1
|
DiAdamo A, Chai H, Chong ML, Wang G, Wen J, Jiang YH, Li P. Patterns of Cytogenomic Findings from a Case Series of Recurrent Pregnancy Loss Provide Insight into the Extent of Genetic Defects Causing Miscarriages. Glob Med Genet 2024; 11:123-131. [PMID: 38560483 PMCID: PMC10980555 DOI: 10.1055/s-0044-1785227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Background A retrospective study was performed to evaluate the patterns of cytogenomic findings detected from a case series of products of conception (POC) in recurrent pregnancy loss (RPL) over a 16-year period from 2007 to 2023. Results This case series of RPL was divided into a single analysis (SA) group of 266 women and a consecutive analysis (CA) group of 225 women with two to three miscarriages analyzed. Of the 269 POC from the SA group and the 469 POC from the CA group, a spectrum of cytogenomic abnormalities of simple aneuploidies, compound aneuploidies, polyploidies, and structural rearrangements/pathogenic copy number variants (pCNVs) were detected in 109 (41%) and 160 cases (34%), five (2%) and 11 cases (2%), 35 (13%) and 36 cases (8%), and 10 (4%) and 19 cases (4%), respectively. Patterns with recurrent normal karyotypes, alternating normal and abnormal karyotypes, and recurrent abnormal karyotypes were detected in 74 (33%), 71 (32%), and 80 (35%) of consecutive miscarriages, respectively. Repeat aneuploidies of monosomy X and trisomy 16, triploidy, and tetraploidy were detected in nine women. Conclusions A comparable spectrum of cytogenomic abnormalities was noted in the SA and CA groups of RPL. A skewed likelihood of 2/3 for recurrent normal and abnormal karyotypes and 1/3 for alternating normal and abnormal karyotypes in consecutive miscarriages was observed. Routine cytogenetic analysis should be performed for consecutive miscarriages. Further genomic sequencing to search for detrimental and embryonic lethal variants causing miscarriages and pathogenic variants inducing aneuploidies and polyploidies should be considered for RPL with recurrent normal and abnormal karyotypes.
Collapse
Affiliation(s)
- Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Mei Ling Chong
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Guilin Wang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
- Yale Center for Genome Analysis, New Haven, Connecticut, United States
| | - Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
- Yale Center for Genomic Health, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
- Yale Center for Genomic Health, Yale University School of Medicine, New Haven, Connecticut, United States
| |
Collapse
|
2
|
Essers R, Lebedev IN, Kurg A, Fonova EA, Stevens SJC, Koeck RM, von Rango U, Brandts L, Deligiannis SP, Nikitina TV, Sazhenova EA, Tolmacheva EN, Kashevarova AA, Fedotov DA, Demeneva VV, Zhigalina DI, Drozdov GV, Al-Nasiry S, Macville MVE, van den Wijngaard A, Dreesen J, Paulussen A, Hoischen A, Brunner HG, Salumets A, Zamani Esteki M. Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss. Nat Med 2023; 29:3233-3242. [PMID: 37996709 PMCID: PMC10719097 DOI: 10.1038/s41591-023-02645-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/11/2023] [Indexed: 11/25/2023]
Abstract
Pregnancy loss is often caused by chromosomal abnormalities of the conceptus. The prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental lineages during intrauterine development remain elusive. In this study, we analyzed 1,745 spontaneous pregnancy losses and found that roughly half (50.4%) of the products of conception (POCs) were karyotypically abnormal, with maternal and paternal age independently contributing to the increased genomic aberration rate. We applied genome haplarithmisis to a subset of 94 pregnancy losses with normal parental and POC karyotypes. Genotyping of parental DNA as well as POC extra-embryonic mesoderm and chorionic villi DNA, representing embryonic and trophoblastic tissues, enabled characterization of the genomic landscape of both lineages. Of these pregnancy losses, 35.1% had chromosomal aberrations not previously detected by karyotyping, increasing the rate of aberrations of pregnancy losses to 67.8% by extrapolation. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to chorionic villi, such as confined placental mosaicism, we found a higher degree of mosaic chromosomal imbalances in extra-embryonic mesoderm rather than chorionic villi. Our results stress the importance of scrutinizing the full allelic architecture of genomic abnormalities in pregnancy loss to improve clinical management and basic research of this devastating condition.
Collapse
Affiliation(s)
- Rick Essers
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Ants Kurg
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Elizaveta A Fonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Rebekka M Koeck
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Ulrike von Rango
- Department of Anatomy & Embryology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Lloyd Brandts
- Department of Clinical Epidemiology and Medical Technology Assessment (KEMTA), Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Spyridon Panagiotis Deligiannis
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Obstetrics and Gynecology, University of Helsinki, Helsinki, Finland
| | - Tatyana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Elena A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Dmitry A Fedotov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Viktoria V Demeneva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Daria I Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Gleb V Drozdov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Salwan Al-Nasiry
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Obstetrics and Gynaecology, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Merryn V E Macville
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Jos Dreesen
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Aimee Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andres Salumets
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.
- Competence Center on Health Technologies, Tartu, Estonia.
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands.
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands.
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
3
|
Peng G, Zhou Q, Chai H, Wen J, Zhao H, Taylor HS, Jiang Y, Li P. Estimation on risk of spontaneous abortions by genomic disorders from a meta-analysis of microarray results on large case series of pregnancy losses. Mol Genet Genomic Med 2023; 11:e2181. [PMID: 37013615 PMCID: PMC10422064 DOI: 10.1002/mgg3.2181] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/25/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
A meta-analysis on seven large case series (>1000 cases) of chromosome microarray analysis (CMA) on products of conceptions (POC) evaluated the diagnostic yields of genomic disorders and syndromic pathogenic copy number variants (pCNVs) from a collection of 35,130 POC cases. CMA detected chromosomal abnormalities and pCNVs in approximately 50% and 2.5% of cases, respectively. The genomic disorders and syndromic pCNVs accounted for 31% of the detected pCNVs, and their incidences in POC ranged from 1/750 to 1/12,000. The newborn incidences of these genomic disorders and syndromic pCNVs were estimated in a range of 1/4000 to 1/50,000 live births from population genetic studies and diagnostic yields of a large case series of 32,587 pediatric patients. The risk of spontaneous abortion (SAB) for DiGeorge syndrome (DGS), Wolf-Hirschhorn syndrome (WHS), and William-Beuren syndrome (WBS) was 42%, 33%, and 21%, respectively. The estimated overall risk of SAB for major genomic disorders and syndromic pCNVs was approximately 38%, which was significantly lower than the 94% overall risk of SAB for chromosomal abnormalities. Further classification on levels of risk of SAB to high (>75%), intermediate (51%-75%), and low (26%-50%) for known chromosomal abnormalities, genomic disorders, and syndromic pCNVs could provide evidence-based interpretation in prenatal diagnosis and genetic counseling.
