1
|
Schubert C, Milverton J, Goodall S, Merlin T. A systematic review to assess the utility of genomic autopsy using exome or genome sequencing in cases of congenital anomalies and perinatal death. Genet Med 2024; 26:101159. [PMID: 38704678 DOI: 10.1016/j.gim.2024.101159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024] Open
Abstract
PURPOSE Exome or genome sequencing (ES or GS) can identify genetic causes of otherwise unexplained congenital anomaly and perinatal death (PND) but is not routine practice. The evidence base for "genomic autopsy" after termination of pregnancy for fetal anomaly (TOPFA) and PND has been synthesized to determine the value of this investigation. METHODS We conducted a systematic review and meta-analysis of studies meeting prespecified inclusion criteria and containing ≥10 cases of TOPFA or PND (with or without major congenital abnormality), in which ES or GS was conducted. We determined test performance, including diagnostic yield, accuracy, and reliability. We also reported outcomes associated with clinical utility and harms, where described. RESULTS From 2245 potentially eligible studies, 32 publications were eligible and had data extracted, representing 2120 cases that could be meta-analyzed. No diagnostic accuracy or comparative studies were identified, although some analysis of concordance between different ES/GS methodologies could be performed. Studies reporting parent-related outcomes or long-term follow-up did not do so in a systematic or quantifiable manner. CONCLUSION Evidence suggests that approximately one-fourth to one-third of fetal losses associated with TOPFA or unexplained PND are associated with a genetic cause identifiable on ES or GS-albeit this estimate varies depending on phenotypic and background risk factors. Despite the large body of evidence on ES and GS, little research has attempted to validate the accuracy of testing, nor measure the clinical or societal outcomes in families that follow the diagnostic investigation in this context.
Collapse
Affiliation(s)
- Camille Schubert
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia.
| | - Joanne Milverton
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Goodall
- Centre for Health Economics Research and Evaluation, Faculty of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Tracy Merlin
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
2
|
Mustafa HJ, Barbera JP, Sambatur EV, Pagani G, Yaron Y, Baptiste CD, Wapner RJ, Brewer CJ, Khalil A. Diagnostic yield of exome sequencing in prenatal agenesis of corpus callosum: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:312-320. [PMID: 37519216 DOI: 10.1002/uog.27440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/25/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVES To determine the incremental diagnostic yield of exome sequencing (ES) after negative chromosomal microarray analysis (CMA) in cases of prenatally diagnosed agenesis of the corpus callosum (ACC) and to identify the associated genes and variants. METHODS A systematic search was performed to identify relevant studies published up until June 2022 using four databases: PubMed, SCOPUS, Web of Science and The Cochrane Library. Studies in English reporting on the diagnostic yield of ES following negative CMA in prenatally diagnosed partial or complete ACC were included. Authors of cohort studies were contacted for individual participant data and extended cohorts were provided for two of them. The increase in diagnostic yield with ES for pathogenic/likely pathogenic (P/LP) variants was assessed in all cases of ACC, isolated ACC, ACC with other cranial anomalies and ACC with extracranial anomalies. To identify all reported genetic variants, the systematic review included all ACC cases; however, for the meta-analysis, only studies with ≥ three ACC cases were included. Meta-analysis of proportions was employed using a random-effects model. Quality assessment of the included studies was performed using modified Standards for Reporting of Diagnostic Accuracy criteria. RESULTS A total of 28 studies, encompassing 288 prenatally diagnosed ACC cases that underwent ES following negative CMA, met the inclusion criteria of the systematic review. We classified 116 genetic variants in 83 genes associated with prenatal ACC with a full phenotypic description. There were 15 studies, encompassing 268 cases, that reported on ≥ three ACC cases and were included in the meta-analysis. Of all the included cases, 43% had a P/LP variant on ES. The highest yield was for ACC with extracranial anomalies (55% (95% CI, 35-73%)), followed by ACC with other cranial anomalies (43% (95% CI, 30-57%)) and isolated ACC (32% (95% CI, 18-51%)). CONCLUSIONS ES demonstrated an incremental diagnostic yield in cases of prenatally diagnosed ACC following negative CMA. While the greatest diagnostic yield was observed in ACC with extracranial anomalies and ACC with other central nervous system anomalies, ES should also be considered in cases of isolated ACC. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- H J Mustafa
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Riley Children and Indiana University Health Fetal Center, Indianapolis, IN, USA
| | - J P Barbera
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - E V Sambatur
- Research Division, Houston Center for Maternal Fetal Medicine, Houston, TX, USA
| | - G Pagani
- Maternal Fetal Medicine Unit, Department of Obstetrics and Gynecology, ASST-Papa Giovanni XXIII, Bergamo, Italy
| | - Y Yaron
- Prenatal Genetic Diagnosis Unit, Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - C D Baptiste
- Obstetrics and Gynecology, Reproductive Genetics, Columbia University Medical Center, New York, NY, USA
| | - R J Wapner
- Obstetrics and Gynecology, Reproductive Genetics, Columbia University Medical Center, New York, NY, USA
| | - C J Brewer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - A Khalil
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
| |
Collapse
|
3
|
Cai M, Chen X, Li Y, Lin N, Huang H, Xu L. Genetic analysis, ultrasound phenotype, and pregnancy outcomes of fetuses with Xp22.33 or Yp11.32 microdeletions. J Perinat Med 2024; 52:96-101. [PMID: 37846158 DOI: 10.1515/jpm-2023-0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/27/2023] [Indexed: 10/18/2023]
Abstract
OBJECTIVES The phenotypes of Xp22.33 or Yp11.32 microdeletions comprising the short-stature homeobox (SHOX) gene have been extensively described in adults and children. Herein, the prenatal ultrasound phenotype and pregnancy outcomes of fetuses with Xp22.33/Yp11.32 microdeletions were analyzed to improve our understanding, diagnosis, and monitoring of this genetic condition in the fetal stage. METHODS A total of 9,100 pregnant women referred to tertiary units for prenatal diagnosis were evaluated by chromosomal microarray analysis(CMA). RESULTS Seven (0.08 %) fetuses had Xp22.33/Yp11.32 microdeletions, ranging from 243 kb to 1.1 Mb, that comprised SHOX. The ultrasonic phenotypes differed among these fetuses, with three fetuses presenting abnormal bone development, one had labial-palatal deformity and strawberry head, two had an abnormal ultrasonic soft marker, and one had no abnormalities. After genetic counseling, only one couple underwent pedigree assessment, which confirmed the paternal origin of the microdeletion. This infant presented delayed speech development, whereas other three infants showed a typical postnatal development. In three cases, the parents chose to terminate the pregnancy. CONCLUSIONS The ultrasonic phenotype of fetuses with Xp22.33/Yp11.32 microdeletions resulting in SHOX heterozygosity loss is variable. Prenatal CMA can quickly and effectively diagnose Xp22.33/Yp11.32 microdeletions and SHOX loss, which may help prenatal counseling.
Collapse
Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| |
Collapse
|
4
|
Vaseghi P, Habibi L, Neidich JA, Cao Y, Fattahi N, Rashidi-Nezhad R, Salehnezhad T, Dalili H, Rahimi Sharbaf F, Zarkesh MR, Malekian M, Mokhberdezfuli M, Mehrtash A, Ardeshirdavani A, Kariminejad R, Ghorbansabagh V, Sadeghimoghadam P, Naddaf A, Esmaeilnia Shirvany T, Mosayebi Z, Sahebdel B, Golshahi F, Shirazi M, Shamel S, Moeini R, Heidari A, Daneshmand MA, Ghasemi R, Akrami SM, Rashidi-Nezhad A. Towards solving the genetic diagnosis odyssey in Iranian patients with congenital anomalies. Eur J Hum Genet 2024:10.1038/s41431-024-01533-x. [PMID: 38278869 DOI: 10.1038/s41431-024-01533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 01/28/2024] Open
Abstract
Understanding the underlying causes of congenital anomalies (CAs) can be a complex diagnostic journey. We aimed to assess the efficiency of exome sequencing (ES) and chromosomal microarray analysis (CMA) in patients with CAs among a population with a high fraction of consanguineous marriage. Depending on the patient's symptoms and family history, karyotype/Quantitative Fluorescence- Polymerase Chain Reaction (QF-PCR) (n = 84), CMA (n = 81), ES (n = 79) or combined CMA and ES (n = 24) were performed on 168 probands (66 prenatal and 102 postnatal) with CAs. Twelve (14.28%) probands were diagnosed by karyotype/QF-PCR and seven (8.64%) others were diagnosed by CMA. ES findings were conclusive in 39 (49.36%) families, and 61.90% of them were novel variants. Also, 64.28% of these variants were identified in genes that follow recessive inheritance in CAs. The diagnostic rate (DR) of ES was significantly higher than that of CMA in children from consanguineous families (P = 0·0001). The highest DR by CMA was obtained in the non-consanguineous postnatal subgroup and by ES in the consanguineous prenatal subgroup. In a population that is highly consanguineous, our results suggest that ES may have a higher diagnostic yield than CMA and should be considered as the first-tier test in the evaluation of patients with congenital anomalies.
Collapse
Affiliation(s)
- Parisa Vaseghi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Photo Healing and Regeneration, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | - Laleh Habibi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | - Julie A Neidich
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang Cao
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Neda Fattahi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | | | | | - Hossein Dalili
- Breastfeeding Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Rahimi Sharbaf
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zarkesh
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | - Mahdieh Mokhberdezfuli
- Ronash Medical Genetics Laboratory, Tehran, Iran
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | - Vafa Ghorbansabagh
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvane Sadeghimoghadam
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Naddaf
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Tahereh Esmaeilnia Shirvany
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ziba Mosayebi
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrokh Sahebdel
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Golshahi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahboobeh Shirazi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Shamel
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | - Roksana Moeini
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | | | - Reza Ghasemi
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Genetics Ward, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
5
|
Wang Y, Yin F, Chai Y, Jin J, Zhang P, Tan Q, Chen Z. Prenatal diagnosis of fetuses with ultrasound anomalies by whole-exome sequencing in Luoyang city, China. Front Genet 2024; 14:1301439. [PMID: 38318287 PMCID: PMC10838985 DOI: 10.3389/fgene.2023.1301439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024] Open
Abstract
Background: There is a great obstacle in prenatal diagnosis of fetal anomalies due to their considerable genetic and clinical heterogeneity. Whole-exome sequencing (WES) has been confirmed as a successful option for genetic diagnosis in pediatrics, but its clinical utility for prenatal diagnosis remains to be limited. Methods: A total of 60 fetuses with abnormal ultrasound findings underwent karyotyping or chromosomal microarray analysis (CMA), and those with negative results were further subjected to WES. The identified variants were classified as pathogenic or likely pathogenic (P/LP) and the variant of uncertain significance (VUS). Pregnancy outcomes were obtained through a telephone follow-up. Results: Twelve (20%, 12/60) fetuses were diagnosed to have chromosomal abnormalities using karyotyping or CMA. Of the remaining 48 cases that underwent WES, P/LP variants were identified in 14 cases (29.2%), giving an additional diagnostic yield of 23.3% (14/60). The most frequently affected organ referred for prenatal WES was the head or neck system (40%), followed by the skeletal system (39.1%). In terms of pathogenic genes, FGFR3 was the most common diagnostic gene in this cohort. For the first time, we discovered five P/LP variants involved in SEC24D, FIG4, CTNNA3, EPG5, and PKD2. In addition, we identified three VUSes that had been reported previously. Outcomes of pregnancy were available for 54 cases, of which 24 cases were terminated. Conclusion: The results confirmed that WES is a powerful tool in prenatal diagnosis, especially for fetuses with ultrasonographic anomalies that cannot be diagnosed using conventional prenatal methods. Additionally, newly identified variants will expand the phenotypic spectrum of monogenic disorders and greatly enrich the prenatal diagnostic database.
