Comparative Genomic Hybridization in the Study of Human Disease


Microarray‐based comparative genomic hybridization (CGH) has made a significant impact on the ability to diagnose human constitutional disease by detecting genomic copy number changes that were previously undetectable by other types of cytogenetic and molecular technologies. Not only can hundreds of well‐characterized genetic syndromes be detected in a single assay, but new genomic disorders and disease‐causing genes are also being discovered through the utilization of this technology. Clinical implementation of array CGH Hybridization has been extended to the prenatal setting, where it is also proving to enhance the diagnostic capabilities in the perinatal period. However, the clinical interpretation of the increasing number of copy number variations detected as the resolution of the microarrays is improved still poses a formidable challenge to laboratorians, health care providers and families.

Key Concepts:

  • Array comparative genomic Hybridization (aCGH) has several advantages over traditional cytogenetic methods for diagnosing human diseases: higher resolution, more robust and automated, and shorter turn around time since no cell culture is required.

  • Copy number variation (CNV) is common in the genome making it challenging for the clinical significance to be determined. Parental testing and utilisation of several internet‐based databases assist with the interpretation of CNVs.

  • The detection rate for clinically relevant CNVs by aCGH (10–20%) is significantly higher than traditional chromosome analysis (3%) making it the recommended first‐tier cytogenetic diagnostic test for patients with unexplained developmental delay/intellectual disability, autism spectrum disorders and multiple congenital anomalies by the International Standard Cytogenomic Array Consortium.

  • The resolution of aCGH has evolved to be sensitive enough to aid in the diagnosis of single gene disorders.

  • Array CGH is a useful tool for discovering new disease‐causing genes.

  • Array CGH has led to the recognition of many new genomic disorders, many of which cannot be diagnosed clinically due to lack cardinal features, variable expressivity and reduced penetrance.

  • CNVs, particularly those that occur de novo, are increasingly being recognised as important in the etiology of both syndromic and nonsyndromic autism as well as other neuropsychiatric disorders.

  • SNP‐based microarrays can be used to diagnosis uniparental disomy.

  • Array CGH is increasingly being used in prenatal diagnosis and has demonstrated its usefulness in clarifying the significance of karyotype findings and providing diagnoses not identifiable by chromosome analysis alone.

  • It is the opinion of The American College of Obstetrician and Gynecologists (2009) that aCGH not currently replace classic cytogenetics for prenatal diagnosis, but that targeted aCGH can be offered as an adjunct tool in prenatal cases with abnormal anatomical findings and normal karyotype, as well as in cases of fetal demise with congenital anomalies and the inability to obtain a conventional karyotype.

Keywords: array comparative genomic Hybridization; copy number variation; genomic disorders; autism; uniparental disomy; prenatal diagnosis; microarray; microdeletion; microduplication

Figure 1.

Array comparative genomic hybridization. A schematic of the array CGH process is shown at the top of the slide. The bottom left portion of the slide shows a typical representation of the array data generated by in‐house software for copy number analysis with an image of the FISH confirmation on the right. (a) Genomic DNA from the patient is labelled with a green fluorescent dye (Cy5) and genomic DNA from a normal control is labelled with a red fluorescent dye (Cy3). (b) The two samples are mixed and co‐hybridized to the array of DNA fragments. (c) A laser scanner reads the fluorescent signals and the intensities of each color are quantified using special software. A copy number loss is indicated by a red spot (more control and less patient DNA) and a copy number gain is indicated by a green spot (more patient and less control DNA). (d) The graph is arranged so that chromosomal data are presented in order from chromosome 1 on the left to chromosome Y on the right. The log2 ratio scale is shown on the Y‐Axis. The centre line represents neutral copy number, and gains and losses are plotted above and below this line, respectively. In this example, a loss in copy number on chromosome 17p12 is shown in red. The table below shows the location, size of deletion, log ratio as well as the number of the oligos within this region. (e) FISH confirmation shows lack of signal (red oval) for target probe on one chromosome 17, confirming the deletion (green signal is control probe, red signal is target probe) Deletions in this region have been reported in patients with hereditary neuropathy with liability to pressure palsies (HNPP, OMIN 162500).

