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Prospective chromosome analysis of 3429 amniocentesis samples in China using copy number variation sequencing

  • Jing Wang
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Lin Chen
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Cong Zhou
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Li Wang
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Hanbing Xie
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Yuanyuan Xiao
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Hongmei Zhu
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Ting Hu
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Zhu Zhang
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Qian Zhu
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Zhiying Liu
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Shanlin Liu
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • He Wang
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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  • Mengnan Xu
    Affiliations
    Berry Genomics Corporation, Beijing, China
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  • Zhilin Ren
    Affiliations
    Berry Genomics Corporation, Beijing, China
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  • Fuli Yu
    Affiliations
    Berry Genomics Corporation, Beijing, China

    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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  • David S. Cram
    Affiliations
    Berry Genomics Corporation, Beijing, China
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  • Hongqian Liu
    Correspondence
    Corresponding author: Hongqian Liu, PhD.
    Affiliations
    Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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      Background

      Next-generation sequencing is emerging as a viable alternative to chromosome microarray analysis for the diagnosis of chromosome disease syndromes. One next-generation sequencing methodology, copy number variation sequencing, has been shown to deliver high reliability, accuracy, and reproducibility for detection of fetal copy number variations in prenatal samples. However, its clinical utility as a first-tier diagnostic method has yet to be demonstrated in a large cohort of pregnant women referred for fetal chromosome testing.

      Objective

      We sought to evaluate copy number variation sequencing as a first-tier diagnostic method for detection of fetal chromosome anomalies in a general population of pregnant women with high-risk prenatal indications.

      Study Design

      This was a prospective analysis of 3429 pregnant women referred for amniocentesis and fetal chromosome testing for different risk indications, including advanced maternal age, high-risk maternal serum screening, and positivity for an ultrasound soft marker. Amniocentesis was performed by standard procedures. Amniocyte DNA was analyzed by copy number variation sequencing with a chromosome resolution of 0.1 Mb. Fetal chromosome anomalies including whole chromosome aneuploidy and segmental imbalances were independently confirmed by gold standard cytogenetic and molecular methods and their pathogenicity determined following guidelines of the American College of Medical Genetics for sequence variants.

      Results

      Clear interpretable copy number variation sequencing results were obtained for all 3429 amniocentesis samples. Copy number variation sequencing identified 3293 samples (96%) with a normal molecular karyotype and 136 samples (4%) with an altered molecular karyotype. A total of 146 fetal chromosome anomalies were detected, comprising 46 whole chromosome aneuploidies (pathogenic), 29 submicroscopic microdeletions/microduplications with known or suspected associations with chromosome disease syndromes (pathogenic), 22 other microdeletions/microduplications (likely pathogenic), and 49 variants of uncertain significance. Overall, the cumulative frequency of pathogenic/likely pathogenic and variants of uncertain significance chromosome anomalies in the patient cohort was 2.83% and 1.43%, respectively. In the 3 high-risk advanced maternal age, high-risk maternal serum screening, and ultrasound soft marker groups, the most common whole chromosome aneuploidy detected was trisomy 21, followed by sex chromosome aneuploidies, trisomy 18, and trisomy 13. Across all clinical indications, there was a similar incidence of submicroscopic copy number variations, with approximately equal proportions of pathogenic/likely pathogenic and variants of uncertain significance copy number variations. If karyotyping had been used as an alternate cytogenetics detection method, copy number variation sequencing would have returned a 1% higher yield of pathogenic or likely pathogenic copy number variations.

      Conclusion

      In a large prospective clinical study, copy number variation sequencing delivered high reliability and accuracy for identifying clinically significant fetal anomalies in prenatal samples. Based on key performance criteria, copy number variation sequencing appears to be a well-suited methodology for first-tier diagnosis of pregnant women in the general population at risk of having a suspected fetal chromosome abnormality.