Collapse
Affiliation(s)
- Yanan Wang
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Fan Yin
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
| | - Yuqiong Chai
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Jiapei Jin
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Pai Zhang
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Qianqian Tan
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
| | - Zhigang Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
| |
Collapse
|
6
|
Maksiutenko EM, Barbitoff YA, Nasykhova YA, Pachuliia OV, Lazareva TE, Bespalova ON, Glotov AS. The Landscape of Point Mutations in Human Protein Coding Genes Leading to Pregnancy Loss. Int J Mol Sci 2023; 24:17572. [PMID: 38139401 PMCID: PMC10743817 DOI: 10.3390/ijms242417572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Pregnancy loss is the most frequent complication of a pregnancy which is devastating for affected families and poses a significant challenge for the health care system. Genetic factors are known to play an important role in the etiology of pregnancy loss; however, despite advances in diagnostics, the causes remain unexplained in more than 30% of cases. In this review, we aggregated the results of the decade-long studies into the genetic risk factors of pregnancy loss (including miscarriage, termination for fetal abnormality, and recurrent pregnancy loss) in euploid pregnancies, focusing on the spectrum of point mutations associated with these conditions. We reviewed the evolution of molecular genetics methods used for the genetic research into causes of pregnancy loss, and collected information about 270 individual genetic variants in 196 unique genes reported as genetic cause of pregnancy loss. Among these, variants in 18 genes have been reported by multiple studies, and two or more variants were reported as causing pregnancy loss for 57 genes. Further analysis of the properties of all known pregnancy loss genes showed that they correspond to broadly expressed, highly evolutionary conserved genes involved in crucial cell differentiation and developmental processes and related signaling pathways. Given the features of known genes, we made an effort to construct a list of candidate genes, variants in which may be expected to contribute to pregnancy loss. We believe that our results may be useful for prediction of pregnancy loss risk in couples, as well as for further investigation and revealing genetic etiology of pregnancy loss.
Collapse
Affiliation(s)
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
| | | | | | | | | | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
| |
Collapse
|
7
|
Deutsche Gesellschaft für Humangenetik e.V. (GfH). MED GENET-BERLIN 2023; 35:307-311. [PMID: 38841554 PMCID: PMC11006311 DOI: 10.1515/medgen-2023-2059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
|
8
|
Di Girolamo R, Rizzo G, Khalil A, Alameddine S, Lisi G, Liberati M, Novelli A, D'Antonio F. Whole exome sequencing in fetuses with isolated increased nuchal translucency: a systematic review and meta-analysis. J Matern Fetal Neonatal Med 2023; 36:2193285. [PMID: 37019452 DOI: 10.1080/14767058.2023.2193285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
OBJECTIVE To estimate the incremental yield of detecting pathogenic or likely pathogenic diagnostic genetic variants (DGV) by whole exome sequencing (WES) over standard karyotype and chromosomal microarray (CMA) analyses in fetuses with isolated increased nuchal translucency (NT) and normal fetal anatomy at the time of 11-14 weeks scan. MATERIALS AND METHODS Medline and Embase databases were searched. Inclusion criteria were fetuses with NT >95th percentile, normal karyotype and CMA and no associated structural anomalies at the time of the 11-14 weeks scan. The primary outcome was to estimate the incremental yield of detecting pathogenic or likely pathogenic genetic variants by WES over standard karyotype and CMA analyses in fetuses with isolated increased nuchal translucency. The secondary outcomes were the detection of a genetic variant of unknown significance. Sub-analysis according to different NT cutoffs (between 3.0 and 5.5 mm and > 5.5 mm) and considering fetuses with isolated NT in which fetal anatomy was confirmed to be normal at the anomaly scan were also performed. Random effects model meta-analyses of proportion were used to analyze the data. RESULTS Eight articles (324 fetuses) were included in the systematic review. Of the fetuses with negative standard karyotype and CMA analysis, the 8.07% (95% CI 5.4-11.3) had pathogenic or likely pathogenic genetic variants detected exclusively by WES. When stratifying the analysis according to NT cutoffs, genetic anomalies detected exclusively at WES analysis were found in 44.70% (95% CI 26.8-63.4) of fetuses with NT between 3.0 mm and 5.5 mm and 55.3% (95% CI 36.6-73.2) in those fetuses with NT >5.5 mm and positive WES results. The 7.84% (95% CI 1.6-18.2) had variants of unknown significance identified by WES. When considering fetuses with isolated increased NT and normal fetal anatomy at the anomaly scan, the rate of pathogenic or likely pathogenic genetic variants detected by WES was 3.87% (95% CI 1.6-7.1), while variants of unknown significance were detected in 4.27% (95% CI 2.2-7.0) of cases. CONCLUSIONS Pathogenic and likely pathogenic genetic variants detected by WES are present in a significant proportion of fetuses with increased NT but normal standard karyotype and CMA analysis, also when no anomalies are detected at the anomaly scan. Further large studies sharing objective protocols of imaging assessment are needed to confirm these findings and to elucidate which gene panels should be assessed in fetuses with isolated increased NT to rule out associated genetic anomalies, which may potentially impact post-natal outcomes.
Collapse
Affiliation(s)
- Raffaella Di Girolamo
- Centre for High-Risk Pregnancy and Fetal Care, Department of Obstetrics and Gynaecology, University of Chieti, Chieti, Italy
| | - Giuseppe Rizzo
- Department of Obstetrics and Gynaecology Fondazione Policlinico Tor Vergata, Università Roma Tor Vergata
| | - Asma Khalil
- Fetal Medicine Unit, Saint George's Hospital, London, United Kingdom
| | - Sara Alameddine
- Centre for High-Risk Pregnancy and Fetal Care, Department of Obstetrics and Gynaecology, University of Chieti, Chieti, Italy
| | - Gabriele Lisi
- Pediatric Surgery Unit, Department of Medicine and Aging Science, University Gabriele D'Annunzio of Chieti-Pescara, Chieti, Italy
| | - Marco Liberati
- Centre for High-Risk Pregnancy and Fetal Care, Department of Obstetrics and Gynaecology, University of Chieti, Chieti, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesco D'Antonio
- Centre for High-Risk Pregnancy and Fetal Care, Department of Obstetrics and Gynaecology, University of Chieti, Chieti, Italy
| |
Collapse
|
9
|
Chhatwal K, Smith JJ, Bola H, Zahid A, Venkatakrishnan A, Brand T. Uncovering the Genetic Basis of Congenital Heart Disease: Recent Advancements and Implications for Clinical Management. CJC PEDIATRIC AND CONGENITAL HEART DISEASE 2023; 2:464-480. [PMID: 38205435 PMCID: PMC10777202 DOI: 10.1016/j.cjcpc.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/13/2023] [Indexed: 01/12/2024]
Abstract
Congenital heart disease (CHD) is the most prevalent hereditary disorder, affecting approximately 1% of all live births. A reduction in morbidity and mortality has been achieved with advancements in surgical intervention, yet challenges in managing complications, extracardiac abnormalities, and comorbidities still exist. To address these, a more comprehensive understanding of the genetic basis underlying CHD is required to establish how certain variants are associated with the clinical outcomes. This will enable clinicians to provide personalized treatments by predicting the risk and prognosis, which might improve the therapeutic results and the patient's quality of life. We review how advancements in genome sequencing are changing our understanding of the genetic basis of CHD, discuss experimental approaches to determine the significance of novel variants, and identify barriers to use this knowledge in the clinics. Next-generation sequencing technologies are unravelling the role of oligogenic inheritance, epigenetic modification, genetic mosaicism, and noncoding variants in controlling the expression of candidate CHD-associated genes. However, clinical risk prediction based on these factors remains challenging. Therefore, studies involving human-induced pluripotent stem cells and single-cell sequencing help create preclinical frameworks for determining the significance of novel genetic variants. Clinicians should be aware of the benefits and implications of the responsible use of genomics. To facilitate and accelerate the clinical integration of these novel technologies, clinicians should actively engage in the latest scientific and technical developments to provide better, more personalized management plans for patients.
Collapse
Affiliation(s)
- Karanjot Chhatwal
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Jacob J. Smith
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Harroop Bola
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Abeer Zahid
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Ashwin Venkatakrishnan
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Thomas Brand
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| |
Collapse
|
10
|
Qin Y, Yao Y, Liu N, Wang B, Liu L, Li H, Gao T, Xu R, Wang X, Zhang F, Song J. Prenatal whole-exome sequencing for fetal structural anomalies: a retrospective analysis of 145 Chinese cases. BMC Med Genomics 2023; 16:262. [PMID: 37880672 PMCID: PMC10601195 DOI: 10.1186/s12920-023-01697-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) significantly improves the diagnosis of the etiology of fetal structural anomalies. This study aims to evaluate the diagnostic value of prenatal WES and to investigate the pathogenic variants in structurally abnormal fetuses. METHODS We recruited 144 fetuses with structural anomalies between 14 and 2020 and 15 December 2021 in the study. Genetic screening was performed by WES combined with karyotyping and chromosomal microarray analysis. The molecular diagnostic yield of prenatal WES for each type of fetal structural anomaly and the identified pathogenic genes and mutations were reported. RESULTS In this study, we retrospectively analyzed the clinical and genetic data of 145 structurally anomalous fetuses. These cases were classified into 9 phenotypic classes based on antenatal ultrasound findings. Thirty-eight pathogenic variants in 24 genes were identified in 35 of the 145 cases, including 14 novel variants in 13 genes (EP300, MYH3, TSC2, MMP9, CPLANE1, INVS, COL1A1, EYA1, TTC21B, MKS1, COL11A2, PDHA1 and L1CAM). Five additional pathogenic variants were classified as incidental findings. Our study showed that the overall diagnosis rate of WES was 28.1% (27/96) in the parent-fetus trio cases and 16.3% (8/49) in the proband-only cases. Fetuses with musculoskeletal anomalies had the highest diagnostic yield (51.4%, 19/37). In addition, FGFR3 and COL1A1 were the most common pathogenic genes. CONCLUSIONS Our work expands the mutation spectrum of the genes associated with fetal structural anomalies and provides valuable information for future parental genetic counselling and pregnancy management of the structurally anomalous fetuses.
Collapse
Affiliation(s)
- Yayun Qin
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Yanyi Yao
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Hui Li
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Tangxinzi Gao
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Runhong Xu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Xiaoyan Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Fanglian Zhang
- Honghu Hospital of Traditional Chinese Medicine, Jingzhou, 433200, Hubei Province, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China.
| |
Collapse
|
11
|
Mustafa HJ, Sambatur EV, Barbera JP, Pagani G, Yaron Y, Baptiste CD, Wapner RJ, Khalil A. Diagnostic yield with exome sequencing in prenatal severe bilateral ventriculomegaly: a systematic review and meta-analysis. Am J Obstet Gynecol MFM 2023; 5:101048. [PMID: 37311485 DOI: 10.1016/j.ajogmf.2023.101048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
OBJECTIVE This study aimed to determine the incremental diagnostic yield of prenatal exome sequencing after negative chromosomal microarray analysis results in prenatally diagnosed bilateral severe ventriculomegaly or hydrocephalus; another objective was to categorize the associated genes and variants. DATA SOURCES A systematic search was performed to identify relevant studies published until June 2022 using 4 databases (Cochrane Library, Web of Science, Scopus, and MEDLINE). STUDY ELIGIBILITY CRITERIA Studies in English reporting on the diagnostic yield of exome sequencing following negative chromosomal microarray analysis results in cases of prenatally diagnosed bilateral severe ventriculomegaly were included. METHODS Authors of cohort studies were contacted for individual participant data, and 2 studies provided their extended cohort data. The incremental diagnostic yield of exome sequencing was assessed for pathogenic/likely pathogenic findings in cases of: (1) all severe ventriculomegaly; (2) isolated severe ventriculomegaly (as the only cranial anomaly); (3) severe ventriculomegaly with other cranial anomalies; and (4) nonisolated severe ventriculomegaly (with extracranial anomalies). To be able to identify all reported genetic associations, the systematic review portion was not limited to any minimal severe ventriculomegaly case numbers; however, for the synthetic meta-analysis, we included studies with ≥3 severe ventriculomegaly cases. Meta-analysis of proportions was done using a random-effects model. Quality assessment of the included studies was performed using the modified STARD (Standards for Reporting of Diagnostic Accuracy Studies) criteria. RESULTS A total of 28 studies had 1988 prenatal exome sequencing analyses performed following negative chromosomal microarray analysis results for various prenatal phenotypes; this included 138 cases with prenatal bilateral severe ventriculomegaly. We categorized 59 genetic variants in 47 genes associated with prenatal severe ventriculomegaly along with their full phenotypic description. There were 13 studies reporting on ≥3 severe ventriculomegaly cases, encompassing 117 severe ventriculomegaly cases that were included in the synthetic analysis. Of all the included cases, 45% (95% confidence interval, 30-60) had positive pathogenic/likely pathogenic exome sequencing results. The highest yield was for nonisolated cases (presence of extracranial anomalies; 54%; 95% confidence interval, 38-69), followed by severe ventriculomegaly with other cranial anomalies (38%; 95% confidence interval, 22-57) and isolated severe ventriculomegaly (35%; 95% confidence interval, 18-58). CONCLUSION There is an apparent incremental diagnostic yield of prenatal exome sequencing following negative chromosomal microarray analysis results in bilateral severe ventriculomegaly. Although the greatest yield was found in cases of nonisolated severe ventriculomegaly, consideration should also be given to performing exome sequencing in cases of isolated severe ventriculomegaly as the only brain anomaly identified on prenatal imaging.
