseases were identified in 12 families (30%), highly suspected Mendelian diseases in 12 families (30%), variants with uncertain significance in 8 families (20%), and no noticeable variants for 8 families (20%). Further analysis showed variants in 22 genes may cause fetal malformations. Four gene variants were detected in fetuses for the first time, which expanded the spectrum of the disease phenotype. Two novel candidate genes may be related to fetal malformations. Of 26 couples receiving PGD on disease-associated genes, 3 healthy newborns were delivered, and 4 couples are undergoing pregnancies. We reported the fetal data and developed an optimized genetic testing strategy. Our finding strongly suggests the presence of single gene Mendelian disorders in 60% of those families, and PGD services for couples to have healthy babies.
Collapse
Affiliation(s)
- Wei Guo
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Yuchen Lai
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhiqiang Yan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yuqian Wang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Yanli Nie
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Shuo Guan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Ying Kuo
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Wenxin Zhang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Xiaohui Zhu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | | | - Xu Zhi
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Liying Yan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| |
Collapse
|
52
|
Abou Tayoun A, Mason-Suares H. Considerations for whole exome sequencing unique to prenatal care. Hum Genet 2019; 139:1149-1159. [PMID: 31701237 DOI: 10.1007/s00439-019-02085-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
Whole exome sequencing (WES) is increasingly being used in the prenatal setting. The emerging data support the clinical utility of prenatal WES based on its diagnostic yield, which can be as high as 80% for certain ultrasound findings. However, detailed practice and laboratory guidelines, addressing the indications for prenatal WES and the surrounding technical, interpretation, ethical, and counseling issues, are still lacking. Herein, we review the literature and summarize the most recent findings and applications of prenatal WES. This review offers specialists and clinical genetic laboratorians a body of evidence and expert opinions that can serve as a resource to assist in their practice. Finally, we highlight the emerging technologies that promise a future of prenatal WES without the risks associated with invasive testing.
Collapse
Affiliation(s)
| | - Heather Mason-Suares
- Departments of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA. .,Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, 65 Landsdowne Street, Cambridge, MA, 02115, USA.
| |
Collapse
|
53
|
Lamont RE, Xi Y, Popko C, Lazier J, Bernier FP, Lauzon JL, Innes AM, Parboosingh JS, Thomas MA. Next-Generation Sequencing Using a Cardiac Gene Panel in Prenatally Diagnosed Cardiac Anomalies. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2019; 40:1417-1423. [PMID: 30473118 DOI: 10.1016/j.jogc.2018.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 02/01/2018] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Most prenatally identified congenital heart defects (CHDs) are the sole structural anomaly detected; however, there is a subgroup of cases where the specific genetic cause will impact prognosis, including chromosome abnormalities and single-gene causes. Next-generation sequencing of all the protein coding regions in the genome or targeted to genes involved in cardiac development is currently possible in the prenatal period, but there are minimal data on the clinical utility of such an approach. This study assessed the outcome of a CHD gene panel that included single-gene causes of syndromic and non-syndromic CHDs. METHOD Sixteen cases with a fetal CHD identified on prenatal ultrasound were studied using a 108 CHD gene panel. DNA was extracted from cultured amniocytes. RESULTS There was no diagnostic pathogenic variant identified in these cases. There was an average of 2.9 reportable variants identified per case and the majority of them were variants of uncertain significance. CONCLUSION Next-generation sequencing has the potential for increased genetic diagnosis for fetal anomalies. However, the large number of variants and the absence of an examinable patient make the interpretation of these variants challenging.
Collapse
Affiliation(s)
- Ryan E Lamont
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB
| | - Yanwei Xi
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB
| | - Claire Popko
- Bachelor of Health Sciences Program, University of Calgary, Calgary, AB
| | - Joanna Lazier
- Department of Medical Genetics, University of Alberta, Edmonton, AB
| | - Francois P Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB
| | - Julie L Lauzon
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB
| | - Jillian S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB
| | - Mary Ann Thomas
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB; Alberta Children's Hospital Research Institute, Calgary, AB.
| |
Collapse
|
54
|
Greenbaum L, Pode-Shakked B, Eisenberg-Barzilai S, Dicastro-Keidar M, Bar-Ziv A, Goldstein N, Reznik-Wolf H, Poran H, Rigbi A, Barel O, Bertoli-Avella AM, Bauer P, Regev M, Raas-Rothschild A, Pras E, Berkenstadt M. Evaluation of Diagnostic Yield in Fetal Whole-Exome Sequencing: A Report on 45 Consecutive Families. Front Genet 2019; 10:425. [PMID: 31428121 PMCID: PMC6688107 DOI: 10.3389/fgene.2019.00425] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 04/17/2019] [Indexed: 11/13/2022] Open
Abstract
Prenatal ultrasound (US) abnormalities often pose a clinical dilemma and necessitate facilitated investigations in the search of diagnosis. The strategy of pursuing fetal whole-exome sequencing (WES) for pregnancies complicated by abnormal US findings is gaining attention, but the reported diagnostic yield is variable. In this study, we describe a tertiary center's experience with fetal WES from both terminated and ongoing pregnancies, and examine the clinical factors affecting the diagnostic rate. A total of 45 consecutive families of Jewish descent were included in the analysis, for which clinical fetal WES was performed under either single (fetus only), trio (fetus and parents) or quatro (two fetuses and parents) design. Except one, all families were non-consanguineous. In 41 of the 45 families, WES was sought following abnormal fetal US findings, and 18 of them had positive relevant family history (two or more fetuses with US abnormalities, or single fetus with US abnormalities and an affected parent). The overall diagnostic yield was 28.9% (13/45 families), and 31.7% among families with fetal US abnormalities (13/41). It was significantly higher in families with prenatal US abnormalities and relevant family history (10/18, 55.6%), compared to families with prenatal US abnormal findings and lack of such history (3/23, 13%) (p = 0.004). WES yield was relatively high (42.9-60%) among families with involvement of brain, renal or musculoskeletal US findings. Taken together, our results in a real-world setting of genetic counseling demonstrates that fetal WES is especially indicated in families with positive family history, as well as in fetuses with specific types of congenital malformation.
Collapse
Affiliation(s)
- Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ben Pode-Shakked
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Michal Dicastro-Keidar
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Anat Bar-Ziv
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Nurit Goldstein
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Haike Reznik-Wolf
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Hana Poran
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Amihai Rigbi
- Faculty of Education, Beit Berl College, Kfar Saba, Israel
| | - Ortal Barel
- Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | | | | | - Miriam Regev
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Annick Raas-Rothschild
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elon Pras
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Berkenstadt
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
55
|
Colley E, Hamilton S, Smith P, Morgan NV, Coomarasamy A, Allen S. Potential genetic causes of miscarriage in euploid pregnancies: a systematic review. Hum Reprod Update 2019; 25:452-472. [PMID: 31150545 DOI: 10.1093/humupd/dmz015] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/07/2019] [Indexed: 12/14/2022] Open
Abstract
Abstract
BACKGROUND
Approximately 50% of pregnancy losses are caused by chromosomal abnormalities, such as aneuploidy. The remainder has an apparent euploid karyotype, but it is plausible that there are cases of pregnancy loss with other genetic aberrations that are not currently routinely detected. Studies investigating the use of exome sequencing and chromosomal microarrays in structurally abnormal pregnancies and developmental disorders have demonstrated their clinical application and/or potential utility in these groups of patients. Similarly, there have been several studies that have sought to identify genes that are potentially causative of, or associated with, spontaneous pregnancy loss, but the evidence has not yet been synthesized.
OBJECTIVE AND RATIONALE
The objective was to identify studies that have recorded monogenic genetic contributions to pregnancy loss in euploid pregnancies, establish evidence for genetic causes of pregnancy loss, identify the limitations of current evidence, and make recommendations for future studies. This evidence is important in considering additional research into Mendelian causes of pregnancy loss and appropriate genetic investigations for couples experiencing recurrent pregnancy loss.
SEARCH METHODS
A systematic review was conducted in MEDLINE (1946 to May 2018) and Embase (1974 to May 2018). The search terms ‘spontaneous abortion’, ‘miscarriage’, ‘pregnancy loss’, or ‘lethal’ were used to identify pregnancy loss terms. These were combined with search terms to identify the genetic contribution including ‘exome’, ‘human genome’, ‘sequencing analysis’, ‘sequencing’, ‘copy number variation’, ‘single-nucleotide polymorphism’, ‘microarray analysis’, and ‘comparative genomic hybridization’. Studies were limited to pregnancy loss up to 20 weeks in humans and excluded if the genetic content included genes that are not lethal in utero, PGD studies, infertility studies, expression studies, aneuploidy with no recurrence risk, methodologies where there is no clinical relevance, and complex genetic studies. The quality of the studies was assessed using a modified version of the Newcastle–Ottawa scale.
OUTCOMES
A total of 50 studies were identified and categorized into three themes: whole-exome sequencing studies; copy number variation studies; and other studies related to pregnancy loss including recurrent molar pregnancies, epigenetics, and mitochondrial DNA aberrations. Putatively causative variants were found in a range of genes, including CHRNA1 (cholinergic receptor, nicotinic, alpha polypeptide 1), DYNC2H1 (dynein, cytoplasmic 2, heavy chain 1), and RYR1 (ryanodine receptor 1), which were identified in multiple studies. Copy number variants were also identified to have a causal or associated link with recurrent miscarriage.
WIDER IMPLICATIONS
Identification of genes that are causative of or predisposing to pregnancy loss will be of significant individual patient impact with respect to counselling and treatment. In addition, knowledge of specific genes that contribute to pregnancy loss could also be of importance in designing a diagnostic sequencing panel for patients with recurrent pregnancy loss and also in understanding the biological pathways that can cause pregnancy loss.
Collapse
Affiliation(s)
- Emily Colley
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Susan Hamilton
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - Paul Smith
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Arri Coomarasamy
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Stephanie Allen
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| |
Collapse
|
56
|
Genetic testing and PGD for unexplained recurrent fetal malformations with MAGEL2 gene mutation. SCIENCE CHINA-LIFE SCIENCES 2019; 62:886-894. [PMID: 31152388 DOI: 10.1007/s11427-019-9541-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 04/15/2019] [Indexed: 12/31/2022]
Abstract
Birth defects are caused by multiple factors, such as chromosome abnormality, environmental factors, and maternal factors. In this study, we focused on exploring the genetic causes of a non-consanguineous couple who suffered from four times of unsuccessful pregnancy due to unexplained recurrent fetal malformations with similar symptoms and normal chromosome copy number variations. Using trio-whole exome sequencing (trio-WES) for this couple and one of the affected fetuses, we found a mutation, c.1996delC on the maternal imprinted gene MAGEL2 that was carried by the affected fetus and husband, leading to Schaaf-Yang syndrome. To screen this mutation, we further performed preimplantation genetic diagnosis (PGD) strategy followed by a gene pedigree validation and pathogenicity analysis. After the transfer of a PGD-screened embryo, a normal newborn without previous abnormal symptoms was born (February 15, 2019). We present the first data that identified a pathogenic gene (MAGEL2 c.1996delC) in a fetus with Schaaf-Yang syndrome in the EAS (East Asian) database and overcame this genetic defect by using processed PGD for this couple based on the WES results.
