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Tamura Y, Santo M, Araki Y, Matsubayashi H, Takaya Y, Kitaya K, Doshida M, Yamaguchi K, Mizuta S, Takahashi C, Kim N, Okuno K, Takeuchi T, Ishikawa T. Chromosomal copy number analysis of products of conception by conventional karyotyping and next-generation sequencing. Reprod Med Biol 2021; 20:71-75. [PMID: 33488285 PMCID: PMC7812460 DOI: 10.1002/rmb2.12351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/28/2020] [Accepted: 09/14/2020] [Indexed: 11/12/2022] Open
Abstract
PURPOSE Chromosomal abnormalities are a major cause of spontaneous abortion, and conventional G-banded karyotyping (G-banding) is mainly utilized for chromosomal analysis. Recently, next-generation sequencing (NGS) has been introduced for chromosomal analysis. Here, we aimed to investigate the applicability and utility of NGS-based chromosomal analysis of products of conception (POC) on chorionic villus samples from spontaneous abortion. METHODS The results of chromosomal analysis of 7 chorionic villus samples from spontaneous abortion were compared between conventional G-banding and NGS-based chromosomal copy number analysis. Age dependency and frequency of each chromosomal aneuploidy were evaluated for 279 cases analyzed by NGS. RESULTS Excluding two cases (culture failure and maternal cell contamination), the results were consistent between G-banding and NGS. For cases analyzed by NGS, the rate of chromosomal abnormality increased in a maternal age-dependent manner. The frequency of each chromosomal aneuploidy detected by NGS was almost the same as that previously reported. Finally, NGS analysis was possible for difficult cases by G-banding analysis, such as culture failure, maternal cell contamination, long-term storage cases, and low cell number. CONCLUSIONS Chromosome analysis using NGS not only obtains comparable results to conventional G-banding, but also can analyze POC more accurately and efficiently.
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Affiliation(s)
| | | | - Yasuhisa Araki
- Nippon Reprogenetics Inc.MaebashiJapan
- Graduate School of Health ScienceGunma Paz UniversityTakasakiJapan
| | | | | | | | | | | | - Shimpei Mizuta
- Reproduction Clinic OsakaOsakaJapan
- Reproduction Clinic TokyoTokyoJapan
| | | | | | | | | | - Tomomoto Ishikawa
- Reproduction Clinic OsakaOsakaJapan
- Reproduction Clinic TokyoTokyoJapan
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Najafi K, Gholami S, Moshtagh A, Bazrgar M, Sadatian N, Abbasi G, Rostami P, Khalili S, Babanejad M, Nourmohammadi B, Faramarzi Garous N, Najmabadi H, Kariminejad R. Chromosomal aberrations in pregnancy and fetal loss: Insight on the effect of consanguinity, review of 1625 cases. Mol Genet Genomic Med 2019; 7:e820. [PMID: 31210028 PMCID: PMC6687859 DOI: 10.1002/mgg3.820] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 04/23/2019] [Accepted: 05/17/2019] [Indexed: 01/16/2023] Open
Abstract
Background Pregnancy loss affects 10%–15% of pregnancies and is caused by several factors, maternal and fetal. Most common cause is chromosomal aneuploidy and has traditionally been detected by karyotyping product of conception and/or fetal tissue. In recent years, array comparative genomic hybridization (a‐CGH) has been used because of its higher detection and lower failure rates. Methods DNA was extracted from 1625 products of abortion or fetal tissue. In 1,104 cases both quantitative fluorescent‐polymerase chain reaction (QF‐PCR) and a‐CGH, and in 521 cases only a‐CGH, was performed. Results The detection rate using QF‐PCR and a‐CGH is 20% compared to 12.7%, overall, and 15.7%, excluding failed samples, by karyotypes in our center. QF‐PCR and a‐CGH failed in 1.9% of cases, while the failure rate for karyotypes was 20.1%. The difference of detection and failure rates is significant (p‐value < 0.001 and p‐value < 0.001 respectively). Unexpectedly we also found a significant difference in frequency of imbalances in related versus unrelated couples. (χ2 = 11.4926, p‐value < 0.001). Conclusion It is highly likely that the pregnancy loss in consanguineous couples is caused by other genetic and immune mechanisms. It is plausible that, through the same mechanism by which single gene disorders have a higher prevalence of manifesting disease in consanguineous couples, they can cause lethal genetic disorders leading to pregnancy loss and intra‐uterine fetal death (IUFD) in these couples. Our findings suggest that this is a matter for further study as it will greatly influence the approach to counseling and managing consanguineous couples with pregnancy loss.
