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Gaspar PC, Miranda AE, Bigolin A, Morais AAC, Aragón MG, Morais JAV, Alonso Neto JB, Lannoy LHD, Sanchez MN, Cravo Neto DB, Bermúdez XPCD, Benzaken AS. [A national network of molecular tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae: a pilot implementation experience in Brazil]. CAD SAUDE PUBLICA 2024; 40:e00123023. [PMID: 39082498 PMCID: PMC11290829 DOI: 10.1590/0102-311xpt123023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/20/2023] [Accepted: 02/08/2024] [Indexed: 08/02/2024] Open
Abstract
This study aimed to know the opinion of professionals participating in an experiment to implement a pilot for molecular tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae at the Brazilian Unified National Health System (SUS). The detection rate of C. trachomatis and/or N. gonorrhoeae and the factors associated with infection were determined. The strategy included laboratories belonging to the HIV and viral hepatitis viral load network. Testing targeted people who are more vulnerable to sexually transmitted infections and collected urine samples and/or vaginal, endocervical, and/or male urethral swabs. Questionnaires were sent to state managers and laboratory professionals about the implementation of the pilot. Reviews were overall positive. Weaknesses included difficulties changing work processes, lack of human resources, poorly sensitized care professionals, and absence of primary urine tubes, the only input not provided. Strengths included the centralized acquisition of tests, sharing of equipment, and storage of samples at room temperature. Of the 16,177 people who were tested, 1,004 (6.21%) were positive for C. trachomatis; 1,036 (6.4%), for N. gonorrhoeae; and 239 (1.48%), for C. trachomatis/N. gonorrhoeae . Detection of any infection occurred more frequently in young people (≤ 24 vs. > 24 years) (adjOR = 2.65; 95%CI: 2.38-2.96), men (adjOR = 1.95; 95%CI: 1.72-2.21), brown/black individuals (adjOR = 1.06; 95%CI: 1.05-1.11), those in Southeastern Brazil (adjOR = 1.08; 95%CI: 1.02-1.13), and in urethral secretion samples (adjOR = 1.46; 95%CI: 1.41-1.52). Results show the importance of making testing available nationwide, which supported the implementation of a definitive network to detection C. trachomatis/N. gonorrhoeae in SUS.
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Affiliation(s)
- Pâmela Cristina Gaspar
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
- Programa de Pós-graduação em Saúde Coletiva, Universidade de Brasília, Brasília, Brasil
| | - Angélica Espinosa Miranda
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
- Programa de Pós-graduação em Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brasil
| | - Alisson Bigolin
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
| | - Amanda Alencar Cabral Morais
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
| | - Mayra Gonçalves Aragón
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
- Programa de Pós-graduação em Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brasil
| | - José Athayde Vasconcelos Morais
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
| | - José Boullosa Alonso Neto
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
| | - Leonor Henriette de Lannoy
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
- Programa de Pós-graduação em Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brasil
| | - Mauro Niskier Sanchez
- Programa de Pós-graduação em Saúde Coletiva, Universidade de Brasília, Brasília, Brasil
| | - Draurio Barreira Cravo Neto
- Departamento de HIV/AIDS, Tuberculose, Hepatites Virais e Infecções Sexualmente Transmissíveis, Ministério da Saúde, Brasília, Brasil
| | | | - Adele Schwartz Benzaken
- Programa de Pós-graduação em Saúde Coletiva, Universidade de Brasília, Brasília, Brasil
- Instituto Leonidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Brasil
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de Koning MA, Pimienta Ramirez PA, Haak MC, Han X, Ruiterkamp-Versteeg MH, de Leeuw N, Schatz UA, Shoukier M, Rieger-Fackeldey E, Ortiz JU, van Duinen SG, Klein WM, Witlox RSGM, Finnell RH, Santen GWE, Lei Y, Suerink M. De novo heterozygous missense variants in CELSR1 as cause of fetal pleural effusions and progressive fetal hydrops. J Med Genet 2024; 61:549-552. [PMID: 38272662 DOI: 10.1136/jmg-2023-109698] [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: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
Fetal hydrops as detected by prenatal ultrasound usually carries a poor prognosis depending on the underlying aetiology. We describe the prenatal and postnatal clinical course of two unrelated female probands in whom de novo heterozygous missense variants in the planar cell polarity gene CELSR1 were detected using exome sequencing. Using several in vitro assays, we show that the CELSR1 p.(Cys1318Tyr) variant disrupted the subcellular localisation, affected cell-cell junction, impaired planar cell polarity signalling and lowered proliferation rate. These observations suggest that deleterious rare CELSR1 variants could be a possible cause of fetal hydrops.
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Affiliation(s)
- Maayke A de Koning
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Monique C Haak
- Department of Obstetrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Xiao Han
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Nicole de Leeuw
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
| | - Ulrich A Schatz
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Department of Obstetrics and Gynecology, Technische Universität München, Munich, Germany
| | - Moneef Shoukier
- Department of Molecular Genetics, Prenatal Medicine Munich, Munich, Germany
| | | | - Javier U Ortiz
- Department of Obstetrics and Gynecology, Technische Universität München, Munich, Germany
| | - Sjoerd G van Duinen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Willemijn M Klein
- Department of Medical Imaging, Radboudumc, Nijmegen, The Netherlands
| | - Ruben S G M Witlox
- Department of Neonatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Richard H Finnell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Departments of Medicine, Molecular and Cellular Biology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yunping Lei
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Rogers A, De Jong L, Waters W, Rawlings LH, Simons K, Gao S, Soubrier J, Kenyon R, Lin M, King R, Lawrence DM, Muller P, Leblanc S, McGregor L, Sallevelt SCEH, Liebelt J, Hardy TSE, Fletcher JM, Scott HS, Kulkarni A, Barnett CP, Kassahn KS. Extending the new era of genomic testing into pregnancy management: A proposed model for Australian prenatal services. Aust N Z J Obstet Gynaecol 2024. [PMID: 38577897 DOI: 10.1111/ajo.13814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Trio exome sequencing can be used to investigate congenital abnormalities identified on pregnancy ultrasound, but its use in an Australian context has not been assessed. AIMS Assess clinical outcomes and changes in management after expedited genomic testing in the prenatal period to guide the development of a model for widespread implementation. MATERIALS AND METHODS Forty-three prospective referrals for whole exome sequencing, including 40 trios (parents and pregnancy), two singletons and one duo were assessed in a tertiary hospital setting with access to a state-wide pathology laboratory. Diagnostic yield, turn-around time (TAT), gestational age at reporting, pregnancy outcome, change in management and future pregnancy status were assessed for each family. RESULTS A clinically significant genomic diagnosis was made in 15/43 pregnancies (35%), with an average TAT of 12 days. Gestational age at time of report ranged from 16 + 5 to 31 + 6 weeks (median 21 + 3 weeks). Molecular diagnoses included neuromuscular and skeletal disorders, RASopathies and a range of other rare Mendelian disorders. The majority of families actively used the results in pregnancy decision making as well as in management of future pregnancies. CONCLUSIONS Rapid second trimester prenatal genomic testing can be successfully delivered to investigate structural abnormalities in pregnancy, providing crucial guidance for current and future pregnancy management. The time-sensitive nature of this testing requires close laboratory and clinical collaboration to ensure appropriate referral and result communication. We found the establishment of a prenatal coordinator role and dedicated reporting team to be important facilitators. We propose this as a model for genomic testing in other prenatal services.