Collapse
Affiliation(s)
- Gang Peng
- Department of GeneticsYale University School of MedicineNew HavenConnecticut06520USA
- Department of Medical & Molecular GeneticsIndiana University School of MedicineIndianapolisIndiana46202USA
- Department of BiostatisticsSchool of Public Health, Yale UniversityNew HavenConnecticutUSA
| | - Qinghua Zhou
- Biomedical Translational Research Institute, Jinan UniversityGuangzhouChina
| | - Hongyan Chai
- Department of GeneticsYale University School of MedicineNew HavenConnecticut06520USA
| | - Jiadi Wen
- Department of GeneticsYale University School of MedicineNew HavenConnecticut06520USA
| | - Hongyu Zhao
- Department of GeneticsYale University School of MedicineNew HavenConnecticut06520USA
- Department of BiostatisticsSchool of Public Health, Yale UniversityNew HavenConnecticutUSA
| | - Hugh S. Taylor
- Department of Obstetrics, Gynecology and Reproductive SciencesYale University School of MedicineNew HavenConnecticut06520USA
| | - Yong‐Hui Jiang
- Department of GeneticsYale University School of MedicineNew HavenConnecticut06520USA
| | - Peining Li
- Department of GeneticsYale University School of MedicineNew HavenConnecticut06520USA
| |
Collapse
|
4
|
Huang W, Zhu X, Sun G, Gao Z, Kong X. Whole-exome sequencing in deceased fetuses with ultrasound anomalies: a retrospective analysis. BMC Med Genomics 2023; 16:25. [PMID: 36797717 PMCID: PMC9936674 DOI: 10.1186/s12920-022-01427-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/23/2022] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) is an effective method in the prenatal setting for identification of the underlying genetic etiology of fetal ultrasound abnormalities. To investigate the diagnostic value of WES in fetuses with ultrasound abnormalities that resulted in fetal demise or pregnancy termination. METHODS 61 deceased fetuses with ultrasound abnormalities and normal copy number variation Sequencing were retrospectively collected. Proband-only or trio-WES were performed on the products of conception. RESULT Collectively, 28 cases were positive with 39 variants (10 pathogenic, 22 likely pathogenic and 7 variants of uncertain significance) of 18 genes, and the overall diagnostic rate was 45.9% (28/61), of which 39.2% (11/28) were de novo variants. In addition, 21 variants in 11 genes among the positive cases had not been previously reported. The diagnostic yield for definitive findings for trio analysis was 55.9% (19/34) compared to 33.3% (9/27) for singletons. The most common ultrasound abnormalities were skeletal system abnormalities 39.2% (11/28), followed by multiple system abnormalities (17.9%, 5/28) and genitourinary abnormalities (17.9%, 5/28). CONCLUSION Our results support the use of WES to identify genetic etiologies of ultrasound abnormalities and improve understanding of pathogenic variants. The identification of disease-related variants provided information for subsequent genetic counseling of recurrence risk and management of subsequent pregnancies.
Collapse
Affiliation(s)
- Wei Huang
- grid.412633.10000 0004 1799 0733Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiaofan Zhu
- grid.412633.10000 0004 1799 0733Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Gege Sun
- grid.412633.10000 0004 1799 0733Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Zhi Gao
- grid.412633.10000 0004 1799 0733Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiangdong Kong
- Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| |
Collapse
|
5
|
Kowalczyk K, Smyk M, Bartnik-Głaska M, Plaskota I, Wiśniowiecka-Kowalnik B, Bernaciak J, Chojnacka M, Paczkowska M, Niemiec M, Dutkiewicz D, Kozar A, Magdziak R, Krawczyk W, Pietras G, Michalak E, Klepacka T, Obersztyn E, Bal J, Nowakowska BA. Application of array comparative genomic hybridization (aCGH) for identification of chromosomal aberrations in the recurrent pregnancy loss. J Assist Reprod Genet 2022; 39:357-367. [PMID: 35079943 PMCID: PMC8956756 DOI: 10.1007/s10815-022-02400-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/13/2022] [Indexed: 12/03/2022] Open
Abstract
Spontaneous abortion occurs in 8–20% of recognized pregnancies and usually takes place in the first trimester (7–11 weeks). There are many causes of pregnancy loss, but the most important (about 75%) is the presence of chromosomal aberrations. We present the results of oligonucleotide array application in a cohort of 62 miscarriage cases. The inclusion criteria for the study were the loss after 8th week of pregnancy and the appearance of recurrent miscarriages. DNA was extracted from trophoblast or fetal skin fibroblasts. In the 62 tested materials from recurrent miscarriages, the detection rate was 56.5% (35/62). The most commonly found were aneuploidies (65%) (chromosomal trisomy 14, 16, 18, 21, and 22), Turner syndrome, and triploidy (17.1%). Other chromosomal abnormalities included pathogenic and likely pathogenic structural aberrations: 1) pathogenic: deletion 7p22.3p12.3 and duplication 9p24.3p13.2 inherited from the normal father, deletion 3q13.31q22.2 and deletion 3q22.3q23 of unknown inheritance and duplication of 17p12 inherited from father with foot malformation; 2) likely pathogenic variants: deletion 17p13.1 inherited from normal mother, deletion 5q14.3 of unknown inheritance and de novo deletion 1q21.1q21.2. Among these aberrations, six CNVs (copy number variants) were responsible for the miscarriage: deletion 7p22.3p12.3 and duplication 9p24.3p13.2, deletion 3q13.31q22.2 and deletion 3q22.3q23, and deletion 17p13.1 and deletion 1q21.1q21.2. Other two findings were classified as incidental findings (deletion 5q14.3 and 17p12 duplication). Our research shows that 17% of the aberrations (6/35 abnormal results) that cannot be identified by the routine kariotype analysis are structural aberrations containing genes important for fetal development, the mutations of which may cause spontaneous abortion.
Collapse
Affiliation(s)
- Katarzyna Kowalczyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.
| | - Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Izabela Plaskota
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Joanna Bernaciak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Marta Chojnacka
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Magdalena Niemiec
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Daria Dutkiewicz
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Agata Kozar
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Róża Magdziak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Wojciech Krawczyk
- Department of Obstetrics and Perinatology, Medical University of Lublin, Lublin, Poland
| | - Grzegorz Pietras
- Department of Obstetrics and Perinatology, Medical University of Lublin, Lublin, Poland
| | - Elżbieta Michalak
- Deparment of Pathomorphology, Institute of Mother and Child, Warsaw, Poland
| | - Teresa Klepacka
- Deparment of Pathomorphology, Institute of Mother and Child, Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Jerzy Bal
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | |
Collapse
|
6
|
Freitas M, Santos AD, Barbosa L, Figueiredo AD, Pellegrini S, Santos N, Paiva I, Rangel-Pozzo A, Sisdelli L, Mai S, Land M, Ribeiro M, Ribeiro M. Cellular consequences of small supernumerary marker chromosome derived from chromosome 12: mosaicism in daughter and father. Braz J Med Biol Res 2022; 55:e12072. [PMID: 35766708 PMCID: PMC9224815 DOI: 10.1590/1414-431x2022e12072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/14/2022] [Indexed: 11/21/2022] Open
Abstract
Constitutional genomic imbalances are known to cause malformations, disabilities, neurodevelopmental delay, and dysmorphia and can lead to dysfunctions in the cell cycle. In extremely rare genetic conditions such as small supernumerary marker chromosomes (sSMC), it is important to understand the cellular consequences of this extra marker, as well the factors that contribute to their maintenance or elimination through successive cell cycles and phenotypic impact. The study of chromosomal mosaicism provides a natural model to characterize the effect of aneuploidy on genome stability and compare cells with the same genetic background and environment exposure, but differing in the presence of sSMC. Here, we report the functional characterization of different cell lines from two familial patients with mosaic sSMC derived from chromosome 12. We performed studies of proliferation dynamics, stability, and variability of these cells using fluorescent in situ hybridization (FISH), sister chromatid exchanges (SCE), and conventional staining. We also quantified the telomere-related genomic instability of sSMC cells using 3D telomeric profile analysis by quantitative-FISH. sSMC cells exhibited differences in the cell cycle dynamics compared to normal cells. First, the sSMC cells exhibited lower proliferation index and higher frequency of SCE than normal cells, associated with a higher level of chromosomal instability. Second, sSMC cells exhibited more telomeric-related genomic instability. Lastly, the differences of sSMC cells distribution among tissues could explain different phenotypic repercussions observed in patients. These results will help in our understanding of the sSMC stability, maintenance during cell cycle, and the cell cycle variables involved in the different phenotypic manifestations.
Collapse
Affiliation(s)
- M.O. Freitas
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil; Universidade Federal do Rio de Janeiro, Brasil
| | - A.O. dos Santos
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil; Universidade Federal do Rio de Janeiro, Brasil
| | - L.S. Barbosa
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil
| | - A.F. de Figueiredo
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil; Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil
| | - S.P. Pellegrini
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil
| | - N.C.K. Santos
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil
| | - I.S. Paiva
- Universidade do Grande Rio, Brasil; UNIFESO (Centro Educacional Serra dos Orgãos), Brasil
| | - A. Rangel-Pozzo
- CancerCare Manitoba Research Institute, University of Manitoba, Cancer Care Manitoba, Canada
| | - L. Sisdelli
- CancerCare Manitoba Research Institute, University of Manitoba, Cancer Care Manitoba, Canada; Universidade Federal de São Paulo, Brasil
| | - S. Mai
- CancerCare Manitoba Research Institute, University of Manitoba, Cancer Care Manitoba, Canada
| | - M.G.P. Land
- Universidade Federal do Rio de Janeiro, Brasil; Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil
| | - M.G. Ribeiro
- Universidade Federal do Rio de Janeiro, Brasil; Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil
| | - M.C.M. Ribeiro
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Brasil; Campus Duque de Caxias, Universidade Federal do Rio de Janeiro, Brasil
| |
Collapse
|
7
|
Kline J, Vardarajan B, Abhyankar A, Kytömaa S, Levin B, Sobreira N, Tang A, Thomas-Wilson A, Zhang R, Jobanputra V. Embryonic lethal genetic variants and chromosomally normal pregnancy loss. Fertil Steril 2021; 116:1351-1358. [PMID: 34756330 DOI: 10.1016/j.fertnstert.2021.06.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/16/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To examine whether rare damaging genetic variants are associated with chromosomally normal pregnancy loss and estimate the magnitude of the association. DESIGN Case-control. SETTING Cases were derived from a consecutive series of karyotyped losses at one New Jersey hospital. Controls were derived from the National Database for Autism Research. PATIENT(S) Cases comprised 19 chromosomally normal loss conceptus-parent trios. Controls comprised 547 unaffected siblings of autism case-parent trios. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) The rate of damaging variants in the exome (loss of function and missense-damaging) and the proportions of probands with at least one such variant among cases vs. controls. RESULTS The proportions of probands with at least one rare damaging variant were 36.8% among cases and 22.9% among controls (odds ratio, 2.0; 99% confidence interval, 0.5-7.3). No case had a variant in a known fetal anomaly gene. The proportion with variants in possibly embryonic lethal genes increased in case probands (odds ratio, 14.5; 99% confidence interval, 1.5-89.7); variants occurred in BAZ1A, FBN2, and TIMP2. CONCLUSION(S) Rare genetic variants in the conceptus may be a cause of chromosomally normal pregnancy loss. A larger sample is needed to estimate the magnitude of the association with precision and identify relevant biologic pathways.
Collapse
Affiliation(s)
- Jennie Kline
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York; Gertrude H. Sergievsky Center, Columbia University, New York, New York.
| | - Badri Vardarajan
- Gertrude H. Sergievsky Center, Columbia University, New York, New York
| | | | - Sonja Kytömaa
- Boston University School of Medicine, Boston, Massachusetts
| | - Bruce Levin
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Andrew Tang
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | | | - Ruiwei Zhang
- Life Sciences Practice, Charles River Associates, New York, New York
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University, New York, New York; New York Genome Center, New York, New York
| |
Collapse
|
8
|
Wen J, Grommisch B, DiAdamo A, Chai H, Ng SME, Hui P, Bale A, Mak W, Wang G, Li P. Detection of cytogenomic abnormalities by OncoScan microarray assay for products of conception from formalin-fixed paraffin-embedded and fresh fetal tissues. Mol Cytogenet 2021; 14:21. [PMID: 33810806 PMCID: PMC8019165 DOI: 10.1186/s13039-021-00542-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 12/02/2022] Open
Abstract
Background The OncoScan microarray assay (OMA) using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP) loci enabled the detection of cytogenomic abnormalities of chromosomal imbalances and pathogenic copy number variants (pCNV). The small size of molecular inversion probes is optimal for SNP genotyping of fragmented DNA from fixed tissues. This retrospective study evaluated the clinical utility of OMA as a uniform platform to detect cytogenomic abnormalities for pregnancy loss from fresh and fixed tissues of products of conception (POC). Results Fresh specimens of POC were routinely subjected to cell culture and then analyzed by karyotyping. POC specimens with a normal karyotype (NK) or culture failure (CF) and from formalin-fixed paraffin-embedded (FFPE) tissues were subjected to DNA extraction for OMA. The abnormality detection rate (ADR) by OMA on 94 cases of POC-NK, 38 cases of POC-CF, and 35 cases of POC-FFPE tissues were 2% (2/94), 26% (10/38), and 57% (20/35), respectively. The detected cytogenomic abnormalities of aneuploidies, triploidies and pCNV accounted for 50%, 40% and 10% in POC-CF and 85%, 10% and 5% in POC-FFPE, respectively. False negative result from cultured maternal cells and maternal cell contamination were each detected in one case. OMA on two cases with unbalanced structural chromosome abnormalities further defined genomic imbalances and breakpoints. Conclusion OMA on POC-CF and POC-FFPE showed a high diagnostic yield of cytogenomic abnormalities. This approach circumvented the obstacles of CF from fresh specimens and fragmented DNA from fixed tissues and provided a reliable and effective platform for detecting cytogenomic abnormalities and monitoring true fetal result from maternal cell contamination.