Figure 2.

Detection of genomic disorders. Detection of 22q.11.2 microdeletion syndrome and reciprocal 22q11.2 microduplication syndrome by array CGH with FISH confirmation. (a1) Array CGH showing a loss in copy number of chromosome band 22q11.2 involving the 22q11.2 deletion syndrome region (red circle). (a2) FISH analysis shows lack of signal (red oval) for target probe on one chromosome 22, confirming the deletion (green signal is control probe, red signal is target probe). Insert‐G‐banded chromosome analysis showing the deletion on one chromosome 22 (black arrow). (b1) Array CGH showing a gain in copy number of chromosome band 22q11.2 involving the 22q11.2 duplication syndrome region (red circle). (b2) FISH analysis shows three signals for the target probe, confirming the duplication (green signal is control probe, red signal is target probe). Insert‐G‐banded chromosome analysis showing the duplication on one chromosome 22 (black arrow).

Figure 3.

Detection of UPD and IBD by SNP array analysis. SNP array analysis showing evidence of uniparental disomy (UPD) and identity by descent (IBD). (a) UPD for the entire chromosome 15 is indicated by absence of heterozygosity (top panel‐lack of signal at 0.5 B allele frequency (BAF) which represents genotype A/B) and no change in copy number (bottom panel‐all signals are at 0 Log ratio). (b) Blocks of absence of heterozygosity (AOH) of the proximal regions of chromosome 9p and 9q as demonstrated by lack of signals at the 0.5 BAF. Within the block of AOH at 9p (red oval) is the gene for galactosaemia, GALT. The patient is affected with galactosaemia due to a homozygous mutation in the GALT gene. The parents are consanguineous, which is consistent with the multiple blocks of AOH.

Figure 4.

Prenatal diagnosis of TAR syndrome. Prenatal diagnosis of TAR syndrome by array CGH, FISH and ultrasound. (a) Array CGH showing a loss in copy number of chromosome band 1q21.1 involving the TAR syndrome region. (b) FISH analysis shows lack of signal for the target probe on one chromosome 1, confirming the deletion (green signal is control probe, red signal is target probe). (c) Ultrasound performed at 17 weeks showed bilateral absence of radii with the hands attached directly to the humeri (indicated by red arrows). (d) Ultrasound performed at 19 weeks showed humeri appeared markedly shortened and more curved but symmetrical and hands include thumbs bilaterally (indicated with red arrow).



ACOG Committee Opinion No. 446 (2009) Array comparative genomic hybridization in prenatal diagnosis. Obstetrics & Gynecology 114: 1161–1163.

Alkan C, Coe BP and Eichler EE (2011) Genome structural variation discovery and genotyping. Nature Reviews Genetics 12(5): 363–376.

Aradhya S and Cherry AM (2007) Array‐based comparative genomic hybridization: clinical contexts for targeted and whole‐genome designs. Genetics in Medicine 9(9): 553–559.

Ballif BC, Rorem EA, Sundin K et al. (2006) Detection of low‐level mosaicism by array CGH in routine diagnostic specimens. American Journal of Medical Genetics Part A 140A(24): 2757–2767.

Berg JS, Brunetti‐Pierri N, Peters SU et al. (2007) Speech delay and autism spectrum behaviors are frequently associated with duplication of the 7q11.23 Williams–Beuren syndrome region. Genetics in Medicine 9(7): 427–441.

Boone PM, Bacino CA, Shaw CA et al. (2010) Detection of clinically relevant exonic copy‐number changes by array CGH. Human Mutation 31(12): 1326–1342.

Cai WW, Mao JH, Chow CW et al. (2002) Genome‐wide detection of chromosomal imbalances in tumors using BAC microarrays. Nature Biotechnology 20(4): 393–396.