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Affiliation(s)
- Alice Rogers
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Lucas De Jong
- Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Wendy Waters
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Lesley H Rawlings
- Genomics Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Keryn Simons
- Genomics Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Song Gao
- Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Julien Soubrier
- Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Rosalie Kenyon
- ACRF SA Cancer Genome Facility, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Ming Lin
- ACRF SA Cancer Genome Facility, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Rob King
- ACRF SA Cancer Genome Facility, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - David M Lawrence
- ACRF SA Cancer Genome Facility, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Peter Muller
- Maternal Fetal Medicine Service (MFMS), Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Shannon Leblanc
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Lesley McGregor
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Suzanne C E H Sallevelt
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Jan Liebelt
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Tristan S E Hardy
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Repromed, Monash IVF, Adelaide, South Australia, Australia
| | - Janice M Fletcher
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Abhi Kulkarni
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Karin S Kassahn
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
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Liu J, Liu Q, Zhao J, Lin S, Zhou Y. Prenatal evaluation of genetic variants in fetuses with small head circumference: A single-center retrospective study. Eur J Obstet Gynecol Reprod Biol 2024; 293:57-66. [PMID: 38113582 DOI: 10.1016/j.ejogrb.2023.12.004] [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: 06/16/2023] [Revised: 10/31/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
OBJECTIVES To comprehensively evaluate the contributions of numerical chromosomal abnormality, copy number variant (CNV), and sequence variant (SV) to fetuses with small head circumference in a Chinese cohort using chromosome microarray analysis and whole exome sequencing. METHODS A total of 157 fetuses with small heads defined as head circumference < - 2 standard deviation (SD) were recruited between October 2014 and March 2023. We used the ultrasonic measurement parameter Z-score to define small head as possible microcephaly (3 < Z ≤ -2), microcephaly (-5 < Z ≤ -3), or pathologic microcephaly (Z ≤ -5). Ultrasound findings and genetic results were analyzed. RESULTS The overall diagnostic yield of chromosomal abnormalities by microarray analysis was 13 %. Whole exome sequencing revealed eight novel variants and two interesting candidate genes and provided a 25.4 % incremental yield compared with microarray analysis. Of the detected SVs, 56 % were de novo and the most common inheritance pattern was autosomal dominant inheritance presented in 11/16 fetuses. Compared with isolated small heads, non-isolated small heads had a significantly higher detection rate of chromosomal abnormalities (16 % vs. 3.0 %, P = 0.049) but not SVs (24 % vs. 5.5 %, P = 0.126). Subgroup analysis showed that intracranial anomalies had a similar high detection rate of SVs in fetuses with all small heads subgroups while no chromosomal abnormalities and causative SVs were found in fetuses with isolated possible microcephaly. CONCLUSIONS Ultrasound findings of small fetal head circumference < 3 SD below the mean, especially those with intracranial structural abnormalities, indicate the need for genetic counseling. Genetic variants, mainly copy number variants and SV, may be responsible for the substantial proportion of small fetal head circumference, while most are de novo. Whole exome sequencing and microarray analysis are effective diagnostic approaches for this population.
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Affiliation(s)
- Jingyu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Quanrui Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jingya Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shaobin Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China.
| | - Yi Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China.
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Diderich KEM, Klapwijk JE, van der Schoot V, van den Born M, Wilke M, Joosten M, Stuurman KE, Hoefsloot LH, Van Opstal D, Brüggenwirth HT, Srebniak MI. The role of a multidisciplinary team in managing variants of uncertain clinical significance in prenatal genetic diagnosis. Eur J Med Genet 2023; 66:104844. [PMID: 37709011 DOI: 10.1016/j.ejmg.2023.104844] [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: 04/24/2023] [Revised: 08/04/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Although in general prenatal exome sequencing only reports (likely) pathogenic variants, in some cases a variant of uncertain significance (VUS) is disclosed. The aims of this retrospective study were to evaluate the types of VUS that have been reported to prospective parents, possible reclassification and to design a standard flow chart to determine which types of VUS could be considered for reporting in prenatal settings. Furthermore, we investigated what the crucial elements are to facilitate rapid management of uncertain results in a prenatal setting. MATERIAL AND METHODS We reviewed exome results from 451 pregnancies performed in 2019-2021. We analyzed which factors that were taken into account by the multidisciplinary team (MDT) contributed towards decision making on reporting VUS after prenatal exome sequencing. RESULTS In 9/451 (2%) pregnancies tested with exome sequencing using a broad panel analysis a VUS was reported. After birth 3/9 VUS could be reclassified to likely pathogenic variants based on new clinical follow up data. We considered reporting VUS in genes: 1) matching the fetal phenotype, 2) associated with a severe disorder when a functional test is available or 3) possibly associated with a disorder where early post-partum diagnosis and treatment are crucial for a better prognosis. Two flowcharts were designed to guide first the laboratory specialist and then the MDT in decisions on reporting VUS. The crucial elements that enabled timely decisions on VUS disclosure were regular meetings, appropriate expertise, professional connections with other experts and psychological safety within the MDT. CONCLUSION In this study three out of nine VUS could be re-classified as likely pathogenic after clinical follow-up. In order to protect pregnant couples from the burden of uncertain results, the genetic professionals have to take the responsibility to limit the reporting of VUS. This can be done not only by automated filtering of data, by following professional guidelines and by building standardized decision flows, but also by discussing individual cases considering personal situations and the involved disease and by sharing professional experience and responsibility in a multidisciplinary prenatal team setting.
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Affiliation(s)
- Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands.
| | - Jasmijn E Klapwijk
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Vyne van der Schoot
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Myrthe van den Born
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Kyra E Stuurman
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Hennie T Brüggenwirth
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Malgorzata I Srebniak
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
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Diderich KEM, Klapwijk JE, van der Schoot V, Brüggenwirth HT, Joosten M, Srebniak MI. Challenges and Pragmatic Solutions in Pre-Test and Post-Test Genetic Counseling for Prenatal Exome Sequencing. Appl Clin Genet 2023; 16:89-97. [PMID: 37216148 PMCID: PMC10198275 DOI: 10.2147/tacg.s411185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The yield of genetic prenatal diagnosis has been notably improved by introducing whole genome chromosomal microarray (CMA) and prenatal exome sequencing (pES). However, together with increased numbers of diagnoses made, the need to manage challenging findings such as variants of unknown significance (VUS) and incidental findings (IF) also increased. We have summarized the current guidelines and recommendations and we have shown current solutions used in our tertiary center in the Netherlands. We discuss four of the most common clinical situations: fetus with normal pES results, fetus with a pathogenic finding explaining the fetal phenotype, fetus with a variant of uncertain clinical significance fitting the phenotype and fetus with a variant leading to an incidental diagnosis. Additionally, we reflect on solutions in order to facilitate genetic counseling in an NGS-era.
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Affiliation(s)
| | | | | | | | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
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7
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Poljak B, Agarwal U, Alfirevic Z, Allen S, Canham N, Higgs J, Kaelin Agten A, Khalil A, Roberts D, Mone F, Navaratnam K. Prenatal exome sequencing and impact on perinatal outcome: cohort study. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2023; 61:339-345. [PMID: 36508432 DOI: 10.1002/uog.26141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
OBJECTIVES First, to determine the uptake of prenatal exome sequencing (pES) and the diagnostic yield of pathogenic (causative) variants in a UK tertiary fetal medicine unit following the introduction of the NHS England Rapid Exome Sequencing Service for fetal anomalies testing (R21 pathway). Second, to identify how the decision to proceed with pES and identification of a causative variant affect perinatal outcomes, specifically late termination of pregnancy (TOP) at or beyond 22 weeks' gestation. METHODS This was a retrospective cohort study of anomalous fetuses referred to the Liverpool Women's Hospital Fetal Medicine Unit between 1 March 2021 and 28 February 2022. pES was performed as part of the R21 pathway. Trio exome sequencing was performed using an Illumina next-generation sequencing platform assessing coding and splice regions of a panel of 974 prenatally relevant genes and 231 expert reviewed genes. Data on demographics, phenotype, pES result and perinatal outcome were extracted and compared. Descriptive statistics and the χ-square or Fisher's exact test were performed using IBM SPSS version 28.0.1.0. RESULTS In total, 72 cases were identified and two-thirds of eligible women (n = 48) consented to trio pES. pES was not feasible in one case owing to a low DNA yield and, therefore, was performed in 47 cases. In one-third of cases (n = 24), pES was not proposed or agreed. In 58.3% (14/24) of these cases, this was because invasive testing was declined and, in 41.7% (10/24) of cases, women opted for testing and underwent chromosomal microarray analysis only. The diagnostic yield of pES was 23.4% (11/47). There was no overall difference in the proportion of women who decided to have late TOP in the group in which pES was agreed compared with the group in which pES was not proposed or agreed (25.0% (12/48) vs 25.0% (6/24); P = 1.0). However, the decision to have late TOP was significantly more frequent when a causative variant was detected compared with when pES was uninformative (63.6% (7/11) vs 13.9% (5/36); P < 0.0009). The median turnaround time for results was longer in cases in which a causative variant was identified than in those in which pES was uninformative (22 days (interquartile range (IQR), 19-34) days vs 14 days (IQR, 10-15 days); P < 0.0001). CONCLUSIONS This study demonstrates the potential impact of identification of a causative variant by pES on decision to have late TOP. As the R21 pathway continues to evolve, we urge clinicians and policymakers to consider introducing earlier screening for anomalies, developing robust guidance for late TOP and ensuring optimized support for couples. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- B Poljak
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - U Agarwal
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - Z Alfirevic
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
- Harris-Wellbeing Research Centre, University of Liverpool, Liverpool, UK
| | - S Allen
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - N Canham
- Clinical Genetics Department, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - J Higgs
- Clinical Genetics Department, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - A Kaelin Agten
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - 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
| | - D Roberts
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - F Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - K Navaratnam
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
- Harris-Wellbeing Research Centre, University of Liverpool, Liverpool, UK
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So PL, Hui ASY, Ma TWL, Shu W, Hui APW, Kong CW, Lo TK, Kan ANC, Kan EYL, Chong SC, Chung BHY, Luk HM, Choy KW, Kan ASY, Leung WC. Implementation of Public Funded Genome Sequencing in Evaluation of Fetal Structural Anomalies. Genes (Basel) 2022; 13:2088. [PMID: 36360323 PMCID: PMC9690018 DOI: 10.3390/genes13112088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 08/20/2023] Open
Abstract
With the advancements in prenatal diagnostics, genome sequencing is now incorporated into clinical use to maximize the diagnostic yield following uninformative conventional tests (karyotype and chromosomal microarray analysis). Hong Kong started publicly funded prenatal genomic sequencing as a sequential test in the investigation of fetal structural anomalies in April 2021. The objective of the study was to evaluate the clinical performance and usefulness of this new service over one year. We established a web-based multidisciplinary team to facilitate case selection among the expert members. We retrospectively analyzed the fetal phenotypes, test results, turnaround time and clinical impact in the first 15 whole exome sequencing and 14 whole genome sequencing. Overall, the molecular diagnostic rate was 37.9% (11/29). De novo autosomal dominant disorders accounted for 72.7% (8/11), inherited autosomal recessive disorders for 18.2% (2/11), and inherited X-linked disorders for 9.1% (1/11). The median turnaround time for ongoing pregnancy was 19.5 days (range, 13-31 days). Our study showed an overall clinical impact of 55.2% (16/29), which influenced reproductive decision-making in four cases, guided perinatal management in two cases and helped future family planning in ten cases. In conclusion, our findings support the important role of genome sequencing services in the prenatal diagnosis of fetal structural anomalies in a population setting. It is important to adopt a multidisciplinary team approach to support the comprehensive genetic service.
