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Ridnõi K, Kurvinen E, Pajusalu S, Reimand T, Õunap K. Two Consecutive Pregnancies with Simpson-Golabi-Behmel Syndrome Type 1: Case Report and Review of Published Prenatal Cases. Mol Syndromol 2018; 9:205-213. [PMID: 30158844 DOI: 10.1159/000490083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2018] [Indexed: 11/19/2022] Open
Abstract
Fetal overgrowth and numerous congenital malformations can be detected in every trimester of pregnancy. New technologies in molecular testing, such as chromosomal microarray analysis and next-generation sequencing, continually demonstrate advantages for definitive diagnosis in fetal life. Simpson-Golabi-Behmel (SGB) syndrome is a rare but well-known overgrowth condition that is rarely diagnosed in the prenatal setting. We report 3 cases of SGB syndrome in 2 consecutive pregnancies. In our series, distinctive prenatal sonographic findings led to molecular diagnosis. Exome sequencing from fetal DNA revealed a hemizygous splice site variant in the GPC3 gene: NM_004484.3:c.1166+ 1G>T. The mother is a heterozygous carrier. We also provide an overview of the previously published 57 prenatal cases of SGB syndrome with prevalence estimation of the symptoms to aid prenatal differential diagnosis of fetal overgrowth syndromes.
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Affiliation(s)
- Konstantin Ridnõi
- Center for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn.,Department of Clinical Genetics, Institute of Clinical Medicine
| | - Elvira Kurvinen
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, Institute of Clinical Medicine.,Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
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Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing. Semin Fetal Neonatal Med 2018; 23:94-101. [PMID: 29305293 DOI: 10.1016/j.siny.2017.12.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities. In addition, the transformation of prenatal genetic testing arising from the introduction of whole genome, exome and targeted NGS produces unprecedented volumes of data requiring complex analysis and interpretation. Now translating these technologies to the clinic has become the goal of clinical genomics, transforming modern healthcare and personalized medicine. The achievement of this goal requires the most progressive technological tools for rapid high-throughput data generation at an affordable cost. Furthermore, as larger proportions of patients with genetic disease are identified we must be ready to offer appropriate genetic counselling to families and potential parents. In addition, the identification of novel treatment targets will continue to be explored, which is likely to introduce ethical considerations, particularly if genome editing techniques are included in these targeted treatments and transferred into mainstream personalized healthcare. Here we review the impact of NGS technology to analyse cell-free DNA (cfDNA) in maternal plasma to deliver NIPD for monogenic disorders and allow more comprehensive investigation of the abnormal fetus through the use of exome sequencing.
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53
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Narayanan S, Blumberg B, Clayman ML, Pan V, Wicklund C. Exploring the Issues Surrounding Clinical Exome Sequencing in the Prenatal Setting. J Genet Couns 2018. [DOI: 10.1007/s10897-018-0245-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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54
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Aggarwal S, Tandon A, Das Bhowmik A, Safarulla JMNJ, Dalal A. A Dysmorphology Based Systematic Approach Toward Perinatal Genetic Diagnosis in a Fetal Autopsy Series. Fetal Pediatr Pathol 2018; 37:49-68. [PMID: 29336636 DOI: 10.1080/15513815.2017.1397070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND This retrospective study assesses the contribution of genetic disorders in fetuses undergoing postmortem evaluation and the performance of a clinical dysmorphology based systematic approach toward genetic diagnosis. MATERIALS AND METHODS Ninety fetuses, including spontaneous losses and terminated pregnancies, underwent a postmortem evaluation including dysmorphological examination, radiological studies, and histopathological examination. Genetic testing including karyotyping, biochemical testing, Sanger sequencing, and exome sequencing were performed selectively. RESULTS A genetic etiology was concluded in 48 fetuses (55%). As a standalone test, dysmorphological examination was able to ascertain a definite genetic diagnosis in sixteen cases, histopathology in six; and karyotyping, biochemical testing and exome sequencing in two cases each (Total 28). Additionally, dysmorphology findings indicated possible genetic disorder in 20 cases. CONCLUSION Genetic etiologies contribute significantly to fetuses undergoing autopsy in this series. A systematic approach to postmortem fetal evaluation guided by dysmorphological examination provides high diagnostic yield toward perinatal genetic diagnosis.