Collapse
Affiliation(s)
- Hiba J Mustafa
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Indiana University School of Medicine, Indianapolis, IN (Dr Mustafa); Fetal Center at Riley Children's Health, Indiana University Health, Indianapolis, IN (Dr Mustafa).
| | - Enaja V Sambatur
- Research Division, Houston Center for Maternal Fetal Medicine, Houston, TX (Ms Sambatur)
| | - Julie P Barbera
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (Ms Barbera)
| | - Giorgio Pagani
- Maternal Fetal Medicine Unit, Department of Obstetrics and Gynecology, ASST Papa Giovanni XXIII, Bergamo, Italy (Dr Pagani)
| | - Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel (Dr Yaron); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel (Dr Yaron)
| | - Caitlin D Baptiste
- Division of Women's Genetics, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY (Drs Baptiste and Wapner)
| | - Ronald J Wapner
- Division of Women's Genetics, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY (Drs Baptiste and Wapner)
| | - Asma Khalil
- Fetal Medicine Unit, St George's Hospital, St George's University of London, London, United Kingdom (Dr Khalil); Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, United Kingdom (Dr Khalil)
| |
Collapse
|
12
|
Vaseghi H, Akrami SM, Rashidi‐Nezhad A. The challenges in the interpretation of genetic variants detected by genomics techniques in patients with congenital anomalies. J Clin Lab Anal 2023; 37:e24967. [PMID: 37823350 PMCID: PMC10623530 DOI: 10.1002/jcla.24967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/28/2023] [Accepted: 09/16/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Despite the efforts that have been made to standardize the interpretation of variants, in some cases, their pathogenicity remains vague and confusing, and sometimes their interpretation does not help clinicians to establish clinical correlation using genetic test results. This study aims to shed more lights on these challenging variants. METHODS In a clinical setting, the variants found from 81 array CGH and 79 whole exome sequencing (WES) in patients with congenital anomalies were interpreted based on American College of Medical Genetics and Genomics guidelines. RESULTS In this study, the interpretation of the disease-causing variants and the variants with uncertain clinical significance detected by WES was far more challenging than the variants detected by array CGH. The presence of unreported clinical symptoms, incomplete penetrance, variable expressivity, parents' reluctance to analyze segregation in the family, and the limitations of prenatal tests, were among the challenging factors in the interpretation of variants in this study. CONCLUSION A careful study of the pedigree and disease mode of inheritance, as well as a careful clinical examination of the carrier parents in diseases with autosomal dominant inheritance, are among the primary strategies for determining the clinical significance of the variants. Continued efforts to mitigate these challenges are needed to improve the interpretation of variants.
Collapse
Affiliation(s)
- Hajar Vaseghi
- Department of Medical Genetics, School of MedicineTehran University of Medical SciencesTehranIran
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of MedicineTehran University of Medical SciencesTehranIran
| | - Ali Rashidi‐Nezhad
- Maternal, Fetal and Neonatal Research Center, Family Health Research InstituteTehran University of Medical SciencesTehranIran
| |
Collapse
|
13
|
Geraghty RM, Orr S, Olinger E, Neatu R, Barroso-Gil M, Mabillard H, Consortium GER, Wilson I, Sayer JA. Use of whole genome sequencing to determine the genetic basis of visceral myopathies including Prune Belly syndrome. JOURNAL OF RARE DISEASES (BERLIN, GERMANY) 2023; 2:9. [PMID: 37288276 PMCID: PMC10241726 DOI: 10.1007/s44162-023-00012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/21/2023] [Indexed: 06/09/2023]
Abstract
Objectives/aims The visceral myopathies (VM) are a group of disorders characterised by poorly contractile or acontractile smooth muscle. They manifest in both the GI and GU tracts, ranging from megacystis to Prune Belly syndrome. We aimed to apply a bespoke virtual genetic panel and describe novel variants associated with this condition using whole genome sequencing data within the Genomics England 100,000 Genomes Project. Methods We screened the Genomics England 100,000 Genomes Project rare diseases database for patients with VM-related phenotypes. These patients were screened for sequence variants and copy number variants (CNV) in ACTG2, ACTA2, MYH11, MYLK, LMOD1, CHRM3, MYL9, FLNA and KNCMA1 by analysing whole genome sequencing data. The identified variants were analysed using variant effect predictor online tool, and any possible segregation in other family members and novel missense mutations was modelled using in silico tools. The VM cohort was also used to perform a genome-wide variant burden test in order to identify confirm gene associations in this cohort. Results We identified 76 patients with phenotypes consistent with a diagnosis of VM. The range of presentations included megacystis/microcolon hypoperistalsis syndrome, Prune Belly syndrome and chronic intestinal pseudo-obstruction. Of the patients in whom we identified heterozygous ACTG2 variants, 7 had likely pathogenic variants including 1 novel likely pathogenic allele. There were 4 patients in whom we identified a heterozygous MYH11 variant of uncertain significance which leads to a frameshift and a predicted protein elongation. We identified one family in whom we found a heterozygous variant of uncertain significance in KCNMA1 which in silico models predicted to be disease causing and may explain the VM phenotype seen. We did not find any CNV changes in known genes leading to VM-related disease phenotypes. In this phenotype selected cohort, ACTG2 is the largest monogenic cause of VM-related disease accounting for 9% of the cohort, supported by a variant burden test approach, which identified ACTG2 variants as the largest contributor to VM-related phenotypes. Conclusions VM are a group of disorders that are not easily classified and may be given different diagnostic labels depending on their phenotype. Molecular genetic analysis of these patients is valuable as it allows precise diagnosis and aids understanding of the underlying disease manifestations. We identified ACTG2 as the most frequent genetic cause of VM. We recommend a nomenclature change to 'autosomal dominant ACTG2 visceral myopathy' for patients with pathogenic variants in ACTG2 and associated VM phenotypes. Supplementary Information The online version contains supplementary material available at 10.1007/s44162-023-00012-z.
Collapse
Affiliation(s)
- Robert M. Geraghty
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Sarah Orr
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Eric Olinger
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Ruxandra Neatu
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Miguel Barroso-Gil
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Holly Mabillard
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Genomics England Research Consortium
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle Upon Tyne, NE4 5PL UK
| | - Ian Wilson
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - John A. Sayer
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle Upon Tyne, NE4 5PL UK
| |
Collapse
|
14
|
The Value of a Comprehensive Genomic Evaluation in Prenatal Diagnosis of Genetic Diseases: A Retrospective Study. Genes (Basel) 2022; 13:genes13122365. [PMID: 36553632 PMCID: PMC9778469 DOI: 10.3390/genes13122365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Currently, there are still many challenges in prenatal diagnosis, such as limited or uncertain fetal phenotyping, variant interpretation, and rapid turnaround times. The aim of this study was to illustrate the value of a comprehensive genomic evaluation in prenatal diagnosis. We retrospectively reviewed 20 fetuses with clinically significant copy number variants (CNVs) detected by chromosomal microarray analysis (CMA) and no further exome sequencing testing in our tertiary center between 2019 and 2020. The residual DNA from the prenatal cases was used for the parallel implementation of CNV sequencing (CNV-seq) and trio-based clinical exome sequencing (trio-CES). CMA revealed 26 clinically significant CNVs (18 deletions and eight duplications) in 20 fetuses, in which five fetuses had two or more CNVs. There were eight fetuses with pathogenic CNVs (e.g., del 1p36), nine fetuses with likely pathogenic CNVs (e.g., dup 22q11.21), and three fetuses with variants of unknown significance (VOUS, e.g., dup 1q21.1q21.2). Trio-CES identified four fetuses with likely pathogenic mutations (SNV/InDels). Of note, a fetus was detected with a maternally inherited hemizygous variant in the SLX4 gene due to a 16p13.3 deletion on the paternal chromosome. The sizes of CNVs detected by CNV-seq were slightly larger than that of the SNP array, and four cases with mosaic CNVs were all identified by CNV-seq. In conclusion, microdeletion/duplication syndromes and monogenic disorders may co-exist in a subject, and CNV deletion may contribute to uncovering additional recessive disease alleles. The application of a comprehensive genomic evaluation (CNVs and SNV/InDels) has great value in the prenatal diagnosis arena. CNV-seq based on NGS technology is a reliable and a cost-effective technique for identifying CNVs.