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Affiliation(s)
- Po Lam So
- Department of Obstetrics and Gynecology, Tuen Mun Hospital, Hong Kong SAR, China
| | - Annie Shuk Yi Hui
- Department of Obstetrics & Gynaecology, Prince of Wales Hospital, Hong Kong SAR, China
| | - Teresa Wei Ling Ma
- Department of Obstetrics & Gynaecology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Wendy Shu
- Department of Obstetrics & Gynaecology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR, China
| | - Amelia Pui Wah Hui
- Department of Obstetrics & Gynaecology, Queen Mary Hospital, Hong Kong SAR, China
| | - Choi Wah Kong
- Department of Obstetrics & Gynaecology, United Christian Hospital, Hong Kong SAR, China
| | - Tsz Kin Lo
- Department of Obstetrics & Gynaecology, Princess Margaret Hospital, Hong Kong SAR, China
| | - Amanda Nim Chi Kan
- Department of Pathology, Hong Kong Children’s Hospital, Hong Kong SAR, China
| | - Elaine Yee Ling Kan
- Department of Radiology, Hong Kong Children’s Hospital, Hong Kong SAR, China
| | - Shuk Ching Chong
- Department of Paediatrics, Prince of Wales Hospital, Hong Kong SAR, China
| | - Brian Hon Yin Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ho Ming Luk
- Clinical Genetics Service Unit, Hong Kong Children’s Hospital, Hong Kong SAR, China
| | - Kwong Wai Choy
- Prenatal Genetic Diagnosis Centre, Department of Obstetrics & Gynaecology, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Anita Sik Yau Kan
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong SAR, China
| | - Wing Cheong Leung
- Department of Obstetrics & Gynaecology, Kwong Wah Hospital, Hong Kong SAR, China
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9
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Almubarak A, Zhang D, Kosak M, Rathwell S, Doonanco J, Eaton AJ, Kannu P, Lazier J, Lui M, Niederhoffer KY, MacPherson MJ, Sorsdahl M, Caluseriu O. Prenatal Genetic Testing in the Era of Next Generation Sequencing: A One-Center Canadian Experience. Genes (Basel) 2022; 13:2019. [PMID: 36360262 PMCID: PMC9690880 DOI: 10.3390/genes13112019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 01/26/2024] Open
Abstract
The introduction of next generation sequencing (NGS) technologies has revolutionized the practice of Medical Genetics, and despite initial reticence in its application to prenatal genetics (PG), it is becoming gradually routine, subject to availability. Guidance for the clinical implementation of NGS in PG, in particular whole exome sequencing (ES), has been provided by several professional societies with multiple clinical studies quoting a wide range of testing yields. ES was introduced in our tertiary care center in 2017; however, its use in relation to prenatally assessed cases has been limited to the postnatal period. In this study, we review our approach to prenatal testing including the use of microarray (CMA), and NGS technology (gene panels, ES) over a period of three years. The overall diagnostic yield was 30.4%, with 43.2% of those diagnoses being obtained through CMA, and the majority by using NGS technology (42% through gene panels and 16.6% by ES testing, respectively). Of these, 43.4% of the diagnoses were obtained during ongoing pregnancies. Seventy percent of the abnormal pregnancies tested went undiagnosed. We are providing a contemporary, one tertiary care center retrospective view of a real-life PG practice in the context of an evolving use of NGS within a Canadian public health care system that may apply to many similar jurisdictions around the world.
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Affiliation(s)
- Asra Almubarak
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Dan Zhang
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mackenzie Kosak
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Sarah Rathwell
- Women’s and Children’s Health Research Institute, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Jasmine Doonanco
- Maternal Fetal Medicine Clinic, Royal Alexandra Hospital, Edmonton, AB T5H 3V9, Canada
| | - Alison J. Eaton
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Maternal Fetal Medicine Clinic, Royal Alexandra Hospital, Edmonton, AB T5H 3V9, Canada
| | - Peter Kannu
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Women’s and Children’s Health Research Institute, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Maternal Fetal Medicine Clinic, Royal Alexandra Hospital, Edmonton, AB T5H 3V9, Canada
| | - Joanna Lazier
- Regional Genetics Program, Children’s Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Monique Lui
- Maternal Fetal Medicine Clinic, Royal Alexandra Hospital, Edmonton, AB T5H 3V9, Canada
| | - Karen Y. Niederhoffer
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Maternal Fetal Medicine Clinic, Royal Alexandra Hospital, Edmonton, AB T5H 3V9, Canada
| | - Melissa J. MacPherson
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Maternal Fetal Medicine Clinic, Royal Alexandra Hospital, Edmonton, AB T5H 3V9, Canada
| | - Melissa Sorsdahl
- Maternal Fetal Medicine Clinic, Royal Alexandra Hospital, Edmonton, AB T5H 3V9, Canada
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Women’s and Children’s Health Research Institute, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Maternal Fetal Medicine Clinic, Royal Alexandra Hospital, Edmonton, AB T5H 3V9, Canada
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10
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Advantages of current fetal neuroimaging and genomic technologies in prenatal diagnosis: A clinical case. Eur J Med Genet 2022; 66:104652. [PMID: 36374791 DOI: 10.1016/j.ejmg.2022.104652] [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: 01/22/2022] [Revised: 07/21/2022] [Accepted: 10/20/2022] [Indexed: 12/14/2022]
Abstract
The diagnosis of prenatal microcephaly, as well as the possibility of underlining a genetic cause, is becoming more frequent thanks to advances in prenatal imaging and parallel massive sequencing. One case of primary microcephaly in three sibs demonstrates how complementary diagnostic exams can help to diagnose and establish the etiology.
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11
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Fu F, Li R, Yu Q, Wang D, Deng Q, Li L, Lei T, Chen G, Nie Z, Yang X, Han J, Pan M, Zhen L, Zhang Y, Jing X, Li F, Li F, Zhang L, Yi C, Li Y, Lu Y, Zhou H, Cheng K, Li J, Xiang L, Zhang J, Tang S, Fang P, Li D, Liao C. Application of exome sequencing for prenatal diagnosis of fetal structural anomalies: clinical experience and lessons learned from a cohort of 1618 fetuses. Genome Med 2022; 14:123. [PMID: 36307859 PMCID: PMC9615232 DOI: 10.1186/s13073-022-01130-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background Exome sequencing (ES) is becoming more widely available in prenatal diagnosis. However, data on its clinical utility and integration into clinical management remain limited in practice. Herein, we report our experience implementing prenatal ES (pES) in a large cohort of fetuses with anomalies detected by ultrasonography using a hospital-based in-house multidisciplinary team (MDT) facilitated by a three-step genotype-driven followed by phenotype-driven analysis framework. Methods We performed pES in 1618 fetal cases with positive ultrasound findings but negative for karyotyping and chromosome microarray analysis between January 2014 and October 2021, including both retrospective (n=565) and prospective (n=1053) cohorts. The diagnostic efficiency and its correlation to organ systems involved, phenotypic spectrum, and the clinical impacts of pES results on pregnancy outcomes were analyzed. Results A genotype-driven followed by phenotype-driven three-step approach was carried out in all trio pES. Step 1, a genotype-driven analysis resulted in a diagnostic rate of 11.6% (187/1618). Step 2, a phenotype-driven comprehensive analysis yielded additional diagnostic findings for another 28 cases (1.7%; 28/1618). In the final step 3, data reanalyses based on new phenotypes and/or clinical requests found molecular diagnosis in 14 additional cases (0.9%; 14/1618). Altogether, 229 fetal cases (14.2%) received a molecular diagnosis, with a higher positive rate in the retrospective than the prospective cohort (17.3% vs. 12.4%, p<0.01). The diagnostic rates were highest in fetuses with skeletal anomalies (30.4%) and multiple organ involvements (25.9%), and lowest in fetuses with chest anomalies (0%). In addition, incidental and secondary findings with childhood-onset disorders were detected in 11 (0.7%) cases. Furthermore, we described the prenatal phenotypes for the first time for 27 gene-associated conditions (20.0%, 27/135) upon a systematic analysis of the diagnosed cases and expanded the phenotype spectrum for 26 (19.3%) genes where limited fetal phenotypic information was available. In the prospective cohort, the combined prenatal ultrasound and pES results had significantly impacted the clinical decisions (61.5%, 648/1053). Conclusions The genotype-driven approach could identify about 81.7% positive cases (11.6% of the total cohort) with the initial limited fetal phenotype information considered. The following two steps of phenotype-driven analysis and data reanalyses helped us find the causative variants in an additional 2.6% of the entire cohort (18.3% of all positive findings). Our extensive phenotype analysis on a large number of molecularly confirmed prenatal cases had greatly enriched our current knowledge on fetal phenotype-genotype correlation, which may guide more focused prenatal ultrasound in the future. This is by far the largest pES cohort study that combines a robust trio sequence data analysis, systematic phenotype-genotype correlation, and well-established MDT in a single prenatal clinical setting. This work underlines the value of pES as an essential component in prenatal diagnosis in guiding medical management and parental decision making. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01130-x.
