Advanced search
Publication Cover
Expert Review of Molecular Diagnostics Volume 11, 2011 - Issue 6
Submit an article Journal homepage
93
Views
22
CrossRef citations to date
0
Altmetric
Review

Copy-number changes in prenatal diagnosis

Melissa Strassberg Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
,
Gary Fruhman Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
&
Ignatia B Van den Veyver Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA;[email protected]
Pages 579-592 | Published online: 09 Jan 2014

References

  • Manning M, Hudgins L. Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet. Med.12(11), 742–745 (2010).
  • Miller DT, Adam MP, 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.86(5), 749–764 (2010).
  • Stankiewicz P, Beaudet AL. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr. Opin. Genet. Dev.17(3), 182–192 (2007).
  • Trask BJ. Human cytogenetics: 46 chromosomes, 46 years and counting. Nat. Rev. Genet.3(10), 769–778 (2002).
  • Feldman B, Ebrahim SA, Hazan SL et al. Routine prenatal diagnosis of aneuploidy by FISH studies in high-risk pregnancies. Am. J. Med. Genet.90(3), 233–238 (2000).
  • Desmaze C, Prieur M, Amblard F et al. Physical mapping by FISH of the DiGeorge critical region (DGCR): involvement of the region in familial cases. Am. J. Hum. Genet.53(6), 1239–1249 (1993).
  • Driscoll DA, Salvin J, Sellinger B et al. Prevalence of 22q11 microdeletions in DiGeorge and velocardiofacial syndromes: implications for genetic counselling and prenatal diagnosis. J. Med. Genet.30(10), 813–817 (1993).
  • Pertl B, Pieber D, Lercher-Hartlieb A et al. Rapid prenatal diagnosis of aneuploidy by quantitative fluorescent PCR on fetal samples from mothers at high risk for chromosome disorders. Mol. Hum. Reprod.5(12), 1176–1179 (1999).
  • Hochstenbach R, Meijer J, van de Brug J et al. Rapid detection of chromosomal aneuploidies in uncultured amniocytes by multiplex ligation-dependent probe amplification (MLPA). Prenat. Diagn.25(11), 1032–1039 (2005).
  • Tabor A, Philip J, Madsen M, Bang J, Obel EB, Norgaard-Pedersen B. Randomised controlled trial of genetic amniocentesis in 4606 low-risk women. Lancet1(8493), 1287–1293 (1986).
  • Eddleman KA, Malone FD, Sullivan L et al. Pregnancy loss rates after midtrimester amniocentesis. Obstet. Gynecol.108(5), 1067–1072 (2006).
  • ACOG. ACOG Practice Bulletin No. 88, December 2007. Invasive prenatal testing for aneuploidy. Obstet. Gynecol.110(6), 1459–1467 (2007).
  • Katz-Jaffe MG, Mantzaris D, Cram DS. DNA identification of fetal cells isolated from cervical mucus: potential for early non-invasive prenatal diagnosis. Br. J. Obstet. Gynecol.112(5), 595–600 (2005).
  • ACOG. ACOG Practice Bulletin No. 77: screening for fetal chromosomal abnormalities. Obstet. Gynecol.109(1), 217–227 (2007).
  • Kallioniemi A, Kallioniemi OP, Sudar D et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science258(5083), 818–821 (1992).
  • Cheung SW, Shaw CA, Yu W et al. Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet. Med.7(6), 422–432 (2005).
  • Ballif BC, Kashork CD, Saleki R et al. Detecting sex chromosome anomalies and common triploidies in products of conception by array-based comparative genomic hybridization. Prenat. Diagn.26(4), 333–339 (2006).
  • Scherer SW, Lee C, Birney E et al. Challenges and standards in integrating surveys of structural variation. Nat. Genet.39(Suppl. 7), S7–S15 (2007).
  • Carter NP. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet.39(Suppl. 7), S16–S21 (2007).
  • Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu. Rev. Med.61, 437–455 (2010).
  • Lu X, Shaw CA, Patel A et al. Clinicalimplementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS One2(3), e327 (2007).
  • Shaffer LG, Kashork CD, Saleki R et al. Targeted genomic microarray analysis for identification of chromosome abnormalities in 1500 consecutive clinical cases. J. Pediatr.149(1), 98–102 (2006).