Collapse
|
15
|
Pauta M, Martinez-Portilla RJ, Borrell A. Diagnostic yield of exome sequencing in fetuses with multisystem malformations: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 59:715-722. [PMID: 35041238 DOI: 10.1002/uog.24862] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To determine the diagnostic yield of exome sequencing (ES) above that of chromosomal microarray analysis (CMA) or karyotyping in fetuses with multisystem structural anomalies (at least two major anomalies in different anatomical systems). METHOD This was a systematic review conducted in accordance with PRISMA guidelines. Searching PubMed, Web of Knowledge and Cochrane database, we identified studies describing ES, whole-genome and/or next-generation sequencing in fetuses with multisystem malformations. Included were observational studies involving five or more eligible fetuses. A fetus was eligible for inclusion if it had at least two major anomalies of different anatomical systems and a negative CMA or karyotyping result. Only positive variants classified as likely pathogenic or pathogenic determined to be causative of the fetal phenotype were considered. A negative CMA or karyotype result was treated as the reference standard. The diagnostic yield of the primary outcome was calculated by single-proportion analysis using random-effects modeling. A subgroup analysis was performed to compare the diagnostic yield of the solo approach (fetus alone sequenced) with that of the trio approach (fetus and both parents sequenced). RESULTS Seventeen articles with data on ES diagnostic yield, including 694 individuals with multisystem malformations, were identified. Overall, a pathogenic or likely pathogenic variant potentially causative of the fetal phenotype was found in 213 fetuses, giving a 33% (95% CI, 27-40%) incremental yield of ES. A stratified analysis showed similar diagnostic yields of ES using the solo approach (30%; 95% CI, 11-52%) and the trio approach (35%; 95% CI, 26-44%). CONCLUSIONS ES applied in fetuses with multisystem structural anomalies was able to identify a potentially causative gene when CMA or karyotyping had failed to do so in an additional one-third of cases. No differences were observed between the solo and trio approaches for ES. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- M Pauta
- BCNatal, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - R J Martinez-Portilla
- Clinical Research Division, Evidence-Based Medicine Department, National Institute of Perinatology, Mexico City, Mexico
| | - A Borrell
- BCNatal, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, Barcelona, Catalonia, Spain
| |
Collapse
|
16
|
A single center experience of prenatal parent‐fetus trio exome sequencing for pregnancies with congenital anomalies. Prenat Diagn 2022; 42:901-910. [DOI: 10.1002/pd.6170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/07/2022]
|
17
|
Yi S, Li M, Yang Q, Qin Z, Yi S, Xu J, Chen J, Wei H, Jiang Y, Wei R, Zhang Q, Yang C, Chen B, Luo J. De Novo SMARCC2 Variant in a Chinese Woman with Coffin-Siris Syndrome 8: a Case Report with Mild Intellectual Disability and Endocrinopathy. J Mol Neurosci 2022; 72:1293-1299. [DOI: 10.1007/s12031-022-02010-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/04/2022] [Indexed: 11/29/2022]
|
18
|
Van den Veyver IB. Prenatal exomes and genomes - so much new and so much more to learn. Prenat Diagn 2022; 42:659-661. [PMID: 35583086 DOI: 10.1002/pd.6152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| |
Collapse
|
19
|
Kucińska-Chahwan A, Roszkowski T, Nowakowska B, Geremek M, Paczkowska M, Bijok J, Massalska D. Extended genetic testing in fetuses with sonographic skeletal system abnormalities. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 59:660-667. [PMID: 34198368 DOI: 10.1002/uog.23722] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/19/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVES To analyze genetic causes of skeletal system abnormalities diagnosed by prenatal sonography and to establish a diagnostic protocol with regard to extended genetic testing in this group of patients. METHODS This prospective observational cohort study included all singleton pregnancies with a sonographic abnormality of the skeletal system evaluated in a single ultrasound department during a 1-year period (2019). Fetuses underwent routine genetic testing by chromosomal microarray analysis (CMA) supplemented with polyploidy testing, and those with either a normal result or an abnormal result not consistent with the observed phenotype underwent exome sequencing (ES). Interpretation of variants was discussed by a panel of specialists to identify pathogenic/likely pathogenic variants. RESULTS The study group comprised 55 fetuses. A chromosomal abnormality consistent with the observed phenotype was detected in 24 (43.6%) cases. After exclusions, 26 (47.3%) cases underwent further molecular testing by ES, of which 18 (69.2%) were classified as having abnormal ES results, thus increasing the diagnostic yield by a further 18 (32.7%) cases and giving an abnormal genetic test result in 42/55 (76.4%) fetuses overall. Pathogenic or likely pathogenic sequence variants in 14 different genes were detected across 18 fetuses. Seven genes are already listed in the International Skeletal Dysplasia Society Nosology and seven are not typically found to be causal for skeletal dysplasias and are not listed in the Nosology. CONCLUSIONS In fetuses with skeletal system anomalies, chromosomal abnormality was the most common genetic diagnosis. Exome sequencing increased the diagnostic yield over that of CMA and polyploidy testing. Fetuses with skeletal abnormalities should undergo extended genetic testing following routine testing, as many genetic anomalies responsible for skeletal defects may otherwise be missed. © 2021 International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- A Kucińska-Chahwan
- Department of Gynecology Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - T Roszkowski
- Department of Gynecology Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - B Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - M Geremek
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - M Paczkowska
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - J Bijok
- Department of Gynecology Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - D Massalska
- Department of Gynecology Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| |
Collapse
|
20
|
Sun H, Zhang S, Wang J, Zhou X, Zhang H, Yang H, He Y. Expanding the phenotype associated with SMARCC2 variants: a fetus with tetralogy of Fallot. BMC Med Genomics 2022; 15:40. [PMID: 35241061 PMCID: PMC8895577 DOI: 10.1186/s12920-022-01185-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coffin-Siris syndrome-8 (CSS8) is a rare autosomal dominant disorder caused by variants in SMARCC2, a core subunit of the chromatin-remodeling complex BRG1-associated factor (BAF). The clinical characteristics of this disorder have not been entirely determined because of the rarity of clinical reports. The BAF complex plays a crucial role in embryogenesis and cardiac development, and pathogenic variants in genes encoding the components of the BAF complex have been associated with congenital heart disease (CHD). However, variants in SMARCC2 have not been reported in patients with CHD. CASE PRESENTATION A 28-year-old primigravida was referred at 24 weeks gestation for prenatal echocardiography. The echocardiographic findings were consistent with a prenatal ultrasound diagnosis of tetralogy of Fallot (TOF). After detailed counseling, the couple decided to terminate the pregnancy and undergo genetic testing. A trio (fetus and the parents) whole-exome sequencing (WES) and copy number variation sequencing (CNV-seq) were performed. CNV-seq identified no chromosomal abnormalities. WES analysis revealed a pathogenic, de novo heterozygous frameshift variant in SMARCC2 (NM_003075.5: c.3561del, p.Leu1188fs). The genetic diagnosis of CSS8 was considered given the identification of the SMARCC2 pathogenic variant. CONCLUSIONS We report the first prenatal case with the SMARCC2 variant. The presence of CHD further broadens the phenotypic spectrum of SMARCC2-related disease.
Collapse
Affiliation(s)
- Hairui Sun
- Department of Echocardiography, Beijing Anzhen Hospital, Capital Medical University, No.2, Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Siyao Zhang
- Department of Echocardiography, Beijing Anzhen Hospital, Capital Medical University, No.2, Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Jingyi Wang
- Department of Echocardiography, Beijing Anzhen Hospital, Capital Medical University, No.2, Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Xiaoxue Zhou
- Department of Echocardiography, Beijing Anzhen Hospital, Capital Medical University, No.2, Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Hongjia Zhang
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, No.2, Anzhen Road, Chaoyang District, Beijing, 100029, China.
| | - Huixia Yang
- Peking University First Hospital, Beijing, China
| | - Yihua He
- Department of Echocardiography, Beijing Anzhen Hospital, Capital Medical University, No.2, Anzhen Road, Chaoyang District, Beijing, 100029, China.
| |
Collapse
|
21
|
Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
Collapse
Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
| | | | | | | | | | | |
Collapse
|
22
|
Mellis R, Oprych K, Scotchman E, Hill M, Chitty LS. Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: A systematic review and meta-analysis. Prenat Diagn 2022; 42:662-685. [PMID: 35170059 PMCID: PMC9325531 DOI: 10.1002/pd.6115] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/10/2022]
Abstract
Objectives We conducted a systematic review and meta‐analysis to determine the diagnostic yield of exome sequencing (ES) for prenatal diagnosis of fetal structural anomalies, where karyotype/chromosomal microarray (CMA) is normal. Methods Following electronic searches of four databases, we included studies with ≥10 structurally abnormal fetuses undergoing ES or whole genome sequencing. The incremental diagnostic yield of ES over CMA/karyotype was calculated and pooled in a meta‐analysis. Sub‐group analyses investigated effects of case selection and fetal phenotype on diagnostic yield. Results We identified 72 reports from 66 studies, representing 4350 fetuses. The pooled incremental yield of ES was 31% (95% confidence interval (CI) 26%–36%, p < 0.0001). Diagnostic yield was significantly higher for cases pre‐selected for likelihood of monogenic aetiology compared to unselected cases (42% vs. 15%, p < 0.0001). Diagnostic yield differed significantly between phenotypic sub‐groups, ranging from 53% (95% CI 42%–63%, p < 0.0001) for isolated skeletal abnormalities, to 2% (95% CI 0%–5%, p = 0.04) for isolated increased nuchal translucency. Conclusion Prenatal ES provides a diagnosis in an additional 31% of structurally abnormal fetuses when CMA/karyotype is non‐diagnostic. The expected diagnostic yield depends on the body system(s) affected and can be optimised by pre‐selection of cases following multi‐disciplinary review to determine that a monogenic cause is likely.
What's already known about this topic?
Prenatal exome sequencing (ES) increases genetic diagnoses in fetuses with structural abnormalities and a normal karyotype and chromosomal microarray. Published diagnostic yields from ES are varied and may be influenced by study size, case selection and fetal phenotype.
What does this study add?
This study provides a comprehensive systematic review of the literature to date and investigates the diagnostic yield of ES for a range of isolated system anomalies, to support clinical decision‐making on how to offer prenatal ES.
Collapse
Affiliation(s)
- Rhiannon Mellis
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | | | - Elizabeth Scotchman
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Melissa Hill
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Lyn S Chitty
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| |
Collapse
|
23
|
Xie M, Li J, Hu H, Wang P, Cong X, Li J, Dai L, Lu Y, Zhang W. Development and validation of a novel 26-plex system for prenatal diagnosis with forensic markers. Int J Legal Med 2022; 136:527-537. [PMID: 35102446 DOI: 10.1007/s00414-022-02780-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
Abstract
Short tandem repeat (STR) loci are commonly used in forensic casework, such as personal identification and paternity testing. In recent years, STR has also been widely used for rapid, accurate and automated prenatal diagnosis, known as quantitative fluorescent PCR (QF-PCR). Despite their usefulness, the current systems often lack the power to detect mosaicism for Turner syndrome. In this study, we developed a novel 26-plex system that combined the 22 STRs in chromosome 21/18/13/X, 3 sex loci and 1 quality control marker (TAF9L). The system was generated to achieve greater diagnostic power of trisomy 21/18/13 and sex chromosome abnormalities. Studies of the sensitivity, specificity, stability and accuracy were performed according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Compared with the results of the chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq), the detection ratio of non-mosaic chromosome abnormalities of this system in the identification of chromosome 21/18/13/X/Y aneuploidies reached 100%, and the rate of negative results was consistently 100% based on 203 prenatal diagnosis sample analyses. In addition, our results suggested that this panel was a useful tool for mosaicism for Turner syndrome cases. Interestingly, we found one case with large segment loss of chromosome X, which indicated that we should be alert to this situation when the STR genotype of the parent-child is inconsistent in forensic genetics. In summary, this study demonstrated that our system is an accurate, cost-effective and rapid approach for the detection of chromosome numerical abnormalities in prenatal diagnosis.
Collapse
Affiliation(s)
- Mingkun Xie
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Huan Hu
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Panpan Wang
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Xueqi Cong
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Jingzhi Li
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Lei Dai
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Yang Lu
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Weishe Zhang
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China.
| |
Collapse
|
24
|
Stevens BK, Nunley PB, Wagner C, Murphy L, Wittman T, Ramdaney A, Jones M, Choates MG. Utility of expanded carrier screening in pregnancies with ultrasound abnormalities. Prenat Diagn 2021; 42:60-78. [PMID: 34792213 DOI: 10.1002/pd.6069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/15/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Explore the utility of expanded carrier screening in evaluating heritable causes of congenital anomalies detected by prenatal ultrasound. METHOD A retrospective chart review was conducted to collect structural abnormality and genetic testing data on infants who were evaluated postnatally by a medical geneticist. These were used to determine if expanded carrier screening could have determined the etiology prior to delivery. Additionally, recessive and X-linked conditions on clinically available carrier screening panels were evaluated to determine the number of conditions associated with abnormal ultrasound findings. RESULTS Our retrospective chart review found 222 patients with genetic etiologies, including eight unique autosomal recessive conditions and six X-linked conditions in the 23% who underwent exome sequencing. Of these 14 unique conditions detected, three were included on a list of 271 conditions for which screening was available in 2019 and five were included on a 500 condition panel available in 2020. A literature review was performed on the list of 271 conditions and 88 were reported to be associated with one or more ultrasound abnormalities. CONCLUSION This study demonstrates limited but potential utility for expanded carrier screening to determine the underlying etiology of congenital anomalies.