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12
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Kernie CG, Wynn J, Rosenbaum A, de Voest J, Galloway S, Giordano J, Stover S, Westerfield L, Gilmore K, Wapner RJ, Van den Veyver IB, Vora NL, Clifton RG, Caughey AB, Chung WK. Information is power: The experiences, attitudes and needs of individuals who chose to have prenatal genomic sequencing for fetal anomalies. Prenat Diagn 2022; 42:947-954. [PMID: 35476893 DOI: 10.1002/pd.6153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE This study sought to evaluate the experiences of individuals who chose to participate in a study and receive prenatal genomic sequencing (pGS) for fetuses with congenital structural anomalies. METHOD Individuals who received research results of prenatal sequencing were invited to participate in semi-structured interviews about their experiences. A constructivist grounded theory approach was used to code and analyze interviews. RESULTS Thirty-three participants from 27 pregnancies were interviewed. Participants were motivated to enroll in the study to find out more about their fetus' condition and prepare for the future. The waiting period was a time of significant anxiety for participants. Most participants felt relief and closure upon receiving results, regardless of the category of result, and had a clear understanding of the implications of the results. CONCLUSION Participants' experiences with pGS were often intertwined with the experience of having a fetus with an abnormality. Participants were satisfied with the decision to participate in research and the support they received from the healthcare team, although waiting for results was associated with anxiety. The healthcare team plays an integral role in setting expectations and validating feelings of anxiety, fear and uncertainty.
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Affiliation(s)
- Catherine G Kernie
- Columbia University Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Allison Rosenbaum
- Columbia University Vagelos College of Physicians & Surgeons, New York, New York, USA
| | - Jessica de Voest
- George Washington University Biostatistics Center, Washington, District of Columbia, USA
| | - Stephanie Galloway
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Jessica Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Samantha Stover
- Department of Obstetrics & Gynecology and Molecular & Human Genetics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Texas, USA
| | - Lauren Westerfield
- Department of Obstetrics & Gynecology and Molecular & Human Genetics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Texas, USA
| | - Kelly Gilmore
- Department of Obstetrics & Gynecology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ignatia B Van den Veyver
- Department of Obstetrics & Gynecology and Molecular & Human Genetics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Texas, USA
| | - Neeta L Vora
- Department of Obstetrics & Gynecology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rebecca G Clifton
- George Washington University Biostatistics Center, Washington, District of Columbia, USA
| | - Aaron B Caughey
- Department of Obstetrics & Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA.,Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
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13
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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: 20] [Impact Index Per Article: 10.0] [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.
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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
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14
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Mellis R, Tapon D, Shannon N, Dempsey E, Pandya P, Chitty LS, Hill M. Implementing a rapid fetal exome sequencing service: What do parents and health professionals think? Prenat Diagn 2022; 42:783-795. [PMID: 35383981 PMCID: PMC9324936 DOI: 10.1002/pd.6140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Prenatal exome sequencing (pES) for the diagnosis of fetal abnormalities is being introduced more widely in clinical practice. Here we explore parents' and professionals' views and experiences of pES, to identify perceived benefits, concerns, and support needs. METHODS Semi-structured interviews were conducted with 11 parents and 20 health professionals (fetal medicine and clinical genetics) with experience of rapid pES prior to implementation in the English National Health Service. Interviews were transcribed verbatim and analysed thematically. RESULTS Parents and professionals were largely positive about pES, emphasising clinical and psychosocial benefits of a timely, definitive diagnosis in pregnancy. Concerns included parental anxiety related to the timing of pES results or uncertain findings, a need for guidelines for case selection and reporting, and ensuring sufficient capacity for counselling, phenotyping and variant interpretation. Professionals were concerned non-genetics professionals may not be equipped to counsel parents on the complexities of pES. CONCLUSION These findings highlight important issues for clinical implementation of pES. Expert counselling is required to enable parents to make informed decisions during a stressful time. To achieve this, professionals need further education and training, and fetal medicine and genetics services must work closely together to ensure parental understanding and appropriate support.
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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
| | - Dagmar Tapon
- Queen Charlotte's & Chelsea HospitalImperial College Healthcare NHS TrustLondonUK
| | - Nora Shannon
- Clinical Genetics ServiceNottingham City HospitalNottinghamUK
| | - Esther Dempsey
- South West Thames Regional Genetics ServiceLondonUK,School of Biological and Molecular SciencesSt George's University of LondonLondonUK
| | - Pranav Pandya
- Elizabeth Garrett Anderson Institute for Women's HealthUniversity College LondonLondonUK,Fetal Medicine UnitUniversity College London HospitalsLondonUK
| | - 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
| | - 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
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15
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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.
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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.)
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16
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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: 77] [Impact Index Per Article: 38.5] [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.
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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
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Mokveld T, Al-Ars Z, Sistermans EA, Reinders M. WisecondorFF: Improved Fetal Aneuploidy Detection from Shallow WGS through Fragment Length Analysis. Diagnostics (Basel) 2021; 12:59. [PMID: 35054227 PMCID: PMC8774687 DOI: 10.3390/diagnostics12010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
In prenatal diagnostics, NIPT screening utilizing read coverage-based profiles obtained from shallow WGS data is routinely used to detect fetal CNVs. From this same data, fragment size distributions of fetal and maternal DNA fragments can be derived, which are known to be different, and often used to infer fetal fractions. We argue that the fragment size has the potential to aid in the detection of CNVs. By integrating, in parallel, fragment size and read coverage in a within-sample normalization approach, it is possible to construct a reference set encompassing both data types. This reference then allows the detection of CNVs within queried samples, utilizing both data sources. We present a new methodology, WisecondorFF, which improves sensitivity, while maintaining specificity, relative to existing approaches. WisecondorFF increases robustness of detected CNVs, and can reliably detect even at lower fetal fractions (<2%).
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Affiliation(s)
- Tom Mokveld
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
| | - Zaid Al-Ars
- Computer Engineering, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands;
| | - Erik A. Sistermans
- Department of Human Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands;
| | - Marcel Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
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18
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Basel-Salmon L, Sukenik-Halevy R. Challenges in variant interpretation in prenatal exome sequencing. Eur J Med Genet 2021; 65:104410. [PMID: 34952236 DOI: 10.1016/j.ejmg.2021.104410] [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: 06/25/2021] [Revised: 12/05/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
The use of exome sequencing (ES) in the prenatal setting improves the diagnostic yield of genetic testing for fetuses with ultrasound anomalies. However, while the purpose of ES is to explain the fetal phenotype, secondary or incidental findings unrelated to the observed abnormalities might be detected. Recently, requests for ES in fetuses with no sonographic abnormalities have been increasing, raising serious ethical and medico-legal concerns. Variant interpretation is complex even in the postnatal setting and performing broad genomic data analyses in the prenatal setting presents additional dilemmas. This article discusses challenges and questions related to prenatal ES, including variant interpretation of incidental findings in cases of indicated prenatal ES, as well as in situations where ES is performed in asymptomatic fetuses.