  • Bejjani BA, Saleki R, Ballif BC et al. Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: is less more? Am. J. Med. Genet. A134(3), 259–267 (2005).
  • Cheung SW, Shaw CA, Scott DA et al. Microarray-based CGH detects chromosomal mosaicism not revealed by conventional cytogenetics. Am. J. Med. Genet. A143A(15), 1679–1686 (2007).
  • Ballif BC, Sulpizio SG, Lloyd RM et al. The clinical utility of enhanced subtelomeric coverage in array CGH. Am. J. Med. Genet. A143A(16), 1850–1857 (2007).
  • Sahoo T, Cheung SW, Ward P et al. Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization. Genet. Med.8(11), 719–727 (2006).
  • Van den Veyver IB, Patel A, Shaw CA et al. Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases. Prenat. Diagn.29(1), 29–39 (2009).
  • Kashork CD, Theisen A, Shaffer LG. Prenatal diagnosis using array CGH. Methods Mol. Biol.444, 59–69 (2008).
  • Veltman JA, de Vries BB. Diagnostic genome profiling: unbiased whole genome or targeted analysis? J. Mol. Diagn.8(5), 534–537; discussion 537–539 (2006).
  • Choy KW, Setlur SR, Lee C, Lau TK. The impact of human copy number variation on a new era of genetic testing. Br. J. Obstet. Gynecol.117(4), 391–398 (2010).
  • Iafrate AJ, Feuk L, Rivera MN et al. Detection of large-scale variation in the human genome. Nat. Genet.36(9), 949–951 (2004).
  • Sebat J, Lakshmi B, Troge J et al. Large-scale copy number polymorphism in the human genome. Science305(5683), 525–528 (2004).
  • Redon R, Ishikawa S, Fitch KR et al. Global variation in copy number in the human genome. Nature444(7118), 444–454 (2006).
  • Conrad DF, Pinto D, Redon R et al. Origins and functional impact of copy number variation in the human genome. Nature464(7289), 704–712 (2010).
  • Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat. Rev. Genet.7(2), 85–97 (2006).
  • Lupski JR. Genomic rearrangements and sporadic disease. Nat. Genet.39(Suppl. 7), S43–S47 (2007).
  • Simovich MJ, Yatsenko SA, Kang SH et al. Prenatal diagnosis of a 9q34.3 microdeletion by array-CGH in a fetus with an apparently balanced translocation. Prenat. Diagn.27(12), 1112–1117 (2007).
  • Warburton D. De novo balanced chromosome rearrangements and extra marker chromosomes identified at prenatal diagnosis: clinical significance and distribution of breakpoints. Am. J. Hum. Genet.49(5), 995–1013 (1991).
  • Youssoufian H, Pyeritz RE. Mechanisms and consequences of somatic mosaicism in humans. Nat. Rev. Genet.3(10), 748–758 (2002).
  • Hahnemann JM, Vejerslev LO. Accuracy of cytogenetic findings on chorionic villus sampling (CVS) – diagnostic consequences of CVS mosaicism and non-mosaic discrepancy in centres contributing to EUCROMIC 1986–1992. Prenat. Diagn.17(9), 801–820 (1997).
  • Ledbetter DH, Zachary JM, Simpson JL et al. Cytogenetic results from the U.S. Collaborative Study on CVS. Prenat. Diagn.12(5), 317–345 (1992).
  • Ballif BC, Rorem EA, Sundin K et al. Detection of low-level mosaicism by array CGH in routine diagnostic specimens. Am. J. Med. Genet. A140(24), 2757–2767 (2006).
  • Bi W, Breman AM, Venable SF et al. Rapid prenatal diagnosis using uncultured amniocytes and oligonucleotide array CGH. Prenat. Diagn.28(10), 943–949 (2008).
  • Schaeffer AJ, Chung J, Heretis K, Wong A, Ledbetter DH, Lese Martin C. Comparative genomic hybridization-array analysis enhances the detection of aneuploidies and submicroscopic imbalances in spontaneous miscarriages. Am. J. Hum. Genet.74(6), 1168–1174 (2004).