Collapse
Affiliation(s)
- Blair K Stevens
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Chelsea Wagner
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lauren Murphy
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Theresa Wittman
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Aarti Ramdaney
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Malorie Jones
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Meagan Giles Choates
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| |
Collapse
|
25
|
Stuurman KE, van der Mespel-Brouwer MH, Engels MAJ, Elting MW, Bhola SL, Meijers-Heijboer H. Isolated Increased Nuchal Translucency in First Trimester Ultrasound Scan: Diagnostic Yield of Prenatal Microarray and Outcome of Pregnancy. Front Med (Lausanne) 2021; 8:737936. [PMID: 34733861 PMCID: PMC8558347 DOI: 10.3389/fmed.2021.737936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Increased nuchal translucency (NT) is associated with aneuploidy. When the karyotype is normal, fetuses are still at risk for structural anomalies and genetic syndromes. Our study researched the diagnostic yield of prenatal microarray in a cohort of fetuses with isolated increased NT (defined as NT ≥ 3.5 mm) and questioned whether prenatal microarray is a useful tool in determining the adverse outcomes of the pregnancy. Materials and Methods: A prospective study was performed, in which 166 women, pregnant with a fetus with isolated increased NT (ranging from 3.5 to 14.3 mm with a mean of 5.4 mm) were offered karyotyping and subsequent prenatal microarray when karyotype was normal. Additionally, all ongoing pregnancies of fetuses with normal karyotype were followed up with regard to postnatal outcome. The follow-up time after birth was maximally 4 years. Results: Totally, 149 of 166 women opted for prenatal testing. Seventy-seven fetuses showed normal karyotype (52%). Totally, 73 of 77 fetuses with normal karyotype did not show additional anomalies on an early first trimester ultrasound. Totally, 40 of 73 fetuses received prenatal microarray of whom 3 fetuses had an abnormal microarray result: two pathogenic findings (2/40) and one incidental carrier finding. In 73 fetuses with an isolated increased NT, 21 pregnancies showed abnormal postnatal outcome (21/73, 28.8%), 29 had a normal outcome (29/73, 40%), and 23 were lost to follow-up (23/73, 31.5%). Seven out of 73 live-born children showed an adverse outcome (9.6%). Conclusions: Prenatal microarray in fetuses with isolated increased NT had a 5% (2/40) increased diagnostic yield compared to conventional karyotyping. Even with a normal microarray, fetuses with an isolated increased NT had a 28.8% risk of either pregnancy loss or an affected child.
Collapse
Affiliation(s)
- Kyra E Stuurman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marjolein H van der Mespel-Brouwer
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Mariet W Elting
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Department of Human Genetics, Amsterdam UMC, Universiteit van Amsterdam, Amsterdam, Netherlands
| | - Shama L Bhola
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Department of Human Genetics, Amsterdam UMC, Universiteit van Amsterdam, Amsterdam, Netherlands
| | - Hanne Meijers-Heijboer
- Department of Human Genetics, Amsterdam UMC, Universiteit van Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
26
|
Mancini GMS, Smits DJ, Dekker J, Schot R, de Wit MCY, Lequin MH, Dremmen M, Brooks AS, van Ham T, Verheijen FW, Fornerod M, Dobyns WB, Wilke M. Multidisciplinary interaction and MCD gene discovery. The perspective of the clinical geneticist. Eur J Paediatr Neurol 2021; 35:27-34. [PMID: 34592643 DOI: 10.1016/j.ejpn.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
The increasing pace of gene discovery in the last decade has brought a major change in the way the genetic causes of brain malformations are being diagnosed. Unbiased genomic screening has gained the first place in the diagnostic protocol of a child with congenital (brain) anomalies and the detected variants are matched with the phenotypic presentation afterwards. This process is defined as "reverse phenotyping". Screening of DNA, through copy number variant analysis of microarrays and analysis of exome data on different platforms, obtained from the index patient and both parents has become a routine approach in many centers worldwide. Clinicians are used to multidisciplinary team interaction in patient care and disease management and this explains why the majority of research that has led to the discovery of new genetic disorders nowadays proceeds from clinical observations to genomic analysis and to data exchange facilitated by open access sharing databases. However, the relevance of multidisciplinary team interaction has not been object of systematic research in the field of brain malformations. This review will illustrate some examples of how diagnostically driven questions through multidisciplinary interaction, among clinical and preclinical disciplines, can be successful in the discovery of new genes related to brain malformations. The first example illustrates the setting of interaction among neurologists, geneticists and neuro-radiologists. The second illustrates the importance of interaction among clinical dysmorphologists for pattern recognition of syndromes with multiple congenital anomalies. The third example shows how fruitful it can be to step out of the "clinical comfort zone", and interact with basic scientists in applying emerging technologies to solve the diagnostic puzzles.
Collapse
Affiliation(s)
- Grazia M S Mancini
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam.
| | - Daphne J Smits
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Jordy Dekker
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Rachel Schot
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| | - Marie Claire Y de Wit
- Department of Child Neurology, Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, Rotterdam, NL, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| | - Maarten H Lequin
- Department of Radiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marjolein Dremmen
- Department of Radiology, Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| | - Alice S Brooks
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Tjakko van Ham
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Frans W Verheijen
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| | - Maarten Fornerod
- Department of Cell Biology, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - William B Dobyns
- Department of Pediatrics (Genetics), University of Minnesota, 420 Delaware Street SE, MMC75, Minneapolis, MN, 55454, USA
| | - Martina Wilke
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| |
Collapse
|
27
|
Ali Alghamdi M, Alrasheedi A, Alghamdi E, Adly N, AlAali WY, Alhashem A, Alshahrani A, Shamseldin H, Alkuraya FS, Alfadhel M. Molecular autopsy by proxy in preconception counseling. Clin Genet 2021; 100:678-691. [PMID: 34406647 PMCID: PMC9290025 DOI: 10.1111/cge.14049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 01/06/2023]
Abstract
Monogenic diseases that result in early pregnancy loss or neonatal death are genetically and phenotypically highly variable. This often poses significant challenges in arriving at a molecular diagnosis for reproductive planning. Molecular autopsy by proxy (MABP) refers to the genetic testing of relatives of deceased individuals to deduce the cause of death. Here, we specifically tested couples who lost one or more children/pregnancies with no available DNA. We developed our testing strategy using whole exome sequencing data from 83 consanguineous Saudi couples. We detected the shared carrier state of 50 pathogenic variants/likely pathogenic variants in 43 families and of 28 variants of uncertain significance in 24 families. Negative results were seen in 16 couples after variant reclassification. In 10 families, the risk of more than one genetic disease was documented. Secondary findings were seen in 10 families: either genetic variants with potential clinical consequences for the tested individual or a female carrier for X‐linked conditions. This couple‐based approach has enabled molecularly informed genetic counseling for 52% (43/83 families). Given the predominance of autosomal recessive causes of pregnancy and child death in consanguineous populations, MABP can be a helpful approach to consanguineous couples who seek counseling but lack molecular data on their deceased offspring.
Collapse
Affiliation(s)
- Malak Ali Alghamdi
- Medical Genetic Division, Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Medical Genetics Division, Department of Pediatrics, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Ameinah Alrasheedi
- Department of Pediatrics, College of Medicine and Medical Sciences, Qassim University, Al Qassim, Saudi Arabia
| | - Esra Alghamdi
- College of Medicine, Imam Mohammed Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Nouran Adly
- College of Medicine Research Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Wajeih Y AlAali
- Dr. Sulaiman Al Habib Medical Group, Riyadh, Saudi Arabia.,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Hanan Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia.,Genetics and Precision Medicine department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| |
Collapse
|
28
|
He M, Du L, Xie H, Zhang L, Gu Y, Lei T, Zheng J, Chen D. The Added Value of Whole-Exome Sequencing for Anomalous Fetuses With Detailed Prenatal Ultrasound and Postnatal Phenotype. Front Genet 2021; 12:627204. [PMID: 34367232 PMCID: PMC8340955 DOI: 10.3389/fgene.2021.627204] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives The objective of the study was to explore the added value of whole-exome sequencing (WES) in abnormal fetuses with detailed prenatal ultrasound and postnatal phenotype with normal karyotype and chromosomal microarray analysis (CMA). Methods Parents of fetuses with structural abnormalities by prenatal ultrasound who consented to provide fetal samples were prospectively recruited from January 2017 to December 2019. With aneuploidies or cases with copy number variations (CNVs) excluded, WES was performed for cases with normal karyotype and CMA results. Detailed prenatal ultrasound and postnatal imaging or pathology features were recommended for further interpretation of genetic variants. Results WES was performed for 94 eligible fetuses, DNA samples of which were extracted from 53 parent-fetus trios and 41 proband-only fetal tissues. A diagnostic genetic variant was identified in 37 (39.4%) of 94 fetuses, and 34 (64.2%) were detected in 53 trios, which was significantly greater than 3 (7.3%) in 41 proband-only cases (p < 0.001). In 34 trios with diagnostic genetic variants, 23 (67.6%) were de novo and 11 (32.4%) were inherited with two homozygous and nine heterozygous variants. Fourteen (14.9%) of 94 fetuses had a variant of uncertain significance (VUS). Among 94 cases, six affected pregnancies continued and 88 terminated, and 57 of 88 terminated cases underwent postmortem examinations. With accurate phenotypes demonstrated by prenatal ultrasound and postnatal autopsies, the clinical phenotypes were correlated in 33 (89.2%) of 37 cases with specific genotypes, with the highest matching ratio in skeletal diseases (20/33, 60.6%). Conclusion WES has added value in the genetic diagnosis of abnormal fetuses with normal karyotypes and CMA, particularly in skeletal diseases. Using WES in various anomalous fetuses can broaden the understanding of prenatal phenotypes and genetic variants.
Collapse
Affiliation(s)
- Miao He
- Department of Ultrasonic Medicine, Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liu Du
- Department of Ultrasonic Medicine, Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongning Xie
- Department of Ultrasonic Medicine, Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lihe Zhang
- Department of Ultrasonic Medicine, Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yujun Gu
- Department of Ultrasonic Medicine, Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ting Lei
- Department of Ultrasonic Medicine, Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ju Zheng
- Department of Ultrasonic Medicine, Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dan Chen
- Guangzhou Kingmed Diagnostics Group, Guangzhou, China
| |
Collapse
|
29
|
Lei L, Zhou L, Xiong JJ. Whole-exome sequencing increases the diagnostic rate for prenatal fetal structural anomalies. Eur J Med Genet 2021; 64:104288. [PMID: 34246755 DOI: 10.1016/j.ejmg.2021.104288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Prenatal whole-exome sequencing (WES) is becoming increasingly used when karyotype and microarray tests are not diagnostic of fetal malformations. Although the value of WES clearly emerges in terms of higher diagnostic rates, the limitations of prenatal phenotyping together with the counseling challenges for variants of uncertain significance and incidental results suggest that the routine application of prenatal WES is not yet easy. METHODS Structurally abnormal fetuses with a mean gestational age of 24 weeks (range 13-38 weeks) were recruited from the Chong Qing Health Center for Women and Children. We performed a retrospective WES investigation in 85 fetuses, using DNA from amniotic fluid (66 samples, 77.6%), umbilical cord blood (10 samples, 11.8%), and fetal tissues (9 samples, 10.6%). Parental DNA was extracted from peripheral blood. RESULTS Molecular diagnosis was obtained in 16 of the 85 fetuses (18.8%). According to the variant segregation mode and family history, 7 fetuses (43.75%) were affected by an autosomal dominant condition (6 variants were de novo and 1 variant was inherited from an unknowingly affected father), 7 fetuses (43.75%) had an autosomal recessive syndrome always associated with compound heterozygosity, and 2 fetuses (12.5%) had an X-linked condition (one mother was a carrier). In addition, the highest diagnostic rate was observed in fetuses with multisystem abnormalities (38.9%, 7/18). A variant of uncertain significance was detected in 16 samples (18.8%, 16/85). CONCLUSION Our study confirms that prenatal WES is an efficient tool for studying fetal abnormalities, although further improvements are needed to establish stronger fetal genotype-phenotype correlations.
Collapse
Affiliation(s)
- Ling Lei
- Chong Qing Health Center for Women and Children, Chongqing, 401120, China.
| | - Lan Zhou
- Chong Qing Health Center for Women and Children, Chongqing, 401120, China
| | - Jiao-Jiao Xiong
- Chong Qing Health Center for Women and Children, Chongqing, 401120, China
| |
Collapse
|
30
|
Abstract
PURPOSE OF REVIEW The current review seeks to provide a comprehensive update on the revolutionary technology of whole exome sequencing (WES) which has been used to interrogate abnormal foetal phenotypes since the last few years, and is changing the paradigms of prenatal diagnosis, facilitating accurate genetic diagnosis and optimal management of pregnancies affected with foetal abnormalities, as well enabling delineation of novel Mendelian disorders. RECENT FINDINGS WES has contributed to identification of more than 1000 Mendelian genes and made rapid strides into clinical diagnostics in recent years. Diagnostic yield of WES in postnatal cohorts has ranged from 25 to 50%, and this test is now a first tier investigation for various clinical presentations. Various abnormal perinatal phenotypes have also been investigated using WES since 2014, with diagnostic yields ranging from 8.5 to 80%. Studies in foetal phenotypes have been challenging and guidelines in this cohort are still evolving. SUMMARY WES has proven to be a disrupting technology, enabling genetic diagnosis for pregnancies complicated by previously unexplained foetal abnormalities, and revealing a significant contribution of single gene disorders in these, thereby changing clinical diagnostic paradigms. The application of this technology in perinatal cohorts is also providing interesting insights into single gene defects presenting as previously unknown genetic syndromes, hence contributing to expansion of Mendelian genetics to encompass various foetal phenotypes.