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Affiliation(s)
- Shagun Aggarwal
- a Department of Medical Genetics , Nizam's Institute of Medical Sciences , Punjagutta, Hyderabad , Telangana , India.,b Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana , India
| | - Ashwani Tandon
- c Department of Pathology , Nizam's Institute of Medical Sciences , Hyderabad , Telangana , India
| | - Aneek Das Bhowmik
- b Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana , India
| | | | - Ashwin Dalal
- b Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana , India
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55
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Aarabi M, Sniezek O, Jiang H, Saller DN, Bellissimo D, Yatsenko SA, Rajkovic A. Importance of complete phenotyping in prenatal whole exome sequencing. Hum Genet 2018; 137:175-181. [PMID: 29392406 DOI: 10.1007/s00439-017-1860-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/16/2017] [Indexed: 12/16/2022]
Abstract
Whole exome sequencing (WES) is an emerging technique in prenatal diagnosis. In this retrospective study, we examined diagnostic utility and limitations of WES in prenatal cases with structural birth defects. DNA from 20 trios (fetal and parental), with normal karyotype and microarray findings, underwent WES and variant interpretation at a reference laboratory. The WES results were later re-evaluated in our academic center utilizing prenatal and postnatal phenotyping. Initial analysis using only prenatal ultrasound findings revealed no pathogenic or likely pathogenic variants in 20 pregnancies with structural birth defects. Re-analysis of WES variants and combination of prenatal and postnatal phenotyping yielded pathogenic variants in at least 20% of cases including PORCN gene in a fetus with split-hand/foot malformation, as well as variants of uncertain significance in NEB and NOTCH1 in fetuses with postnatal muscle weakness and Adams-Oliver syndrome, respectively. Furthermore, Sanger sequencing in a patient with holoprosencephaly, elucidated by postnatal MRI, revealed a pathogenic 47-base pairs deletion in ZIC2 which was missed by prenatal WES. This study suggests that incomplete prenatal phenotyping and lack of prenatal ultrasound-genotype databases are the limiting factors for current interpretation of WES data in prenatal diagnosis. Development of prenatal phenotype-genotype databases would significantly help WES interpretation in this setting. Patients who underwent prenatal clinical WES may benefit from the re-analysis based on detailed postnatal findings.
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Affiliation(s)
- Mahmoud Aarabi
- Medical Genetics and Genomics Laboratories, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Olivia Sniezek
- Westminster College, New Wilmington, PA, USA.,Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Huaiyang Jiang
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Devereux N Saller
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daniel Bellissimo
- Medical Genetics and Genomics Laboratories, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Svetlana A Yatsenko
- Medical Genetics and Genomics Laboratories, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aleksandar Rajkovic
- Medical Genetics and Genomics Laboratories, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA. .,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA. .,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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56
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Chong K, Saleh M, Injeyan M, Miron I, Fong K, Shannon P. Nonisolated diaphragmatic hernia in Simpson-Golabi-Behmel syndrome. Prenat Diagn 2018; 38:117-122. [PMID: 29240237 DOI: 10.1002/pd.5198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/01/2017] [Accepted: 12/09/2017] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Congenital diaphragmatic hernia (CDH) is associated with Simpson-Golabi-Behmel syndrome (SGBS), but few cases diagnosed prenatally have been reported. The aim of this series is to highlight the association of nonisolated CDH with SGBS type I on prenatal ultrasound and emphasize the importance of genetic testing, fetal autopsy, and family history in confirming this diagnosis. METHOD Retrospective review of 3 cases of SGBS type I in a single tertiary care centre. Family history, fetal ultrasound, autopsy findings, and genetic testing for GPC3 was performed for each case. RESULTS Fetal ultrasound findings in the second trimester were CDH, omphalocele, increased nuchal fold, renal anomaly, and cleft lip and palate. Fetal autopsy confirmed the prenatal ultrasound findings and also showed dysmorphic facial features and premalignant lesions on renal and gonadal histology. Microarray and DNA analysis of the GPC3 gene confirmed the diagnosis of SGBS type I in each case. CONCLUSION Nonisolated CDH in a male fetus suggests a diagnosis of SGBS type I. Fetal autopsy, pedigree analysis, and genetic testing for GPC3 are all essential to confirming the diagnosis. The histological findings of ovotestes and nephroblastomatosis indicate that cancer predisposition is established early in fetal life.