Collapse
|
57
|
Update on the use of exome sequencing in the diagnosis of fetal abnormalities. Eur J Med Genet 2019; 62:103663. [PMID: 31085342 DOI: 10.1016/j.ejmg.2019.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/26/2019] [Accepted: 05/04/2019] [Indexed: 12/18/2022]
Abstract
Unexpected fetal abnormalities detected through ultrasound scanning in pregnancy may have a monogenic aetiology but are difficult to diagnose. Next generation sequencing now enables us to sequence fetal exomes, providing increased resolution and broader diagnostic capability compared to traditional cytogenetic prenatal tests, improving the yield and accuracy of diagnoses and allowing better counselling for expectant parents. Here we review published studies of exome sequencing (ES) for prenatal diagnosis over the last 5 years and address important questions for its clinical implementation, including clinical utility, which groups benefit most, and practical and ethical challenges for interpreting and reporting results. We observe that fetal ES substantially improves diagnostic yield relative to cytogenetic techniques. However, diagnostic rates vary widely between studies, largely attributable to differences in case selection. Recently several large studies report variations in diagnostic yield between phenotypic groups, with fetuses with multisystem abnormalities most likely to receive a diagnosis from fetal ES. Challenges for prenatal ES include the limitations of ultrasound-based fetal phenotyping, the need for rapid return of results in pregnancy, and technical limitations compared to whole genome sequencing. We also consider ethical issues around potential secondary findings and variants of uncertain significance and the complex counselling needs these present. Prenatal ES is a valuable tool to diagnose fetal abnormalities and, as it is implemented in the clinic, more large-scale research will serve to further delineate its clinical utility, as well as generating new knowledge about fetal phenotypes and informing guidelines for case selection, reporting results and genetic counselling.
Collapse
|
58
|
de Koning MA, Haak MC, Adama van Scheltema PN, Peeters-Scholte CMPCD, Koopmann TT, Nibbeling EAR, Aten E, den Hollander NS, Ruivenkamp CAL, Hoffer MJV, Santen GWE. From diagnostic yield to clinical impact: a pilot study on the implementation of prenatal exome sequencing in routine care. Genet Med 2019; 21:2303-2310. [PMID: 30918357 DOI: 10.1038/s41436-019-0499-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/14/2019] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Exome sequencing (ES) is an efficient tool to diagnose genetic disorders postnatally. Recent studies show that it may have a considerable diagnostic yield in fetuses with structural anomalies on ultrasound. We report on the clinical impact of the implementation of prenatal ES (pES) for ongoing pregnancies in routine care. METHODS We retrospectively analyzed the impact of pES on pregnancy outcome and pre- or perinatal management in the first 22 patients counseled for pES because of one or more structural anomalies on fetal ultrasound. RESULTS In two cases, a diagnosis was made by chromosomal microarray analysis after ES counseling. The remaining 20 cases were divided in three groups: (1) pES to aid parental decision making (n = 12), (2) pES in the context of late pregnancy termination requests (n = 5), and (3) pES to guide pre- or perinatal management (n = 3). pES had a clinical impact in 75% (9/12), 40% (2/5), and 100% (3/3) respectively, showing an overall clinical impact of pES of 70% (14/20). CONCLUSION We show that clinical implementation of pES is feasible and affects parental decision making or pre- and perinatal management supporting further implementation of ES in the prenatal setting.
Collapse
Affiliation(s)
- Maayke A de Koning
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique C Haak
- Department of Obstetrics and Fetal Medicine, Leiden University Medical Centre, Leiden, the Netherlands
| | | | | | - Tamara T Koopmann
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands.
| |
Collapse
|
59
|
Brew CE, Castro BA, Pan V, Hart A, Blumberg B, Wicklund C. Genetics professionals' attitudes toward prenatal exome sequencing. J Genet Couns 2019; 28:229-239. [PMID: 30888706 DOI: 10.1002/jgc4.1112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 02/11/2019] [Accepted: 12/21/2019] [Indexed: 11/11/2022]
Abstract
Prenatal exome sequencing (ES) currently has limited use in the clinical setting, but research suggests that it has added diagnostic utility over karyotyping and array techniques for prenatal diagnosis of fetuses presenting with ultrasound abnormalities. The purpose of this study was to assess the attitudes of genetics professionals toward the clinical implementation of prenatal ES in order to guide development of professional guidelines. A survey was developed using themes identified in previous qualitative studies and was distributed to members of the American College of Medical Genetics and Genomics (ACMG), the American Society of Human Genetics (ASHG), and the National Society of Genetic Counselors (NSGC). A total of 498 participants completed some portion of the survey. There was consensus among participants that there would be clinical utility of prenatal ES when used for diagnosis, pregnancy management, and termination decisions. The majority also agreed that prenatal ES was distinct from its current use in the pediatric and adult settings. There were many areas of contention regarding which types of results should be returned to families and whether or not the current ACMG guidelines for return of incidental findings should also apply to the prenatal setting. Overall, professional guidance is needed to address the continuing concerns surrounding prenatal ES as its utilization in this setting is expected to grow.
Collapse
Affiliation(s)
- Casey E Brew
- Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital, Chicago, Illinois
| | | | - Vivian Pan
- Kaiser Permanente Research Bank, Oakland, California
| | - Alexa Hart
- Fetal and Neonatal Medicine Center, Rush University Medical Center, Chicago, Illinois
| | - Bruce Blumberg
- Kaiser Permanente School of Medicine, Pasadena, California
| | | |
Collapse
|
60
|
Lord J, McMullan DJ, Eberhardt RY, Rinck G, Hamilton SJ, Quinlan-Jones E, Prigmore E, Keelagher R, Best SK, Carey GK, Mellis R, Robart S, Berry IR, Chandler KE, Cilliers D, Cresswell L, Edwards SL, Gardiner C, Henderson A, Holden ST, Homfray T, Lester T, Lewis RA, Newbury-Ecob R, Prescott K, Quarrell OW, Ramsden SC, Roberts E, Tapon D, Tooley MJ, Vasudevan PC, Weber AP, Wellesley DG, Westwood P, White H, Parker M, Williams D, Jenkins L, Scott RH, Kilby MD, Chitty LS, Hurles ME, Maher ER. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study. Lancet 2019; 393:747-757. [PMID: 30712880 PMCID: PMC6386638 DOI: 10.1016/s0140-6736(18)31940-8] [Citation(s) in RCA: 362] [Impact Index Per Article: 72.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Fetal structural anomalies, which are detected by ultrasonography, have a range of genetic causes, including chromosomal aneuploidy, copy number variations (CNVs; which are detectable by chromosomal microarrays), and pathogenic sequence variants in developmental genes. Testing for aneuploidy and CNVs is routine during the investigation of fetal structural anomalies, but there is little information on the clinical usefulness of genome-wide next-generation sequencing in the prenatal setting. We therefore aimed to evaluate the proportion of fetuses with structural abnormalities that had identifiable variants in genes associated with developmental disorders when assessed with whole-exome sequencing (WES). METHODS In this prospective cohort study, two groups in Birmingham and London recruited patients from 34 fetal medicine units in England and Scotland. We used whole-exome sequencing (WES) to evaluate the presence of genetic variants in developmental disorder genes (diagnostic genetic variants) in a cohort of fetuses with structural anomalies and samples from their parents, after exclusion of aneuploidy and large CNVs. Women were eligible for inclusion if they were undergoing invasive testing for identified nuchal translucency or structural anomalies in their fetus, as detected by ultrasound after 11 weeks of gestation. The partners of these women also had to consent to participate. Sequencing results were interpreted with a targeted virtual gene panel for developmental disorders that comprised 1628 genes. Genetic results related to fetal structural anomaly phenotypes were then validated and reported postnatally. The primary endpoint, which was assessed in all fetuses, was the detection of diagnostic genetic variants considered to have caused the fetal developmental anomaly. FINDINGS The cohort was recruited between Oct 22, 2014, and June 29, 2017, and clinical data were collected until March 31, 2018. After exclusion of fetuses with aneuploidy and CNVs, 610 fetuses with structural anomalies and 1202 matched parental samples (analysed as 596 fetus-parental trios, including two sets of twins, and 14 fetus-parent dyads) were analysed by WES. After bioinformatic filtering and prioritisation according to allele frequency and effect on protein and inheritance pattern, 321 genetic variants (representing 255 potential diagnoses) were selected as potentially pathogenic genetic variants (diagnostic genetic variants), and these variants were reviewed by a multidisciplinary clinical review panel. A diagnostic genetic variant was identified in 52 (8·5%; 95% CI 6·4-11·0) of 610 fetuses assessed and an additional 24 (3·9%) fetuses had a variant of uncertain significance that had potential clinical usefulness. Detection of diagnostic genetic variants enabled us to distinguish between syndromic and non-syndromic fetal anomalies (eg, congenital heart disease only vs a syndrome with congenital heart disease and learning disability). Diagnostic genetic variants were present in 22 (15·4%) of 143 fetuses with multisystem anomalies (ie, more than one fetal structural anomaly), nine (11·1%) of 81 fetuses with cardiac anomalies, and ten (15·4%) of 65 fetuses with skeletal anomalies; these phenotypes were most commonly associated with diagnostic variants. However, diagnostic genetic variants were least common in fetuses with isolated increased nuchal translucency (≥4·0 mm) in the first trimester (in three [3·2%] of 93 fetuses). INTERPRETATION WES facilitates genetic diagnosis of fetal structural anomalies, which enables more accurate predictions of fetal prognosis and risk of recurrence in future pregnancies. However, the overall detection of diagnostic genetic variants in a prospectively ascertained cohort with a broad range of fetal structural anomalies is lower than that suggested by previous smaller-scale studies of fewer phenotypes. WES improved the identification of genetic disorders in fetuses with structural abnormalities; however, before clinical implementation, careful consideration should be given to case selection to maximise clinical usefulness. FUNDING UK Department of Health and Social Care and The Wellcome Trust.