Collapse
|
31
|
Najafi K, Mehrjoo Z, Ardalani F, Ghaderi-Sohi S, Kariminejad A, Kariminejad R, Najmabadi H. Identifying the causes of recurrent pregnancy loss in consanguineous couples using whole exome sequencing on the products of miscarriage with no chromosomal abnormalities. Sci Rep 2021; 11:6952. [PMID: 33772059 PMCID: PMC7997959 DOI: 10.1038/s41598-021-86309-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/08/2021] [Indexed: 12/26/2022] Open
Abstract
Recurrent miscarriages occur in about 5% of couples trying to conceive. In the past decade, the products of miscarriage have been studied using array comparative genomic hybridization (a-CGH). Within the last decade, an association has been proposed between miscarriages and single or multigenic changes, introducing the possibility of detecting other underlying genetic factors by whole exome sequencing (WES). We performed a-CGH on the products of miscarriage from 1625 Iranian women in consanguineous or non-consanguineous marriages. WES was carried out on DNA extracted from the products of miscarriage from 20 Iranian women in consanguineous marriages and with earlier normal genetic testing. Using a-CGH, a statistically significant difference was detected between the frequency of imbalances in related vs. unrelated couples (P < 0.001). WES positively identified relevant alterations in 11 genes in 65% of cases. In 45% of cases, we were able to classify these variants as pathogenic or likely pathogenic, according to the American College of Medical Genetics and Genomics guidelines, while in the remainder, the variants were classified as of unknown significance. To the best of our knowledge, our study is the first to employ WES on the products of miscarriage in consanguineous families with recurrent miscarriages regardless of the presence of fetal abnormalities. We propose that WES can be helpful in making a diagnosis of lethal disorders in consanguineous couples after prior genetic testing.
Collapse
Affiliation(s)
- Kimia Najafi
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Zohreh Mehrjoo
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
| | - Fariba Ardalani
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
| | - Siavash Ghaderi-Sohi
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Ariana Kariminejad
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Roxana Kariminejad
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Hossein Najmabadi
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran.
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran.
| |
Collapse
|
32
|
Guadagnolo D, Mastromoro G, Di Palma F, Pizzuti A, Marchionni E. Prenatal Exome Sequencing: Background, Current Practice and Future Perspectives-A Systematic Review. Diagnostics (Basel) 2021; 11:diagnostics11020224. [PMID: 33540854 PMCID: PMC7913004 DOI: 10.3390/diagnostics11020224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/16/2022] Open
Abstract
The introduction of Next Generation Sequencing (NGS) technologies has exerted a significant impact on prenatal diagnosis. Prenatal Exome Sequencing (pES) is performed with increasing frequency in fetuses with structural anomalies and negative chromosomal analysis. The actual diagnostic value varies extensively, and the role of incidental/secondary or inconclusive findings and negative results has not been fully ascertained. We performed a systematic literature review to evaluate the diagnostic yield, as well as inconclusive and negative-result rates of pES. Papers were divided in two groups. The former includes fetuses presenting structural anomalies, regardless the involved organ; the latter focuses on specific class anomalies. Available findings on non-informative or negative results were gathered as well. In the first group, the weighted average diagnostic yield resulted 19%, and inconclusive finding rate 12%. In the second group, the percentages were extremely variable due to differences in sample sizes and inclusion criteria, which constitute major determinants of pES efficiency. Diagnostic pES availability and its application have a pivotal role in prenatal diagnosis, though more homogeneity in access criteria and a consensus on clinical management of controversial information management is envisageable to reach widespread use in the near future.
Collapse
Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Francesca Di Palma
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Clinical Genomics Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Correspondence:
| |
Collapse
|
33
|
Mone F, Eberhardt RY, Morris RK, Hurles ME, McMullan DJ, Maher ER, Lord J, Chitty LS, Giordano JL, Wapner RJ, Kilby MD. COngenital heart disease and the Diagnostic yield with Exome sequencing (CODE) study: prospective cohort study and systematic review. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:43-51. [PMID: 32388881 DOI: 10.1002/uog.22072] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To determine the incremental yield of antenatal exome sequencing (ES) over chromosomal microarray analysis (CMA) or conventional karyotyping in prenatally diagnosed congenital heart disease (CHD). METHODS A prospective cohort study of 197 trios undergoing ES following CMA or karyotyping owing to CHD identified prenatally and a systematic review of the literature were performed. MEDLINE, EMBASE, CINAHL and ClinicalTrials.gov (January 2000 to October 2019) databases were searched electronically for studies reporting on the diagnostic yield of ES in prenatally diagnosed CHD. Selected studies included those with more than three cases, with initiation of testing based upon prenatal phenotype only and that included cases in which CMA or karyotyping was negative. The incremental diagnostic yield of ES was assessed in: (1) all cases of CHD; (2) isolated CHD; (3) CHD associated with extracardiac anomaly (ECA); and (4) CHD according to phenotypic subgroup. RESULTS In our cohort, ES had an additional diagnostic yield in all CHD, isolated CHD and CHD associated with ECA of 12.7% (25/197), 11.5% (14/122) and 14.7% (11/75), respectively (P = 0.81). The corresponding pooled incremental yields from 18 studies (encompassing 636 CHD cases) included in the systematic review were 21% (95% CI, 15-27%), 11% (95% CI, 7-15%) and 37% (95% CI, 18-56%), respectively. The results did not differ significantly when subanalysis was limited to studies including more than 20 cases, except for CHD associated with ECA, in which the incremental yield was greater (49% (95% CI, 17-80%)). In cases of CHD associated with ECA in the primary analysis, the most common extracardiac anomalies associated with a pathogenic variant were those affecting the genitourinary system (23/52 (44.2%)). The greatest incremental yield was in cardiac shunt lesions (41% (95% CI, 19-63%)), followed by right-sided lesions (26% (95% CI, 9-43%)). In the majority (68/96 (70.8%)) of instances, pathogenic variants occurred de novo and in autosomal dominant (monoallelic) disease genes. The most common (19/96 (19.8%)) monogenic syndrome identified was Kabuki syndrome. CONCLUSIONS There is an apparent incremental yield of prenatal ES in CHD. While the greatest yield is in CHD associated with ECA, consideration could also be given to performing ES in the presence of an isolated cardiac abnormality. A policy of routine application of ES would require the adoption of robust bioinformatic, clinical and ethical pathways. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- F Mone
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - R K Morris
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - D J McMullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - E R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - J Lord
- Wellcome Sanger Institute, Hinxton, UK
| | - L S Chitty
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust and UCL Great Ormond Street Institute of Child Health, London, UK
| | - J 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 Vagelos Medical Center, New York, NY, USA
| | - R 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 Vagelos Medical Center, New York, NY, USA
| | - M D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| |
Collapse
|
34
|
Nunley PB, Hashmi SS, Johnson A, Ashfaq M, Farach LS, Singletary CN, Stevens BK. Exploring the predicted yield of prenatal testing by evaluating a postnatal population with structural abnormalities using a novel mathematical model. Prenat Diagn 2020; 41:354-361. [PMID: 33128384 DOI: 10.1002/pd.5858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 08/29/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To determine the yield of prenatal testing and screening options after identification of fetal structural abnormalities using a novel mathematical model. METHOD A retrospective chart review was conducted to collect structural abnormality and genetic testing data on infants who were evaluated postnatally by a medical geneticist. A novel mathematical model was used to determine and compare the predicted diagnostic yields of prenatal testing and screening options. RESULTS Over a quarter of patients with at least one structural abnormality (28.1%, n = 222) had a genetic aberration identified that explained their phenotype. Chromosomal microarray (CMA) had the highest predicted diagnostic yield (26.8%, P < .001). Karyotype (20.8%) had similar yields as genome wide NIPT (21.2%, P = .859) and NIPT with select copy number variants (CNVs) (17.9%, P = .184). Among individuals with an isolated structural abnormality, whole exome sequencing (25.9%) and CMA (14.9%) had the highest predicted yields. CONCLUSION This study introduces a novel mathematical model for predicting the potential yield of prenatal testing and screening options. This study provides further evidence that CMA has the highest predicted diagnostic yield in cases with structural abnormalities. Screening with expanded NIPT options shows potential for patients who decline invasive testing, but only in the setting of adequate pre-test counseling.
Collapse
Affiliation(s)
- Peyton B Nunley
- Department of Obstetrics and Gynecology, University of South Carolina School of Medicine, Columbia, South Carolina, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Syed S Hashmi
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Anthony Johnson
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Myla Ashfaq
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Laura S Farach
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Claire N Singletary
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Blair K Stevens
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| |
Collapse
|
35
|
Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 163:87-108. [PMID: 33035590 PMCID: PMC8021618 DOI: 10.1016/j.pbiomolbio.2020.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/12/2020] [Accepted: 09/29/2020] [Indexed: 01/26/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.
Collapse
Affiliation(s)
- James P Lees-Miller
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander Cobban
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, And Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI, 48824, USA
| | - Dave W Anderson
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.
| |
Collapse
|
36
|
Cai M, Lin N, Lin Y, Huang H, Xu L. Evaluation of chromosomal abnormalities and copy number variations in late trimester pregnancy using cordocentesis. Aging (Albany NY) 2020; 12:15556-15565. [PMID: 32805723 PMCID: PMC7467360 DOI: 10.18632/aging.103575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/09/2020] [Indexed: 01/30/2023]
Abstract
Because the numbers of detected fetal abnormalities increase as gestation progresses, we evaluated the safety and efficacy of cordocentesis for single nucleotide polymorphism (SNP) analysis tests in 754 women during third trimester pregnancy. Conventional karyotyping was performed on all fetuses, and Affymetrix CytoScan HD was used for SNP-array testing. In addition to the 24 cases with chromosomal abnormalities detected with conventional karyotyping analysis, the SNP-array test identified 56 (7.4%) cases with normal karyotypes but abnormal copy number variations (CNVs). Of those, 24 were pathogenic CNVs and 32 were of uncertain clinical significance. In 742 of the cases, there were abnormal sonographic findings, and cytogenetic abnormalities were detected in 76 cases (10.2%). The largest number of abnormalities involved multiple malformations (21.7%), followed by defects in the lymphatics or effusion (19.0%) or urogenital system (15.3%). The use of SNP-array test fully complemented chromosome karyotype analysis after late cordocentesis. It also improved the detection rate for fetal chromosomal abnormalities and was effective for preventing and controlling the occurrence of birth defects.
Collapse
Affiliation(s)
- Meiying Cai
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuan Lin
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| |
Collapse
|
37
|
Application of exome sequencing for prenatal diagnosis: a rapid scoping review. Genet Med 2020; 22:1925-1934. [PMID: 32747765 DOI: 10.1038/s41436-020-0918-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/20/2020] [Indexed: 01/03/2023] Open
Abstract
Genetic diagnosis provides important information for prenatal decision-making and management. Promising results from exome sequencing (ES) for genetic diagnosis in fetuses with structural anomalies are emerging. The objective of this scoping review was to identify what is known about the use of ES for genetic testing in prenatal cases with known or suspected genetic disease. A rapid scoping review was conducted over a six-week timeframe of English-language peer-reviewed studies. Search strategies for major databases (e.g., Medline) and gray literature were developed, and peer reviewed by information specialists. Identified studies were categorized and charted using tables and diagrams. Twenty-four publications were included from seven countries published between 2014 and 2019. Most commonly reported outcomes were diagnostic yields, which varied widely from 5% to 57%, and prenatal phenotype. Few studies reported clinical outcomes related to impact, decision-making, and clinical utility. Qualitative studies (n = 6) provided useful insights into patient and health-care provider experiences with ES. Findings suggest prenatal ES is beneficial, but more research is needed to better understand the clinical utility, circumstances for ideal use, feasibility, and costs of offering rapid ES as a routine option for prenatal genetic testing.