  • Veenma D, Beurskens N, Douben H et al. Comparable low-level mosaicism in affected and non affected tissue of a complex CDH patient. PLoS One5(12), e15348 (2010).
  • Rodriguez-Santiago B, Malats N, Rothman N et al. Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome. Am. J. Hum. Genet.87(1), 129–138 (2010).
  • Conlin LK, Thiel BD, Bonnemann CG et al. Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum. Mol. Genet.19(7), 1263–1275 (2010).
  • Cross J, Peters G, Wu Z, Brohede J, Hannan GN. Resolution of trisomic mosaicism in prenatal diagnosis: estimated performance of a 50K SNP microarray. Prenat. Diagn.27(13), 1197–1204 (2007).
  • Liehr T, Claussen U, Starke H. Small supernumerary marker chromosomes (sSMC) in humans. Cytogenet. Genome Res.107(1–2), 55–67 (2004).
  • Graf MD, Christ L, Mascarello JT et al. Redefining the risks of prenatally ascertained supernumerary marker chromosomes: a collaborative study. J. Med. Genet.43(8), 660–664 (2006).
  • Ballif BC, Hornor SA, Sulpizio SG et al. Development of a high-density pericentromeric region BAC clone set for the detection and characterization of small supernumerary marker chromosomes by array CGH. Genet. Med.9(3), 150–162 (2007).
  • Choe J, Kang JK, Bae CJ et al. Identification of origin of unknown derivative chromosomes by array-based comparative genomic hybridization using pre- and postnatal clinical samples. J. Hum. Genet.52(11), 934–942 (2007).
  • Tyreman M, Abbott KM, Willatt LR et al. High resolution array analysis: diagnosing pregnancies with abnormal ultrasound findings. J. Med. Genet.46(8), 531–541 (2009).
  • Schaaf CP, Scott DA, Wiszniewska J, Beaudet AL. Identification of incestuous parental relationships by SNP-based DNA microarrays. Lancet377(9765), 555–556 (2011).
  • Shaffer LG, Bejjani BA, Torchia B, Kirkpatrick S, Coppinger J, Ballif BC. The identification of microdeletion syndromes and other chromosome abnormalities: cytogenetic methods of the past, new technologies for the future. Am. J. Med. Genet. C Semin. Med. Genet.145C(4), 335–345 (2007).
  • Ben-Shachar S, Ou Z, Shaw CA et al. 22q11.2 distal deletion: a recurrent genomic disorder distinct from DiGeorge syndrome and velocardiofacial syndrome. Am. J. Hum. Genet.82(1), 214–221 (2008).
  • Berg JS, Brunetti-Pierri N, Peters SU et al. Speech delay and autism spectrum behaviors are frequently associated with duplication of the 7q11.23 Williams–Beuren syndrome region. Genet. Med.9(7), 427–441 (2007).
  • Lupski JR. Genome structural variation and sporadic disease traits. Nat. Genet.38(9), 974–976 (2006).
  • Koolen DA, Vissers LE, Pfundt R et al. A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat. Genet.38(9), 999–1001 (2006).
  • Kirchhoff M, Bisgaard AM, Duno M, Hansen FJ, Schwartz M. A 17q21.31 microduplication, reciprocal to the newly described 17q21.31 microdeletion, in a girl with severe psychomotor developmental delay and dysmorphic craniofacial features. Eur J. Med. Genet.50(4), 256–263 (2007).
  • Potocki L, Bi W, Treadwell-Deering D et al. Characterization of Potocki–Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype. Am. J. Hum. Genet.80(4), 633–649 (2007).
  • del Gaudio D, Fang P, Scaglia F et al. Increased MECP2 gene copy number as the result of genomic duplication in neurodevelopmentally delayed males. Genet. Med.8(12), 784–792 (2006).
  • Somerville MJ, Mervis CB, Young EJ et al. Severe expressive-language delay related to duplication of the Williams–Beuren locus. N. Engl. J. Med.353(16), 1694–1701 (2005).
  • Vissers LE, van Ravenswaaij CM, Admiraal R et al. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat. Genet.36(9), 955–957 (2004).