Collapse
Affiliation(s)
| | - Dominic J McMullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | | | | | - Susan J Hamilton
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Elizabeth Quinlan-Jones
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK; Centre for Women's and Newborn Health, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | | | - Rebecca Keelagher
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Sunayna K Best
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Georgina K Carey
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Rhiannon Mellis
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Sarah Robart
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Ian R Berry
- The Leeds Genetics Laboratory, St James's University Hospital, Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Deirdre Cilliers
- Oxford Genomic Medicine Centre, Nuffield Orthopaedic Centre, Oxford, UK
| | - Lara Cresswell
- Department of Cytogenetics, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Sandra L Edwards
- Cytogenetics Service, Norfolk and Norwich University Hospital Foundation Trust, Norwich, UK
| | - Carol Gardiner
- West of Scotland Genetics Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Alex Henderson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Simon T Holden
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Tessa Homfray
- South West Thames Regional Genetics Centre, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Tracy Lester
- Oxford Regional Genetics Services, The Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rebecca A Lewis
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, St Michael's Hospital, University Hospitals Bristol, Bristol, UK
| | - Katrina Prescott
- Chapel Allerton Hospital, Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Oliver W Quarrell
- Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Eileen Roberts
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - Dagmar Tapon
- Centre for Fetal Care, Queen Charlotte's and Chelsea Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Madeleine J Tooley
- Department of Clinical Genetics, St Michael's Hospital, University Hospitals Bristol, Bristol, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Astrid P Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Diana G Wellesley
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Paul Westwood
- West of Scotland Genetics Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Helen White
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Michael Parker
- The Ethox Centre, Nuffield Department of Population Health and Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Lucy Jenkins
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Richard H Scott
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Mark D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK; Centre for Women's and Newborn Health, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Lyn S Chitty
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | | | - Eamonn R Maher
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK; Cambridge Biomedical Research Centre, National Institute for Health Research, Cambridge, UK.
| |
Collapse
|
61
|
Petrovski S, Aggarwal V, Giordano JL, Stosic M, Wou K, Bier L, Spiegel E, Brennan K, Stong N, Jobanputra V, Ren Z, Zhu X, Mebane C, Nahum O, Wang Q, Kamalakaran S, Malone C, Anyane-Yeboa K, Miller R, Levy B, Goldstein DB, Wapner RJ. Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study. Lancet 2019; 393:758-767. [PMID: 30712878 DOI: 10.1016/s0140-6736(18)32042-7] [Citation(s) in RCA: 323] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 08/14/2018] [Accepted: 08/28/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Identification of chromosomal aneuploidies and copy number variants that are associated with fetal structural anomalies has substantial value. Although whole-exome sequencing (WES) has been applied to case series of a few selected prenatal cases, its value in routine clinical settings has not been prospectively assessed in a large unselected cohort of fetuses with structural anomalies. We therefore aimed to determine the incremental diagnostic yield (ie, the added value) of WES following uninformative results of standard investigations with karyotype testing and chromosomal microarray in an unselected cohort of sequential pregnancies showing fetal structural anomalies. METHODS In this prospective cohort study, the parents of fetuses who were found to have a structural anomaly in a prenatal ultrasound were screened for possible participation in the study. These participants were predominantly identified in or were referred to the Columbia University Carmen and John Thain Center for Prenatal Pediatrics (New York, NY, USA). Fetuses with confirmed aneuploidy or a causal pathogenic copy number variant were excluded from WES analyses. By use of WES of the fetuses and parents (parent-fetus trios), we identified genetic variants that indicated an underlying cause (diagnostic genetic variants) and genetic variants that met the criteria of bioinformatic signatures that had previously been described to be significantly enriched among diagnostic genetic variants. FINDINGS Between April 24, 2015, and April 19, 2017, 517 sequentially identified pregnant women found to have fetuses with a structural anomaly were screened for their eligibility for inclusion in our study. 71 (14%) couples declined testing, 87 (17%) trios were missing at least one DNA sample (from either parent or the fetus), 69 (13%) trios had a clinically relevant abnormal karyotype or chromosomal microarray finding, 51 (10%) couples did not consent to WES or withdrew consent, and five (1%) samples were not of good enough quality for analysis. DNA samples from 234 (45%) eligible trios were therefore used for analysis of the primary outcome. By use of trio sequence data, we identified diagnostic genetic variants in 24 (10%) families. Mutations with bioinformatic signatures that were indicative of pathogenicity but with insufficient evidence to be considered diagnostic were also evaluated; 46 (20%) of the 234 fetuses assessed were found to have such signatures. INTERPRETATION Our analysis of WES data in a prospective cohort of unselected fetuses with structural anomalies shows the value added by WES following the use of routine genetic tests. Our findings suggest that, in cases of fetal anomalies in which assessment with karyotype testing and chromosomal microarray fail to determine the underlying cause of a structural anomaly, WES can add clinically relevant information that could assist current management of a pregnancy. The unique challenges of WES-based prenatal diagnostics require analysis by a multidisciplinary team of perinatal practitioners and laboratory specialists. FUNDING Institute for Genomic Medicine (Columbia University Irving Medical Center).
Collapse
Affiliation(s)
- Slavé Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jessica L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Melissa Stosic
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Karen Wou
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Erica Spiegel
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Kelly Brennan
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Vaidehi Jobanputra
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Xiaolin Zhu
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Caroline Mebane
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Odelia Nahum
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Quanli Wang
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Colin Malone
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Russell Miller
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Brynn Levy
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Ronald J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA.
| |
Collapse
|
62
|
Meier N, Bruder E, Lapaire O, Hoesli I, Kang A, Hench J, Hoeller S, De Geyter J, Miny P, Heinimann K, Chaoui R, Tercanli S, Filges I. Exome sequencing of fetal anomaly syndromes: novel phenotype-genotype discoveries. Eur J Hum Genet 2019; 27:730-737. [PMID: 30679815 PMCID: PMC6461982 DOI: 10.1038/s41431-018-0324-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/02/2018] [Accepted: 12/04/2018] [Indexed: 01/05/2023] Open
Abstract
The monogenic etiology of most severe fetal anomaly syndromes is poorly understood. Our objective was to use exome sequencing (ES) to increase our knowledge on causal variants and novel candidate genes associated with specific fetal phenotypes. We employed ES in a cohort of 19 families with one or more fetuses presenting with a distinctive anomaly pattern and/or phenotype recurrence at increased risk for lethal outcomes. Candidate variants were identified in 12 families (63%); in 6 of them a definite diagnosis was achieved including known or novel variants in recognized disease genes (MKS1, OTX2, FGFR2, and RYR1) and variants in novel disease genes describing new fetal phenotypes (CENPF, KIF14). We identified variants likely causal after clinical and functional review (SMAD3, KIF4A, and PIGW) and propose novel candidate genes (PTK7, DNHD1, and TTC28) for early human developmental disease supported by functional and cross-species phenotyping evidence. We describe rare and novel fetal anomaly syndromes and highlight the diagnostic utility of ES, but also its contribution to discovery. The diagnostic yield of the future application of prenatal ES will depend on our ability to increase our knowledge on the specific phenotype–genotype correlations during fetal development.
Collapse
Affiliation(s)
- Nicole Meier
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Elisabeth Bruder
- University of Basel, Basel, Switzerland.,Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Olav Lapaire
- Department of Obstetrics and Gynecology, University Hospital Basel, Basel, Switzerland
| | - Irene Hoesli
- Department of Obstetrics and Gynecology, University Hospital Basel, Basel, Switzerland
| | - Anjeung Kang
- Centre for Prenatal Ultrasound, Freie Strasse, Basel, Switzerland
| | - Jürgen Hench
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Sylvia Hoeller
- University of Basel, Basel, Switzerland.,Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Julie De Geyter
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Peter Miny
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Karl Heinimann
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Rabih Chaoui
- Centre for Prenatal Diagnosis, Friedrichstrasse, Berlin, Germany
| | - Sevgi Tercanli
- University of Basel, Basel, Switzerland.,Centre for Prenatal Ultrasound, Freie Strasse, Basel, Switzerland
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland. .,Department of Clinical Research, University Hospital Basel, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| |
Collapse
|
63
|
Abstract
Whole-exome sequencing (WES) has been used as a standard of care for postnatal diagnosis in the clinical setting in the past few years for children and adults with undiagnosed disease. Many rare disorders have been diagnosed through WES, which is less expensive than the traditional serial genetic testing where patients had previously spent years on an uninformative diagnostic odyssey. Seeking a diagnosis often entails enduring time consuming, and sometimes invasive procedures which may be associated with medical risks that are stressful for families and impose a heavy burden on the health-care system. However, the use of WES is considered impractical in the prenatal and neonatal testing period because of the technical and computational challenges of performing genomic sequencing from small amounts of genetic material, and the need for faster turnaround time (TAT) than the current 6-8 weeks TAT provided by most clinical labs offering postnatal testing. With the rapidly evolving methods of sequence analysis, there are clinical challenges such as the constantly increasing number of genes being identified which are not yet fully phenotypically characterized, especially when ascertained prenatally or neonatally before all the clinical features may be evident. Despite these challenges, there are many clinical benefits to acquiring genomic information in the prenatal and neonatal period. These include superior prognostic information which allows for prenatal planning of mode of delivery and hospital for delivery and optimized neonatal management. We have developed a clinical WES assay using small amounts of DNA with a TAT of 10 days for use in the prenatal or neonatal setting. This test is used to detect small nucleotide variants and indels in fetuses and neonates with structural abnormalities.
Collapse
|
64
|
Daum H, Meiner V, Elpeleg O, Harel T. Fetal exome sequencing: yield and limitations in a tertiary referral center. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 53:80-86. [PMID: 29947050 DOI: 10.1002/uog.19168] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To explore the indications for and diagnostic outcomes of fetal exome sequencing in a tertiary referral center. METHODS Between 2012 and 2017, 77 unrelated fetal samples from pregnancies referred to our center underwent exome sequencing. The cohort included 37 fetuses, 36 products of conception (from cases of pregnancy termination or intrauterine fetal death), one case with DNA from both the fetus and a previous termination of pregnancy, and three cases with DNA of unknown origin. Exome sequencing was performed on DNA extracted from amniocytes or fetal tissue and, in some cases, from parental peripheral blood. Indications, turnaround time, diagnostic rates and pregnancy outcomes were investigated. Diagnostic yield was analyzed according to consanguinity (yes or no), sample type (proband only, or trio or other) and referral indication (malformation or isolated nuchal translucency (NT)). RESULTS The most common indication for fetal exome sequencing was multiple malformations (21/77, 27%), followed by isolated brain malformation (15/77, 19%). Twelve (16%) fetuses were referred for isolated increased NT. Exome analysis was diagnostic for 16 fetuses (21%); when subclassified into fetal malformations vs isolated increased NT it became clear that exome analysis did not reveal any known or probable pathogenic variants in cases referred for isolated increased NT, whereas, among the remaining fetuses, a molecular diagnosis was reached in 16/65 (25%). Proband-only cases received a diagnosis more often than did cases that had trio exome sequencing. CONCLUSIONS Exome sequencing has the potential to provide molecular diagnoses in cases in which conventional prenatal cytogenetic testing is negative. Referral bias of consanguineous cases could account for the high diagnostic rate of proband-only sequencing. Syndrome-specific prognostic information enables parents to make informed decisions, whereas challenges include time limitations and variant interpretation in the setting of non-specific fetal findings. As we report only established disease-gene associations, further segregation and functional studies in a research setting are expected to increase significantly the diagnostic yield. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- H Daum
- Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - V Meiner
- Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - O Elpeleg
- Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - T Harel
- Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| |
Collapse
|
65
|
Yadava SM, Ashkinadze E. Whole exome sequencing for prenatal diagnosis in cases with fetal anomalies: Criteria to improve diagnostic yield. J Genet Couns 2018; 28:251-255. [PMID: 30629328 DOI: 10.1002/jgc4.1045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/30/2018] [Accepted: 10/06/2018] [Indexed: 01/31/2023]
Abstract
Whole exome sequencing (WES) for prenatal diagnosis has a reported diagnostic yield of 6.2%-57%. Our aim was to identify patients with a high likelihood of genetic diagnosis using WES in cases with fetal ultrasound anomalies. This is a series of five selected cases for prenatal WES at our institution. Pregnant couples were initially identified due to fetal ultrasound anomalies. Candidates for WES for fetal diagnosis had a normal fetal karyotype and negative microarray with at least one of the following: parental consanguinity, large regions of homozygosity on fetal microarray, or high likelihood of single gene disorder based on ultrasound findings. All trios underwent sequencing of parental and fetal samples. WES was diagnostic in four of the five cases (80%). We identified two recessive conditions and two de novo mutations. Four couples consented to secondary findings and in one case, the father was found to have an MSH2 mutation associated with Lynch syndrome. The use of specific selection criteria for WES increased diagnostic yield to 80%. This is higher than previously reported. Wide application of our criteria can help identify those who may benefit most from this testing in prenatal diagnosis.