Collapse
Affiliation(s)
- Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sok Meng Evelyn Ng
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, CT, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Winifred Mak
- Department of Women's Health, Dell Medical School, The University of Texas At Austin, Austin, TX, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, CT, USA.
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
9
|
Gou L, Liu T, Wang Y, Wu Q, Hu S, Dong B, Wang C, Zhang Y, Shan X, Wang X, Suo F, Gu M. Clinical utilization of chromosomal microarray analysis for the genetic analysis in subgroups of pregnancy loss. J Matern Fetal Neonatal Med 2020; 35:4404-4411. [PMID: 33228446 DOI: 10.1080/14767058.2020.1849126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
OBJECTIVE The underlying etiologies of pregnancy loss are heterogeneous and in many cases unexplained. This study was to explore the genetic causes of early and late pregnancy loss using chromosomal microarray analysis (CMA). METHODS A cohort of 222 specimens of conceptions underwent genetic analysis using Affymetrix CytoScan 750 K arrays, which includes both SNP markers and copy number markers. RESULTS Of the 222-products of conception (POC), the overall detection rate for clinical significantly chromosomal anomalies was 40.54%, including 53 autosomal aneuploidy (23.87%), 16 sex chromosome aneuploidy (7.21%), 5 mutiple aneuploidy (2.25%), 4 triploidy (1.80%), and 12 pathogenic copy number variants (pCNVs) (5.41%). In addition, variants of uncertain significance and loss of heterozygosity were detected in 9 samples and 2 samples, respectively. The detection rates for total chromosomal abnormalities, autosomal aneuploidy, sex chromosome aneuploidy, multiple aneuploidy, and triploidy in specimens of early pregnancy loss was higher than that of late pregnancy loss, while had lower detection rate of pCNVs. Moreover, the detection rate in POC of mothers younger than 35 years was lower than that of advanced maternal age. The detection rate was 40.57% in POC of mothers with adverse pregnancy histories, in which was comparable with that of mothers without adverse pregnancy histories. CONCLUSIONS CMA yielded a superior detection rate in early pregnancy loss than that of late pregnancy loss. Moreover, the incidence of chromosome abnormality in cases with advanced maternal age was higher than that of cases with younger maternal age, while adverse pregnancy history seemed not to be the factors affecting the detection rate for chromosomal abnormality in pregnancy loss.
Collapse
Affiliation(s)
- Lingshan Gou
- Center for Genetic Medicine, Maternity and Child Health Care Hospital, Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Tianya Liu
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yi Wang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital, Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qin Wu
- Zhejiang Biosan Biochemical Technologies Co.Ltd., Hangzhou, Zhejiang, China
| | - Shunan Hu
- Office of Scientific Research & Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Bulian Dong
- Center for Genetic Medicine, Maternity and Child Health Care Hospital, Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chuanxia Wang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital, Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yan Zhang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital, Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xinghu Shan
- Center for Genetic Medicine, Maternity and Child Health Care Hospital, Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaona Wang
- Office of Scientific Research & Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Feng Suo
- Center for Genetic Medicine, Maternity and Child Health Care Hospital, Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Maosheng Gu
- Center for Genetic Medicine, Maternity and Child Health Care Hospital, Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| |
Collapse
|
10
|
Smits MA, van Maarle M, Hamer G, Mastenbroek S, Goddijn M, van Wely M. Cytogenetic testing of pregnancy loss tissue: a meta-analysis. Reprod Biomed Online 2020; 40:867-879. [DOI: 10.1016/j.rbmo.2020.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/12/2023]
|
11
|
Chai H, DiAdamo A, Grommisch B, Xu F, Zhou Q, Wen J, Mahoney M, Bale A, McGrath J, Spencer-Manzon M, Li P, Zhang H. A Retrospective Analysis of 10-Year Data Assessed the Diagnostic Accuracy and Efficacy of Cytogenomic Abnormalities in Current Prenatal and Pediatric Settings. Front Genet 2019; 10:1162. [PMID: 31850057 PMCID: PMC6902283 DOI: 10.3389/fgene.2019.01162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023] Open
Abstract
Background: Array comparative genomic hybridization (aCGH), karyotyping and fluorescence in situ hybridization (FISH) analyses have been used in a clinical cytogenetic laboratory. A systematic analysis on diagnostic findings of cytogenomic abnormalities in current prenatal and pediatric settings provides approaches for future improvement. Methods: A retrospective analysis was performed on abnormal findings by aCGH, karyotyping, and FISH from 3,608 prenatal cases and 4,509 pediatric cases during 2008–2017. The diagnostic accuracy was evaluated by comparing the abnormality detection rate (ADR) and the relative frequency (RF) of different types of cytogenomic abnormalities between prenatal and pediatric cases. A linear regression correlation between known prevalence and ADR of genomic disorders was used to extrapolate the prevalence of other genomic disorders. The diagnostic efficacy was estimated as percentage of detected abnormal cases by expected abnormal cases from served population. Results: The composite ADR for numerical chromosome abnormalities, structural chromosome abnormalities, recurrent genomic disorders, and sporadic pathogenic copy number variants (pCNVs) in prenatal cases were 13.03%, 1.77%, 1.69%, and 0.9%, respectively, and were 5.13%, 2.84%, 7.08%, and 2.69% in pediatric cases, respectively. The chromosomal abnormalities detected in prenatal cases (14.80%) were significantly higher than that of pediatric cases (7.97%) (p < 0.05), while the pCNVs detected in prenatal cases (2.59%) were significantly lower than that of pediatric cases (9.77%) (p < 0.05). The prevalence of recurrent genomic disorders and total pCNVs was estimated to be 1/396 and 1/291, respectively. Approximately, 29% and 35% of cytogenomic abnormalities expected from the population served were detected in current prenatal and pediatric diagnostic practice, respectively. Conclusion: For chromosomal abnormalities, effective detection of Down syndrome (DS) and Turner syndrome (TS) and under detection of sex chromosome numerical abnormalities in both prenatal and pediatric cases were noted. For pCNVs, under detection of pCNVs in prenatal cases and effective detection of DiGeorge syndrome (DGS) and variable efficacy in detecting other pCNVs in pediatric cases were noted. Extend aCGH analysis to more prenatal cases with fetal ultrasonographic anomalies, enhanced non-invasive prenatal (NIPT) testing screening for syndromic genomic disorders, and better clinical indications for pCNVs are approaches that could improve diagnostic yield of cytogenomic abnormalities.
