Advertisement

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

      Noninvasive prenatal testing (NIPT) is now clinically available for screening fetal subchromosomal copy number variations (CNVs).

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribers receive full online access to your subscription and archive of back issues up to and including 2002.

      Content published before 2002 is available via pay-per-view purchase only.

      Subscribe:

      Subscribe to Clinics in Laboratory Medicine
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      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:)