      Key words

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      References

        • Trask B.J.
        Human cytogenetics: 46 chromosomes, 46 years and counting.
        Nat Rev Genet. 2002; 3: 769-778
        • Chitty L.S.
        • Lo Y.M.
        Noninvasive prenatal screening for genetic diseases using massively parallel sequencing of maternal plasma DNA.
        Cold Spring Harb Perspect Med. 2015; 5: a023085
        • Beaudet A.L.
        Using fetal cells for prenatal diagnosis: history and recent progress.
        Am J Med Genet C Semin Med Genet. 2016; 172: 123-127
        • Smeets D.F.
        Historical prospective of human cytogenetics: from microscope to microarray.
        Clin Biochem. 2004; 37: 439-446
        • Wapner R.J.
        • Martin C.L.
        • Levy B.
        • et al.
        Chromosomal microarray versus karyotyping for prenatal diagnosis.
        N Engl J Med. 2012; 367: 2175-2184
        • Batzir N.A.
        • Shohat M.
        • Maya I.
        Chromosomal microarray analysis (CMA) a clinical diagnostic tool in the prenatal and postnatal settings.
        Pediatr Endocrinol Rev. 2015; 13: 448-454
        • Oneda B.
        • Rauch A.
        Microarrays in prenatal diagnosis.
        Best Pract Res Clin Obstet Gynaecol. 2017; 42: 53-63
        • Liang D.
        • Peng Y.
        • Lv W.
        • et al.
        Copy number variation sequencing for comprehensive diagnosis of chromosome disease syndromes.
        J Mol Diagn. 2014; 16: 519-526
        • Dong Z.
        • Zhang J.
        • Hu P.
        • et al.
        Low-pass whole-genome sequencing in clinical cytogenetics: a validated approach.
        Genet Med. 2016; 18: 940-948
        • Liang D.
        • Wang Y.
        • Ji X.
        • et al.
        Clinical application of whole-genome low-coverage next-generation sequencing to detect and characterize balanced chromosomal translocations.
        Clin Genet. 2017; 91: 605-610
        • Chen Y.
        • Bartanus J.
        • Liang D.
        • et al.
        Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development.
        Hum Mutat. 2017; 38: 669-677
        • Wang Y.
        • Chen Y.
        • Tian F.
        • et al.
        Maternal mosaicism is a significant contributor to discordant sex chromosomal aneuploidies associated with noninvasive prenatal testing.
        Clin Chem. 2014; 60: 251-259
        • Zhou X.
        • Sui L.
        • Xu Y.
        • et al.
        Contribution of maternal copy number variations to false-positive fetal trisomies detected by noninvasive prenatal testing.
        Prenat Diagn. 2017; 37: 318-322
        • Liu S.
        • Song L.
        • Cram D.S.
        • et al.
        Traditional karyotyping vs copy number variation sequencing for detection of chromosomal abnormalities associated with spontaneous miscarriage.
        Ultrasound Obstet Gynecol. 2015; 46: 472-477
        • Hillman S.C.
        • McMullan D.J.
        • Hall G.
        • et al.
        Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta-analysis.
        Ultrasound Obstet Gynecol. 2013; 41: 610-620
        • Saldarriaga W.
        • García-Perdomo H.A.
        • Arango-Pineda J.
        • Fonseca J.
        Karyotype versus genomic hybridization for the prenatal diagnosis of chromosomal abnormalities: a metaanalysis.
        Am J Obstet Gynecol. 2015; 212: 330.e1-330.e10
        • Fiorentino F.
        • Napoletano S.
        • Caiazzo F.
        • et al.
        Chromosomal microarray analysis as a first-line test in pregnancies with a priori low risk for the detection of submicroscopic chromosomal abnormalities.
        Eur J Hum Genet. 2013; 21: 725-730
        • Xu H.B.
        • Yang H.
        • Liu G.
        • Chen H.
        Systematic review of accuracy of prenatal diagnosis for abnormal chromosome diseases by microarray technology.
        Genet Mol Res. 2014; 13: 9115-9121
        • Ferreira J.C.
        • Grati F.R.
        • Bajaj K.
        • et al.