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Affiliation(s)
- Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel; Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel.
| | - Rivka Sukenik-Halevy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Genetics Institute, Meir Medical Center, Kfar Saba, Israel
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Marangoni M, Smits G, Ceysens G, Costa E, Coulon R, Daelemans C, De Coninck C, Derisbourg S, Gajewska K, Garofalo G, Gounongbe C, Guizani M, Holoye A, Houba C, Makhoul J, Norgaard C, Regnard C, Romée S, Soto J, Stagel-Trabbia A, Van Rysselberge M, Vercoutere A, Zaytouni S, Bouri S, D'Haene N, D'Onle D, Dugauquier C, Racu ML, Rocq L, Segers V, Verocq C, Avni EF, Cassart M, Massez A, Blaumeiser B, Brischoux-Boucher E, Bulk S, De Ravel T, Debray G, Dimitrov B, Janssens S, Keymolen K, Laterre M, van Berkel K, Van Maldergem L, Vandernoot I, Vilain C, Donner C, Tecco L, Thomas D, Désir J, Abramowicz M, Migeotte I. Implementation of fetal clinical exome sequencing: Comparing prospective and retrospective cohorts. Genet Med 2021; 24:344-363. [PMID: 34906519 DOI: 10.1016/j.gim.2021.09.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/23/2021] [Accepted: 09/22/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE We compared the diagnostic yield of fetal clinical exome sequencing (fCES) in prospective and retrospective cohorts of pregnancies presenting with anomalies detected using ultrasound. We evaluated factors that led to a higher diagnostic efficiency, such as phenotypic category, clinical characterization, and variant analysis strategy. METHODS fCES was performed for 303 fetuses (183 ongoing and 120 ended pregnancies, in which chromosomal abnormalities had been excluded) using a trio/duo-based approach and a multistep variant analysis strategy. RESULTS fCES identified the underlying genetic cause in 13% (24/183) of prospective and 29% (35/120) of retrospective cases. In both cohorts, recessive heterozygous compound genotypes were not rare, and trio and simplex variant analysis strategies were complementary to achieve the highest possible diagnostic rate. Limited prenatal phenotypic information led to interpretation challenges. In 2 prospective cases, in-depth analysis allowed expansion of the spectrum of prenatal presentations for genetic syndromes associated with the SLC17A5 and CHAMP1 genes. CONCLUSION fCES is diagnostically efficient in fetuses presenting with cerebral, skeletal, urinary, or multiple anomalies. The comparison between the 2 cohorts highlights the importance of providing detailed phenotypic information for better interpretation and prenatal reporting of genetic variants.
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Affiliation(s)
- Martina Marangoni
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.
| | - Guillaume Smits
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Gilles Ceysens
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium; Department of Obstetrics and Gynecology, Hôpital Ambroise Paré, Mons, Belgium
| | - Elena Costa
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Robert Coulon
- Department of Obstetrics and Gynecology, Centre Hospitalier EpiCURA, Ath, Belgium
| | - Caroline Daelemans
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Caroline De Coninck
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Sara Derisbourg
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Kalina Gajewska
- Department of Obstetrics and Gynecology, Hôpital Civil Marie Curie, Charleroi, Belgium
| | - Giulia Garofalo
- Department of Fetal Medicine, CHU Saint-Pierre, Brussels, Belgium
| | | | - Meriem Guizani
- Department of Fetal Medicine, CHU Saint-Pierre, Brussels, Belgium
| | - Anne Holoye
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Catherine Houba
- Department of Fetal Medicine, CHU Saint-Pierre, Brussels, Belgium
| | - Jean Makhoul
- Department of Gynecology and Obstetrics, Hôpitaux Iris Sud-Etterbeek-Ixelles, Brussels, Belgium
| | - Christian Norgaard
- Department of Obstetrics and Gynecology, CHIREC - Braine-l'Alleud-Waterloo Hospital, Braine l'Alleud, Belgium
| | - Cecile Regnard
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Stephanie Romée
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Jamil Soto
- Department of Gynecology and Obstetrics, Hôpitaux Iris Sud-Etterbeek-Ixelles, Brussels, Belgium
| | - Aurore Stagel-Trabbia
- Department of Gynecology and Obstetrics, Hôpitaux Iris Sud-Etterbeek-Ixelles, Brussels, Belgium
| | | | - An Vercoutere
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Siham Zaytouni
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah Bouri
- Department of Pathology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicky D'Haene
- Department of Pathology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Dominique D'Onle
- Department of Anatomopathology, Institut Jules Bordet, Brussels, Belgium
| | - Christian Dugauquier
- Department of Pathology, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Marie-Lucie Racu
- Department of Pathology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Laureen Rocq
- Department of Pathology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Valérie Segers
- Department of Anatomopathology, CHU Brugmann, Brussels, Belgium
| | - Camille Verocq
- Department of Pathology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Marie Cassart
- Department of Fetal Medicine, CHU Saint-Pierre, Brussels, Belgium; Department of Perinatal Imaging Radiology, Etterbeek-Ixelles Hospital, Brussels, Belgium
| | - Anne Massez
- Department of Radiology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Bettina Blaumeiser
- Center for Medical Genetics, Universiteit en Universitair Ziekenhuis Antwerpen, Antwerp, Belgium
| | | | - Saskia Bulk
- Center of Human Genetics, CHU de Liège, Liège, Belgium
| | - Thomy De Ravel
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, Brussels, Belgium
| | | | - Boyan Dimitrov
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, Brussels, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, University Hospital Ghent, Ghent, Belgium
| | - Kathelijn Keymolen
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, Brussels, Belgium
| | - Marie Laterre
- Center of Human Genetics, CHU de Liège, Liège, Belgium
| | - Kim van Berkel
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, Brussels, Belgium
| | | | - Isabelle Vandernoot
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Catheline Vilain
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium; Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Brussels, Belgium
| | - Catherine Donner
- Department of Obstetrics and Gynecology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Laura Tecco
- Department of Fetal Medicine, CHU Saint-Pierre, Brussels, Belgium
| | - Dominique Thomas
- Department of Gynecology and Obstetrics, Hôpitaux Iris Sud-Etterbeek-Ixelles, Brussels, Belgium
| | - Julie Désir
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium; Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Marc Abramowicz
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium; Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Isabelle Migeotte
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium; Fonds de la Recherche Scientifique (FNRS), Brussels, Belgium.
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20
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de Koning MA, Hoffer MJV, Nibbeling EAR, Bijlsma EK, Toirkens MJP, Adama-Scheltema PN, Verweij EJ, Veenhof MB, Santen GWE, Peeters-Scholte CMPCD. Prenatal exome sequencing: A useful tool for the fetal neurologist. Clin Genet 2021; 101:65-77. [PMID: 34611884 PMCID: PMC9297851 DOI: 10.1111/cge.14070] [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: 05/18/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 01/08/2023]
Abstract
Prenatal exome sequencing (pES) is a promising tool for diagnosing genetic disorders when structural anomalies are detected on prenatal ultrasound. The aim of this study was to investigate the diagnostic yield and clinical impact of pES as an additional modality for fetal neurologists who counsel parents in case of congenital anomalies of the central nervous system (CNS). We assessed 20 pregnancies of 19 couples who were consecutively referred to the fetal neurologist for CNS anomalies. pES had a diagnostic yield of 53% (10/19) with most diagnosed pregnancies having agenesis or hypoplasia of the corpus callosum (7/10). Overall clinical impact was 63% (12/19), of which the pES result aided parental decision making in 55% of cases (6/11), guided perinatal management in 75% of cases (3/4), and was helpful in approving a late termination of pregnancy request in 75% of cases (3/4). Our data suggest that pES had a high diagnostic yield when CNS anomalies are present, although this study is limited by its small sample size. Moreover, pES had substantial clinical impact, which warrants implementation of pES in the routine care of the fetal neurologist in close collaboration with gynecologists and clinical geneticists.
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Affiliation(s)
- Maayke A de Koning
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Menno J P Toirkens
- Department of Radiology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - E Joanne Verweij
- Department of Obstetrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marieke B Veenhof
- Department of Obstetrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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21
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Lemmers RJLF, Vliet PJ, Granado DSL, Stoep N, Buermans H, Schendel R, Schimmel J, Visser M, Coster R, Jeanpierre M, Laforet P, Upadhyaya M, Engelen B, Sacconi S, Tawil R, Voermans NC, Rogers M, van der Maarel SM. High resolution breakpoint junction mapping of proximally extended D4Z4 deletions in FSHD1 reveals evidence for a founder effect. Hum Mol Genet 2021; 31:748-760. [PMID: 34559225 DOI: 10.1093/hmg/ddab250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 01/09/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an inherited myopathy clinically characterized by weakness in the facial, shoulder girdle and upper arm muscles. FSHD is caused by chromatin relaxation of the D4Z4 macrosatellite repeat, mostly by a repeat contraction, facilitating ectopic expression of DUX4 in skeletal muscle. Genetic diagnosis for FSHD is generally based on the sizing and haplotyping of the D4Z4 repeat on chromosome 4 by Southern blotting, molecular combing or single-molecule optical mapping, which is usually straight forward but can be complicated by atypical rearrangements of the D4Z4 repeat. One of these rearrangements is a D4Z4 proximally-extended deletion (DPED) allele, where not only the D4Z4 repeat is partially deleted, but also sequences immediately proximal to the repeat are lost, which can impede accurate diagnosis in all genetic methods. Previously, we identified several DPED alleles in FSHD and estimated the size of the proximal deletions by a complex pulsed-field gel electrophoresis and Southern blot strategy. Here, using next generation sequencing, we have defined the breakpoint junctions of these DPED alleles at the base pair resolution in 12 FSHD families and 4 control individuals facilitating a PCR-based diagnosis of these DPED alleles. Our results show that half of the DPED alleles are derivates of an ancient founder allele. For some DPED alleles we found that genetic elements are deleted such as DUX4c, FRG2, DBE-T and myogenic enhancers necessitating re-evaluation of their role in FSHD pathogenesis.
