The clinical utility of microarray technologies applied to prenatal cytogenetics in the presence of a normal conventional karyotype: a review of the literature

Jonathan L A Callaway, Lisa G Shaffer, Lyn S Chitty, Jill A Rosenfeld, John A Crolla, Jonathan L A Callaway, Lisa G Shaffer, Lyn S Chitty, Jill A Rosenfeld, John A Crolla

Abstract

The clinical utility of microarray technologies when used in the context of prenatal diagnosis lies in the technology's ability to detect submicroscopic copy number changes that are associated with clinically significant outcomes. We have carried out a systematic review of the literature to calculate the utility of prenatal microarrays in the presence of a normal conventional karyotype. Amongst 12,362 cases in studies that recruited cases from all prenatal ascertainment groups, 295/12,362 (2.4%) overall were reported to have copy number changes with associated clinical significance (pCNC), 201/3090 (6.5%) when ascertained with an abnormal ultrasound, 50/5108 (1.0%) when ascertained because of increased maternal age and 44/4164 (1.1%) for all other ascertainment groups (e.g. parental anxiety and abnormal serum screening result). When additional prenatal microarray studies are included in which ascertainment was restricted to fetuses with abnormal ultrasound scans, 262/3730 (7.0%) were reported to have pCNCs.

© 2013 John Wiley & Sons, Ltd.

References

    1. Shaw-Smith C, Redon R, Rickman L, et al. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet. 2004;41(4):241–8.
    1. de Vries BB, Pfundt R, Leisink M. Diagnostic genome profiling in mental retardation. Am J Hum Genet. 2005;77(4):606–16.
    1. Miller DT, Adam MP, Aradhya S. 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(5):749–64.
    1. Shaffer LG, Bejjani BA, Torchia B. 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. 2007;145C(4):335–45.
    1. Tyreman M, Abbott KM, Willatt LR. High resolution array analysis: diagnosing pregnancies with abnormal ultrasound findings. J Med Genet. 2009;46:531–41.
    1. D'Amours G, Kibar Z, Mathonnet G. Whole-genome array CGH identifies pathogenic copy number variations in fetuses with major malformations and a normal karyotype. Clin Genet. 2012;81:128–41.
    1. Evangelidou P, Sismani C, Ioannides M. Clinical application of whole-genome array CGH during prenatal diagnosis: study of 25 selected pregnancies with abnormal ultrasound findings or apparently balanced structural aberrations. Mol Cytogenet. 2010;3:24.
    1. Valduga M, Philippe C, Bach Segura P. A retrospective study by oligonucleotide array-CGH analysis in 50 fetuses with multiple malformations. Prenat Diagn. 2010;30:333–341.
    1. Faas BH, van der Burgt I, Kooper AJ. Identification of clinically significant, submicroscopic chromosome alterations and UPD in fetuses with ultrasound anomalies using genome-wide 250k SNP array analysis. J Med Genet. 2010;47:586–94.
    1. Srebniak MI, Boter M, Oudesluijs GO. Genomic SNP array as a gold standard for prenatal diagnosis of foetal ulltrasound abnormalities. Mol Cytogenet. 2012;5:14.
    1. Le Caignec C, Boceno M, Saugier-Veber P. Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J Med Genet. 2005;42:121–128.
    1. Rooryck C, Toutain J, Cailley D. Prenatal diagnosis using array-CGH: a French experience. Eur J Med Genet. 2013 doi: [Epub ahead of print]
    1. Kleeman L, Bianchi DW, Shaffer LG. Use of array comparative genomic hybridization for prenatal diagnosis of fetuses with sonographic anomalies and normal metaphase karyotype. Prenat Diagn. 2009;29:1213–7.
    1. Wapner RJ, Martin CL, Levy B. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 2012;367:2175–84.
    1. Shaffer LG, Dabell MP, Fisher AJ. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diag. 2012;32:1–10.
    1. Lee C-N, Lin S-Y, Lin C-H. Clinical utility of array comparative genomic hybridisation for prenatal diagnosis: a cohort study of 3171 pregnancies. BJOG. 2012;119:614–25.
    1. Fiorentino F, Napoletano S, Caiazzo F. 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. 2012 doi: [Epub ahead of print]
    1. Armengol L, Nevado J, Serra-Juhe C. Clinical utility of chromosomal microarray analysis in invasive prenatal diagnosis. Hum Genet. 2012;131:513–23.
    1. Breman A, Pursley AN, Hixson P. Prenatal chromosomal microarray analysis in a diagnostic laboratory; experience with >1000 cases and review of the literature. Prenat Diagn. 2012;32:351–61.
    1. Park SJ, Jung EH, Ryu RS. Clinical implementation of whole-genome array CGH as a first-tier test in 5080 pre and postnatal cases. Mol Cytogenet. 2011;4:12.
    1. Maya I, Davidov B, Gershovitz L. Diagnostic utility of array-based comparative genomic hybridization (aCGH) in a prenatal setting. Prenat Diagn. 2010;30:1131–7.
    1. Coppinger J, Alliman S, Lamb AN. Whole-genome microarray analysis in prenatal specimens identifies clinically significant chromosome alterations without increase in results of unclear significance compared to targeted microarray. Prenat Diagn. 2009;29:1156–66.
    1. Reddy UM, Page GP, Saade GR. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med. 2012;367:2185–93.
    1. Filges I, Kang A, Klug V. Array comparative genomic hybridization in prenatal diagnosis of first trimester pregnancies at high risk for chromosomal anomalies. Mol Cytogenet. 2012;5:38.
    1. Leung TY, Vogel I, Lau TK. Identification of submicroscopic chromosomal aberrations in fetuses with increased nuchal translucency and apparently normal karyotype. Ultrasound Obstet Gynecol. 2011;38:314–319.
    1. Yatsenko SA, Davis S, Hendrix NW. Application of chromosomal microarray in the evaluation of abnormal prenatal findings. Clin Genet. 2012 doi: [Epub ahead of print]
    1. Tabor A, Alfirevic Z. Update on procedure-related risks for prenatal diagnosis techniques. Fetal Diagn Ther. 2010;27(1):1–7.
    1. Rosenfeld JA, Coe BP, Eichler EE. Estimates of penetrance for pathogenic copy-number variations. Genet Med. 2012 doi: [Epub ahead of print]
    1. Srinivsan A, Bianchi D, Huang H. Noninvasive detection of fetal subchromosome abnormalities via deep sequencing of maternal plasma. Am J Hum Genet. 2013;92:1–10.
    1. Dan S, Chen F, Choy KW. Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing. PLoS ONE. 2012 doi: [Epub ahead of print]
    1. Lau TK, Jiang FM, Stevenson RJ. Secondary findings from non-invasive prenatal testing for common fetal aneuploidies by whole genome sequencing as a clinical service. Prenat Diagn. 2013;33(6):602–8.
    1. Chen S, Lau TK, Zhang C. A method for noninvasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing. Prenat Diagn. 2013;33(6):584–90.

Source: PubMed

Sponsors en medewerkers

Medische omstandigheden

Geneesmiddelinterventies

3
Abonneren