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Affiliation(s)
- Karen Chong
- Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, ON, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | - Maha Saleh
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | - Marie Injeyan
- Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | - Ioana Miron
- Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | - Katherine Fong
- Department of Medical Imaging, Mount Sinai Hospital, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | - Patrick Shannon
- Department of Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
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57
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Best S, Wou K, Vora N, Van der Veyver IB, Wapner R, Chitty LS. Promises, pitfalls and practicalities of prenatal whole exome sequencing. Prenat Diagn 2018; 38:10-19. [PMID: 28654730 PMCID: PMC5745303 DOI: 10.1002/pd.5102] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Abstract
Prenatal genetic diagnosis provides information for pregnancy and perinatal decision-making and management. In several small series, prenatal whole exome sequencing (WES) approaches have identified genetic diagnoses when conventional tests (karyotype and microarray) were not diagnostic. Here, we review published prenatal WES studies and recent conference abstracts. Thirty-one studies were identified, with diagnostic rates in series of five or more fetuses varying between 6.2% and 80%. Differences in inclusion criteria and trio versus singleton approaches to sequencing largely account for the wide range of diagnostic rates. The data suggest that diagnostic yields will be greater in fetuses with multiple anomalies or in cases preselected following genetic review. Beyond its ability to improve diagnostic rates, we explore the potential of WES to improve understanding of prenatal presentations of genetic disorders and lethal fetal syndromes. We discuss prenatal phenotyping limitations, counselling challenges regarding variants of uncertain significance, incidental and secondary findings, and technical problems in WES. We review the practical, ethical, social and economic issues that must be considered before prenatal WES could become part of routine testing. Finally, we reflect upon the potential future of prenatal genetic diagnosis, including a move towards whole genome sequencing and non-invasive whole exome and whole genome testing. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sunayna Best
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Karen Wou
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Neeta Vora
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ignatia B. Van der Veyver
- Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Lyn S. Chitty
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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Abstract
There have been major advances in genetic testing especially over the last 10 years. We have advanced from looking at simple chromosomes under a microscope to more sophisticated analysis of the DNA makeup of chromosomes and from testing a single gene to sequencing almost all of our genetic material. Similarly, in the field of prenatal testing we have made great strides in screening and diagnostic testing in the hope of detecting significant abnormalities in the fetus while decreasing the risk to the pregnancy. In this article the major types of genetic screening and diagnostic testing, both prenatal and postnatal, will be reviewed. [Pediatr Ann. 2017;46(11):e423-e427.].
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59
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Vora NL, Powell B, Brandt A, Strande N, Hardisty E, Gilmore K, Foreman AKM, Wilhelmsen K, Bizon C, Reilly J, Owen P, Powell CM, Skinner D, Rini C, Lyerly AD, Boggess KA, Weck K, Berg JS, Evans JP. Prenatal exome sequencing in anomalous fetuses: new opportunities and challenges. Genet Med 2017; 19:1207-1216. [PMID: 28518170 PMCID: PMC5675748 DOI: 10.1038/gim.2017.33] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022] Open
Abstract
PurposeWe investigated the diagnostic and clinical performance of exome sequencing in fetuses with sonographic abnormalities with normal karyotype and microarray and, in some cases, normal gene-specific sequencing.MethodsExome sequencing was performed on DNA from 15 anomalous fetuses and from the peripheral blood of their parents. Parents provided consent to be informed of diagnostic results in the fetus, medically actionable findings in the parents, and their identification as carrier couples for significant autosomal recessive conditions. We assessed the perceptions and understanding of exome sequencing using mixed methods in 15 mother-father dyads.ResultsIn seven (47%) of 15 fetuses, exome sequencing provided a diagnosis or possible diagnosis with identification of variants in the following genes: COL1A1, MUSK, KCTD1, RTTN, TMEM67, PIEZO1 and DYNC2H1. One additional case revealed a de novo nonsense mutation in a novel candidate gene (MAP4K4). The perceived likelihood that exome sequencing would explain the results (5.2 on a 10-point scale) was higher than the approximately 30% diagnostic yield discussed in pretest counseling.ConclusionExome sequencing had diagnostic utility in a highly select population of fetuses where a genetic diagnosis was highly suspected. Challenges related to genetics literacy and variant interpretation must be addressed by highly tailored pre- and posttest genetic counseling.