Collapse
Affiliation(s)
- Stacy M Yadava
- Department of Obstetrics, Gynecology and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Elena Ashkinadze
- Department of Obstetrics, Gynecology and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| |
Collapse
|
66
|
Borrell A. A new comprehensive paradigm for prenatal diagnosis: seeing the forest through the trees. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 52:563-568. [PMID: 29484739 DOI: 10.1002/uog.19035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/06/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Affiliation(s)
- A Borrell
- Barcelona Center for Maternofetal and Neonatal Medicine, Hospital Clínic Barcelona, Catalonia, Spain
| |
Collapse
|
67
|
Leung GKC, Mak CCY, Fung JLF, Wong WHS, Tsang MHY, Yu MHC, Pei SLC, Yeung KS, Mok GTK, Lee CP, Hui APW, Tang MHY, Chan KYK, Liu APY, Yang W, Sham PC, Kan ASY, Chung BHY. Identifying the genetic causes for prenatally diagnosed structural congenital anomalies (SCAs) by whole-exome sequencing (WES). BMC Med Genomics 2018; 11:93. [PMID: 30359267 PMCID: PMC6202811 DOI: 10.1186/s12920-018-0409-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/01/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) has become an invaluable tool for genetic diagnosis in paediatrics. However, it has not been widely adopted in the prenatal setting. This study evaluated the use of WES in prenatal genetic diagnosis in fetuses with structural congenital anomalies (SCAs) detected on prenatal ultrasound. METHOD Thirty-three families with fetal SCAs on prenatal ultrasonography and normal chromosomal microarray results were recruited. Genomic DNA was extracted from various fetal samples including amniotic fluid, chorionic villi, and placental tissue. Parental DNA was extracted from peripheral blood when available. We used WES to sequence the coding regions of parental-fetal trios and to identify the causal variants based on the ultrasonographic features of the fetus. RESULTS Pathogenic mutations were identified in three families (n = 3/33, 9.1%), including mutations in DNAH11, RAF1 and CHD7, which were associated with primary ciliary dyskinesia, Noonan syndrome, and CHARGE syndrome, respectively. In addition, variants of unknown significance (VUSs) were detected in six families (18.2%), in which genetic changes only partly explained prenatal features. CONCLUSION WES identified pathogenic mutations in 9.1% of fetuses with SCAs and normal chromosomal microarray results. Databases for fetal genotype-phenotype correlations and standardized guidelines for variant interpretation in prenatal diagnosis need to be established to facilitate the use of WES for routine testing in prenatal diagnosis.
Collapse
Affiliation(s)
- Gordon K C Leung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - Jasmine L F Fung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - Wilfred H S Wong
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - Mandy H Y Tsang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - Mullin H C Yu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - Steven L C Pei
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - K S Yeung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - Gary T K Mok
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - C P Lee
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, China
| | - Amelia P W Hui
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, China
| | - Mary H Y Tang
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, China.,Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Hong Kong, HKSAR, China
| | - Kelvin Y K Chan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, China.,Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Hong Kong, HKSAR, China
| | - Anthony P Y Liu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China
| | - P C Sham
- Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, HKSAR, China
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, China. .,Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Hong Kong, HKSAR, China.
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Room 103, 1/F, New Clinical Building, Hong Kong, Hong Kong Special Administrative Region, China. .,Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, China. .,Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Hong Kong, HKSAR, China.
| |
Collapse
|
68
|
Reches A, Hiersch L, Simchoni S, Barel D, Greenberg R, Ben Sira L, Malinger G, Yaron Y. Whole-exome sequencing in fetuses with central nervous system abnormalities. J Perinatol 2018; 38:1301-1308. [PMID: 30108342 DOI: 10.1038/s41372-018-0199-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/29/2022]
Abstract
OBJECTIVE We describe our experience with whole-exome sequencing (WES) in fetuses with central nervous system (CNS) abnormalities following a normal chromosomal microarray result. METHODS During the study period (2014-2017) 7 cases (9 fetuses) with prenatally diagnosed CNS abnormality, whose chromosomal microarray analysis was negative, were offered whole-exome sequencing analysis. RESULTS A pathogenic or a likely pathogenic variant was found in 5 cases including a previously described, likely pathogenic de novo TUBA1A variant (Case #1); a previously described homozygous VRK1 variant (Case #2); an X-linked ARX variant (Case #3); a likely pathogenic heterozygous variant in the TUBB3 gene (Case #5). Finally, in two fetuses of the same couple (Case #6), a compound heterozygous state was detected, consisting of the NPHP1 gene deletion and a sequence variant of uncertain significance. Two additional cases had normal WES results. CONCLUSION Whole-exome sequencing may improve prenatal diagnosis in fetuses with CNS abnormalities.
Collapse
Affiliation(s)
- Adi Reches
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Liran Hiersch
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel. .,Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.
| | - Sharon Simchoni
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Dalit Barel
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Rotem Greenberg
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Liat Ben Sira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.,Radiology Department, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Gustavo Malinger
- Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| |
Collapse
|
69
|
Guo W, Zhu X, Yan L, Qiao J. The present and future of whole-exome sequencing in studying and treating human reproductive disorders. J Genet Genomics 2018; 45:517-525. [DOI: 10.1016/j.jgg.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
|
70
|
Normand EA, Braxton A, Nassef S, Ward PA, Vetrini F, He W, Patel V, Qu C, Westerfield LE, Stover S, Dharmadhikari AV, Muzny DM, Gibbs RA, Dai H, Meng L, Wang X, Xiao R, Liu P, Bi W, Xia F, Walkiewicz M, Van den Veyver IB, Eng CM, Yang Y. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Med 2018; 10:74. [PMID: 30266093 PMCID: PMC6162951 DOI: 10.1186/s13073-018-0582-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting. Methods We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive “fetal exomes” performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher’s exact test. Results Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families. Conclusion Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis. Electronic supplementary material The online version of this article (10.1186/s13073-018-0582-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Salma Nassef
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Lauren E Westerfield
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Stover
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Present address: The National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
| |
Collapse
|
71
|
Abstract
Prenatal whole exome sequencing (WES) has the potential to increase the ability to provide more diagnostic capabilities in fetuses with sonographic abnormalities, which would then improve the ability to counsel families. It is also often the first step in improving the path toward informed diagnosis and treatment, which is especially important in the era of advancing in utero fetal therapy. This article discusses the current literature regarding prenatal WES, clinical indications for WES, challenges with interpretation/counseling (variants of unknown significance), research priorities, ethical issues, and potential future advances.
Collapse
Affiliation(s)
- Angie C Jelin
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, Johns Hopkins School of Medicine, 500 North Wolfe Street, Phipps 222, Baltimore, MD 21218, USA
| | - Neeta Vora
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, 3010 Old Clinic Building/Cb# 7516, Chapel Hill, NC 27599, USA.
| |
Collapse
|
72
|
Vora NL, Hui L. Next-generation sequencing and prenatal 'omics: advanced diagnostics and new insights into human development. Genet Med 2018; 20:791-799. [PMID: 30032162 PMCID: PMC6123255 DOI: 10.1038/s41436-018-0087-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/01/2018] [Indexed: 12/16/2022] Open
Abstract
Prenatal genetics has evolved over the last decade to include application of new 'omics technologies to improve perinatal care. The clinical utility of these technologies when applied to direct fetal specimens from amniocentesis or chorionic villus sampling is being explored. In this review, we provide an overview of use of prenatal exome sequencing and role in evaluation of the structurally abnormal fetus, potential applications of genome sequencing, and finally, use of transcriptomics to assess placental and fetal well-being.
Collapse
Affiliation(s)
- Neeta L Vora
- Department of Obstetrics & Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Lisa Hui
- Department of Obstetrics & Gynaecology, University of Melbourne, Heidelberg, Victoria, Australia
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, Public Health Genetics Group, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, The Northern Hospital, Epping, Victoria, Australia
| |
Collapse
|
73
|
Das Bhowmik A, Dalal A, Tandon A, Aggarwal S. Exome sequencing identifies novel ACE splice-site variant in a fetus with renal tubular dysgenesis. J Obstet Gynaecol Res 2018; 44:2181-2185. [PMID: 30058238 DOI: 10.1111/jog.13771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 07/04/2018] [Indexed: 11/29/2022]
Abstract
We report a 32-week fetus conceived of consanguineous parentage which presented with severe early onset oligohydramnios and history of a similarly affected sibling in previous pregnancy. Ultrasonography and autopsy were inconclusive, prompting exome sequencing on fetal DNA. This resulted in identification of a homozygous novel 3' splice-site variation in intron 17 of the ACE gene (NM_000789.3:c.2642-1G>A), confirming diagnosis of autosomal recessive renal tubular dysgenesis, and facilitating prenatal diagnosis in subsequent pregnancy.
Collapse
Affiliation(s)
- Aneek Das Bhowmik
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwani Tandon
- Department of Pathology, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Shagun Aggarwal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| |
Collapse
|
74
|
Zhou X, Chandler N, Deng L, Zhou J, Yuan M, Sun L. Prenatal diagnosis of skeletal dysplasias using a targeted skeletal gene panel. Prenat Diagn 2018; 38:692-699. [PMID: 29907962 DOI: 10.1002/pd.5298] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/24/2018] [Accepted: 05/31/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE This study aimed to perform an accurate and precise diagnosis for fetuses with suspected skeletal anomalies based on an incomplete and limited ultrasound phenotype. METHODS Proband-only targeted skeletal gene panel sequencing was performed on 12 families who had fetuses with suspected skeletal anomalies based on ultrasound evaluations at a mean gestational age of 24 weeks and 3 days. The fetuses all had normal standard genetic testing yield (karyotyping and microarray). RESULTS In 10 of 12 fetuses, panel sequencing provided a diagnosis or possible diagnosis with identification of variants in the following genes: FGFR3, COL1A2, IHH, COL2A1, and DYNC2H1. Two cases revealed novel variants in COL2A1 and DYNC2H1. CONCLUSIONS Our study suggests that targeted skeletal gene panel sequencing is highly sensitive for prenatal diagnosis of fetuses presenting with unexpected ultrasound findings suggestive of a skeletal dysplasia.
Collapse
Affiliation(s)
- Xinyao Zhou
- Unit of Fetal Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Natalie Chandler
- North East Thames Regional Genetics Laboratory, Great Ormond Street NHS Foundation Trust, London, UK
| | - Linbei Deng
- Unit of Fetal Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Jia Zhou
- Unit of Fetal Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Meizhen Yuan
- Unit of Fetal Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Luming Sun
- Unit of Fetal Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| |
Collapse
|
75
|
Aggarwal S, Das Bhowmik A, Tandon A, Dalal A. Exome sequencing reveals blended phenotype of double heterozygous FBN1 and FBN2 variants in a fetus. Eur J Med Genet 2018; 61:399-402. [DOI: 10.1016/j.ejmg.2018.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/13/2018] [Accepted: 02/26/2018] [Indexed: 02/03/2023]
|
76
|
Ridnõi K, Kurvinen E, Pajusalu S, Reimand T, Õunap K. Two Consecutive Pregnancies with Simpson-Golabi-Behmel Syndrome Type 1: Case Report and Review of Published Prenatal Cases. Mol Syndromol 2018; 9:205-213. [PMID: 30158844 DOI: 10.1159/000490083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2018] [Indexed: 11/19/2022] Open
Abstract
Fetal overgrowth and numerous congenital malformations can be detected in every trimester of pregnancy. New technologies in molecular testing, such as chromosomal microarray analysis and next-generation sequencing, continually demonstrate advantages for definitive diagnosis in fetal life. Simpson-Golabi-Behmel (SGB) syndrome is a rare but well-known overgrowth condition that is rarely diagnosed in the prenatal setting. We report 3 cases of SGB syndrome in 2 consecutive pregnancies. In our series, distinctive prenatal sonographic findings led to molecular diagnosis. Exome sequencing from fetal DNA revealed a hemizygous splice site variant in the GPC3 gene: NM_004484.3:c.1166+ 1G>T. The mother is a heterozygous carrier. We also provide an overview of the previously published 57 prenatal cases of SGB syndrome with prevalence estimation of the symptoms to aid prenatal differential diagnosis of fetal overgrowth syndromes.