Collapse
Affiliation(s)
- Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Fang Xu
- Prevention Genetics, Marshfield, WI, United States
| | - Qinghua Zhou
- The First Affiliated Hospital, Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Maurice Mahoney
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - James McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Michele Spencer-Manzon
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| |
Collapse
|
12
|
Mao J, Wang H, Li H, Song X, Wang T, Xiang J, Li H. Genetic analysis of products of conception using a HLPA/SNP-array strategy. Mol Cytogenet 2019; 12:40. [PMID: 31687045 PMCID: PMC6822274 DOI: 10.1186/s13039-019-0452-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/23/2019] [Indexed: 11/29/2022] Open
Abstract
Background Fetal chromosomal abnormalities was the most frequent cause of miscarriage, and the traditional testing method G-banded karyotyping has limitations. Then high-throughput ligation-dependent probe amplification (HLPA) and single nucleotide polymorphism array (SNP-array) were introduced for genetic analysis on products of conception (POC). Methods HLPA and SNP-array analysis were combined. POC samples were initially tested using HLPA, followed by SNP-array analysis on samples that were found to be normal by HLPA. Results Of the 326 POC samples tested, the overall abnormality rate was 54.6% (178/326), including 44.8% (146/326) chromosomal abnormalities identified by HLPA and 9.8% (32/326) additional chromosomal abnormalities further detected by SNP-array. Conclusions The combination of HLPA and SNP-array analysis is an efficient and cost-effective strategy for genetic analysis of POC.
Collapse
Affiliation(s)
- Jun Mao
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| | - Huiling Wang
- 3Department of Gynaecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China
| | - Haibo Li
- Ningbo Municipal Key Laboratory of Comprehensive Prevention and Treatment of Birth Defects, Ningbo Women & Children's Hospital, Ningbo, Zhejiang, China
| | - Xiaoyan Song
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| | - Ting Wang
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| | - Jingjing Xiang
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| | - Hong Li
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| |
Collapse
|
13
|
Chai H, Grommisch B, DiAdamo A, Wen J, Hui P, Li P. Inverted duplication, triplication and quintuplication through sequential breakage-fusion-bridge events induced by a terminal deletion at 5p in a case of spontaneous abortion. Mol Genet Genomic Med 2019; 7:e00965. [PMID: 31478360 PMCID: PMC6785443 DOI: 10.1002/mgg3.965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 01/09/2023] Open
Abstract
Background Integrated chromosome, fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) analyses have been effective in defining unbalanced chromosomal rearrangements. Discordant chromosome and aCGH results are rarely reported. Methods Routine cytogenomic analyses and literature review were performed in the study of a case from products of conception (POC). Results Chromosome and FISH analysis revealed a mosaic pattern consisting of a primary aberration of an inverted duplication of 5p and derived secondary and tertiary aberrations from sequential triplication and quintuplication of 5p, respectively. The aCGH analysis detected only a 1.521 Mb terminal deletion at 5p15.33 with no other pathogenic copy number variants in the genome. This mosaic karyotypic pattern likely resulted from chromosome instability induced by sequential breakage‐fusion‐bridge events during in vitro cell culture. A review of literature found heterogeneous distal deletion and inverted duplication of 5p in prenatal and pediatric cases. Conclusion This is the first case reported in POC with a unique mosaic pattern and discordant chromosome and aCGH results. Caution should be applied in reporting and interpreting these discordant results and further analysis for underlying mechanism should be considered.
Collapse
Affiliation(s)
- Hongyan Chai
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Brittany Grommisch
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Autumn DiAdamo
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Jiadi Wen
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Peining Li
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
14
|
Colley E, Hamilton S, Smith P, Morgan NV, Coomarasamy A, Allen S. Potential genetic causes of miscarriage in euploid pregnancies: a systematic review. Hum Reprod Update 2019; 25:452-472. [PMID: 31150545 DOI: 10.1093/humupd/dmz015] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/07/2019] [Indexed: 12/14/2022] Open
Abstract
Abstract
BACKGROUND
Approximately 50% of pregnancy losses are caused by chromosomal abnormalities, such as aneuploidy. The remainder has an apparent euploid karyotype, but it is plausible that there are cases of pregnancy loss with other genetic aberrations that are not currently routinely detected. Studies investigating the use of exome sequencing and chromosomal microarrays in structurally abnormal pregnancies and developmental disorders have demonstrated their clinical application and/or potential utility in these groups of patients. Similarly, there have been several studies that have sought to identify genes that are potentially causative of, or associated with, spontaneous pregnancy loss, but the evidence has not yet been synthesized.
OBJECTIVE AND RATIONALE
The objective was to identify studies that have recorded monogenic genetic contributions to pregnancy loss in euploid pregnancies, establish evidence for genetic causes of pregnancy loss, identify the limitations of current evidence, and make recommendations for future studies. This evidence is important in considering additional research into Mendelian causes of pregnancy loss and appropriate genetic investigations for couples experiencing recurrent pregnancy loss.
SEARCH METHODS
A systematic review was conducted in MEDLINE (1946 to May 2018) and Embase (1974 to May 2018). The search terms ‘spontaneous abortion’, ‘miscarriage’, ‘pregnancy loss’, or ‘lethal’ were used to identify pregnancy loss terms. These were combined with search terms to identify the genetic contribution including ‘exome’, ‘human genome’, ‘sequencing analysis’, ‘sequencing’, ‘copy number variation’, ‘single-nucleotide polymorphism’, ‘microarray analysis’, and ‘comparative genomic hybridization’. Studies were limited to pregnancy loss up to 20 weeks in humans and excluded if the genetic content included genes that are not lethal in utero, PGD studies, infertility studies, expression studies, aneuploidy with no recurrence risk, methodologies where there is no clinical relevance, and complex genetic studies. The quality of the studies was assessed using a modified version of the Newcastle–Ottawa scale.
OUTCOMES
A total of 50 studies were identified and categorized into three themes: whole-exome sequencing studies; copy number variation studies; and other studies related to pregnancy loss including recurrent molar pregnancies, epigenetics, and mitochondrial DNA aberrations. Putatively causative variants were found in a range of genes, including CHRNA1 (cholinergic receptor, nicotinic, alpha polypeptide 1), DYNC2H1 (dynein, cytoplasmic 2, heavy chain 1), and RYR1 (ryanodine receptor 1), which were identified in multiple studies. Copy number variants were also identified to have a causal or associated link with recurrent miscarriage.
WIDER IMPLICATIONS
Identification of genes that are causative of or predisposing to pregnancy loss will be of significant individual patient impact with respect to counselling and treatment. In addition, knowledge of specific genes that contribute to pregnancy loss could also be of importance in designing a diagnostic sequencing panel for patients with recurrent pregnancy loss and also in understanding the biological pathways that can cause pregnancy loss.