  • Wang X, Reid Sutton V, Omar Peraza-Llanes J et al. Mutations in X-linked PORCN, a putative regulator of Wnt signaling, cause focal dermal hypoplasia. Nat. Genet.39(7), 836–838 (2007).
  • Grzeschik KH, Bornholdt D, Oeffner F et al. Deficiency of PORCN, a regulator of Wnt signaling, is associated with focal dermal hypoplasia. Nat. Genet.39(7), 833–835 (2007).
  • Scott DA, Klaassens M, Holder AM et al. Genome-wide oligonucleotide-based array comparative genome hybridization analysis of non-isolated congenital diaphragmatic hernia. Hum. Mol. Genet.16(4), 424–430 (2007).
  • Klaassens M, van Dooren M, Eussen HJ et al. Congenital diaphragmatic hernia and chromosome 15q26: determination of a candidate region by use of fluorescent in situ hybridization and array-based comparative genomic hybridization. Am. J. Hum. Genet.76(5), 877–882 (2005).
  • Slavotinek AM, Moshrefi A, Davis R et al. Array comparative genomic hybridization in patients with congenital diaphragmatic hernia: mapping of four CDH-critical regions and sequencing of candidate genes at 15q26.1–15q26.2. Eur J. Hum. Genet.14(9), 999–1008 (2006).
  • Greenberg F, Guzzetta V, Montes de Oca-Luna R et al. Molecular analysis of the Smith–Magenis syndrome: a possible contiguous-gene syndrome associated with del(17)(p11.2). Am. J. Hum. Genet.49(6), 1207–1218 (1991).
  • Shaw-Smith C, Pittman AM, Willatt L et al. Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability. Nat. Genet.38(9), 1032–1037 (2006).
  • Sharp AJ, Hansen S, Selzer RR et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat. Genet.38(9), 1038–1042 (2006).
  • Gajecka M, Mackay KL, Shaffer LG. Monosomy 1p36 deletion syndrome. Am. J. Med. Genet. C Semin. Med. Genet.145C(4), 346–356 (2007).
  • Sebat J. Major changes in our DNA lead to major changes in our thinking. Nat. Genet.39(Suppl. 7), S3–S5 (2007).
  • Szatmari P, Paterson AD, Zwaigenbaum L et al. Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat. Genet.39(3), 319–328 (2007).
  • Le Caignec C, Boceno M, Saugier-Veber P et al. Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J. Med. Genet.42(2), 121–128 (2005).
  • Rickman L, Fiegler H, Shaw-Smith C et al. Prenatal detection of unbalanced chromosomal rearrangements by array CGH. J. Med. Genet.43(4), 353–361 (2006).
  • Kleeman L, Bianchi DW, Shaffer LG et al. Use of array comparative genomic hybridization for prenatal diagnosis of fetuses with sonographic anomalies and normal metaphase karyotype. Prenat. Diagn.29(13), 1213–1217 (2009).
  • Vialard F, Molina Gomes D, Leroy B et al. Array comparative genomic hybridization in prenatal diagnosis: another experience. Fetal Diagn. Ther.25(2), 277–284 (2009).
  • Valduga M, Philippe C, Bach Segura P et al. A retrospective study by oligonucleotide array-CGH analysis in 50 fetuses with multiple malformations. Prenat. Diagn.30(4), 333–341 (2010).
  • Faas BH, van der Burgt I, Kooper AJ et al. Identification of clinically significant, submicroscopic chromosome alterations and UPD in fetuses with ultrasound anomalies using genome-wide 250k SNP array analysis. J. Med. Genet.47(9), 586–594 (2010).
  • Hillman SC, Pretlove S, Coomarasamy A et al. Additional information from array comparative genomic hybridisation (array CGH) technology over conventional karyotyping in prenatal diagnosis – a systematic review and meta-analysis. Ultrasound Obstet. Gynecol.37(1), 6–14 (2011).
  • Leung TY, Vogel I, Lau TK et al. Identification of submicroscopic chromosomal aberrations in fetuses with increased nuchal translucency and an apparently normal karyotype. Ultrasound Obstet. Gynecol. DOI: 10.1002/uog.8988 (2011) (Epub ahead of print).