Collapse
|
38
|
Lefebvre M, Bruel AL, Tisserant E, Bourgon N, Duffourd Y, Collardeau-Frachon S, Attie-Bitach T, Kuentz P, Assoum M, Schaefer E, El Chehadeh S, Antal MC, Kremer V, Girard-Lemaitre F, Mandel JL, Lehalle D, Nambot S, Jean-Marçais N, Houcinat N, Moutton S, Marle N, Lambert L, Jonveaux P, Foliguet B, Mazutti JP, Gaillard D, Alanio E, Poirisier C, Lebre AS, Aubert-Lenoir M, Arbez-Gindre F, Odent S, Quélin C, Loget P, Fradin M, Willems M, Bigi N, Perez MJ, Blesson S, Francannet C, Beaufrere AM, Patrier-Sallebert S, Guerrot AM, Goldenberg A, Brehin AC, Lespinasse J, Touraine R, Capri Y, Saint-Frison MH, Laurent N, Philippe C, Tran Mau-Them F, Thevenon J, Faivre L, Thauvin-Robinet C, Vitobello A. Genotype-first in a cohort of 95 fetuses with multiple congenital abnormalities: when exome sequencing reveals unexpected fetal phenotype-genotype correlations. J Med Genet 2020; 58:400-413. [PMID: 32732226 DOI: 10.1136/jmedgenet-2020-106867] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/04/2020] [Accepted: 05/21/2020] [Indexed: 11/03/2022]
Abstract
PURPOSE Molecular diagnosis based on singleton exome sequencing (sES) is particularly challenging in fetuses with multiple congenital abnormalities (MCA). Indeed, some studies reveal a diagnostic yield of about 20%, far lower than in live birth individuals showing developmental abnormalities (30%), suggesting that standard analyses, based on the correlation between clinical hallmarks described in postnatal syndromic presentations and genotype, may underestimate the impact of the genetic variants identified in fetal analyses. METHODS We performed sES in 95 fetuses with MCA. Blind to phenotype, we applied a genotype-first approach consisting of combined analyses based on variants annotation and bioinformatics predictions followed by reverse phenotyping. Initially applied to OMIM-morbid genes, analyses were then extended to all genes. We complemented our approach by using reverse phenotyping, variant segregation analysis, bibliographic search and data sharing in order to establish the clinical significance of the prioritised variants. RESULTS sES rapidly identified causal variant in 24/95 fetuses (25%), variants of unknown significance in OMIM genes in 8/95 fetuses (8%) and six novel candidate genes in 6/95 fetuses (6%). CONCLUSIONS This method, based on a genotype-first approach followed by reverse phenotyping, shed light on unexpected fetal phenotype-genotype correlations, emphasising the relevance of prenatal studies to reveal extreme clinical presentations associated with well-known Mendelian disorders.
Collapse
Affiliation(s)
- Mathilde Lefebvre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Laboratoire d'Anatomo-Pathologie, Plateforme de Biologie Hospitalo-Universitaire, CHU de Dijon Bourgogne, Dijon, France
| | - Ange-Line Bruel
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Emilie Tisserant
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Nicolas Bourgon
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Yannis Duffourd
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | | | - Tania Attie-Bitach
- Laboratoire d'Embryologie et de Génétique des Malformations Congénitales, Hopital Necker, APHP, Paris Cedex 15, France
| | - Paul Kuentz
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Mirna Assoum
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Elise Schaefer
- Service de Génétique Médicale, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Maria Cristina Antal
- Service de Fœtopathologie, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Valérie Kremer
- Laboratoire de Cytogénétique constitutionnelle et prénatale, CHU de Strasbourg, Strasbourg, France
| | - Françoise Girard-Lemaitre
- Département Médecine translationnelle et neurogénétique, Institut de génétique et de biologie moléculaire et cellulaire, Strasbourg, France
| | - Jean-Louis Mandel
- Département Médecine translationnelle et neurogénétique, Institut de génétique et de biologie moléculaire et cellulaire, Strasbourg, France
| | - Daphne Lehalle
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nada Houcinat
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sébastien Moutton
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire de Génétique chromosomique et moléculaire, CHU de Dijon Bourgogne, Dijon, France
| | - Laetita Lambert
- UF de Génétique médicale, Maternité régionale, CHU de Nancy, Nancy, France
| | | | - Bernard Foliguet
- Laboratoire de Biologie de la Reproduction et du Développement Maternité de Nancy, CHU de Nancy, Nancy, France
| | - Jean-Pierre Mazutti
- Laboratoire de Biologie de la Reproduction et du Développement Maternité de Nancy, CHU de Nancy, Nancy, France
| | | | | | | | - Anne-Sophie Lebre
- Service de Génétique et Biologie de la Reproduction, CHU de Reims, Reims, France
| | | | | | - Sylvie Odent
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France
| | - Chloé Quélin
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France.,Service de Fœtopathologie, CHU de Rennes, Rennes, France
| | - Philippe Loget
- Service de Fœtopathologie, CHU de Rennes, Rennes, France
| | - Melanie Fradin
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France
| | - Marjolaine Willems
- Equipe Maladies Génétiques de l'Enfant et de l'Adulte, CHU de Montpellier, Montpellier, France
| | - Nicole Bigi
- Service de Fœtopathologie, CHU de Montpellier, Montpellier, France
| | - Marie-José Perez
- Service de Fœtopathologie, CHU de Montpellier, Montpellier, France
| | | | - Christine Francannet
- Service de Génétique médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | | | | | | | | | | | | | - Renaud Touraine
- Service de Genetique Clinique, C.H.U. De Saint Etienne-Hopital Nord, Saint Etienne Cedex 2, France
| | - Yline Capri
- Service de génétique clinique, Hôpital Robert Debré - APHP, Paris, France
| | | | - Nicole Laurent
- Laboratoire d'Anatomo-Pathologie, Plateforme de Biologie Hospitalo-Universitaire, CHU de Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Frederic Tran Mau-Them
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julien Thevenon
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Département de Génétique et Procréation, CHU Grenoble Alpes, Université Grenoble Alpes, Grenoble, France
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France .,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France .,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| |
Collapse
|
39
|
Chen M, Chen J, Wang C, Chen F, Xie Y, Li Y, Li N, Wang J, Zhang VW, Chen D. Clinical application of medical exome sequencing for prenatal diagnosis of fetal structural anomalies. Eur J Obstet Gynecol Reprod Biol 2020; 251:119-124. [PMID: 32502767 DOI: 10.1016/j.ejogrb.2020.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To evaluate the clinical application of medical exome sequencing (MES) for prenatal diagnosis of genetic diseases related to fetal structural anomalies detected by prenatal ultrasound examination. STUDY DESIGN A total of 105 fetuses with structural anomalies were negative results in both Quantitative fluorescent polymerase chain reaction (QF-PCR) and chromosomal microarray analysis (CMA). Then trio-based MES was further used for identifying the potential monogenic diseases in these fetuses. Coding regions and known pathogenic non-coding regions of over 4000 disease-related genes were interrogated, and variants were classified following the guidelines of American College of Medical Genetics (ACMG). RESULTS The 105 fetuses with structural anomalies were categorized into 12 phenotypic groups. A definitive diagnosis was achieved in 19% (20/105) of the cases, with the identification of 21 pathogenic or likely pathogenic variants in 14 genes. The proportion of patients with diagnostic genetic variants varied between the phenotypic groups, with the highest diagnostic yield in the cardiovascular abnormalities (44%), followed by the skeletal and limb abnormalities (38%) and brain structural abnormalities (25%). In addition, 12 fetuses were detected variants of unknown significance (VOUS), while the relevance of phenotypes and variants would further evaluated. CONCLUSION MES can identify the underlying genetic cause in fetal structural anomalies. It can further assist the management of pregnancy and genetic counseling. It was demonstrated the importance of translating prenatal MES into clinical practice.
Collapse
Affiliation(s)
- Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes.
| | - Jingsi Chen
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes
| | - Chunli Wang
- AmCare Genomics Laboratory, Guangzhou, 510300, Guangdong, China
| | - Fei Chen
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes
| | - Yinong Xie
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes
| | - Yufan Li
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes
| | - Nan Li
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes
| | - Jing Wang
- AmCare Genomics Laboratory, Guangzhou, 510300, Guangdong, China
| | - Victor Wei Zhang
- AmCare Genomics Laboratory, Guangzhou, 510300, Guangdong, China; Baylor College of Medicine, Department of Human and Molecular Genetics, Houston, USA
| | - Dunjin Chen
- Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes
| |
Collapse
|
40
|
Tang J, Zhou C, Shi H, Mo Y, Tan W, Sun T, Zhu J, Li Q, Li H, Li Y, Wang S, Hong Y, Li N, Zeng Q, Tan J, Ma W, Luo L. Prenatal diagnosis of skeletal dysplasias using whole exome sequencing in China. Clin Chim Acta 2020; 507:187-193. [PMID: 32360156 DOI: 10.1016/j.cca.2020.04.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/04/2020] [Accepted: 04/27/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Skeletal dysplasias account for nearly 10% of fetal structural malformations detected by ultrasonography. This clinically heterogeneous group of genetic anomaly includes at least 461 genetic skeletal disorders with extreme clinical, phenotypic, and genetic heterogeneities, thus, significantly complicates accurate diagnosis. Researches have used whole exome sequencing (WES) for prenatal molecular diagnoses of skeletal dysplasias, however, data are still limited. METHODS DNA extracted from umbilical cord blood or amniocytes from fetuses suspected of skeletal dysplasias based on ultrasound evaluations were analyzed by WES. Blood samples were taken from the parents of the positive fetuses for co-segregation analysis using Sanger sequencing. RESULT Definitive molecular diagnosis was made in 6/8 (75%) cases, comprised of 5 de novo disease-causing changes in 3 genes (FGFR3, COL2A1, and COL1A2) and one proband with a biallelic deficiency for Lamin B Receptor(LBR),and including 3 novel variants. All fetuses had no detectable copy number variation (CNV) from sequencing results. CONCLUSIONS Our study suggests that WES is an efficient approach for prenatal diagnosis of fetuses suspected of skeletal abnormalities and contributes to parental genetics counseling and pregnancy management.
Collapse
Affiliation(s)
- Jia Tang
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China; Department of Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510080, China.
| | - Chenglong Zhou
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China; Halo Genetics, Guangzhou, Guangdong 510000, China
| | - Haihong Shi
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China; Halo Genetics, Guangzhou, Guangdong 510000, China
| | - Yuying Mo
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Weilan Tan
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Tielan Sun
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Jinling Zhu
- Department of Biology, School of Basic Medicine, Jiamusi University, Jiamusi, Heilongjiang 154007, China
| | - Qing Li
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Hui Li
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Yuping Li
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Songbai Wang
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Yan Hong
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Ning Li
- Halo Genetics, Guangzhou, Guangdong 510000, China
| | - Qinlong Zeng
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Jieliang Tan
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Wei Ma
- Department of Biology, School of Basic Medicine, Jiamusi University, Jiamusi, Heilongjiang 154007, China
| | - Liangping Luo
- Department of Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510080, China.
| |
Collapse
|
41
|
Tosca L, Giltay JC, Bouvattier C, Klijn AJ, Bouligand J, Lambert AS, Lecerf L, Josso N, Tachdjian G, Picard JY. Persistent Müllerian duct syndrome due to anti-Müllerian hormone receptor 2 microdeletions: a diagnostic challenge. Hum Reprod 2020; 35:999-1003. [PMID: 32187366 DOI: 10.1093/humrep/deaa014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/09/2020] [Indexed: 11/12/2022] Open
Abstract
The persistent Müllerian duct syndrome (PMDS) is defined by the persistence of Müllerian derivatives in an otherwise normally virilized 46,XY male. It is usually caused by mutations in either the anti-Müllerian hormone (AMH) or AMH receptor type 2 (AMHR2) genes. We report the first cases of PMDS resulting from a microdeletion of the chromosomal region 12q13.13, the locus of the gene for AMHR2. One case involved a homozygous microdeletion of five exons of the AMHR2 gene. In the second case, the whole AMHR2 gene was deleted from the maternally inherited chromosome. The patient's paternal allele carried a stop mutation, which was initially thought to be homozygous by Sanger sequencing. Diagnostic methods are discussed, with an emphasis on comparative genomic hybridization and targeted massive parallel sequencing.