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Affiliation(s)
- Kimia Najafi
- Cytogenetic divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
- Genetic Research CenterUniversity of Social Welfare and Rehabilitation SciencesTehranIran
| | - Soheila Gholami
- Cytogenetic divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | - Azadeh Moshtagh
- Cytogenetic divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | - Masood Bazrgar
- Cytogenetic divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | - Neda Sadatian
- Cytogenetic divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | - Golemaryam Abbasi
- Cytogenetic divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | - Parvin Rostami
- Molecular divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | - Soheila Khalili
- Molecular divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | - Mojgan Babanejad
- Genetic Research CenterUniversity of Social Welfare and Rehabilitation SciencesTehranIran
- Molecular divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | | | | | - Hossein Najmabadi
- Genetic Research CenterUniversity of Social Welfare and Rehabilitation SciencesTehranIran
- Molecular divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
| | - Roxana Kariminejad
- Cytogenetic divisionKariminejad ‐ Najmabadi Pathology & Genetics CenterTehranIran
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Pauta M, Grande M, Rodriguez-Revenga L, Kolomietz E, Borrell A. Added value of chromosomal microarray analysis over karyotyping in early pregnancy loss: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51:453-462. [PMID: 29055063 DOI: 10.1002/uog.18929] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 09/29/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To estimate the increased test success rate and incremental yield of chromosomal microarray analysis (CMA) over conventional karyotyping in detection of pathogenic copy number variants (CNVs) and variants of unknown significance (VOUS) in early pregnancy loss. METHOD This was a systematic review conducted in accordance with PRISMA criteria. All articles identified in PubMed, Ovid MEDLINE and Web of Science, between January 2000 and April 2017, that described CNVs in early pregnancy losses (up to 20 weeks) were included. Risk differences were pooled to estimate the incremental yield of CMA over karyotyping overall, and after stratification. In addition, test success rate, defined as the proportion of informative results, was compared in series in which CMA and karyotyping were performed concurrently. RESULTS Twenty-three studies, reporting on 5507 pregnancy losses up to 20 weeks with full data available, met the inclusion criteria for analysis. In the series in which CMA and karyotyping were performed concurrently, CMA showed a significant improvement in success rate, providing informative results in 95% (95% CI, 94-96%) of cases compared with karyotyping in which informative results were provided in 68% (95% CI, 66-70%) of cases. Combined data from reviewed studies revealed that incremental yields of CMA over karyotyping were 2% (95% CI, 1-2%) for pathogenic CNVs and 4% (95% CI, 3-6%) for VOUS. The most common pathogenic CNVs reported were 22q11.21 and 1p36.33 deletion. CONCLUSION In comparison with conventional karyotyping, CMA provides a significant increase in test success rate and incremental diagnostic yield in early pregnancy loss. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- M Pauta
- BCNatal Hospital Clínic Barcelona and IDIBAPS, Barcelona, Spain
| | - M Grande
- BCNatal Hospital Clínic Barcelona and IDIBAPS, Barcelona, Spain
| | - L Rodriguez-Revenga
- Biochemistry and Molecular Genetics Department, Hospital Clínic Barcelona and IDIBAPS, Barcelona, Spain
| | - E Kolomietz
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Ontario, Canada
| | - A Borrell
- BCNatal Hospital Clínic Barcelona and IDIBAPS, Barcelona, Spain
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Rosenfeld JA, Tucker ME, Escobar LF, Neill NJ, Torchia BS, McDaniel LD, Schultz RA, Chong K, Chitayat D. Diagnostic utility of microarray testing in pregnancy loss. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 46:478-486. [PMID: 25846569 DOI: 10.1002/uog.14866] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/25/2015] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVES To determine the frequency of clinically significant chromosomal abnormalities identified by chromosomal microarray in pregnancy losses at any gestational age and to compare microarray performance with that of traditional cytogenetic analysis when testing pregnancy losses. METHODS Among 535 fetal demise specimens of any gestational age, clinical microarray-based comparative genomic hybridization (aCGH) was performed successfully on 515, and a subset of 107 specimens underwent additional single nucleotide polymorphism (SNP) analysis. RESULTS Overall, clinically significant abnormalities were identified in 12.8% (64/499) of specimens referred with normal or unknown karyotypes. Detection rates were significantly higher with earlier gestational age. In the subset with normal karyotype, clinically significant abnormalities were identified in 6.9% (20/288). This detection rate did not vary significantly with gestational age, suggesting that, unlike aneuploidy, the contribution of submicroscopic chromosomal abnormalities to fetal demise does not vary with gestational age. In the 107 specimens that underwent aCGH and SNP analysis, seven cases (6.5%) had abnormalities of potential clinical significance detected by the SNP component, including female triploidy. aCGH failed to yield fetal results in 8.3%, which is an improvement over traditional cytogenetic analysis of fetal demise specimens. CONCLUSIONS Both the provision of results in cases in which karyotype fails and the detection of abnormalities in the presence of a normal karyotype demonstrate the increased diagnostic utility of microarray in pregnancy loss. Thus, chromosomal microarray testing is a preferable, robust method of analyzing cases of pregnancy loss to better delineate possible genetic etiologies, regardless of gestational age.