Collapse
Affiliation(s)
- Emily Colley
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Susan Hamilton
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - Paul Smith
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Arri Coomarasamy
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Stephanie Allen
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| |
Collapse
|
15
|
Wen J, Comerford K, Xu Z, Wu W, Amato K, Grommisch B, DiAdamo A, Xu F, Chai H, Li P. Analytical validation and chromosomal distribution of regions of homozygosity by oligonucleotide array comparative genomic hybridization from normal prenatal and postnatal case series. Mol Cytogenet 2019; 12:12. [PMID: 30886647 PMCID: PMC6404290 DOI: 10.1186/s13039-019-0424-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022] Open
Abstract
Background Regions of homozygosity (ROH) are continuous homozygous segments commonly seen in the human genome. The integration of single nucleotide polymorphism (SNP) probes into current array comparative genomic hybridization (aCGH) analysis has enabled the detection of the ROH. However, for detecting and reporting biologically relevant ROH in a clinical setting, it is necessary to assess the analytical validity of SNP calling and the chromosomal distribution of ROH in normal populations. Methods The analytical validity was evaluated by correlating the consistency of SNP calling with the quality parameters of aCGH and by accessing the accuracy of SNP calling using PCR based restriction enzyme digestion and Sanger sequencing. The distribution of ROH was evaluated by the numbers, sizes, locations, and frequencies of ROH from the collection of data from parental, postnatal, and prenatal case series that had normal aCGH and chromosome results. Results The SNP calling failure rate was 20–30% with a derivative Log2 ratio (DLR) below 0.2 and increased significantly to 30–40% with DLR of 0.2–0.4. The accuracy of SNP calling is 93%. Of the 958 cases tested, 34% had no ROH, 64% had one to four ROH, and less than 1% had more than five ROH. Of the 1196 ROH detected, 95% were less than 10 Mb. The distribution of numbers and sizes of ROH showed no differences among the parental, pediatric and prenatal case series and test tissues. The chromosomal distribution of ROH was non-random with ROH seen most frequently in chromosome 8, less frequently in chromosomes 2, 6, 10, 12, 11 and 18, and most rarely seen on chromosomes 15, 19, 21 and 22. Recurrent ROH occurring with a frequency greater than 1% were detected in 17 chromosomal loci which locates either in the pericentric or interstitial regions. Conclusion With a quality control parameter of DLR set at below 0.2, the consistency of SNP calling would be 75%, the accuracy of SNP call could be 93%, and the observed chromosomal distribution of ROH could be used as a reference. This aCGH analysis could be a reliable screening tool to document biologically relevant ROH and recommend further molecular analysis. Electronic supplementary material The online version of this article (10.1186/s13039-019-0424-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jiadi Wen
- 1Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Kathleen Comerford
- 2Diagnostic Genetics Program, University of Connecticut, Storrs, CT 06269 USA
| | - Zhiyong Xu
- 3Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| | - Weiqing Wu
- 3Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| | - Katherine Amato
- 1Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Brittany Grommisch
- 1Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Autumn DiAdamo
- 1Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Fang Xu
- PreventionGenetics, Marshfield, WI 54449 USA
| | - Hongyan Chai
- 1Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Peining Li
- 1Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 USA
| |
Collapse
|
16
|
Yang X, Song Z, Wu C, Wang W, Li G, Zhang W, Wu L, Lu K. Constructing a database for the relations between CNV and human genetic diseases via systematic text mining. BMC Bioinformatics 2018; 19:528. [PMID: 30598077 PMCID: PMC6311945 DOI: 10.1186/s12859-018-2526-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The detection and interpretation of CNVs are of clinical importance in genetic testing. Several databases and web services are already being used by clinical geneticists to interpret the medical relevance of identified CNVs in patients. However, geneticists or physicians would like to obtain the original literature context for more detailed information, especially for rare CNVs that were not included in databases. RESULTS The resulting CNVdigest database includes 440,485 sentences for CNV-disease relationship. A total number of 1582 CNVs and 2425 diseases are involved. Sentences describing CNV-disease correlations are indexed in CNVdigest, with CNV mentions and disease mentions annotated. CONCLUSIONS In this paper, we use a systematic text mining method to construct a database for the relationship between CNVs and diseases. Based on that, we also developed a concise front-end to facilitate the analysis of CNV/disease association, providing a user-friendly web interface for convenient queries. The resulting system is publically available at http://cnv.gtxlab.com /.
Collapse
Affiliation(s)
- Xi Yang
- School of Computer Science, National University of Defense Technology, Changsha, 410073, China
| | - Zhuo Song
- Genetalks Biotech Inc., Beijing, 100176, China
| | - Chengkun Wu
- School of Computer Science, National University of Defense Technology, Changsha, 410073, China. .,Institute for Quantum Information & State Key Laboratory of High Performance Computing, College of Computer, National University of Defense Technology, Changsha, 410073, China.
| | - Wei Wang
- School of Computer Science, National University of Defense Technology, Changsha, 410073, China
| | - Gen Li
- Genetalks Biotech Inc., Beijing, 100176, China
| | - Wei Zhang
- Genetalks Biotech Inc., Beijing, 100176, China
| | - Lingqian Wu
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China.
| | - Kai Lu
- School of Computer Science, National University of Defense Technology, Changsha, 410073, China.
| |
Collapse
|
17
|
Kubendran S, Duong J, Dong F, Lueking A, Farley D. Implementing a Protocol to Optimize Detection of Chromosome Abnormalities in Cases of Miscarriage or Stillbirth at a Midwestern Teaching Hospital. Perm J 2018; 22:17-204. [PMID: 30010531 DOI: 10.7812/tpp/17-204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CONTEXT Results from chromosome testing after spontaneous abortion (SAB) or intrauterine fetal demise (IUFD) are useful in patient counseling; however, results can be inconclusive when cell cultures for chromosomes are unable to grow from products of conception. Chromosomal microarray analysis (CMA) can analyze DNA from nonviable fetal tissue. OBJECTIVE To examine whether establishing a genetic testing protocol for karyotype and CMA on SAB and IUFD tissues increases diagnostic yield. DESIGN A retrospective chart review was conducted in cases of SAB or IUFD when karyotyping and/or CMA was requested, comparing two periods: Preprotocol and postprotocol implementation. MAIN OUTCOME MEASURES Diagnostic yield was compared by using the number of determinate test results in the preprotocol and postprotocol study periods. A case was considered to have indeterminate results when the final genetic test results reported no fetal tissue or no cell culture growth. RESULTS A total of 55 preprotocol and 52 postprotocol patients were analyzed. Diagnostic yield increased from 72.7% to 94.2% after implementation of the genetic testing protocol (p = 0.0004). Indeterminate results occurred more frequently before compared with after implementation of the protocol. CONCLUSION A protocol of reflexing to CMA or proceeding directly with CMA gives a higher diagnostic yield in the genetic evaluation of SAB or IUFD. Institutions should consider implementing a genetic testing protocol to improve diagnostic yield. Our study results emphasize the importance of proceeding directly to microarray analysis and give support for current clinical recommendations for genetic testing after fetal demise.
