Applications of Noninvasive Prenatal Testing for Subchromosomal Copy Number Variations Using Cell-Free DNA

  • Jiale Xiang
    Affiliations
    BGI Genomics, BGI-Shenzhen, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China

    College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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  • Zhiyu Peng
    Correspondence
    Corresponding author.
    Affiliations
    BGI Genomics, BGI-Shenzhen, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China

    College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
    Search for articles by this author
Published:September 01, 2021DOI:https://doi.org/10.1016/j.yamp.2021.07.002
      Noninvasive prenatal testing (NIPT) is now clinically available for screening fetal subchromosomal copy number variations (CNVs).

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      References

        • Lo Y.M.
        • Corbetta N.
        • Chamberlain P.F.
        • et al.
        Presence of fetal DNA in maternal plasma and serum.
        Lancet. 1997; 350: 485-487
        • Bianchi D.W.
        • Chiu R.W.K.
        Sequencing of circulating cell-free DNA during pregnancy.
        N Engl J Med. 2018; 379: 464-473
        • Gadsboll K.
        • Petersen O.B.
        • Gatinois V.
        • et al.
        Current use of noninvasive prenatal testing in Europe, Australia and the USA: a graphical presentation.
        Acta Obstet Gynecol Scand. 2020; 99: 722-730
        • Van Den Bogaert K.
        • Lannoo L.
        • Brison N.
        • et al.
        Outcome of publicly funded nationwide first-tier noninvasive prenatal screening.
        Genet Med. 2021; 23: 1137-1142
        • 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
        • Wang H.
        • Dong Z.
        • Zhang R.
        • et al.
        Low-pass genome sequencing versus chromosomal microarray analysis: implementation in prenatal diagnosis.
        Genet Med. 2020; 22: 500-510
        • Capalbo A.
        • Rienzi L.
        • Ubaldi F.M.
        Diagnosis and clinical management of duplications and deletions.
        Fertil Steril. 2017; 107: 12-18
        • Gregg A.R.
        • Skotko B.G.
        • Benkendorf J.L.
        • et al.
        Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics.
        Genet Med. 2016; 18: 1056-1065
        • Liang D.
        • Cram D.S.
        • Tan H.
        • et al.
        Clinical utility of noninvasive prenatal screening for expanded chromosome disease syndromes.
        Genet Med. 2019; 21: 1998-2006
        • van der Meij K.R.M.
        • Sistermans E.A.
        • Macville M.V.E.
        • et al.
        TRIDENT-2: national implementation of genome-wide non-invasive prenatal testing as a first-tier screening test in the Netherlands.
        Am J Hum Genet. 2019; 105: 1091-1101
        • Liao G.J.
        • Chan K.C.
        • Jiang P.
        • et al.
        Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA.
        PLoS One. 2012; 7: e38154
        • Chiu R.W.
        • Chan K.C.
        • Gao Y.
        • et al.
        Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma.
        Proc Natl Acad Sci U S A. 2008; 105: 20458-20463
        • Helgeson J.
        • Wardrop J.
        • Boomer T.
        • et al.
        Clinical outcome of subchromosomal events detected by whole-genome noninvasive prenatal testing.
        Prenat Diagn. 2015; 35: 999-1004
        • 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 e1-9
        • Martin K.
        • Iyengar S.
        • Kalyan A.
        • et al.
        Clinical experience with a single-nucleotide polymorphism-based non-invasive prenatal test for five clinically significant microdeletions.
        Clin Genet. 2018; 93: 293-300
        • Lefkowitz R.B.
        • Tynan J.A.
        • Liu T.
        • et al.
        Clinical validation of a noninvasive prenatal test for genomewide detection of fetal copy number variants.
        Am J Obstet Gynecol. 2016; 215: 227.e1-227.e16
        • Li R.
        • Wan J.
        • Zhang Y.
        • et al.
        Detection of fetal copy number variants by non-invasive prenatal testing for common aneuploidies.
        Ultrasound Obstet Gynecol. 2016; 47: 53-57
        • Liu H.
        • Gao Y.
        • Hu Z.
        • et al.
        Performance evaluation of NIPT in detection of chromosomal copy number variants using low-coverage whole-genome sequencing of plasma DNA.
        PLoS One. 2016; 11: e0159233
        • Dong Z.
        • Yan J.
        • Xu F.
        • et al.
        Genome sequencing explores complexity of chromosomal abnormalities in recurrent miscarriage.