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Affiliation(s)
- J A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - M E Tucker
- St. Vincent Hospital, Indianapolis, IN, USA
| | | | - N J Neill
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - B S Torchia
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - L D McDaniel
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - R A Schultz
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - K Chong
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Ontario, Canada
| | - D Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Ontario, Canada
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Dhillon RK, Hillman SC, Morris RK, McMullan D, Williams D, Coomarasamy A, Kilby MD. Additional information from chromosomal microarray analysis (CMA) over conventional karyotyping when diagnosing chromosomal abnormalities in miscarriage: a systematic review and meta-analysis. BJOG 2013; 121:11-21. [DOI: 10.1111/1471-0528.12382] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2013] [Indexed: 02/03/2023]
Affiliation(s)
- RK Dhillon
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
| | - SC Hillman
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
- School of Clinical and Experimental Medicine; College of Medicine and Dentistry; University of Birmingham; Edgbaston Birmingham UK
| | - RK Morris
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
- School of Clinical and Experimental Medicine; College of Medicine and Dentistry; University of Birmingham; Edgbaston Birmingham UK
| | - D McMullan
- West Midlands Regional Genetics Laboratories and the Department of Clinical Genetics; Birmingham Women's Foundation Trust; Edgbaston Birmingham UK
| | - D Williams
- West Midlands Regional Genetics Laboratories and the Department of Clinical Genetics; Birmingham Women's Foundation Trust; Edgbaston Birmingham UK
| | - A Coomarasamy
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
- School of Clinical and Experimental Medicine; College of Medicine and Dentistry; University of Birmingham; Edgbaston Birmingham UK
| | - MD Kilby
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
- School of Clinical and Experimental Medicine; College of Medicine and Dentistry; University of Birmingham; Edgbaston Birmingham UK
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Gao J, Liu C, Yao F, Hao N, Zhou J, Zhou Q, Zhang L, Liu X, Bian X, Liu J. Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion. Mol Cytogenet 2012; 5:33. [PMID: 22794168 PMCID: PMC3488553 DOI: 10.1186/1755-8166-5-33] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/20/2012] [Indexed: 12/15/2022] Open
Abstract
Background Array-based comparative genomic hybridization (aCGH) is a new technique for detecting submicroscopic deletions and duplications, and can overcome many of the limitations associated with classic cytogenetic analysis. However, its clinical use in spontaneous abortion needs comprehensive evaluation. We used aCGH to investigate chromosomal imbalances in 100 spontaneous abortions and compared the results with G-banding karyotyping and fluorescence in situ hybridization (FISH). Inconsistent results were verified by quantitative fluorescence PCR. Results Abnormalities were detected in 61 cases. aCGH achieved the highest detection rate (93.4%, 57/61) compared with traditional karyotyping (77%, 47/61) and FISH analysis (68.9%, 42/61). aCGH identified all chromosome abnormalities reported by traditional karyotyping and interphase FISH analysis, with the exception of four triploids. It also detected three additional aneuploidy cases in 37 specimens with ‘normal’ karyotypes, one mosaicism and 10 abnormalities in 14 specimens that failed to grow in vitro. Conclusions aCGH analysis circumvents many limitations in traditional karyotyping or FISH. The accuracy and efficiency of aCGH in spontaneous abortions highlights its clinical usefulness for the future. As aborted tissues have the potential to be contaminated with maternal cells, the threshold value of detection in aCGH should be lowered to avoid false negatives.
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Affiliation(s)
- Jinsong Gao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Shuai Fu Yuan No,1, Dongdan, Beijing 100730, People's Republic of China.
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