Collapse
Affiliation(s)
- Shobana Kubendran
- Associate Professor in Pediatrics at the University of Kansas School of Medicine in Wichita.
| | - Jennifer Duong
- Research Associate in Obstetrics and Gynecology at the University of Kansas School of Medicine in Wichita.
| | - Fanglong Dong
- Associate Professor in the Graduate College of Biomedical Science at Western University of Health Sciences in Pomona, CA.
| | - Amy Lueking
- Obstetrician-Gynecologist for the Avera Medical Group in Pierre, SD.
| | - Darren Farley
- Clinical Assistant Professor in Obstetrics and Gynecology at the University of Kansas School of Medicine in Wichita.
| |
Collapse
|
18
|
Zhu X, Li J, Zhu Y, Wang W, Wu X, Yang Y, Gu L, Gu Y, Hu Y. Application of chromosomal microarray analysis in products of miscarriage. Mol Cytogenet 2018; 11:44. [PMID: 30140311 PMCID: PMC6098645 DOI: 10.1186/s13039-018-0396-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022] Open
Abstract
Background Chromosomal abnormality is one of the major cause of spontaneous abortion. Most available guidelines suggest genetic testing after three miscarriages, which has been proved to be difficult to adhere to and somewhat of low cost-effectiveness. As chromosomal microarray analysis has been recommended to be applied on miscarriage products, we managed a retrospective study on our experience investigate the potential impact of this technique on previous guidelines and our present management on miscarried couples and products. Results Of the 405 products of conceptions, the overall detection rate of pathogenetic results was 55.3% (224/405), including 7.1% (16/224) copy number changes which could be missed by conventional karyotyping analysis. Of the 222 natural conception samples, abnormal genetic results were found in 126 cases (56.8%). The detection rate in the assistant reproductive treatment group was 53.6% (98/183). No significant difference was found between these two groups (p = 0.645, OR = 1.110 with 95% CI: 0.713–1.726). The detection rate was 53.2% (75/141) in 141 product-of-conceptions (POCs) of mothers with adverse pregnancy histories. Of the 264 POC samples of mothers without abnormal pregnancy histories, 56.4% (149/264) were genetically abnormal. The detection rate and maternal age between these two groups were all compatible. Conclusions Chromosomal microarray testing should be referred to couples at their first miscarriage regardless of the way how they get pregnant.
Collapse
Affiliation(s)
- Xiangyu Zhu
- 1Department of Obstetrics and Gynecology, Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital, Nanjing, 210008 Jiangsu China
| | - Jie Li
- 1Department of Obstetrics and Gynecology, Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital, Nanjing, 210008 Jiangsu China
| | - Yujie Zhu
- 1Department of Obstetrics and Gynecology, Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital, Nanjing, 210008 Jiangsu China
| | - Wanjun Wang
- 1Department of Obstetrics and Gynecology, Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital, Nanjing, 210008 Jiangsu China
| | - Xing Wu
- 1Department of Obstetrics and Gynecology, Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital, Nanjing, 210008 Jiangsu China
| | - Ying Yang
- 1Department of Obstetrics and Gynecology, Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital, Nanjing, 210008 Jiangsu China
| | - Leilei Gu
- 1Department of Obstetrics and Gynecology, Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital, Nanjing, 210008 Jiangsu China
| | - Yuanyuan Gu
- 1Department of Obstetrics and Gynecology, Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital, Nanjing, 210008 Jiangsu China
| | - Yali Hu
- 2Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008 Jiangsu China
| |
Collapse
|
19
|
Hu Q, Chai H, Shu W, Li P. Human ring chromosome registry for cases in the Chinese population: re-emphasizing Cytogenomic and clinical heterogeneity and reviewing diagnostic and treatment strategies. Mol Cytogenet 2018; 11:19. [PMID: 29492108 PMCID: PMC5828142 DOI: 10.1186/s13039-018-0367-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/13/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Constitutional ring chromosomes are rare orphan chromosomal disorders. Ring chromosome syndrome featuring growth retardation and mild to intermediate intellectual disability is likely caused by the dynamic behavior of ring chromosome through cell cycles. Chromosomal and regional specific phenotypes likely result from segmental losses and gains during the ring formation. Although recent applications of genomic copy number and sequencing analyses revealed various ring chromosome structures from an increasing number of case studies, there was no organized effort for compilating and curating cytogenomic and clinical finding for ring chromosomes. METHODS A web-based interactive 'Human Ring Chromosome Registry' using Microsoft Access based relational database was developed to present genetic and phenotypic findings of ring chromosome cases. Chinese ring chromosome cases reported in the literature was reviewed and compiled as a testing data set to validate this registry. RESULTS A total of 113 cases of ring chromosomes were retrieved in all chromosomes except for chromosomes 16, 17 and 19. The most frequently seen ring chromosomes by a decreasing order of relative frequencies were ring 13 (14%), X (12%), 22 (10%), 15 (9%), 14 (7%), and 18 (7%). Genomic imbalances were detected in 18 out of 19 cases analyzed by microarray or sequencing. Variable clinical manifestations of developmental delay, dysmorphic facial features, intellectual disability, microcephaly, and hypotonia were noted in most autosomal rings. Chromosomal specific syndromic phenotypes included Wolf-Hirschhorn syndrome in a ring chromosome 4, cri-du-chat syndrome in a ring chromosome 5, epilepsy in ring chromosomes 14 and 20, Turner syndrome in ring chromosome X, and infertility in ring chromosomes 13, 21, 22 and Y. Effective growth hormone supplemental treatment for growth retardation in a ring chromosome 18 was noted. CONCLUSIONS Based on findings from these Chinese ring chromosome cases, guidelines for cytogenomic diagnosis and criteria for case registration were proposed. Further research to define underlying mechanisms of ring chromosome formation and dynamic mosaicism, to delineate the genotype-phenotype correlations, and to develop chromosome therapy for ring chromosomes were discussed.