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Affiliation(s)
- Neeta L. Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bradford Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Natasha Strande
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emily Hardisty
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ann Katherine M. Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- North Carolina Translational and Clinical Sciences (NC TraCS) Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kirk Wilhelmsen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Chris Bizon
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jason Reilly
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Phil Owen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Cynthia M. Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Debra Skinner
- FPG Child Development Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christine Rini
- Department of Health Behavior, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anne D. Lyerly
- Department of Social Medicine and Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kim A. Boggess
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Karen Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jonathan S. Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James P. Evans
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Social Medicine and Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Powis Z, Hart A, Cherny S, Petrik I, Palmaer E, Tang S, Jones C. Clinical diagnostic exome evaluation for an infant with a lethal disorder: genetic diagnosis of TARP syndrome and expansion of the phenotype in a patient with a newly reported RBM10 alteration. BMC MEDICAL GENETICS 2017; 18:60. [PMID: 28577551 PMCID: PMC5455125 DOI: 10.1186/s12881-017-0426-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 05/22/2017] [Indexed: 11/11/2022]
Abstract
Background Diagnostic Exome Sequencing (DES) has been shown to be an effective tool for diagnosis individuals with suspected genetic conditions. Case Presentation We report a male infant born with multiple anomalies including bilateral dysplastic kidneys, cleft palate, bilateral talipes, and bilateral absence of thumbs and first toes. Prenatal testing including chromosome analysis and microarray did not identify a cause for the multiple congenital anomalies. Postnatal diagnostic exome studies (DES) were utilized to find a molecular diagnosis for the patient. Exome sequencing of the proband, mother, and father showed a previously unreported maternally inherited RNA binding motif protein 10 (RBM10) c.1352_1353delAG (p.E451Vfs*66) alteration. Mutations in RBM10 are associated with TARP syndrome, an X-linked recessive disorder originally described with cardinal features of talipes equinovarus, atrial septal defect, Robin sequence, and persistent left superior vena cava. Conclusion DES established a molecular genetic diagnosis of TARP syndrome for a neonatal patient with a poor prognosis in whom traditional testing methods were uninformative and allowed for efficient diagnosis and future reproductive options for the parents. Other reported cases of TARP syndrome demonstrate significant variability in clinical phenotype. The reported features in this infant including multiple hemivertebrae, imperforate anus, aplasia of thumbs and first toes have not been reported in previous patients, thus expanding the clinical phenotype for this rare disorder. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0426-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zöe Powis
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA.
| | - Alexa Hart
- Rush University Medical Center, Chicago, IL, USA
| | - Sara Cherny
- Rush University Medical Center, Chicago, IL, USA
| | - Igor Petrik
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Erika Palmaer
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Sha Tang
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
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61
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Westerfield LE, Braxton AA, Walkiewicz M. Prenatal Diagnostic Exome Sequencing: a Review. CURRENT GENETIC MEDICINE REPORTS 2017. [DOI: 10.1007/s40142-017-0120-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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62
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Whole-exome sequencing on deceased fetuses with ultrasound anomalies: expanding our knowledge of genetic disease during fetal development. Genet Med 2017; 19:1171-1178. [PMID: 28425981 DOI: 10.1038/gim.2017.31] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/08/2017] [Indexed: 12/27/2022] Open
Abstract
PurposeThe aim of this study was to determine the diagnostic yield of whole-exome sequencing (WES) in fetuses with ultrasound anomalies that resulted in fetal demise or pregnancy termination. The results were also utilized to aid in the identification of candidate genes for fetal development and to expand the clinical phenotype of known genetic conditions.MethodsWES was performed on specimens from 84 deceased fetuses. Data were analyzed and final results were classified into one of four categories: positive, possible, negative, and candidate gene only. WES analysis was predominantly performed in fetus-parent trios or quads (61%, n=52).ResultsOverall, 20% (n = 17) of cases were positive, 45% (n=38) were possible, 9% (n=7) had only candidate gene variants and 26% (n = 22) tested negative. The diagnostic yield for definitive findings for trio analysis was 24% (n = 11) compared to 14% (n = 4) for singletons. The most frequently reported ultrasound anomalies were central nervous system (37%, n = 31), hydrops/edema (36%, n = 30), and cardiovascular anomalies (31%, n = 26).ConclusionOur experience supports the use of WES to identify the molecular etiology of fetal ultrasound anomalies, to identify candidate genes involved in fetal development, and to expand our knowledge of the clinical phenotype of known genetic conditions.