Collapse
Affiliation(s)
- Konstantin Ridnõi
- Center for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn.,Department of Clinical Genetics, Institute of Clinical Medicine
| | - Elvira Kurvinen
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, Institute of Clinical Medicine.,Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| |
Collapse
|
77
|
Non invasive prenatal diagnosis of fetal aneuploidy using cell free fetal DNA. Eur J Obstet Gynecol Reprod Biol 2018; 225:5-8. [DOI: 10.1016/j.ejogrb.2018.03.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/13/2018] [Accepted: 03/19/2018] [Indexed: 01/21/2023]
|
78
|
Fu F, Li R, Li Y, Nie ZQ, Lei T, Wang D, Yang X, Han J, Pan M, Zhen L, Ou Y, Li J, Li FT, Jing X, Li D, Liao C. Whole exome sequencing as a diagnostic adjunct to clinical testing in fetuses with structural abnormalities. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51:493-502. [PMID: 28976722 DOI: 10.1002/uog.18915] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVES To evaluate the diagnostic yield of prenatal whole exome sequencing (WES) for monogenic disorders in fetuses with structural malformations and normal results on cytogenetic testing, and to describe information on pathogenic variants that is provided by WES. METHODS Karyotyping, chromosomal microarray analysis (CMA) and WES were performed sequentially on stored samples from a cohort of 3949 pregnancies with fetal structural abnormalities detected on ultrasound and/or magnetic resonance imaging, referred between January 2011 and December 2015. Diagnostic rates of the three techniques were investigated overall, for phenotypic subgroups and for proband-only vs fetus-mother-father samples. Information on pathogenic variants was identified by WES. RESULTS Overall, 18.2% (720/3949) of fetuses had an abnormal karyotype. Pathogenic copy number variants were detected on CMA in 8.2% (138/1680) of fetuses that had a normal karyotype result. WES performed on a subgroup of 196 fetuses with normal CMA and karyotype results revealed the putative genetic variants responsible for the abnormal phenotypes in 47 cases (24%). The molecular diagnosis rates for fetus-mother-father and proband-only samples were 26.5% (13/49) and 23.1% (34/147), respectively. Variants of uncertain significance were detected in 12.8% (25/196) of fetuses, of which 22 were identified in the fetal proband-only group (15%; 22/147) and three in the fetus-mother-father group (6.1%; 3/49). The incidental finding rate was 6.1% (12/196). CONCLUSIONS WES is a promising method for the identification of genetic variants that cause structural abnormalities in fetuses with normal results on karyotyping and CMA. This enhanced diagnostic yield has the potential to improve the clinical management of pregnancies and to inform better the reproductive decisions of affected families. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- F Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - R Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Y Li
- Guanzghou Umbilical Cord Blood Bank, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Z-Q Nie
- Epidemiology Division, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangzhou, Guangdong, China
| | - T Lei
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - D Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - X Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - J Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - M Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - L Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Y Ou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - J Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - F-T Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - X Jing
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - D Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - C Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
79
|
Narayanan S, Blumberg B, Clayman ML, Pan V, Wicklund C. Exploring the Issues Surrounding Clinical Exome Sequencing in the Prenatal Setting. J Genet Couns 2018. [DOI: 10.1007/s10897-018-0245-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
80
|
Aggarwal S, Tandon A, Das Bhowmik A, Safarulla JMNJ, Dalal A. A Dysmorphology Based Systematic Approach Toward Perinatal Genetic Diagnosis in a Fetal Autopsy Series. Fetal Pediatr Pathol 2018; 37:49-68. [PMID: 29336636 DOI: 10.1080/15513815.2017.1397070] [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] [Indexed: 10/18/2022]
Abstract
BACKGROUND This retrospective study assesses the contribution of genetic disorders in fetuses undergoing postmortem evaluation and the performance of a clinical dysmorphology based systematic approach toward genetic diagnosis. MATERIALS AND METHODS Ninety fetuses, including spontaneous losses and terminated pregnancies, underwent a postmortem evaluation including dysmorphological examination, radiological studies, and histopathological examination. Genetic testing including karyotyping, biochemical testing, Sanger sequencing, and exome sequencing were performed selectively. RESULTS A genetic etiology was concluded in 48 fetuses (55%). As a standalone test, dysmorphological examination was able to ascertain a definite genetic diagnosis in sixteen cases, histopathology in six; and karyotyping, biochemical testing and exome sequencing in two cases each (Total 28). Additionally, dysmorphology findings indicated possible genetic disorder in 20 cases. CONCLUSION Genetic etiologies contribute significantly to fetuses undergoing autopsy in this series. A systematic approach to postmortem fetal evaluation guided by dysmorphological examination provides high diagnostic yield toward perinatal genetic diagnosis.
Collapse
Affiliation(s)
- Shagun Aggarwal
- a Department of Medical Genetics , Nizam's Institute of Medical Sciences , Punjagutta, Hyderabad , Telangana , India.,b Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana , India
| | - Ashwani Tandon
- c Department of Pathology , Nizam's Institute of Medical Sciences , Hyderabad , Telangana , India
| | - Aneek Das Bhowmik
- b Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana , India
| | | | - Ashwin Dalal
- b Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana , India
| |
Collapse
|
81
|
Aarabi M, Sniezek O, Jiang H, Saller DN, Bellissimo D, Yatsenko SA, Rajkovic A. Importance of complete phenotyping in prenatal whole exome sequencing. Hum Genet 2018; 137:175-181. [PMID: 29392406 DOI: 10.1007/s00439-017-1860-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/16/2017] [Indexed: 12/16/2022]
Abstract
Whole exome sequencing (WES) is an emerging technique in prenatal diagnosis. In this retrospective study, we examined diagnostic utility and limitations of WES in prenatal cases with structural birth defects. DNA from 20 trios (fetal and parental), with normal karyotype and microarray findings, underwent WES and variant interpretation at a reference laboratory. The WES results were later re-evaluated in our academic center utilizing prenatal and postnatal phenotyping. Initial analysis using only prenatal ultrasound findings revealed no pathogenic or likely pathogenic variants in 20 pregnancies with structural birth defects. Re-analysis of WES variants and combination of prenatal and postnatal phenotyping yielded pathogenic variants in at least 20% of cases including PORCN gene in a fetus with split-hand/foot malformation, as well as variants of uncertain significance in NEB and NOTCH1 in fetuses with postnatal muscle weakness and Adams-Oliver syndrome, respectively. Furthermore, Sanger sequencing in a patient with holoprosencephaly, elucidated by postnatal MRI, revealed a pathogenic 47-base pairs deletion in ZIC2 which was missed by prenatal WES. This study suggests that incomplete prenatal phenotyping and lack of prenatal ultrasound-genotype databases are the limiting factors for current interpretation of WES data in prenatal diagnosis. Development of prenatal phenotype-genotype databases would significantly help WES interpretation in this setting. Patients who underwent prenatal clinical WES may benefit from the re-analysis based on detailed postnatal findings.
Collapse
Affiliation(s)
- Mahmoud Aarabi
- Medical Genetics and Genomics Laboratories, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Olivia Sniezek
- Westminster College, New Wilmington, PA, USA.,Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Huaiyang Jiang
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Devereux N Saller
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daniel Bellissimo
- Medical Genetics and Genomics Laboratories, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Svetlana A Yatsenko
- Medical Genetics and Genomics Laboratories, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aleksandar Rajkovic
- Medical Genetics and Genomics Laboratories, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA. .,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA. .,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
82
|
Best S, Wou K, Vora N, Van der Veyver IB, Wapner R, Chitty LS. Promises, pitfalls and practicalities of prenatal whole exome sequencing. Prenat Diagn 2018; 38:10-19. [PMID: 28654730 PMCID: PMC5745303 DOI: 10.1002/pd.5102] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Abstract
Prenatal genetic diagnosis provides information for pregnancy and perinatal decision-making and management. In several small series, prenatal whole exome sequencing (WES) approaches have identified genetic diagnoses when conventional tests (karyotype and microarray) were not diagnostic. Here, we review published prenatal WES studies and recent conference abstracts. Thirty-one studies were identified, with diagnostic rates in series of five or more fetuses varying between 6.2% and 80%. Differences in inclusion criteria and trio versus singleton approaches to sequencing largely account for the wide range of diagnostic rates. The data suggest that diagnostic yields will be greater in fetuses with multiple anomalies or in cases preselected following genetic review. Beyond its ability to improve diagnostic rates, we explore the potential of WES to improve understanding of prenatal presentations of genetic disorders and lethal fetal syndromes. We discuss prenatal phenotyping limitations, counselling challenges regarding variants of uncertain significance, incidental and secondary findings, and technical problems in WES. We review the practical, ethical, social and economic issues that must be considered before prenatal WES could become part of routine testing. Finally, we reflect upon the potential future of prenatal genetic diagnosis, including a move towards whole genome sequencing and non-invasive whole exome and whole genome testing. © 2017 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Sunayna Best
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Karen Wou
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Neeta Vora
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ignatia B. Van der Veyver
- Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Lyn S. Chitty
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| |
Collapse
|
83
|
de Wit MC, Boekhorst F, Mancini GM, Smit LS, Groenenberg IAL, Dudink J, de Vries FAT, Go ATJI, Galjaard RJH. Advanced genomic testing may aid in counseling of isolated agenesis of the corpus callosum on prenatal ultrasound. Prenat Diagn 2017; 37:1191-1197. [PMID: 28921563 DOI: 10.1002/pd.5158] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Isolated agenesis of the corpus callosum on fetal ultrasound has a varied prognosis. Microarray and exome sequencing (ES) might aid in prenatal counseling. METHOD This study includes 25 fetuses with apparently isolated complete corpus callosum (cACC) on ultrasound. All cases were offered single nucleotide polymorphism array. Complementary ES was offered postnatally in selected cases. Clinical physical and neurodevelopmental follow-up was collected. RESULTS Eighteen cases opted for single nucleotide polymorphism array testing, which detected a causal anomaly in 2/18 (11.1%; 95% CI 2.0%-31%). Among ongoing pregnancies without a causal anomaly on microarray, 30% (95% CI 8.5%-60%) showed intellectual disability. Postnatal magnetic resonance imaging and physical examination often (64%; 95% CI 38%-85%, and 64%; 95% CI 38%-85%, respectively) revealed additional physical anomalies in cases without a causal anomaly on microarray. Two cases appeared truly isolated after birth. Postnatal sequencing in 4 of 16 cases without a causal anomaly on microarray but with intellectual disability and/or additional postnatal physical anomalies revealed 2 single-gene disorders. Therefore, the estimated diagnostic yield of ES in chromosomally normal cACC fetuses is between 2/4 (50%; 95% CI 11%-89%) and 2/16 (13.3%; 95% CI 2.4%-36%). CONCLUSION In accordance with current guidelines, we conclude that microarray should be offered in case of isolated cACC on ultrasound. ES is likely to be informative for prenatal counseling and should be offered if microarray is normal.