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Affiliation(s)
- Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Patrick J Vliet
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Nienke Stoep
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Henk Buermans
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robin Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marianne Visser
- Academic Medical Center, Department of Neurology, Amsterdam, The Netherlands
| | - Rudy Coster
- Department of Pediatrics, Division of Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | | | - Pascal Laforet
- Nord-Est/Ile-de-France Neuromuscular Reference Center, FHU PHENIX, Neurology Department, Raymond-Poincaré Hospital, Versailles Saint-Quentin-en-Yvelines - Paris Saclay University, Garches, France
| | - Meena Upadhyaya
- Department of Medical Genetics, Cardiff University, Cardif, UK
| | - Baziel Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, The Netherlands
| | - Sabrina Sacconi
- Centre de référence des Maladies neuromusculaires, Nice University Hospital, Nice, France
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, The Netherlands
| | - Mark Rogers
- Department of Medical Genetics, Cardiff University, Cardif, UK
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22
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Qiao F, Wang Y, Zhang C, Zhou R, Wu Y, Wang C, Meng L, Mao P, Cheng Q, Luo C, Hu P, Xu Z. Comprehensive evaluation of genetic variants using chromosomal microarray analysis and exome sequencing in fetuses with congenital heart defect. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:377-387. [PMID: 33142350 DOI: 10.1002/uog.23532] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To evaluate comprehensively, using chromosomal microarray analysis (CMA) and exome sequencing (ES), the prevalence of chromosomal abnormalities and sequence variants in unselected fetuses with congenital heart defect (CHD) and to evaluate the potential diagnostic yields of CMA and ES for different CHD subgroups. METHODS This was a study of 360 unselected singleton fetuses with CHD detected by echocardiography, referred to our department for genetic testing between February 2018 and December 2019. We performed CMA, as a routine test for aneuploidy and copy number variations (CNV), and then, in cases without aneuploidy or pathogenic CNV on CMA, we performed ES. RESULTS Overall, positive genetic diagnoses were made in 84 (23.3%) fetuses: chromosomal abnormalities were detected by CMA in 60 (16.7%) and sequence variants were detected by ES in a further 24 (6.7%) cases. The detection rate of pathogenic and likely pathogenic genetic variants in fetuses with non-isolated CHD (32/83, 38.6%) was significantly higher than that in fetuses with isolated CHD (52/277, 18.8%) (P < 0.001), this difference being due mainly to the difference in frequency of aneuploidy between the two groups. The prevalence of a genetic defect was highest in fetuses with an atrioventricular septal defect (36.8%), ventricular septal defect with or without atrial septal defect (28.4%), conotruncal defect (22.2%) or right ventricular outflow tract obstruction (20.0%). We also identified two novel missense mutations (c.2447G>C, p.Arg816Pro; c.1171C>T, p.Arg391Cys) and a new phenotype caused by variants in PLD1. CONCLUSIONS Chromosomal abnormalities were identified in 16.7% and sequence variants in a further 6.7% of fetuses with CHD. ES should be offered to all pregnant women with a CHD fetus without chromosomal abnormality or pathogenic CNV identified by CMA, regardless of whether the CHD is isolated. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- F Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Y Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - R Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Y Wu
- Department of Ultrasound, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - L Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - P Mao
- Personnel Division, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Q Cheng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - P Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Z Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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23
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So PL, Luk HM, Cheung KW, Hui W, Chung MY, Mak ASL, Lok WY, Yu KPT, Cheng SSW, Hau EWL, Ho S, Lam STS, Lo IFM. Prenatal phenotype of Kabuki syndrome: A case series and literature review. Prenat Diagn 2021; 41:1089-1100. [PMID: 34185329 DOI: 10.1002/pd.5998] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Kabuki syndrome (KS) is a genetic disorder characterized by intellectual disability, facial dysmorphism and congenital anomalies. We aim to investigate the prenatal features of fetuses with KS and to provide a comprehensive review of the literature on prenatal sonographic abnormalities associated with KS. METHODS We retrospectively reviewed the prenatal ultrasound findings of all mothers of children with molecularly confirmed KS in Hong Kong, between 1991 and 2019. We also performed systematic review of the literature to identify studies on the prenatal findings in KS. RESULTS We identified 11 cases with KS with detectable fetal ultrasound findings ranging from no detectable abnormalities to a variety of non-specific findings including increased nuchal translucency, pleural effusion, cardiac anomalies, renal anomalies, intrauterine growth restriction, polyhydramnios, oligohydramnios and single umbilical artery. In combining our cases with the 77 cases published, 42 (50.6%) of them had more than one abnormal antenatal ultrasound finding. The most frequent ultrasound features observed were cardiac anomalies (49.4%), followed by polyhydramnios (28.9%), genitourinary anomalies (26.5%), single umbilical artery (15.7%), intrauterine growth restriction (14.5%) and hydrops fetalis/pleural effusion/ascites (12.0%). CONCLUSIONS These cases demonstrate the prenatal phenotypic heterogeneity associated with KS. Although the ultrasound abnormalities are non-specific, KS should be considered in the differential diagnosis when these fetal findings following normal microarray analysis/karyotyping.
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Affiliation(s)
- Po Lam So
- Department of Obstetrics and Gynecology, Tuen Mun Hospital, Hong Kong SAR
| | - Ho Ming Luk
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| | - Ka Wang Cheung
- Department of Obstetrics and Gynecology, Queen Mary Hospital, Hong Kong SAR
| | - Winnie Hui
- Department of Obstetrics & Gynecology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR
| | - Man Yan Chung
- Department of Obstetrics and Gynecology, Prince of Wales Hospital, Hong Kong SAR
| | - Annisa S L Mak
- Department of Obstetrics and Gynecology, Queen Elizabeth Hospital, Hong Kong SAR
| | - Wing Yi Lok
- Department of Obstetrics and Gynecology, United Christian Hospital, Hong Kong SAR
| | - Kris Pui Tak Yu
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| | | | - Edgar W L Hau
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| | - Stephanie Ho
- Clinical Genetic Service, Department of Health, Hong Kong SAR
| | - Stephen T S Lam
- Clinical Genetics Service, Hong Kong Sanatorium & Hospital, Hong Kong SAR
| | - Ivan F M Lo
- Clinical Genetic Service, Department of Health, Hong Kong SAR
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24
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Ashfield T, McCready E, Shago M, Wang H, Sinclair-Bourque E, Cappa E, Piche Marolt A, Chun K. Practice patterns of prenatal and perinatal testing in Canadian cytogenetics laboratories. Prenat Diagn 2021; 41:843-854. [PMID: 33882154 DOI: 10.1002/pd.5951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 02/04/2021] [Accepted: 03/22/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To survey patterns of practice in Canadian cytogenetics laboratories and evaluate whether newer technologies have influenced testing algorithms for the detection of common aneuploidies and other genomic imbalances in the prenatal and perinatal settings. METHODS Cytogenetics laboratories across Canada were invited to participate in two patterns-of-practice surveys: one in 2016 and one in 2019. They were asked to identify the prenatal and perinatal specimen types tested at their facility and which testing methods were used for initial testing and for follow-up. RESULTS All clinical laboratories performing prenatal testing offer rapid aneuploidy detection (RAD). Most laboratories also offer microarray analysis. A positive result is either followed up by karyotyping or no further testing is performed. For prenatal samples, a negative result may be followed up by microarray or karyotyping and is dependent on the reason for referral. For perinatal samples, availability of microarray to follow up a negative result is increasing. CONCLUSIONS Since 2016, the availability of RAD as a first-line test in Canadian cytogenetics laboratories remains consistent, while microarray has become the preferred follow-up testing method over traditional karyotyping following a normal RAD result. Despite a universal healthcare system, disparities in prenatal and perinatal cytogenetic testing algorithms are apparent.
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Affiliation(s)
- Tamara Ashfield
- Institute for Quality Management in Healthcare, Toronto, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Canada
| | - Mary Shago
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Hong Wang
- Genetics Program, North York General Hospital, Toronto, Canada
| | | | - Eva Cappa
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital - Joseph & Wolf Lebovic Health Complex, Toronto, Canada
| | | | - Kathy Chun
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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25
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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.
