Prevalence of chromosomal abnormalities identified by copy number
variation sequencing in high-risk pregnancies, spontaneous abortions, and
suspected genetic disorders

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Abstract

Objective

High-throughput sequencing based on copy number variation (CNV-seq) is commonly used to detect chromosomal abnormalities including aneuploidy. This study provides evidence for the prevalence of chromosomal abnormalities in target populations.

Methods

A total of 160 samples, including 83 high-risk pregnancies, 37 spontaneous abortions, and 40 suspected genetic disorders, were analyzed by CNV-seq. Relationships between the incidence of these chromosomal abnormalities and risk factors (e.g. advanced maternal age, abnormal pregnancy history, and family history of congenital disease) were further analyzed by subgroup.

Results

A total of 37 (44.6%) high-risk pregnancies, 25 (67.6%) spontaneous abortions, and 22 (55%) suspected genetic disorders had chromosomal abnormalities including aneuploidy and CNVs. There was an increased risk association between the prevalence of aneuploidy and pathogenic-relevant CNV in the fetus or abortive tissue and advanced maternal age. Moreover, a family history of congenital disease was also positively correlated with fetal chromosomal abnormalities in high-risk pregnancies.

Conclusion

A relatively high prevalence of chromosomal abnormalities was detected in high-risk pregnancies, spontaneous abortions, and suspected genetic disorders, indicating the importance of CNV detection in such populations.

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Most cited references 26

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CNV-seq, a new method to detect copy number variation using high-throughput sequencing

Chao Xie, Martti T Tammi (2009)

Background DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. Results Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. Conclusion Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.

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Copy number variants, diseases and gene expression.

Charlotte N Henrichsen, Alexandre Reymond, Charlotte N Henrichsen … (2009)

Copy number variation (CNV) has recently gained considerable interest as a source of genetic variation likely to play a role in phenotypic diversity and evolution. Much effort has been put into the identification and mapping of regions that vary in copy number among seemingly normal individuals in humans and a number of model organisms, using bioinformatics or hybridization-based methods. These have allowed uncovering associations between copy number changes and complex diseases in whole-genome association studies, as well as identify new genomic disorders. At the genome-wide scale, however, the functional impact of CNV remains poorly studied. Here we review the current catalogs of CNVs, their association with diseases and how they link genotype and phenotype. We describe initial evidence which revealed that genes in CNV regions are expressed at lower and more variable levels than genes mapping elsewhere, and also that CNV not only affects the expression of genes varying in copy number, but also have a global influence on the transcriptome. Further studies are warranted for complete cataloguing and fine mapping of CNVs, as well as to elucidate the different mechanisms by which they influence gene expression.

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Copy number variation sequencing for comprehensive diagnosis of chromosome disease syndromes.

Desheng Liang, Ying Peng, Weigang Lv … (2014)

Detection of chromosome copy number variation (CNV) plays an important role in the diagnosis of patients with unexplained clinical symptoms and for the identification of chromosome disease syndromes in the established fetus. In current clinical practice, karyotyping, in conjunction with array-based methods, is the gold standard for detection of CNV. To increase accessibility and reduce patient costs for diagnostic CNV tests, we speculated that next-generation sequencing methods could provide a similar degree of sensitivity and specificity as commercial arrays. CNV in patient samples was assessed on a medium-density single nucleotide polymorphism array and by low-coverage massively parallel CNV sequencing (CNV-seq), with mate pair sequencing used to confirm selected CNV deletion breakpoints. A total of 10 ng of input DNA was sufficient for accurate CNV-seq diagnosis, although 50 ng was optimal. Validation studies of samples with small CNVs showed that CNV-seq was specific and reproducible, suggesting that CNV-seq may have a potential genome resolution of approximately 0.1 Mb. In a blinded study of 72 samples with known gross and submicroscopic CNVs originally detected by single nucleotide polymorphism array, there was high diagnostic concordance with CNV-seq. We conclude that CNV-seq is a viable alternative to arrays for the diagnosis of chromosome disease syndromes.

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Author and article information

Journal

Journal ID (nlm-ta): J Int Med Res

Journal ID (iso-abbrev): J. Int. Med. Res

Journal ID (publisher-id): IMR

Journal ID (hwp): spimr

Title: The Journal of International Medical Research

Publisher: SAGE Publications (Sage UK: London, England )

ISSN (Print): 0300-0605

ISSN (Electronic): 1473-2300

Publication date (Electronic): 07 February 2019

Publication date (Print): March 2019

Volume: 47

Issue: 3

Pages: 1169-1178

Affiliations

[1 ]Prenatal Diagnosis Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China

[2 ]Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China

[3 ]Berry Genomics, Beijing, China

[4 ]Department of Obstetrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China

Author notes

[*]Jingcui Yu, Scientific Research Centre, the Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin 150081, China. Email: yujingcui@ 123456ems.hrbmu.edu.cn

Author information

Jingcui Yu https://orcid.org/0000-0001-5182-987X

Article

Publisher ID: 10.1177_0300060518818020

DOI: 10.1177/0300060518818020

PMC ID: 6421393

PubMed ID: 30732499

SO-VID: 1e3a8e3a-aec5-47aa-9edf-e34d1e3385bd

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Creative Commons Non Commercial CC BY-NC: This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License ( http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages ( https://us.sagepub.com/en-us/nam/open-access-at-sage).

Prevalence of chromosomal abnormalities identified by copy number variation sequencing in high-risk pregnancies, spontaneous abortions, and suspected genetic disorders

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Abstract

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International Journal of Medicine and Medical Research

Most cited references 26

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

Copy number variants, diseases and gene expression.

Copy number variation sequencing for comprehensive diagnosis of chromosome disease syndromes.

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