Collapse
Affiliation(s)
- Qiping Hu
- Department of Cell Biology and Genetics, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021 China
- Laboratory of Clinical Cytogenetics and Genomics, Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Hongyan Chai
- Laboratory of Clinical Cytogenetics and Genomics, Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Wei Shu
- Department of Cell Biology and Genetics, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021 China
| | - Peining Li
- Laboratory of Clinical Cytogenetics and Genomics, Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| |
Collapse
|
20
|
Fletcher E, Porteous M, McKenzie KJ, Maher EJ, Evans MJ. Fetal Dysmorphology-Still an Essential Art. Analysis of the Limitations of Microarray in a Fetal Population and a Look Toward the Genome Sequencing Era. Pediatr Dev Pathol 2017; 20:288-297. [PMID: 28727969 DOI: 10.1177/1093526617693104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cytogenomic microarray allows assessment of the genome at higher resolutions than traditional karyotyping. The objective of this study is to evaluate the utility of microarray in a routine fetal autopsy setting before the advent of routine fetal exome/genome sequencing and the issues these technologies may generate. A systematic review of fetal postmortems at 12-24 weeks gestation between January 2011 and December 2014 was undertaken. Cases where there was no consent for audit, research, or genetic testing were excluded as were cases referred to the Procurator Fiscal, stillbirths, and neonatal deaths. Copy number variations were detected in 16 cases. In addition, there was 1 case of uniparental disomy; not all of these were related to the phenotype. There were a number of cases with phenotypic abnormalities and normal array results. Five of these underwent directed mutation analysis-3 were positive. Genetic laboratory investigations such as microarray and Quantitative Fluorescent-Polymerase Chain Reaction may increase the diagnostic yield in the assessment of fetal dysmorphology. However, this study shows that genetic results not only require careful review given the potential uncertain significance but also require phenotypic assessment of the fetus by a competent fetal dysmorphologist to determine the likely causative effect of any detected anomaly. This best practice will also extend to next generation sequencing and interpretation of variants of unknown significance. Fetal medicine teams should ideally include specialists well versed in assessment of fetal anomaly to provide families with the best possible information about the cause of their pregnancy loss and their options for future pregnancies.
Collapse
Affiliation(s)
- E Fletcher
- 1 Department of Clinical Genetics, South East Scotland NHS Service, Western General Hospital, Edinburgh, Scotland
| | - M Porteous
- 1 Department of Clinical Genetics, South East Scotland NHS Service, Western General Hospital, Edinburgh, Scotland
| | - K J McKenzie
- 3 Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, Scotland
| | - E J Maher
- 2 Department of Cytogenetics, South East Scotland NHS Service, Western General Hospital, Edinburgh, Scotland
| | - M J Evans
- 3 Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, Scotland
| |
Collapse
|
21
|
Lantieri F, Malacarne M, Gimelli S, Santamaria G, Coviello D, Ceccherini I. Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation. Int J Mol Sci 2017; 18:E609. [PMID: 28287439 PMCID: PMC5372625 DOI: 10.3390/ijms18030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/07/2017] [Indexed: 12/16/2022] Open
Abstract
The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software. The Aberration Detection Method 2 (ADM-2) algorithm with a threshold of 6 performed quite well, and the array design proved to be reliable, provided that some additional filters are applied, such as considering only intervals with average absolute log₂ratio above 0.3. We also propose an additional filter that takes into account the proportion of probes with log₂ratio exceeding suggestive values for gain or loss. In addition, the quality of samples was confirmed to be a crucial parameter. Finally, this work raises the importance of evaluating the samples profiles by eye and the necessity of validating the imbalances detected.
Collapse
Affiliation(s)
- Francesca Lantieri
- Dipartimento di Scienzedella Salute, Sezione di Biostatistica, Università degli Studi di Genova, Via Pastore 1, 16132 Genoa, Italy.
| | - Michela Malacarne
- Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy.
| | - Stefania Gimelli
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Bâtiment de Base 8C-3-840.3, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Giuseppe Santamaria
- UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy.
| | - Domenico Coviello
- Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy.
| | - Isabella Ceccherini
- UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy.
| |
Collapse
|
22
|
Massalska D, Zimowski JG, Bijok J, Pawelec M, Czubak-Barlik M, Jakiel G, Roszkowski T. First trimester pregnancy loss: Clinical implications of genetic testing. J Obstet Gynaecol Res 2016; 43:23-29. [DOI: 10.1111/jog.13179] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/21/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Diana Massalska
- I Department of Obstetrics and Gynecology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| | | | - Julia Bijok
- I Department of Obstetrics and Gynecology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| | - Magdalena Pawelec
- Department of Genetics; Institute of Psychiatry and Neurology; Warsaw Poland
| | - Małgorzata Czubak-Barlik
- Department of Pathology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| | - Grzegorz Jakiel
- I Department of Obstetrics and Gynecology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| | - Tomasz Roszkowski
- I Department of Obstetrics and Gynecology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| |
Collapse
|
23
|
Cui C, Shu W, Li P. Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications. Front Cell Dev Biol 2016; 4:89. [PMID: 27656642 PMCID: PMC5011256 DOI: 10.3389/fcell.2016.00089] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/11/2016] [Indexed: 12/14/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH techniques have visualized intra-nuclear genomic structure and sub-cellular transcriptional dynamics of many genes and revealed their functions in various biological processes.
Collapse
Affiliation(s)
- Chenghua Cui
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of MedicineNew Haven, CT, USA; Department of Pathology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical SciencesTianjin, China
| | - Wei Shu
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of MedicineNew Haven, CT, USA; Department of Cell Biology and Genetics, Guangxi Medical UniversityNanning, China
| | - Peining Li
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of Medicine New Haven, CT, USA
| |
Collapse
|
24
|
Ozawa N, Sago H, Matsuoka K, Maruyama T, Migita O, Aizu Y, Inazawa J. Cytogenetic analysis of spontaneously discharged products of conception by array-based comparative genomic hybridization. SPRINGERPLUS 2016; 5:874. [PMID: 27386323 PMCID: PMC4920787 DOI: 10.1186/s40064-016-2594-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/15/2016] [Indexed: 12/12/2022]
Abstract
Background Cytogenetic analysis of products of conception (POC) is essential for the management of recurrent pregnancy loss (RPL), but the currently-performed G-banding method is not necessarily applicable to spontaneously discharged POC because of poor quality for culture. We analyzed the karyotypes of 15 spontaneously discharged POC by array-based comparative genomic hybridization (array-CGH). Results All specimens were successfully analyzed and 10 cases had abnormal results: gain in copy number (n = 7) and loss in copy number (n = 3). Most of them were estimated to be whole chromosome aneuploidy, whereas one case was compatible with microdeletion. Two cases were suspected to be male diploid contaminated by maternal DNA or triploid because of the unsatisfactory signal patterns on X/Y chromosomes. Two of three cases with normal female DNA pattern were identified to be contaminated with maternal DNA by the additional analysis of short tandem repeats. Conclusions Given the potential to analyze non-viable POC specimens, array-CGH is a feasible cytogenetic tool for women, in particular, with a history of RPL who desire non-surgical or expectant management of miscarriages and/or a thorough investigation on the cause for recurrent miscarriage, although it needs to take into account high incidence of maternal contamination in spontaneously discharged POC. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2594-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nobuaki Ozawa
- Center of Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535 Japan
| | - Haruhiko Sago
- Center of Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535 Japan
| | - Kentaro Matsuoka
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan ; Department of Pathology, Kitasato Institute Hospital, Tokyo, Japan
| | - Tetsuo Maruyama
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Ohsuke Migita
- Department of Clinical Genetics and Molecular Medicine, National Center for Child Health and Development, Tokyo, Japan ; Department of Clinical Genetics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshinori Aizu
- Division of Advanced Technology and Development, BML, Inc., Kawagoe, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan ; Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|