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63
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Van Mieghem T, Bianchi DW, Levy B, Deprest J, Chitty LS, Ghidini A. In case you missed it: the Prenatal Diagnosis
editors bring you the most significant advances of 2016. Prenat Diagn 2017; 37:117-122. [DOI: 10.1002/pd.5007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 01/15/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Tim Van Mieghem
- Department of Obstetrics and Gynaecology; Mount Sinai Hospital and University of Toronto; Toronto Canada
| | - Diana W. Bianchi
- Mother Infant Research Institute at Tufts Medical Center; Boston MA USA
| | - Brynn Levy
- Department of Pathology and Cell Biology; Columbia University; New York NY USA
| | - Jan Deprest
- Department of Obstetrics and Gynecology; University Hospitals Leuven; Leuven Belgium
| | - Lyn S. Chitty
- North Thames NHS Genomic Medicine Centre; Great Ormond Street NHS Foundation Trust; London UK
- Genetics and Genomic Medicine; UCL Great Ormond Street Institute of Child Health; London UK
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64
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Konialis C, Assimakopoulos E, Hagnefelt B, Karapanou S, Sotiriadis A, Pangalos C. Prenatal diagnosis of X-linked myopathy associated with a VMA21 gene mutation afforded through a novel targeted exome sequencing strategy applied in fetuses with abnormal ultrasound findings. Clin Case Rep 2017; 5:308-311. [PMID: 28265396 PMCID: PMC5331204 DOI: 10.1002/ccr3.822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/13/2016] [Accepted: 12/25/2016] [Indexed: 01/23/2023] Open
Abstract
Fetal malformations detected through routine prenatal ultrasound examination comprise a heterogeneous group potentially associated with genetic disorders where the underlying cause is difficult to establish. We present the prenatal diagnosis of a rare X‐linked myopathy involving a new VMA21 gene mutation, detected through a novel prenatal exome sequencing‐based approach.
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Affiliation(s)
- Christopher Konialis
- InterGenetics - Diagnostic Genetics Centre Athens 11526 Greece; Genomis Ltd, Lynton House London WC1H 9BQ UK
| | - Efstratios Assimakopoulos
- 2nd Department of Obstetrics and Gynecology Ippokrateion General Hospital Aristotle University of Thessaloniki Thessaloniki Greece
| | - Birgitta Hagnefelt
- InterGenetics - Diagnostic Genetics Centre Athens 11526 Greece; Genomis Ltd, Lynton House London WC1H 9BQ UK
| | | | - Alexandros Sotiriadis
- 2nd Department of Obstetrics and Gynecology Ippokrateion General Hospital Aristotle University of Thessaloniki Thessaloniki Greece
| | - Constantinos Pangalos
- InterGenetics - Diagnostic Genetics Centre Athens 11526 Greece; Genomis Ltd, Lynton House London WC1H 9BQ UK
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65
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Abstract
The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively. All of these options have benefits and limitations, and genetic counseling has become increasingly complex for providers who are responsible for guiding patients in their decisions about screening and testing before and during pregnancy.
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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, 77030, USA
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A Clinician's perspective on clinical exome sequencing. Hum Genet 2016; 135:643-54. [PMID: 27126233 DOI: 10.1007/s00439-016-1662-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/23/2016] [Indexed: 12/22/2022]
Abstract
Clinical exome sequencing has clearly improved our ability as clinicians to identify the cause of a wide variety of disorders. Prior to exome sequencing, a majority of patients with apparent syndromes never received a specific molecular genetic diagnosis despite extensive diagnostic odysseys. Even for those receiving an answer to the question of what caused their disorder, the diagnostic odyssey often spanned years to decades. Determining the particular genetic cause in an individual patient can be challenging due to inherent phenotypic and genetic heterogeneity of disease, technical limitations of testing or both. Blended phenotypes, due to multiple monogenic disorders in the same patient, are true dilemmas for traditional genetic evaluations, but are increasingly being diagnosed through clinical exome sequencing. New sequencing technologies have increased the proportion of patients receiving molecular diagnoses, while significantly shortening the time scale, providing multiple benefits for the health-care team, patient and family.