Collapse
Affiliation(s)
- M C de Wit
- Department of Obstetrics and Gynecology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - F Boekhorst
- Department of Obstetrics and Gynecology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - G M Mancini
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - L S Smit
- Department of Neurology, Division of Pediatric Neurology, Erasmus Medical Centre, University Medical Centre, Rotterdam, the Netherlands.,Department of Pediatrics, Division of Neonatology, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, the Netherlands
| | - I A L Groenenberg
- Department of Obstetrics and Gynecology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - J Dudink
- Department of Pediatrics, Division of Neonatology, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, the Netherlands.,Department of Neonatology, Wilhelmina Children's Hospital, UMC Utrecht, Utrecht, the Netherlands
| | - F A T de Vries
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - A T J I Go
- Department of Obstetrics and Gynecology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - R J H Galjaard
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| |
Collapse
|
84
|
Quinlan-Jones E, Hillman SC, Kilby MD, Greenfield SM. Parental experiences of prenatal whole exome sequencing (WES) in cases of ultrasound diagnosed fetal structural anomaly. Prenat Diagn 2017; 37:1225-1231. [DOI: 10.1002/pd.5172] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/06/2017] [Accepted: 10/12/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Elizabeth Quinlan-Jones
- Fetal Medicine Centre; Birmingham Women's and Children's NHS Foundation Trust; Birmingham UK
| | - Sarah C. Hillman
- Unit of Primary Care, Warwick Medical School; University of Warwick; Birmingham UK
| | - Mark D. Kilby
- Fetal Medicine Centre; Birmingham Women's and Children's NHS Foundation Trust; Birmingham UK
- Birmingham Centre for Women's and New-born Health, College of Medical and Dental Sciences; University of Birmingham; Birmingham UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences; University of Birmingham; Birmingham UK
| | - Sheila M. Greenfield
- Institute of Applied Health Research, College of Medical and Dental Sciences; University of Birmingham; Birmingham UK
| |
Collapse
|
85
|
Borghesi A, Mencarelli MA, Memo L, Ferrero GB, Bartuli A, Genuardi M, Stronati M, Villani A, Renieri A, Corsello G. Intersociety policy statement on the use of whole-exome sequencing in the critically ill newborn infant. Ital J Pediatr 2017; 43:100. [PMID: 29100554 PMCID: PMC5670717 DOI: 10.1186/s13052-017-0418-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/17/2017] [Indexed: 01/05/2023] Open
Abstract
The rapid advancement of next-generation sequencing (NGS) technology and the decrease in costs for whole-exome sequencing (WES) and whole-genome sequening (WGS), has prompted its clinical application in several fields of medicine. Currently, there are no specific guidelines for the use of NGS in the field of neonatal medicine and in the diagnosis of genetic diseases in critically ill newborn infants. As a consequence, NGS may be underused with reduced diagnostic success rate, or overused, with increased costs for the healthcare system. Most genetic diseases may be already expressed during the neonatal age, but their identification may be complicated by nonspecific presentation, especially in the setting of critical clinical conditions. The differential diagnosis process in the neonatal intensive care unit (NICU) may be time-consuming, uncomfortable for the patient due to repeated sampling, and ineffective in reaching a molecular diagnosis during NICU stay. Serial gene sequencing (Sanger sequencing) may be successful only for conditions for which the clinical phenotype strongly suggests a diagnostic hypothesis and for genetically homogeneous diseases. Newborn screenings with Guthrie cards, which vary from country to country, are designed to only test for a few dozen genetic diseases out of the more than 6000 diseases for which a genetic characterization is available. The use of WES in selected cases in the NICU may overcome these issues. We present an intersociety document that aims to define the best indications for the use of WES in different clinical scenarios in the NICU. We propose that WES is used in the NICU for critically ill newborn infants when an early diagnosis is desirable to guide the clinical management during NICU stay, when a strong hypothesis cannot be formulated based on the clinical phenotype or the disease is genetically heterogeneous, and when specific non-genetic laboratory tests are not available. The use of WES may reduce the time for diagnosis in infants during NICU stay and may eventually result in cost-effectiveness.
Collapse
Affiliation(s)
- Alessandro Borghesi
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinco San Matteo, Piazzale Golgi, 19, 27100 Pavia, Italy
| | | | - Luigi Memo
- Pediatric Department, S. Martino Hospital, Belluno, Italy
| | | | - Andrea Bartuli
- Rare Diseases and Medical Genetic Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maurizio Genuardi
- Institute of Genomic Medicine, Università Cattolica Del Sacro Cuore, Fondazione Policlinico A. Gemelli, Rome, Italy
| | - Mauro Stronati
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinco San Matteo, Piazzale Golgi, 19, 27100 Pavia, Italy
| | - Alberto Villani
- Pediatric and Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Alessandra Renieri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Giovanni Corsello
- Operative Unit of Pediatrics and Neonatal Intensive Therapy, Mother and Child Department, University of Palermo, Palermo, Italy
| |
Collapse
|
86
|
Vora NL, Powell B, Brandt A, Strande N, Hardisty E, Gilmore K, Foreman AKM, Wilhelmsen K, Bizon C, Reilly J, Owen P, Powell CM, Skinner D, Rini C, Lyerly AD, Boggess KA, Weck K, Berg JS, Evans JP. Prenatal exome sequencing in anomalous fetuses: new opportunities and challenges. Genet Med 2017; 19:1207-1216. [PMID: 28518170 PMCID: PMC5675748 DOI: 10.1038/gim.2017.33] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022] Open
Abstract
PurposeWe investigated the diagnostic and clinical performance of exome sequencing in fetuses with sonographic abnormalities with normal karyotype and microarray and, in some cases, normal gene-specific sequencing.MethodsExome sequencing was performed on DNA from 15 anomalous fetuses and from the peripheral blood of their parents. Parents provided consent to be informed of diagnostic results in the fetus, medically actionable findings in the parents, and their identification as carrier couples for significant autosomal recessive conditions. We assessed the perceptions and understanding of exome sequencing using mixed methods in 15 mother-father dyads.ResultsIn seven (47%) of 15 fetuses, exome sequencing provided a diagnosis or possible diagnosis with identification of variants in the following genes: COL1A1, MUSK, KCTD1, RTTN, TMEM67, PIEZO1 and DYNC2H1. One additional case revealed a de novo nonsense mutation in a novel candidate gene (MAP4K4). The perceived likelihood that exome sequencing would explain the results (5.2 on a 10-point scale) was higher than the approximately 30% diagnostic yield discussed in pretest counseling.ConclusionExome sequencing had diagnostic utility in a highly select population of fetuses where a genetic diagnosis was highly suspected. Challenges related to genetics literacy and variant interpretation must be addressed by highly tailored pre- and posttest genetic counseling.
Collapse
Affiliation(s)
- Neeta L. Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bradford Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Natasha Strande
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emily Hardisty
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ann Katherine M. Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- North Carolina Translational and Clinical Sciences (NC TraCS) Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kirk Wilhelmsen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Chris Bizon
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jason Reilly
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Phil Owen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Cynthia M. Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Debra Skinner
- FPG Child Development Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christine Rini
- Department of Health Behavior, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anne D. Lyerly
- Department of Social Medicine and Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kim A. Boggess
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Karen Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jonathan S. Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James P. Evans
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Social Medicine and Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| |
Collapse
|
87
|
Genomic study of severe fetal anomalies and discovery of GREB1L mutations in renal agenesis. Genet Med 2017; 20:745-753. [PMID: 29261186 DOI: 10.1038/gim.2017.173] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/24/2017] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Fetal anomalies represent a poorly studied group of developmental disorders. Our objective was to assess the impact of whole-exome sequencing (WES) on the investigation of these anomalies. METHODS We performed WES in 101 fetuses or stillborns who presented prenatally with severe anomalies, including renal a/dysgenesis, VACTERL association (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities), brain anomalies, suspected ciliopathies, multiple major malformations, and akinesia. RESULTS A molecular diagnosis was obtained in 19 cases (19%). In 13 of these cases, the diagnosis was not initially suspected by the clinicians because the phenotype was nonspecific or atypical, corresponding in some cases to the severe end of the spectrum of a known disease (e.g., MNX1-, RYR1-, or TUBB-related disorders). In addition, we identified likely pathogenic variants in genes (DSTYK, ACTB, and HIVEP2) previously associated with phenotypes that were substantially different from those found in our cases. Finally, we identified variants in novel candidate genes that were associated with perinatal lethality, including de novo mutations in GREB1L in two cases with bilateral renal agenesis, which represents a significant enrichment of such mutations in our cohort. CONCLUSION Our study opens a window on the distinctive genetic landscape associated with fetal anomalies and highlights the power-but also the challenges-of WES in prenatal diagnosis.
Collapse
|
88
|
Vetro A, Goidin D, Lesende I, Limongelli I, Ranzani GN, Novara F, Bonaglia MC, Rinaldi B, Franchi F, Manolakos E, Lonardo F, Scarano F, Scarano G, Costantino L, Tedeschi S, Giglio S, Zuffardi O. Diagnostic application of a capture based NGS test for the concurrent detection of variants in sequence and copy number as well as LOH. Clin Genet 2017; 93:545-556. [PMID: 28556904 DOI: 10.1111/cge.13060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 01/08/2023]
Abstract
Whole exome sequencing (WES) has made the identification of causative SNVs/InDels associated with rare Mendelian conditions increasingly accessible. Incorporation of softwares allowing CNVs detection into the WES bioinformatics pipelines may increase the diagnostic yield. However, no standard protocols for this analysis are so far available and CNVs in non-coding regions are totally missed by WES, in spite of their possible role in the regulation of the flanking genes expression. So, in a number of cases the diagnostic workflow contemplates an initial investigation by genomic arrays followed, in the negative cases, by WES. The opposite workflow may also be applied, according to the familial segregation of the disease. We show preliminary results for a diagnostic application of a single next generation sequencing panel permitting the concurrent detection of LOH and variations in sequences and copy number. This approach allowed us to highlight compound heterozygosity for a CNV and a sequence variant in a number of cases, the duplication of a non-coding region responsible for sex reversal, and a whole-chromosome isodisomy causing reduction to homozygosity for a WFS1 variant. Moreover, the panel enabled us to detect deletions, duplications, and amplifications with sensitivity comparable to that of the most widely used array-CGH platforms.