  • Shaffer LG, Coppinger J, Alliman S et al. Comparison of microarray-based detection rates for cytogenetic abnormalities in prenatal and neonatal specimens. Prenat. Diagn.28(9), 789–795 (2008).
  • Coppinger J, Alliman S, Lamb AN, Torchia BS, Bejjani BA, Shaffer LG. Whole-genome microarray analysis in prenatal specimens identifies clinically significant chromosome alterations without increase in results of unclear significance compared with targeted microarray. Prenat. Diagn.29(12), 1156–1166 (2009).
  • Benkhalifa M, Kasakyan S, Clement P et al. Array comparative genomic hybridization profiling of first-trimester spontaneous abortions that fail to grow in vitro. Prenat. Diagn.25(10), 894–900 (2005).
  • Shimokawa O, Harada N, Miyake N et al. Array comparative genomic hybridization analysis in first-trimester spontaneous abortions with ‘normal’ karyotypes. Am. J. Med. Genet. A140(18), 1931–1935 (2006).
  • Menten B, Swerts K, Delle Chiaie B et al. Array comparative genomic hybridization and flow cytometry analysis of spontaneous abortions and mors in utero samples. BMC Med. Genet.10, 89 (2009).
  • Zhang YX, Zhang YP, Gu Y et al. Genetic analysis of first-trimester miscarriages with a combination of cytogenetic karyotyping, microsatellite genotyping and array CGH. Clin. Genet.75(2), 133–140 (2009).
  • Robberecht C, Schuddinck V, Fryns JP, Vermeesch JR. Diagnosis of miscarriages by molecular karyotyping: benefits and pitfalls. Genet. Med.11(9), 646–654 (2009).
  • Rajcan-Separovic E, Qiao Y, Tyson C et al. Genomic changes detected by array CGH in human embryos with developmental defects. Mol. Hum. Reprod.16(2), 125–134 (2010).
  • Rajcan-Separovic E, Diego-Alvarez D, Robinson WP et al. Identification of copy number variants in miscarriages from couples with idiopathic recurrent pregnancy loss. Hum. Reprod.25(11), 2913–2922 (2010).
  • Larrabee PB, Johnson KL, Pestova E et al. Microarray analysis of cell-free fetal DNA in amniotic fluid: a prenatal molecular karyotype. Am. J. Hum. Genet.75(3), 485–491 (2004).
  • Miura S, Miura K, Masuzaki H et al. Microarray comparative genomic hybridization (CGH)-based prenatal diagnosis for chromosome abnormalities using cell-free fetal DNA in amniotic fluid. J. Hum. Genet.51(5), 412–417 (2006).
  • Lapaire O, Lu XY, Johnson KL et al. Array-CGH analysis of cell-free fetal DNA in 10 ml of amniotic fluid supernatant. Prenat. Diagn.27(7), 616–621 (2007).
  • Klopocki E, Schulze H, Strauss G et al. Complex inheritance pattern resembling autosomal recessive inheritance involving a microdeletion in thrombocytopenia-absent radius syndrome. Am. J. Hum. Genet.80(2), 232–240 (2007).
  • Hills A, Ahn JW, Donaghue C, Thomas H, Mann K, Ogilvie CM. MLPA for confirmation of array CGH results and determination of inheritance. Mol. Cytogenet.3, 19 (2010).
  • Park JH, Woo JH, Shim SH et al. Application of a target array comparative genomic hybridization to prenatal diagnosis. BMC Med. Genet.11, 102 (2010).
  • ACOG. ACOG Committee Opinion No. 446: array comparative genomic hybridization in prenatal diagnosis. Obstet. Gynecol.114(5), 1161–1163 (2009).
  • Shuster E. Microarray genetic screening: a prenatal roadblock for life? Lancet369(9560), 526–529 (2007).
  • Darilek S, Ward P, Pursley A et al. Pre- and postnatal genetic testing by array-comparative genomic hybridization: genetic counseling perspectives. Genet. Med.10(1), 13–18 (2008).
  • Wapner R, Jackson L. Chromosomal microarray analysis for prenatal diagnosis: a prospective comparison with conventional cytogenetics. Prenat. Diagn.28, S8–S9 (2008).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.