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Pangalos C, Hagnefelt B, Lilakos K, Konialis C. First applications of a targeted exome sequencing approach in fetuses with ultrasound abnormalities reveals an important fraction of cases with associated gene defects. PeerJ 2016; 4:e1955. [PMID: 27168972 PMCID: PMC4860337 DOI: 10.7717/peerj.1955] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/30/2016] [Indexed: 01/15/2023] Open
Abstract
Background. Fetal malformations and other structural abnormalities are relatively frequent findings in the course of routine prenatal ultrasonographic examination. Due to their considerable genetic and clinical heterogeneity, the underlying genetic cause is often elusive and the resulting inability to provide a precise diagnosis precludes proper reproductive and fetal risk assessment. We report the development and first applications of an expanded exome sequencing-based test, coupled to a bioinformatics-driven prioritization algorithm, targeting gene disorders presenting with abnormal prenatal ultrasound findings. Methods. We applied the testing strategy to14 euploid fetuses, from 11 on-going pregnancies and three products of abortion, all with various abnormalities or malformations detected through prenatal ultrasound examination. Whole exome sequencing (WES) was followed by variant prioritization, utilizing a custom analysis pipeline (Fetalis algorithm), targeting 758 genes associated with genetic disorders which may present with abnormal fetal ultrasound findings. Results. A definitive or highly-likely diagnosis was made in 6 of 14 cases (43%), of which 3 were abortuses (Ellis-van Creveld syndrome, Ehlers-Danlos syndrome and Nemaline myopathy 2) and 3 involved on-going pregnancies (Citrullinemia, Noonan syndrome, PROKR2-related Kallmann syndrome). In the remaining eight on-going pregnancy cases (57%), a ZIC1 variant of unknown clinical significance was detected in one case, while in seven cases testing did not reveal any pathogenic variant(s). Pregnancies were followed-up to birth, resulting in one neonate harboring the PROKR2 mutation, presenting with isolated minor structural cardiac abnormalities, and in seven apparently healthy neonates. Discussion. The expanded targeted exome sequencing-based approach described herein (Fetalis), provides strong evidence suggesting a definite and beneficial increase in our diagnostic capabilities in prenatal diagnosis of otherwise chromosomally balanced fetuses with troubling ultrasound abnormalities. Furthermore, the proposed targeted exome sequencing strategy, designed primarily as a diagnostic rather than a research discovery tool, overcomes many of the problems and limitations associated with clinical wide-scale WES testing in a prenatal setting.
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Affiliation(s)
- Constantinos Pangalos
- Genomis Ltd, London, United Kingdom; InterGenetics-Diagnostic Genetic Centre, Athens, Greece
| | | | - Konstantinos Lilakos
- Department of Haematology, "Laikon" General Hospital - University of Athens Medical School , Athens , Greece
| | - Christopher Konialis
- Genomis Ltd, London, United Kingdom; InterGenetics-Diagnostic Genetic Centre, Athens, Greece
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Prenatal diagnosis of fetal akinesia deformation sequence (FADS): a study of 79 consecutive cases. Arch Gynecol Obstet 2016; 294:697-707. [DOI: 10.1007/s00404-016-4017-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/05/2016] [Indexed: 10/22/2022]
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Pan M, Han J, Zhen L, Yang X, Li R, Liao C, Li DZ. Prenatal diagnosis of fetuses with increased nuchal translucency using an approach based on quantitative fluorescent polymerase chain reaction and genomic microarray. Eur J Obstet Gynecol Reprod Biol 2015; 197:164-7. [PMID: 26771907 DOI: 10.1016/j.ejogrb.2015.12.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/21/2015] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To assess the clinical value of prenatal diagnosis of fetuses with increased nuchal translucency (NT) using an approach based on quantitative fluorescent polymerase chain reaction (QF-PCR) and chromosomal microarray (CMA). STUDY DESIGN From January 2013 to October 2014, we included 175 pregnancies with fetal NT ≥ 3.5mm at 11-13 weeks' gestation who received chorionic villus sampling. QF-PCR was first used to rapidly detect common aneuploidies. The cases with a normal QF-PCR result were analyzed by CMA. RESULTS Of the 175 cases, common aneuploidies were detected by QF-PCR in 53 (30.2%) cases (30 cases of trisomy 21, 12 cases of monosomy X, 7 cases of trisomy 18, 3 cases of trisomy 13 and 1 case of 47, XXY). Among the 122 cases with a normal QF-PCR result, microarray detected additional pathogenic copy number variants (CNVs) in 5.7% (7/122) of cases. Four cases would have expected to be detectable by conventional karyotyping because of large deletions/duplications (>10 Mb), leaving three cases (2.5%; 3/118) with pathogenic CNVs only detectable by CMA. CONCLUSION It is rational to use a diagnostic strategy in which CMA is preceded by the less expensive, rapid, QF-PCR to detect common aneuploidies. CMA allows detection of a number of pathogenic chromosomal aberrations in fetuses with a high NT.
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Affiliation(s)
- Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China.
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Chitty LS, Friedman JM, Langlois S. Current controversies in prenatal diagnosis 2: should a fetal exome be used in the assessment of a dysmorphic or malformed fetus? Prenat Diagn 2015; 36:15-9. [PMID: 26525746 DOI: 10.1002/pd.4718] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/21/2015] [Accepted: 10/27/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Lyn S Chitty
- Genetics and Genomic Medicine, UCL Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, England
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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