        Am J Hum Genet. 2019; 105: 1102-1111
        • Shaffer L.G.
        • Bejjani B.A.
        A cytogeneticist's perspective on genomic microarrays.
        Hum Reprod Update. 2004; 10: 221-226
        • Huber D.
        • Voith von Voithenberg L.
        • Kaigala G.V.
        Fluorescence in situ hybridization (FISH): history, limitations and what to expect from micro-scale FISH?.
        Micro Nano Eng. 2018; 1: 15-24
        • Levy B.
        • Burnside R.D.
        Are all chromosome microarrays the same? What clinicians need to know.
        Prenat Diagn. 2019; 39: 157-164
        • Miller D.T.
        • Adam M.P.
        • Aradhya S.
        • et al.
        Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.
        Am J Hum Genet. 2010; 86: 749-764
        • 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
        • Rose N.C.
        • Kaimal A.J.
        • Dugoff L.
        • et al.
        Screening for fetal chromosomal abnormalities: ACOG Practice Bulletin, Number 226.
        Obstet Gynecol. 2020; 136: e48-e69
        • Dondorp W.
        • de Wert G.
        • Bombard Y.
        • et al.
        Non-invasive prenatal testing for aneuploidy and beyond: challenges of responsible innovation in prenatal screening.
        Eur J Hum Genet. 2015; 23: 1438-1450
        • Zhao C.
        • Tynan J.
        • Ehrich M.
        • et al.
        Detection of fetal subchromosomal abnormalities by sequencing circulating cell-free DNA from maternal plasma.
        Clin Chem. 2015; 61: 608-616
        • Canick J.A.
        • Palomaki G.E.
        • Kloza E.M.
        • et al.
        The impact of maternal plasma DNA fetal fraction on next generation sequencing tests for common fetal aneuploidies.
        Prenat Diagn. 2013; 33: 667-674
        • Yin A.H.
        • Peng C.F.
        • Zhao X.
        • et al.
        Noninvasive detection of fetal subchromosomal abnormalities by semiconductor sequencing of maternal plasma DNA.
        Proc Natl Acad Sci U S A. 2015; 112: 14670-14675
        • Welker N.C.
        • Lee A.K.
        • Kjolby R.A.S.
        • et al.
        High-throughput fetal fraction amplification increases analytical performance of noninvasive prenatal screening.
        Genet Med. 2021; 23: 443-450
        • Liang B.
        • Li H.
        • He Q.
        • et al.
        Enrichment of the fetal fraction in non-invasive prenatal screening reduces maternal background interference.
        Sci Rep. 2018; 8: 17675
        • Hu P.
        • Liang D.
        • Chen Y.
        • et al.
        An enrichment method to increase cell-free fetal DNA fraction and significantly reduce false negatives and test failures for non-invasive prenatal screening: a feasibility study.
        J Transl Med. 2019; 17: 124
        • He Q.Z.
        • Wu X.J.
        • He Q.Y.
        • et al.
        A method for improving the accuracy of non-invasive prenatal screening by cell-free foetal DNA size selection.
        Br J Biomed Sci. 2018; 75: 133-138
        • Quail M.A.
        • Gu Y.
        • Swerdlow H.
        • et al.
        Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation.
        Electrophoresis. 2012; 33: 3521-3528
        • Vong J.S.L.
        • Jiang P.
        • Cheng S.H.
        • et al.
        Enrichment of fetal and maternal long cell-free DNA fragments from maternal plasma following DNA repair.
        Prenat Diagn. 2019; 39: 88-99
        • Lo Y.M.
        • Chan K.C.
        • Sun H.
        • et al.
        Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus.
        Sci Transl Med. 2010; 2: 61ra91
        • Fan H.C.
        • Blumenfeld Y.J.
        • Chitkara U.
        • et al.
        Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing.
        Clin Chem. 2010; 56: 1279-1286
        • Zhang B.
        • Zhao S.
        • Wan H.
        • et al.
        High-resolution DNA size enrichment using a magnetic nano-platform and application in non-invasive prenatal testing.
        Analyst. 2020; 145: 5733-5739
        • Qiao L.
        • Yu B.
        • Liang Y.
        • et al.
        Sequencing shorter cfDNA fragments improves the fetal DNA fraction in noninvasive prenatal testing.
        Am J Obstet Gynecol. 2019; 221: 345.e1-345.e11
        • Qiao L.
        • Zhang Q.
        • Liang Y.
        • et al.
        Sequencing of short cfDNA fragments in NIPT improves fetal fraction with higher maternal BMI and early gestational age.
        Am J Transl Res. 2019; 11: 4450-4459
        • Quail M.A.
        • Swerdlow H.
        • Turner D.J.