Collapse
Affiliation(s)
- L Tosca
- Service d'Histologie, Embryologie et Cytogénétique, Assistance Publique-Hôpitaux de Paris, Université Paris-Saclay, Hôpital Antoine Béclère, 92140 Clamart, France.,Faculté de Médecine, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - J C Giltay
- Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
| | - C Bouvattier
- Faculté de Médecine, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France.,Service Endocrinologie et Diabète de l'Enfant, Assistance Publique-Hôpitaux de Paris, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - A J Klijn
- Department Pediatric Urology Wilhelmina Kinderziekenhuis. University Medical Center Utrecht, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
| | - J Bouligand
- Faculté de Médecine, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France.,Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Assistance Publique-Hôpitaux de Paris, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - A S Lambert
- Faculté de Médecine, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France.,Service Endocrinologie et Diabète de l'Enfant, Assistance Publique-Hôpitaux de Paris, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - L Lecerf
- Faculté de Médecine, Institut National de la Santé et de la Recherche Médicale, Université Paris-Est, Unité 955, 94000 Créteil, France
| | - N Josso
- UMR_S938 Centre de Recherche Saint Antoine, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, 75012 Paris, France
| | - G Tachdjian
- Service d'Histologie, Embryologie et Cytogénétique, Assistance Publique-Hôpitaux de Paris, Université Paris-Saclay, Hôpital Antoine Béclère, 92140 Clamart, France.,Faculté de Médecine, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - J Y Picard
- UMR_S938 Centre de Recherche Saint Antoine, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, 75012 Paris, France
| |
Collapse
|
42
|
Application of next-generation sequencing for the diagnosis of fetuses with congenital heart defects. Curr Opin Obstet Gynecol 2020; 31:132-138. [PMID: 30608255 DOI: 10.1097/gco.0000000000000520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Congenital heart defects (CHDs) are the most common type of birth defects, and are thought to result from genetic-environmental interactions. Currently, karyotype and chromosomal microarray analyses are the primary methods used to detect chromosomal abnormalities and copy number variations in fetuses with CHD. Recently, with the introduction of next-generation sequencing (NGS) in prenatal diagnosis, gene mutations have been identified in cases of CHD. The purpose of this review is to summarize current studies about the genetic cause of fetal CHD, paying particular attention to the application of NGS for fetuses with CHD. RECENT FINDINGS In addition to chromosomal abnormalities, gene mutations are an important genetic cause of fetal CHD. Furthermore, incidences of pathogenic mutations in fetuses with CHD are associated with the presence of other structural anomalies, but are irrelevant to the categories of CHD. SUMMARY Gene mutations are important causes of fetal CHD and NGS should be applied to all fetuses with normal karyotype and copy number variations, regardless of whether the CHD is isolated or syndromic.
Collapse
|
43
|
Witkowski L, Dillon MW, Murphy E, S Lebo M, Mason-Suares H. Expanding the Noonan spectrum/RASopathy NGS panel: Benefits of adding NF1 and SPRED1. Mol Genet Genomic Med 2020; 8:e1180. [PMID: 32107864 PMCID: PMC7196473 DOI: 10.1002/mgg3.1180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/28/2019] [Accepted: 01/30/2020] [Indexed: 01/13/2023] Open
Abstract
Background RASopathies are a group of disorders caused by disruptions to the RAS‒MAPK pathway. Despite being in the same pathway, Neurofibromatosis Type 1 (NF1) and Legius syndrome (LS) typically present with phenotypes distinct from Noonan spectrum disorders (NSDs). However, some NF1/LS individuals also exhibit NSD phenotypes, often referred to as Neurofibromatosis‐Noonan syndrome (NFNS), and may be mistakenly evaluated for NSDs, delaying diagnosis, and affecting patient management. Methods A derivation cohort of 28 patients with a prior negative NSD panel and either NFNS or a suspicion of NSD and café‐au‐lait spots underwent NF1 and SPRED1 sequencing. To further determine the utility and burden of adding these genes, a validation cohort of 505 patients with a suspected RASopathy were tested on a 14‐gene RASopathy‐associated panel. Results In the derivation cohort, six (21%) patients had disease‐causing NF1 or SPRED1 variants. In the validation cohort, 11 (2%) patients had disease‐causing variants and 15 (3%) had variants of uncertain significance in NF1 or SPRED1. Of those with disease‐causing variants, 5/17 only had an NSD diagnosis. Conclusions Adding NF1 and SPRED1 to RASopathy panels can speed diagnosis and improve patient management, without significantly increasing the burden of inconclusive results.
Collapse
Affiliation(s)
- Leora Witkowski
- Departments of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.,Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Mitchell W Dillon
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Elissa Murphy
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Matthew S Lebo
- Departments of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.,Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - 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, Cambridge, MA, USA
| |
Collapse
|
44
|
Xue S, Yan H, Chen J, Li N, Wang J, Liu Y, Zhang H, Li S, Zhang W, Chen D, Chen M. Genetic Examination for Fetuses with Increased Fetal Nuchal Translucency by Genomic Technology. Cytogenet Genome Res 2020; 160:57-62. [PMID: 32036363 DOI: 10.1159/000506095] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2020] [Indexed: 01/23/2023] Open
Abstract
This study aims to investigate the value of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in fetuses with increased nuchal translucency (defined as NT above the 95th centile for the crown-rump length). A total of 374 singleton pregnancies with gestational ages ranging from 11 to 13 + 6 weeks were investigated. Ultrasound displayed increased NT and no detectable structural malformations in these fetuses. Pregnancies were divided into 4 groups according to the NT values: 95th centile-3.4 mm (114 cases); 3.5-4.4 mm (150 cases); 4.5-5.4 mm (55 cases); and ≥5.5 mm (55 cases). The possible chromosomal anomalies were all analyzed by CMA first. Furthermore, 24 cases with increased NT but negative CMA results were investigated by WES, and the outcomes were followed up. Among all the 374 cases, causative genetic defects were detected in 100/374 (26.7%) of the cases along with 9 variants of unknown significance (VOUS) by CMA. CMA testing yielded 30 pathogenic variants (30/55), accounting for a detection rate of 54.5%, and 1 VOUS in the group of NT ≥5.5 mm, indicating the highest detection rate in the 4 groups. The 24 cases of the CMA negative sub-cohort with WES analysis further yielded 2 VOUS and 3 likely pathogenic variants, including 2 dominant de novo mutations in SOS1 and ECE1 and 1 recessive inherited compound heterozygous mutation in PIGN, which are associated with cardiac defects. All 3 cases opted for termination of pregnancy (TOP). In addition, 2 cases with increased NT were negative by both CMA and WES analysis, and fetal demise occurred. In conclusion, for the investigation of fetuses with increased NT exome sequencing is suggested to be considered in cases with negative CMA findings. However, appropriate genetic counseling should be given to optimizing its utilization in prenatal diagnosis.
Collapse
|
45
|
Lou C, Goodier JL, Qiang R. A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. Reprod Biol Endocrinol 2020; 18:6. [PMID: 31964400 PMCID: PMC6971995 DOI: 10.1186/s12958-020-0564-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
LINE1 retrotransposons are mobile DNA elements that copy and paste themselves into new sites in the genome. To ensure their evolutionary success, heritable new LINE-1 insertions accumulate in cells that can transmit genetic information to the next generation (i.e., germ cells and embryonic stem cells). It is our hypothesis that LINE1 retrotransposons, insertional mutagens that affect expression of genes, may be causal agents of early miscarriage in humans. The cell has evolved various defenses restricting retrotransposition-caused mutation, but these are occasionally relaxed in certain somatic cell types, including those of the early embryo. We predict that reduced suppression of L1s in germ cells or early-stage embryos may lead to excessive genome mutation by retrotransposon insertion, or to the induction of an inflammatory response or apoptosis due to increased expression of L1-derived nucleic acids and proteins, and so disrupt gene function important for embryogenesis. If correct, a novel threat to normal human development is revealed, and reverse transcriptase therapy could be one future strategy for controlling this cause of embryonic damage in patients with recurrent miscarriages.
Collapse
Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| | - John L. Goodier
- 0000 0001 2171 9311grid.21107.35McKusick-Nathans Deartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| |
Collapse
|
46
|
Kang L, Liu Y, Jin Y, Li M, Song J, Zhang Y, Zhang Y, Yang Y. Mutations of MACF1, Encoding Microtubule-Actin Crosslinking-Factor 1, Cause Spectraplakinopathy. Front Neurol 2020; 10:1335. [PMID: 32010038 PMCID: PMC6974614 DOI: 10.3389/fneur.2019.01335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
As a member of spectraplakin family of cytoskeletal crosslinking proteins, microtubule-actin crosslinking factor 1 (MACF1) controls cytoskeleton network dynamics. Knockout of Macf1 in mice resulted in the developmental retardation and embryonic lethality. Spectraplakinopathy type I, a novel neuromuscular condition characterized by periodic hypotonia, lax muscles, joint contracture, and diminished motor skill, was reported to be associated with heterozygous genomic duplication involving the MACF1 loci, with incomplete penetrance and highly variable clinical presentation in a single pedigree. In this study, parental-derived compound heterozygous novel missense mutations of MACF1, c.1517C>T (p.Thr506Ile) and c.11654T>C (p.Ile3885Thr), were found to co-segregate with disease status in two affected brothers presenting with progressive spastic tetraplegia, dystonia, joint contracture, feeding difficulty and developmental delay. We speculated that MACF1 mutations cause spectraplakinopathy inherited in an autosomal recessive manner. Our clinical findings expanded the phenotype of this neuromuscular disorder and provided new insights into the function of MACF1.
Collapse
Affiliation(s)
- Lulu Kang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yi Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ying Jin
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Mengqiu Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jinqing Song
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | | | - Yao Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| |
Collapse
|
47
|
Aggarwal S, Vineeth VS, Das Bhowmik A, Tandon A, Kulkarni A, Narayanan DL, Bhattacherjee A, Dalal A. Exome sequencing for perinatal phenotypes: The significance of deep phenotyping. Prenat Diagn 2019; 40:260-273. [PMID: 31742715 DOI: 10.1002/pd.5616] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To ascertain the performance of exome sequencing (ES) technology for determining the etiological basis of abnormal perinatal phenotypes and to study the impact of comprehensive phenotyping on variant prioritization. METHODS A carefully selected cohort of 32/204 fetuses with abnormal perinatal phenotypes following postmortem/postnatal deep phenotyping underwent ES to identify a causative variant for the fetal phenotype. A retrospective comparative analysis of the prenatal versus postmortem/postnatal phenotype-based variant prioritization was performed with aid of Phenolyzer software. A review of selected literature reports was done to examine the completeness of phenotypic information for cases in those reports and how it impacted the performance of fetal ES. RESULTS In 18/32 (56%) fetuses, a pathogenic/likely pathogenic variant was identified. This included novel genotype-phenotype associations, expanded prenatal phenotypes of known Mendelian disorders and dual Mendelian diagnoses. The retrospective analysis revealed that the putative diagnostic variant could not be identified on basis of prenatal findings alone in 15/22 (68%) cases, indicating the importance of comprehensive postmortem/postnatal phenotype information. Literature review was supportive of these findings but could not be conclusive due to marked heterogeneity of involved studies. CONCLUSION Comprehensive phenotyping is essential for improving diagnostic performance and facilitating identification of novel genotype-phenotype associations in perinatal cohorts undergoing ES.
Collapse
Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Aneek Das Bhowmik
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwani Tandon
- Department of Pathology, All India Institute of Medical Sciences, Bhopal, India
| | | | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Amrita Bhattacherjee
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
48
|
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: 22] [Impact Index Per Article: 4.4] [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
|
49
|
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
|
50
|
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
|