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26
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Kilby MD. The role of next-generation sequencing in the investigation of ultrasound-identified fetal structural anomalies. BJOG 2021; 128:420-429. [PMID: 32975887 PMCID: PMC8607475 DOI: 10.1111/1471-0528.16533] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2020] [Indexed: 12/14/2022]
Abstract
Fetal structural anomalies have an impact on fetal mortality and morbidity. Next-generation sequencing (NGS) may be incorporated into clinical pathways for investigation of paediatric morbidity but can also be used to delineate the prognosis of fetal anomalies. This paper reviews the role of NGS in the investigation of fetal malformations, the literature defining the clinical utility, the technique most commonly used and potential promise and challenges for implementation into clinical practice. Prospective case selection with informative pre-test counselling by multidisciplinary teams is imperative. Regulated laboratory sequencing, bioinformatic pathways with potential variant identification and conservative matching with the phenotype is important. TWEETABLE ABSTRACT: Prenatal exome sequencing in fetal structural anomalies yields diagnostic information in up to 20% of cases.
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Affiliation(s)
- M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's Foundation Trust, Birmingham, UK.,Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
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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.
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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:
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Dempsey E, Haworth A, Ive L, Dubis R, Savage H, Serra E, Kenny J, Elmslie F, Greco E, Thilaganathan B, Mansour S, Homfray T, Drury S. A report on the impact of rapid prenatal exome sequencing on the clinical management of 52 ongoing pregnancies: a retrospective review. BJOG 2021; 128:1012-1019. [PMID: 32981126 DOI: 10.1111/1471-0528.16546] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Studies have shown that prenatal exome sequencing (PES) improves diagnostic yield in cases of fetal structural malformation. We have retrospectively analysed PES cases from two of the largest fetal medicine centres in the UK to determine the impact of results on management of a pregnancy. DESIGN A retrospective review of clinical case notes. SETTING Two tertiary fetal medicine centres. POPULATION Pregnancies with fetal structural abnormalities referred to clinical genetics via a multidisciplinary team. METHODS We retrospectively reviewed the notes of all patients who had undergone PES. DNA samples were obtained via chorionic villus sampling or amniocentesis. Variants were filtered using patient-specific panels and interpreted using American College of Medical Genetics guidelines. RESULTS A molecular diagnosis was made in 42% (18/43) ongoing pregnancies; of this group, there was a significant management implication in 44% (8/18). A positive result contributed to the decision to terminate a pregnancy in 16% (7/43) of cases. A negative result had a significant impact on management in two cases by affirming the decision to continue pregnancy. CONCLUSIONS We demonstrate that the results of PES can inform pregnancy management. Challenges include variant interpretation with limited phenotype information. These results emphasise the importance of the MDT and collecting phenotype and variant data. As this testing is soon to be widely available, we should look to move beyond diagnostic yield as a measure of the value of PES. TWEETABLE ABSTRACT Prenatal exome sequencing can aid decision-making in pregnancy management; review ahead of routine implementation in NHS.
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Affiliation(s)
- E Dempsey
- South West Thames Regional Genetics Service, London, UK.,School of Biological and Molecular Sciences, St George's University of London, London, UK
| | - A Haworth
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - L Ive
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - R Dubis
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - H Savage
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - E Serra
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - J Kenny
- South West Thames Regional Genetics Service, London, UK
| | - F Elmslie
- South West Thames Regional Genetics Service, London, UK
| | - E Greco
- Harris Birthright Centre, King's College London, London, UK.,Barts Health NHS Trust, London, UK
| | - B Thilaganathan
- Fetal Medicine Centre, St George's Hospital, London, UK.,Vascular Biology Unit, St George's University of London, London, UK
| | - S Mansour
- South West Thames Regional Genetics Service, London, UK.,School of Biological and Molecular Sciences, St George's University of London, London, UK
| | - T Homfray
- South West Thames Regional Genetics Service, London, UK
| | - S Drury
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
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Guillemyn B, Nampoothiri S, Syx D, Malfait F, Symoens S. Loss of TANGO1 Leads to Absence of Bone Mineralization. JBMR Plus 2021; 5:e10451. [PMID: 33778321 PMCID: PMC7990155 DOI: 10.1002/jbm4.10451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 12/03/2022] Open
Abstract
TANGO1 (transport and Golgi organization‐1 homolog) encodes a transmembrane protein, which is located at endoplasmic reticulum (ER) exit sites where it binds bulky cargo, such as collagens, in the lumen and recruits membranes from the ER‐Golgi intermediate compartment (ERGIC) to create an export route for cargo secretion. Mice lacking Mia3 (murine TANGO1 orthologue) show defective secretion of numerous procollagens and lead to neonatal lethality due to insufficient bone mineralization. Recently, aberrant expression of truncated TANGO1 in humans has been shown to cause a mild‐to‐moderate severe collagenopathy associated with dentinogenesis imperfecta, short stature, skeletal abnormalities, diabetes mellitus, and mild intellectual disability. We now show for the first time that complete loss of TANGO1 results in human embryonic lethality with near‐total bone loss and phenocopies the situation of Mia3−/− mice. Whole‐exome sequencing on genomic DNA (gDNA) of an aborted fetus of Indian descent revealed a homozygous 4‐base pair (4‐bp) deletion in TANGO1 that is heterozygously present in both healthy parents. Parental fibroblast studies showed decreased TANGO1 mRNA expression and protein levels. Type I collagen secretion and extracellular matrix organization were normal, supporting a threshold model for clinical phenotype development. As such, our report broadens the phenotypic and mutational spectrum of TANGO1‐related collagenopathies, and underscores the crucial role of TANGO1 for normal bone development, of which deficiency results in a severe‐to‐lethal form of osteochondrodysplasia. © 2021 American Society for Bone and Mineral Research © 2020 The Authors. JBMR Plus published by Wiley Periodicals LLC. on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Brecht Guillemyn
- Department of Biomolecular Medicine Center for Medical Genetics Ghent, Ghent University Hospital Ghent Belgium
| | - Sheela Nampoothiri
- Department of Pediatric Genetics Amrita Institute of Medical Sciences & Research Centre Cochin India
| | - Delfien Syx
- Department of Biomolecular Medicine Center for Medical Genetics Ghent, Ghent University Hospital Ghent Belgium
| | - Fransiska Malfait
- Department of Biomolecular Medicine Center for Medical Genetics Ghent, Ghent University Hospital Ghent Belgium
| | - Sofie Symoens
- Department of Biomolecular Medicine Center for Medical Genetics Ghent, Ghent University Hospital Ghent Belgium
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Beyond diagnostic yield: prenatal exome sequencing results in maternal, neonatal, and familial clinical management changes. Genet Med 2021; 23:909-917. [PMID: 33442022 PMCID: PMC7804210 DOI: 10.1038/s41436-020-01067-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/30/2022] Open
Abstract
Purpose Previous studies have reported that prenatal exome sequencing (pES) can detect monogenic diseases in fetuses with congenital anomalies with diagnostic yields ranging from 6% to 81%, but there are few reports of its clinical utility. Methods We conducted a retrospective chart review of patients who had pES to determine whether results led to clinical management changes. Results Of 20 patients, 8 (40%) received a definitive diagnosis. Seven patients (35%) had medical management changes based on the pES results, including alterations to their delivery plan and neonatal management (such as use of targeted medications, subspecialty referrals, additional imaging and/or procedures). All patients who received a definitive diagnosis and one who received a likely pathogenic variant (n = 9; 45%) received specific counseling about recurrence risk and the medical/developmental prognosis for the baby. In five (25%) cases, the result facilitated a diagnosis in parents and/or siblings. Conclusion pES results can have significant impacts on clinical management, some of which would not be possible if testing is deferred until after birth. To maximize the clinical utility, pES should be prioritized in cases where multiple care options are available and the imaging findings alone are not sufficient to guide parental decision-making, or where postnatal testing will not be feasible.
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31
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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.
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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
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32
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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.
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Abstract
Many genetic disorders are detectable in the prenatal period, and the capacity to identify them has increased remarkably as molecular genetic testing techniques continue to improve and become incorporated into clinical practice. The indications for prenatal genetic testing vary widely, including follow-up of an anomaly found by routine ultrasound or maternal aneuploidy screening, a family history of genetic disease, advanced maternal or paternal age, or evaluation of a low-risk pregnancy due to parental concern. The interpretation of genetic variants identified in the prenatal period poses unique challenges due to the lack of ability for deep phenotyping as well as the option to make critical decisions regarding pregnancy continuation and perinatal management. In this review, we address the various modalities currently available and commonly used for genetic testing, including preimplantation genetic testing of embryos, cell-free DNA testing, and diagnostic procedures such as chorionic villous sampling, amniocentesis, or percutaneous umbilical blood sampling, from which samples may be sent for a wide variety of genetic tests. We discuss the difference between these modalities for the genetic diagnosis of a fetus, their strengths and weaknesses, and strategies for their optimal use in order to direct perinatal care.