Cheung SW, Shaw CA, Scott DA et al. (2007) Microarray‐based CGH detects chromosomal mosaicism not revealed by conventional cytogenetics. American Journal of Medical Genetics Part A 143A(15): 1679–1686.

Cheung SW, Shaw CA, Yu W et al. (2005) Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genetics in Medicine 7(6): 422–432.

Conrad DF, Pinto D, Redon R et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704–712.

Darilek S, Ward P, Pursley A et al. (2008) Pre‐ and postnatal genetic testing by array‐comparative genomic hybridization: genetic counseling perspectives. Genetics in Medicine 10(1): 13–18 [PMID: 18197052].

Gilman SR, Iossifov I, Levy D et al. (2011) Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron 70(5): 898–907.

Jacobs PA (1977) Epidemiology of chromosomal abnormalities in man. American Journal of Epidemiology 105: 180–191.

Jacquemont ML, Sanlaville D, Redon R et al. (2006) Array‐based comparative genomic Hybridization identifies high frequency of cryptic chromosomal rearrangements in patients with syndromic autism spectrum disorders. Journal of Medical Genetics 43(11): 843–849.

Kallioniemi A, Kallioniemi OP, Sudar D et al. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818–821.

Kim YS, Leventhal BL, Koh YJ et al. (2011) Prevalence of autism spectrum disorders in a total population sample. American Journal of Psychiatry 9 [Epub ahead of print].

Ledbetter DH and Engel E (1995) Uniparental disomy in humans: development of an imprinting map and its implications for prenatal diagnosis. Human Molecular Genetics 4: 1757–1764.

Lee C, Iafrate AJ, Brothman AR et al. (2007) Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nature Genetics 39: S48–S54.

Levy D, Ronemus M, Yamrom B et al. (2011) Rare de novo and transmitted copy‐number variation in autistic spectrum disorders. Neuron 70(5): 886–897.

Lu X, Shaw CA, Patel A et al. (2007) Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS One 2(3): e327.

Lu XY, Phung MT, Shaw CA et al. (2008) Genomic imbalances in neonates with birth defects: high detection rates by using chromosomal microarray analysis. Pediatrics 122(6): 1310–1318.

Lupski JR (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends in Genetics 14(10): 417–422.

Mefford HC and Eichler EE (2009) Duplication hotspots, rare genomic disorders and common disease. Current Opinion in Genetics & Development 19(3): 196–204.

Miles JH (2011) Autism spectrum disorders – a genetics review. Genetics in Medicine 13(4): 278–294.

Miller DT, Adam MP, Aradhya S et al. (2010) Consensus statement: chromosomal microarray is a first‐tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. American Journal of Human Genetics 86(5): 749–764.

Muhle R, Trentacoste SV and Rapin I (2004) The genetics of autism. Pediatrics 113(5): e472–486.

Ou Z, Berg JS, Yonath H et al. (2008) Microduplications of 22q11.2 are frequently inherited and are associated with variable phenotypes. Genetics in Medicine 10(4): 267–277.

Ou Z, Kang SH, Shaw CA et al. (2008b) Bacterial artificial chromosome‐emulation oligonucleotide arrays for targeted clinical array‐comparative genomic hybridization analyses. Genetics in Medicine 10(4): 278–289.

Papenhausen P, Schwartz S, Risheg H et al. (2011) UPD detection using homozygosity profiling with a SNP Genotyping Microarray. American Journal of Medical Genetics Part A 155: 757–768.

Pinkel D, Seagraves R, Sudar D et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics 20(2): 207–211.

Pinto D, Pagnamenta AT, Klei L et al. (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466: 368–372.

Ravnan JB, Tepperberg JH, Papenhausen P et al. (2006) Subtelomere FISH analysis of 11 688 cases: an evaluation of the frequency and pattern of subtelomere rearrangements in individuals with developmental disabilities. Journal of Medical Genetics 43(6): 478–489.

Redon R, Ishikawa S, Fitch KR et al. (2006) Global variation in copy number in the human genome. Nature 444: 444–454.