        Frequency of fetal karyotype abnormalities in women undergoing invasive testing in the absence of ultrasound and other high-risk indications.
        Prenat Diagn. 2016; 36: 1146-1155
        • Izetbegovic S.
        • Mehmedbasic S.
        Early amniocentesis as a method of choice in diagnosing gynecological diseases.
        Acta Inform Med. 2013; 21: 270-273
        • Huang L.
        • Jiang T.
        • Liu C.
        Fetal loss after amniocentesis: analysis of a single center’s 7,957 cases in China.
        Clin Exp Obstet Gynecol. 2015; 42: 184-187
        • Li H.
        • Durbin R.
        Fast and accurate short read alignment with Burrows–Wheeler transform.
        Bioinformatics. 2009; 25: 1754-1760
        • Richards S.
        • Aziz N.
        • Bale S.
        • et al.
        Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
        Genet Med. 2015; 17: 405-424
        • Steele M.W.
        • Berg Jr., W.R.
        Chromosome analysis of human amniotic fluid cells.
        Lancet. 1966; 1: 383-385
        • Committee on the Application of Fluorescence Hybridization Technique in Prenatal Diagnosis
        Common Opinion on the application of fluorescence in situ hybridization in prenatal diagnosis.
        Zonghua Fu Chan Ke Za Zhi. 2016; 51 ([in Chinese]): 241-244
        • Mann K.
        • Fox S.P.
        • Abbs S.J.
        • et al.
        Development and implementation of a new rapid aneuploidy diagnostic service within the UK National Health Service and implications for the future of prenatal diagnosis.
        Lancet. 2001; 358: 1057-1061
        • Wapner R.J.
        • Babiarz J.E.
        • Levy B.
        • et al.
        Expanding the scope of noninvasive prenatal testing: detection of fetal microdeletion syndromes.
        Am J Obstet Gynecol. 2015; 212: 332.e1-332.e9
        • Scott Jr., R.T.
        Introduction: Subchromosomal abnormalities in preimplantation embryonic screening.
        Fertil Steril. 2017; 107: 4-5
        • Zilina O.
        • Teek R.
        • Tammur P.
        • et al.
        Chromosomal microarray analysis as a first-tier clinical diagnostic test: Estonian experience.
        Mol Genet Genomic Med. 2014; 2: 166-175
        • Reddy U.M.
        • Page G.P.
        • Saade G.R.
        • et al.
        Karyotype versus microarray testing for genetic abnormalities after stillbirth.
        N Engl J Med. 2012; 367: 2185-2193
        • Battaglia A.
        • Doccini V.
        • Bernardini L.
        • et al.
        Confirmation of chromosomal microarray as a first-tier clinical diagnostic test for individuals with developmental delay, intellectual disability, autism spectrum disorders and dysmorphic features.
        Eur J Paediatr Neurol. 2013; 17: 589-599
        • Kersting A.
        • Kroker K.
        • Steinhard J.
        • et al.
        Psychological impact on women after second and third trimester termination of pregnancy due to fetal anomalies versus women after preterm birth—a 14-month follow up study.
        Arch Womens Ment Health. 2009; 12: 193-201
        • Cram D.S.
        • Zhou D.
        Next generation sequencing: coping with rare genetic diseases in China.
        Intractable Rare Dis Res. 2016; 5: 140-144
        • Nowakowska B.J.
        Clinical interpretation of copy number variants in the human genome.
        Appl Genet. 2017; 58: 449-457
        • Evans M.I.
        • Wapner R.J.
        • Berkowitz R.L.
        Noninvasive prenatal screening or advanced diagnostic testing: caveat emptor.
        Am J Obstet Gynecol. 2016; 215: 298-305
        • Petersen A.K.
        • Cheung S.W.
        • Smith J.L.
        • et al.
        Positive predictive value estimates for cell-free noninvasive prenatal screening from data of a large referral genetic diagnostic laboratory.
        Am J Obstet Gynecol. 2017; 217: 691.e1-691.e6
        • Fiorentino F.
        • Bono S.
        • Pizzuti F.
        • et al.
        The clinical utility of genome-wide noninvasive prenatal screening.
        Prenat Diagn. 2017; 37: 593-601