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Heide S, Spentchian M, Valence S, Buratti J, Mach C, Lejeune E, Olin V, Massimello M, Lehalle D, Mouthon L, Whalen S, Faudet A, Mignot C, Garel C, Blondiaux E, Lefebvre M, Quenum-Miraillet G, Chantot-Bastaraud S, Milh M, Bretelle F, Portes VD, Guibaud L, Putoux A, Tsatsaris V, Spodenkiewic M, Layet V, Dard R, Mandelbrot L, Guet A, Moutton S, Gorce M, Nizon M, Vincent M, Beneteau C, Rocchisanni MA, Benachi A, Saada J, Attié-Bitach T, Guilbaud L, Maurice P, Friszer S, Jouannic JM, de Villemeur TB, Moutard ML, Keren B, Héron D. Prenatal exome sequencing in 65 fetuses with abnormality of the corpus callosum: contribution to further diagnostic delineation. Genet Med 2020; 22:1887-1891. [PMID: 32565546 DOI: 10.1038/s41436-020-0872-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/26/2020] [Accepted: 06/07/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Abnormality of the corpus callosum (AbnCC) is etiologically a heterogeneous condition and the prognosis in prenatally diagnosed cases is difficult to predict. The purpose of our research was to establish the diagnostic yield using chromosomal microarray (CMA) and exome sequencing (ES) in cases with prenatally diagnosed isolated (iAbnCC) and nonisolated AbnCC (niAbnCC). METHODS CMA and prenatal trio ES (pES) were done on 65 fetuses with iAbnCC and niAbnCC. Only pathogenic gene variants known to be associated with AbnCC and/or intellectual disability were considered. RESULTS pES results were available within a median of 21.5 days (9-53 days). A pathogenic single-nucleotide variant (SNV) was identified in 12 cases (18%) and a pathogenic CNV was identified in 3 cases (4.5%). Thus, the genetic etiology was determined in 23% of cases. In all diagnosed cases, the results provided sufficient information regarding the neurodevelopmental prognosis and helped the parents to make an informed decision regarding the outcome of the pregnancy. CONCLUSION Our results show the significant diagnostic and prognostic contribution of CMA and pES in cases with prenatally diagnosed AbnCC. Further prospective cohort studies with long-term follow-up of the born children will be needed to provide accurate prenatal counseling after a negative pES result.
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Affiliation(s)
- Solveig Heide
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France.
| | - Myrtille Spentchian
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Stéphanie Valence
- Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP Sorbonne Université, Paris, France
| | - Julien Buratti
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Corinne Mach
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Elodie Lejeune
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Valérie Olin
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Marta Massimello
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Daphné Lehalle
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Linda Mouthon
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Sandra Whalen
- Service de Génétique Clinique, Hôpital Armand Trousseau, APHP Sorbonne Université, Paris, France
| | - Anne Faudet
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Cyril Mignot
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Catherine Garel
- Service de Radiologie Pédiatrique, Hôpital Armand Trousseau, HUEP, APHP Sorbonne Université, Paris, France
| | - Eleonore Blondiaux
- Service de Radiologie Pédiatrique, Hôpital Armand Trousseau, HUEP, APHP Sorbonne Université, Paris, France
| | - Mathilde Lefebvre
- Service de Foetopathologie, Hôpital Armand Trousseau, HUEP, APHP Sorbonne Université, Paris, France
| | | | - Sandra Chantot-Bastaraud
- Service de Cytogénétique, Hôpital Armand Trousseau, HUEP, APHP Sorbonne Université, Paris, France
| | - Mathieu Milh
- Service de Neurologie Pédiatrique, Hôpital La Timone, APHM, Marseille, France
| | - Florence Bretelle
- Service de Gynécologie Obstétrique, Hôpital Nord, APHM, Aix-Marseille Université, Marseille, France
| | - Vincent des Portes
- Service de Neurologie Pédiatrique, Hospices Civils de Lyon, Bron, France
| | - Laurent Guibaud
- Service de Radiologie Pédiatrique, Hospices Civils de Lyon, Bron, France
| | - Audrey Putoux
- Service de Génétique Clinique, Hospices Civils de Lyon, Bron, France
| | | | | | - Valérie Layet
- Service de Génétique Clinique, Hôpital du Havre, Le Havre, France
| | - Rodolphe Dard
- Service de Génétique Clinique, Hôpital de Poissy, Poissy, France
| | - Laurent Mandelbrot
- Service de Gynécologie Obstétrique, APHP, Université de Paris, Hôpital Louis Mourier, Colombes, France
| | - Agnès Guet
- Service de Pédiatrie, APHP, Hôpital Louis Mourier, Colombes, France
| | | | - Magali Gorce
- Service de Génétique Clinique, CHU d'Angers, Angers, France
| | - Mathilde Nizon
- Service de Génétique Clinique, CHU de Nantes, Nantes, France
| | - Marie Vincent
- Service de Génétique Clinique, CHU de Nantes, Nantes, France
| | - Claire Beneteau
- Service de Génétique Clinique, CHU de Nantes, Nantes, France
| | | | - Alexandra Benachi
- Service de Gynécologie-Obstétrique, Hôpital Antoine Béclère, APHP, Université Paris Saclay, Clamart, France
| | - Julien Saada
- Service de Gynécologie-Obstétrique, Hôpital Antoine Béclère, APHP, Université Paris Saclay, Clamart, France
| | - Tania Attié-Bitach
- Embryofoetopathologie, Service Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Lucie Guilbaud
- Fetal Medicine Département, Hôpital Armand Trousseau, APHP, Sorbonne Université, Paris, France
| | - Paul Maurice
- Fetal Medicine Département, Hôpital Armand Trousseau, APHP, Sorbonne Université, Paris, France
| | - Stéphanie Friszer
- Fetal Medicine Département, Hôpital Armand Trousseau, APHP, Sorbonne Université, Paris, France
| | - Jean-Marie Jouannic
- Fetal Medicine Département, Hôpital Armand Trousseau, APHP, Sorbonne Université, Paris, France
| | | | - Marie-Laure Moutard
- Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP Sorbonne Université, Paris, France
| | - Boris Keren
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Delphine Héron
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
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Deden C, Neveling K, Zafeiropopoulou D, Gilissen C, Pfundt R, Rinne T, de Leeuw N, Faas B, Gardeitchik T, Sallevelt SCEH, Paulussen A, Stevens SJC, Sikkel E, Elting MW, van Maarle MC, Diderich KEM, Corsten-Janssen N, Lichtenbelt KD, Lachmeijer G, Vissers LELM, Yntema HG, Nelen M, Feenstra I, van Zelst-Stams WAG. Rapid whole exome sequencing in pregnancies to identify the underlying genetic cause in fetuses with congenital anomalies detected by ultrasound imaging. Prenat Diagn 2020; 40:972-983. [PMID: 32333414 PMCID: PMC7497059 DOI: 10.1002/pd.5717] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/01/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Abstract
Objective The purpose of this study was to explore the diagnostic yield and clinical utility of trio‐based rapid whole exome sequencing (rWES) in pregnancies of fetuses with a wide range of congenital anomalies detected by ultrasound imaging. Methods In this observational study, we analyzed the first 54 cases referred to our laboratory for prenatal rWES to support clinical decision making, after the sonographic detection of fetal congenital anomalies. The most common identified congenital anomalies were skeletal dysplasia (n = 20), multiple major fetal congenital anomalies (n = 17) and intracerebral structural anomalies (n = 7). Results A conclusive diagnosis was identified in 18 of the 54 cases (33%). Pathogenic variants were detected most often in fetuses with skeletal dysplasia (n = 11) followed by fetuses with multiple major fetal congenital anomalies (n = 4) and intracerebral structural anomalies (n = 3). A survey, completed by the physicians for 37 of 54 cases, indicated that the rWES results impacted clinical decision making in 68% of cases. Conclusions These results suggest that rWES improves prenatal diagnosis of fetuses with congenital anomalies, and has an important impact on prenatal and peripartum parental and clinical decision making.
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Affiliation(s)
- Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Dimitra Zafeiropopoulou
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Brigitte Faas
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Suzanne C E H Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Aimee Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Esther Sikkel
- Department of Obstetrics and Gynecology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Mariet W Elting
- Department of Clinical Genetics, AMsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Merel C van Maarle
- Department of Clinical Genetics, AMsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nicole Corsten-Janssen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Klaske D Lichtenbelt
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Guus Lachmeijer
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Wendy A G van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
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He P, Xu LL, Li DZ. From sub-microscopic variants to the resolution of a single base pair: Exome sequencing in prenatal diagnosis. Eur J Med Genet 2019; 63:103779. [PMID: 31586466 DOI: 10.1016/j.ejmg.2019.103779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Ping He
- Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Li-Li Xu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China.
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