        Improved protocols for the Illumina genome analyzer sequencing system.
        Curr Protoc Hum Genet. 2009; (Chapter 18:Unit 18 2)
        • Lo K.K.
        • Karampetsou E.
        • Boustred C.
        • et al.
        Limited clinical utility of non-invasive prenatal testing for subchromosomal abnormalities.
        Am J Hum Genet. 2016; 98: 34-44
        • Rampasek L.
        • Arbabi A.
        • Brudno M.
        Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing.
        Bioinformatics. 2014; 30: i212-i218
        • Srinivasan A.
        • Bianchi D.W.
        • Huang H.
        • et al.
        Noninvasive detection of fetal subchromosome abnormalities via deep sequencing of maternal plasma.
        Am J Hum Genet. 2013; 92: 167-176
        • Kucharik M.
        • Gnip A.
        • Hyblova M.
        • et al.
        Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: detection limits of screened chromosomal microdeletions.
        PLoS One. 2020; 15: e0238245
        • Liao C.
        • Yin A.H.
        • Peng C.F.
        • et al.
        Noninvasive prenatal diagnosis of common aneuploidies by semiconductor sequencing.
        Proc Natl Acad Sci U S A. 2014; 111: 7415-7420
        • Maya I.
        • Sharony R.
        • Yacobson S.
        • et al.
        When genotype is not predictive of phenotype: implications for genetic counseling based on 21,594 chromosomal microarray analysis examinations.
        Genet Med. 2018; 20: 128-131
        • Rosenfeld J.A.
        • Coe B.P.
        • Eichler E.E.
        • et al.
        Estimates of penetrance for recurrent pathogenic copy-number variations.
        Genet Med. 2013; 15: 478-481
        • Hu H.
        • Wang L.
        • Wu J.
        • et al.
        Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 8141 single pregnancies.
        Hum Genomics. 2019; 13: 14
        • Riggs E.R.
        • Andersen E.F.
        • Cherry A.M.
        • et al.
        Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).
        Genet Med. 2020; 22: 245-257
        • Girirajan S.
        • Rosenfeld J.A.
        • Coe B.P.
        • et al.
        Phenotypic heterogeneity of genomic disorders and rare copy-number variants.
        N Engl J Med. 2012; 367: 1321-1331
        • Sachs A.
        • Blanchard L.
        • Buchanan A.
        • et al.
        Recommended pre-test counseling points for noninvasive prenatal testing using cell-free DNA: a 2015 perspective.
        Prenat Diagn. 2015; 35: 968-971
        • McDonald-McGinn D.M.
        • Hain H.S.
        • Emanuel B.S.
        • et al.
        22q11.2 deletion syndrome.
        in: Adam M.P. Ardinger H.H. Pagon R.A. GeneReviews® [Internet]. University of Washington, Seattle, Seattle (WA)2020: 1993-2021 (Available at:)
        • Driscoll D.J.
        • Miller J.L.
        • Schwartz S.
        • et al.
        Prader-Willi syndrome.
        in: Adam M.P. Ardinger H.H. Pagon R.A. GeneReviews® [Internet]. University of Washington, Seattle, Seattle (WA)1998: 1993-2021 (Available at:)
        • Dagli A.I.
        • Mueller J.
        • CA W.
        Angelman syndrome.
        in: Adam M.P. Ardinger H.H. Pagon R.A. GeneReviews® [Internet]. University of Washington, Seattle, Seattle (WA)1998 (1993-2021. Available at:)
        • Cerruti Mainardi P.
        Cri du chat syndrome.
        Orphanet J Rare Dis. 2006; 1: 33
        • Firth H.V.
        • Richards S.M.
        • Bevan A.P.
        • et al.
        DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.
        Am J Hum Genet. 2009; 84: 524-533
        • Jordan V.K.
        • Zaveri H.P.
        • Scott D.A.
        1p36 deletion syndrome: an update.
        Appl Clin Genet. 2015; 8: 189-200
        • Battaglia A.
        • Carey J.C.
        • ST S.
        Wolf-Hirschhorn syndrome – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY.
        ([Updated 2015 Aug 20])in: Adam M.P. Ardinger H.H. Pagon R.A. GeneReviews® [Internet]. University of Washington, Seattle, Seattle (WA)2002 (1993-2021. Available at:)
        • Battaglia A.
        • Carey J.C.
        • South S.T.
        Wolf-Hirschhorn syndrome: a review and update.
        Am J Med Genet C Semin Med Genet. 2015; 169: 216-223
        • Mattina T.
        • Perrotta C.S.
        • Grossfeld P.
        Jacobsen syndrome.
        Orphanet J Rare Dis. 2009; 4: 9
        • Maas S.
        • Shaw A.
        • Bikker H.
        • et al.
        Trichorhinophalangeal syndrome.
        in: Adam M.P. Ardinger H.H. Pagon R.A. GeneReviews® [Internet]. University of Washington, Seattle, Seattle (WA)2017: 1993-2021 (Available at:)