Collapse
Affiliation(s)
- A Vetro
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - D Goidin
- Diagnostics and Genomics Group, Agilent Technologies Inc., Santa Clara, California
| | - I Lesende
- Diagnostics and Genomics Group, Agilent Technologies Inc., Santa Clara, California
| | | | - G N Ranzani
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - F Novara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - M C Bonaglia
- Cytogenetics Laboratory, Scientific Institute IRCCS E. Medea, Lecco, Italy
| | - B Rinaldi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - F Franchi
- Laboratorio Genetica, Azienda Ospedaliera Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - E Manolakos
- Clinical Laboratory Genetics, Access to Genome, Athens, Greece.,Clinical Laboratory Genetics, Access to Genome, Thessaloniki, Greece
| | - F Lonardo
- U.O.S.D. Genetica Medica-A.O.R.N, Benevento, Italy
| | - F Scarano
- U.O.S.D. Genetica Medica-A.O.R.N, Benevento, Italy
| | - G Scarano
- U.O.S.D. Genetica Medica-A.O.R.N, Benevento, Italy
| | - L Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - S Tedeschi
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - S Giglio
- Medical Genetics Unit, Meyer Children's University Hospital, Firenze, Italy
| | - O Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| |
Collapse
|
89
|
McPherson E, Nestoridi E, Heinke D, Roberts DJ, Fretts R, Yazdy MM, Lin AE. Alternatives to Autopsy for Fetal and Early Neonatal (Perinatal) Deaths: Insights from the Wisconsin Stillbirth Service Program. Birth Defects Res 2017; 109:1430-1441. [DOI: 10.1002/bdr2.1112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 01/16/2023]
Affiliation(s)
- Elspeth McPherson
- Center for Human Genetics; Marshfield Clinic Research Institute; Marshfield Wisconsin
| | - Eirini Nestoridi
- Massachusetts Center for Birth Defects Research and Prevention; Massachusetts; Department of Public Health; Boston Massachusetts
| | - Dominique Heinke
- Massachusetts Center for Birth Defects Research and Prevention; Massachusetts; Department of Public Health; Boston Massachusetts
| | - Drucilla J. Roberts
- Department of Pathology; Massachusetts General Hospital; Boston Massachusetts
| | - Ruth Fretts
- Harvard Vanguard Medical Associates; Wellesley Massachusetts
| | - Mahsa M. Yazdy
- Massachusetts Center for Birth Defects Research and Prevention; Massachusetts; Department of Public Health; Boston Massachusetts
| | - Angela E. Lin
- Massachusetts Center for Birth Defects Research and Prevention; Massachusetts; Department of Public Health; Boston Massachusetts
- Genetics Unit; MassGeneral Hospital for Children; Boston Massachusetts
| |
Collapse
|
90
|
Kardon G, Ackerman KG, McCulley DJ, Shen Y, Wynn J, Shang L, Bogenschutz E, Sun X, Chung WK. Congenital diaphragmatic hernias: from genes to mechanisms to therapies. Dis Model Mech 2017; 10:955-970. [PMID: 28768736 PMCID: PMC5560060 DOI: 10.1242/dmm.028365] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Congenital diaphragmatic hernias (CDHs) and structural anomalies of the diaphragm are a common class of congenital birth defects that are associated with significant morbidity and mortality due to associated pulmonary hypoplasia, pulmonary hypertension and heart failure. In ∼30% of CDH patients, genomic analyses have identified a range of genetic defects, including chromosomal anomalies, copy number variants and sequence variants. The affected genes identified in CDH patients include transcription factors, such as GATA4, ZFPM2, NR2F2 and WT1, and signaling pathway components, including members of the retinoic acid pathway. Mutations in these genes affect diaphragm development and can have pleiotropic effects on pulmonary and cardiac development. New therapies, including fetal endoscopic tracheal occlusion and prenatal transplacental fetal treatments, aim to normalize lung development and pulmonary vascular tone to prevent and treat lung hypoplasia and pulmonary hypertension, respectively. Studies of the association between particular genetic mutations and clinical outcomes should allow us to better understand the origin of this birth defect and to improve our ability to predict and identify patients most likely to benefit from specialized treatment strategies.
Collapse
Affiliation(s)
- Gabrielle Kardon
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Kate G Ackerman
- Departments of Pediatrics (Critical Care) and Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - David J McCulley
- Department of Pediatrics, University of Wisconsin, Madison, WI 53792, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Departments of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Linshan Shang
- Departments of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Eric Bogenschutz
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Xin Sun
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wendy K Chung
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| |
Collapse
|
91
|
Shamseldin HE, Kurdi W, Almusafri F, Alnemer M, Alkaff A, Babay Z, Alhashem A, Tulbah M, Alsahan N, Khan R, Sallout B, Al Mardawi E, Seidahmed MZ, Meriki N, Alsaber Y, Qari A, Khalifa O, Eyaid W, Rahbeeni Z, Kurdi A, Hashem M, Alshidi T, Al-Obeid E, Abdulwahab F, Ibrahim N, Ewida N, El-Akouri K, Al Mulla M, Ben-Omran T, Pergande M, Cirak S, Al Tala S, Shaheen R, Faqeih E, Alkuraya FS. Molecular autopsy in maternal-fetal medicine. Genet Med 2017; 20:420-427. [PMID: 28749478 DOI: 10.1038/gim.2017.111] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/14/2017] [Indexed: 12/16/2022] Open
Abstract
PurposeThe application of genomic sequencing to investigate unexplained death during early human development, a form of lethality likely enriched for severe Mendelian disorders, has been limited.MethodsIn this study, we employed exome sequencing as a molecular autopsy tool in a cohort of 44 families with at least one death or lethal fetal malformation at any stage of in utero development. Where no DNA was available from the fetus, we performed molecular autopsy by proxy, i.e., through parental testing.ResultsPathogenic or likely pathogenic variants were identified in 22 families (50%), and variants of unknown significance were identified in further 15 families (34%). These variants were in genes known to cause embryonic or perinatal lethality (ALPL, GUSB, SLC17A5, MRPS16, THSD1, PIEZO1, and CTSA), genes known to cause Mendelian phenotypes that do not typically include embryonic lethality (INVS, FKTN, MYBPC3, COL11A2, KRIT1, ASCC1, NEB, LZTR1, TTC21B, AGT, KLHL41, GFPT1, and WDR81) and genes with no established links to human disease that we propose as novel candidates supported by embryonic lethality of their orthologs or other lines of evidence (MS4A7, SERPINA11, FCRL4, MYBPHL, PRPF19, VPS13D, KIAA1109, MOCS3, SVOPL, FEN1, HSPB11, KIF19, and EXOC3L2).ConclusionOur results suggest that molecular autopsy in pregnancy losses is a practical and high-yield alternative to traditional autopsy, and an opportunity for bringing precision medicine to the clinical practice of perinatology.
Collapse
Affiliation(s)
- Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wesam Kurdi
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatima Almusafri
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Qatar
| | - Maha Alnemer
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Alya Alkaff
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Zeneb Babay
- Department of Obstetrics and Gynecology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Price Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Maha Tulbah
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nada Alsahan
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rubina Khan
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bahauddin Sallout
- Maternal-Fetal Medicine Department, Women's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Elham Al Mardawi
- Department of Obstetrics and Gynecology, Security Forces Hospital, Riyadh, Saudi Arabia
| | | | - Niema Meriki
- Department of Obstetrics and Gynecology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Yasser Alsaber
- Department of Obstetrics and Gynecology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Alya Qari
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ola Khalifa
- Genetics Unit, Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Wafaa Eyaid
- Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ahmed Kurdi
- Department of Obstetrics and Gynecology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman Al-Obeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Karen El-Akouri
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Qatar
| | - Mariam Al Mulla
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Qatar
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Qatar
| | | | - Sebahattin Cirak
- Cologne Center for Genomics, University of Cologne, Köln, Germany
| | - Saeed Al Tala
- Department of Pediatrics, Armed Forces Hospital Program Southwest Region, Khamis Mushait, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| |
Collapse
|
92
|
Powis Z, Hart A, Cherny S, Petrik I, Palmaer E, Tang S, Jones C. Clinical diagnostic exome evaluation for an infant with a lethal disorder: genetic diagnosis of TARP syndrome and expansion of the phenotype in a patient with a newly reported RBM10 alteration. BMC MEDICAL GENETICS 2017; 18:60. [PMID: 28577551 PMCID: PMC5455125 DOI: 10.1186/s12881-017-0426-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 05/22/2017] [Indexed: 11/11/2022]
Abstract
Background Diagnostic Exome Sequencing (DES) has been shown to be an effective tool for diagnosis individuals with suspected genetic conditions. Case Presentation We report a male infant born with multiple anomalies including bilateral dysplastic kidneys, cleft palate, bilateral talipes, and bilateral absence of thumbs and first toes. Prenatal testing including chromosome analysis and microarray did not identify a cause for the multiple congenital anomalies. Postnatal diagnostic exome studies (DES) were utilized to find a molecular diagnosis for the patient. Exome sequencing of the proband, mother, and father showed a previously unreported maternally inherited RNA binding motif protein 10 (RBM10) c.1352_1353delAG (p.E451Vfs*66) alteration. Mutations in RBM10 are associated with TARP syndrome, an X-linked recessive disorder originally described with cardinal features of talipes equinovarus, atrial septal defect, Robin sequence, and persistent left superior vena cava. Conclusion DES established a molecular genetic diagnosis of TARP syndrome for a neonatal patient with a poor prognosis in whom traditional testing methods were uninformative and allowed for efficient diagnosis and future reproductive options for the parents. Other reported cases of TARP syndrome demonstrate significant variability in clinical phenotype. The reported features in this infant including multiple hemivertebrae, imperforate anus, aplasia of thumbs and first toes have not been reported in previous patients, thus expanding the clinical phenotype for this rare disorder. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0426-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zöe Powis
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA.
| | - Alexa Hart
- Rush University Medical Center, Chicago, IL, USA
| | - Sara Cherny
- Rush University Medical Center, Chicago, IL, USA
| | - Igor Petrik
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Erika Palmaer
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Sha Tang
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | | |
Collapse
|
93
|
Vermeesch JR, Voet T, Devriendt K. Prenatal and pre-implantation genetic diagnosis. Nat Rev Genet 2017; 17:643-56. [PMID: 27629932 DOI: 10.1038/nrg.2016.97] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.
Collapse
Affiliation(s)
- Joris Robert Vermeesch
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Thierry Voet
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| |
Collapse
|
94
|
Westerfield LE, Braxton AA, Walkiewicz M. Prenatal Diagnostic Exome Sequencing: a Review. CURRENT GENETIC MEDICINE REPORTS 2017. [DOI: 10.1007/s40142-017-0120-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
95
|
Whole-exome sequencing on deceased fetuses with ultrasound anomalies: expanding our knowledge of genetic disease during fetal development. Genet Med 2017; 19:1171-1178. [PMID: 28425981 DOI: 10.1038/gim.2017.31] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/08/2017] [Indexed: 12/27/2022] Open
Abstract
PurposeThe aim of this study was to determine the diagnostic yield of whole-exome sequencing (WES) in fetuses with ultrasound anomalies that resulted in fetal demise or pregnancy termination. The results were also utilized to aid in the identification of candidate genes for fetal development and to expand the clinical phenotype of known genetic conditions.MethodsWES was performed on specimens from 84 deceased fetuses. Data were analyzed and final results were classified into one of four categories: positive, possible, negative, and candidate gene only. WES analysis was predominantly performed in fetus-parent trios or quads (61%, n=52).ResultsOverall, 20% (n = 17) of cases were positive, 45% (n=38) were possible, 9% (n=7) had only candidate gene variants and 26% (n = 22) tested negative. The diagnostic yield for definitive findings for trio analysis was 24% (n = 11) compared to 14% (n = 4) for singletons. The most frequently reported ultrasound anomalies were central nervous system (37%, n = 31), hydrops/edema (36%, n = 30), and cardiovascular anomalies (31%, n = 26).ConclusionOur experience supports the use of WES to identify the molecular etiology of fetal ultrasound anomalies, to identify candidate genes involved in fetal development, and to expand our knowledge of the clinical phenotype of known genetic conditions.
Collapse
|
96
|
Abou Tayoun AN, Spinner NB, Rehm HL, Green RC, Bianchi DW. Prenatal DNA Sequencing: Clinical, Counseling, and Diagnostic Laboratory Considerations. Prenat Diagn 2017; 38:26-32. [PMID: 28345240 PMCID: PMC10066604 DOI: 10.1002/pd.5038] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/06/2017] [Accepted: 03/12/2017] [Indexed: 12/18/2022]
Abstract
Clinical diagnostic laboratories are producing next-generation sequencing-based test results that are becoming increasingly incorporated into patient care. Whole genome and exome sequencing on fetal material derived from amniocytes, chorionic villi, or products of conception is starting to be offered clinically in specialized centers, but it has not yet become routine practice. The technical, interpretation, and ethical challenges are greatest in the area of prenatal medicine because the fetus has a limited health history, and the physical examination is only indirectly available via prenatal sonography. Here, we provide an overview of these challenges and highlight the clinical utility, reporting, and counseling issues associated with prenatal DNA sequencing. Future considerations are also discussed. © 2017 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Ahmad N. Abou Tayoun
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine; The Children's Hospital of Philadelphia, and the Perelman School of Medicine at The University of Pennsylvania Perelman School of Medicine; Philadelphia PA USA
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine; The Children's Hospital of Philadelphia, and the Perelman School of Medicine at The University of Pennsylvania Perelman School of Medicine; Philadelphia PA USA
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA USA
- Department of Pathology; Brigham and Women's Hospital, Harvard Medical School; Boston MA USA
- The Broad Institute of MIT and Harvard; Cambridge MA USA
| | - Robert C. Green
- The Broad Institute of MIT and Harvard; Cambridge MA USA
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital, Harvard Medical School; Boston MA USA
| | - Diana W. Bianchi
- Mother Infant Research Institute; Tufts Medical Center; Boston MA USA
- National Human Genome Research Institute; National Institutes of Health; Bethesda MD USA
| |
Collapse
|
97
|
de Wit MC, Srebniak MI, Joosten M, Govaerts LCP, Kornelisse RF, Papatsonis DNM, de Graaff K, Knapen MFCM, Bruggenwirth HT, de Vries FAT, Van Veen S, Van Opstal D, Galjaard RJH, Go ATJI. Prenatal and postnatal findings in small-for-gestational-age fetuses without structural ultrasound anomalies at 18-24 weeks. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2017; 49:342-348. [PMID: 27102944 DOI: 10.1002/uog.15949] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/09/2016] [Accepted: 04/15/2016] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To assess phenotypic and genotypic characteristics of small-for-gestational-age (SGA) fetuses without structural anomalies at 18-24 weeks' gestation. METHODS This retrospective study included structurally normal singleton fetuses with an abdominal circumference ≤ 5th percentile on detailed ultrasound examination between 18 and 24 weeks' gestation. Cases were stratified according to the absence or presence of other abnormal ultrasound findings, such as abnormal amniotic fluid or soft markers. All patients were offered invasive prenatal testing with rapid aneuploidy detection by qualitative fluorescence polymerase chain reaction (QF-PCR) and, if normal, consecutive single nucleotide polymorphism (SNP) array was also offered. Detailed postnatal follow-up (≥ 5 months) was performed. In cases in which a syndromic phenotype became apparent within 5 months after birth and SNP array had not been performed prenatally, it was performed postnatally. RESULTS A total of 211 pregnancies were eligible for inclusion. Of the 158 cases with isolated SGA on ultrasound, 36 opted for invasive prenatal testing. One case of trisomy 21 and one case of a submicroscopic abnormality (a susceptibility locus for neurodevelopmental disease) were detected. Postnatal follow-up showed a postnatal apparent syndromic phenotype in 10 cases. In one case this was due to trisomy 21 and the other nine (5.8%; 95% CI, 2.8-10.0%) cases had normal SNP array results. In 32/53 cases with SGA and associated ultrasound abnormalities, parents opted for invasive testing. One case of trisomy 21 and one of triploidy were found. In 11 cases a syndromic phenotype became apparent after birth. One was due to trisomy 21 and in one case a submicroscopic anomaly (a susceptibility locus) was found. The remaining syndromic cases (17.3%; 95% CI, 8.7-29.0%) had normal SNP array results. CONCLUSION Testing for chromosomal anomalies should be offered in cases of SGA between 18 and 24 weeks' gestation. Whole chromosome anomalies occur in 1.3% (95% CI, 0.2-3.9%) of isolated SGA and 5.8% (95% CI, 1.5-14.0%) of associated SGA. In 0.6% (95% CI, 0.1-2.8%) and 1.9% (95% CI, 0.2-8.2%), respectively, SNP array detected a susceptibility locus for neurodevelopmental disease that would not be detected by karyotyping, QF-PCR or non-invasive prenatal testing. Therefore, and because the genetic causes of SGA are diverse, we suggest SNP array testing in cases of SGA. Thorough postnatal examination and follow-up of infants that presented with reduced fetal growth is important because chromosomally normal syndromic phenotypes occur frequently in SGA fetuses. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- M C de Wit
- Department of Obstetrics and Gynecology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M I Srebniak
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M Joosten
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - L C P Govaerts
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - R F Kornelisse
- Department of Neonatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - D N M Papatsonis
- Department of Obstetrics and Gynecology, Amphia Hospital, Breda, The Netherlands
| | - K de Graaff
- Department of Obstetrics and Gynecology, Reinier de Graaf Groep, Delft, The Netherlands
| | - M F C M Knapen
- Foundation Prenatal Screening Southwestern region of The Netherlands, Rotterdam, The Netherlands
| | - H T Bruggenwirth
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - F A T de Vries
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - S Van Veen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - D Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - R J H Galjaard
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - A T J I Go
- Department of Obstetrics and Gynecology, Erasmus Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
98
|
Choi R, Park HD, Yang M, Ki CS, Lee SY, Kim JW, Song J, Chang YS, Park WS. Novel Pathogenic Variant (c.580C>T) in the CPS1 Gene in a Newborn With Carbamoyl Phosphate Synthetase 1 Deficiency Identified by Whole Exome Sequencing. Ann Lab Med 2017; 37:58-62. [PMID: 27834067 PMCID: PMC5107619 DOI: 10.3343/alm.2017.37.1.58] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/21/2016] [Accepted: 10/19/2016] [Indexed: 12/31/2022] Open
Abstract
Diagnosis of the urea cycle disorder (USD) carbamoyl-phosphate synthetase 1 (CPS1) deficiency (CPS1D) based on only the measurements of biochemical intermediary metabolites is not sufficient to properly exclude other UCDs with similar symptoms. We report the first Korean CPS1D patient using whole exome sequencing (WES). A four-day-old female neonate presented with respiratory failure due to severe metabolic encephalopathy with hyperammonemia (1,690 µmol/L; reference range, 11.2-48.2 µmol/L). Plasma amino acid analysis revealed markedly elevated levels of alanine (2,923 µmol/L; reference range, 131-710 µmol/L) and glutamine (5,777 µmol/L; reference range, 376-709 µmol/L), whereas that of citrulline was decreased (2 µmol/L; reference range, 10-45 µmol/L). WES revealed compound heterozygous pathogenic variants in the CPS1 gene: one novel nonsense pathogenic variant of c.580C>T (p.Gln194*) and one known pathogenic frameshift pathogenic variant of c.1547delG (p.Gly516Alafs*5), which was previously reported in Japanese patients with CPS1D. We successfully applied WES to molecularly diagnose the first Korean patient with CPS1D in a clinical setting. This result supports the clinical applicability of WES for cost-effective molecular diagnosis of UCDs.
Collapse
Affiliation(s)
- Rihwa Choi
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyung Doo Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Mina Yang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Junghan Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Yun Sil Chang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Soon Park
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul, Korea.
| |
Collapse
|
99
|
Konialis C, Assimakopoulos E, Hagnefelt B, Karapanou S, Sotiriadis A, Pangalos C. Prenatal diagnosis of X-linked myopathy associated with a VMA21 gene mutation afforded through a novel targeted exome sequencing strategy applied in fetuses with abnormal ultrasound findings. Clin Case Rep 2017; 5:308-311. [PMID: 28265396 PMCID: PMC5331204 DOI: 10.1002/ccr3.822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/13/2016] [Accepted: 12/25/2016] [Indexed: 01/23/2023] Open
Abstract
Fetal malformations detected through routine prenatal ultrasound examination comprise a heterogeneous group potentially associated with genetic disorders where the underlying cause is difficult to establish. We present the prenatal diagnosis of a rare X‐linked myopathy involving a new VMA21 gene mutation, detected through a novel prenatal exome sequencing‐based approach.
Collapse
Affiliation(s)
- Christopher Konialis
- InterGenetics - Diagnostic Genetics Centre Athens 11526 Greece; Genomis Ltd, Lynton House London WC1H 9BQ UK
| | - Efstratios Assimakopoulos
- 2nd Department of Obstetrics and Gynecology Ippokrateion General Hospital Aristotle University of Thessaloniki Thessaloniki Greece
| | - Birgitta Hagnefelt
- InterGenetics - Diagnostic Genetics Centre Athens 11526 Greece; Genomis Ltd, Lynton House London WC1H 9BQ UK
| | | | - Alexandros Sotiriadis
- 2nd Department of Obstetrics and Gynecology Ippokrateion General Hospital Aristotle University of Thessaloniki Thessaloniki Greece
| | - Constantinos Pangalos
- InterGenetics - Diagnostic Genetics Centre Athens 11526 Greece; Genomis Ltd, Lynton House London WC1H 9BQ UK
| |
Collapse
|
100
|
Bertier G, Sénécal K, Borry P, Vears DF. Unsolved challenges in pediatric whole-exome sequencing: A literature analysis. Crit Rev Clin Lab Sci 2017; 54:134-142. [PMID: 28132577 DOI: 10.1080/10408363.2016.1275516] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Whole-exome sequencing (WES) has been instrumental in the discovery of novel genes and mechanisms causing Mendelian diseases. While this technology is now being successfully applied in a number of clinics, particularly to diagnose patients with rare diseases, it also raises a number of ethical, legal and social issues. In order to identify what challenges were directly foreseen by technology users, we performed a systematic review of the literature. In this paper, we focus on recent publications related to the use of WES in the pediatric context and analyze the most prominent challenges raised by technology users. This is particularly relevant considering that a) most patients currently undergoing testing using WES to identify the genetic basis for rare diseases are children and b) their lack of capacity to consent for themselves makes them a vulnerable population and generates the need for specific ethical, legal and regulatory procedures. We identified key challenges that related to four main categories: (1) intake; (2) sequence production and analysis; (3) reporting of results and counseling considerations and (4) collaborative data interpretation and data sharing. We then contextualize these challenges in light of the recent recommendations and guidelines, published by professional societies that have significant potential to impact the field.
Collapse
Affiliation(s)
- Gabrielle Bertier
- a Department of Human Genetics , Centre of Genomics and Policy, McGill University , Montreal , QC , Canada.,b UMR 1027, Inserm, Université Toulouse III - Paul Sabatier , Toulouse , France
| | - Karine Sénécal
- a Department of Human Genetics , Centre of Genomics and Policy, McGill University , Montreal , QC , Canada
| | - Pascal Borry
- c Department of Public Health and Primary Care , Leuven Institute for Human Genomics and Society , KU Leuven , Leuven , Belgium and
| | - Danya F Vears
- c Department of Public Health and Primary Care , Leuven Institute for Human Genomics and Society , KU Leuven , Leuven , Belgium and.,d Center for Biomedical Ethics and Law , KU Leuven , Leuven , Belgium
| |
Collapse
|