Reiter LT, Hastings PJ, Nelis E et al. (1998) Human meiotic recombination products revealed by sequencing a hotspot for homologous strand exchange in multiple HNPP deletion patients. American Journal of Human Genetics 62(5): 1023–1033.

Sakai Y, Shaw CA, Dawson BC et al. (2011) Protein interactome reveals converging molecular pathways among autism disorders. Science Translational Medicine 3(86): 86ra49.

Sanders SJ, Ercan‐Sencicek AG, Hus V et al. (2011) Multiple recurrent de novo CNVs, including duplication of the 7q11.23 Williams syndrome region, are strongly associated with autism. Neuron 70(5): 863–885.

Schaaf CP, Scott DA, Wiszniewska J and Beaudet AL (2011) Identification of incestuous parental relationships by SNP‐based DNA microarrays. Lancet 377: 555–556.

Sharp AJ, Hansen S, Selzer RR et al. (2006) Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nature Genetics 38(9): 1038–1042.

Shinawi M, Shao L, Jeng LJ et al. (2008) Low‐level mosaicism of trisomy 14: phenotypic and molecular characterization. American Journal of Medical Genetics Part A 146A(11): 1395–1405.

Solinas‐Toldo S, Lampel S, Stilgenbauer S et al. (1997) Matrix‐based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes, Chromosomes and Cancer 20(4): 399–407.

Stankiewicz P and Lupski JR (2002) Genomic architecture, rearrangements and genomic disorders. Trends in Genetics 18(2): 74–82.

Stankiewicz P and Lupski JR (2010) Structural variation in the human genome and its role in disease. Annual Review of Medicine 61: 437–455.

Stankiewicz P, Pursley AN and Cheung SW (2009) Challenges in clinical interpretation of microduplications detected by array CGH analysis. American Journal of Medical Genetics Part A 152A(5): 1089–1100.

Van den Veyver IB, Patel A, Shaw CA et al. (2009) Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases. Prenatal Diagnosis 29(1): 29–39.

Vissers LE, van Ravenswaaij CM, Admiraal R et al. (2004) Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nature Genetics 36(9): 955–957.

Vissers LE, Veltman JA, van Kessel AG and Brunner HG (2005) Identification of disease genes by whole genome CGH arrays. Human Molecular Genetics 14(suppl. 2): R215–R223.

Vorstman JA, Staal WG, van Daalen E et al. (2006) Identification of novel autism candidate regions through analysis of reported cytogenetic abnormalities associated with autism. Molecular Psychiatry 11(1): 18–28.

Weiss LA, Shen Y, Korn JM et al. (2008) Association between microdeletion and microduplication at 16p11.2 and autism. New England Journal of Medicine 358(7): 667–675.

Zhang S, Li FY, Bass HN et al. (2010) Application of oligonucleotide array CGH to the simultaneous detection of a deletion in the nuclear TK2 gene and mtDNA depletion. Molecular Genetics and Metabolism 99(1): 53–57.

Zoghbi HY (2003) Postnatal neurodevelopmental disorders: meeting at the synapse? Science 302: 826–830.

Further Reading

Betancur C (2011) Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Research 1380: 42–77.

Girirajan S and Eichler EE (2010) Phenotypic variability and genetic susceptibility to genomic disorders. Human Molecular Genetics 19(R2): R176–187.

Kearney HM, Thorland EC, Brown KK et al. (2011) American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genetics in Medicine 7: 680–685.

Lee C and Scherer SW (2010) The clinical context of copy number variation in the human genome. Expert Reviews in Molecular Medicine 12: e8.

Mills RE, Walter K, Stewart C et al. (2011) Mapping copy number variation by population‐scale genome sequencing. Nature 470(7332): 59–65.

Morrow EM (2010) Genomic copy number variation in disorders of cognitive development. Journal of the American Academy of Child and Adolescent Psychiatry 49(11): 1091–1104.

Savage MS, Mourad MJ and Wapner RJ (2011) Evolving applications of microarray analysis in prenatal diagnosis. Current Opinion in Obstetrics and Gynecology 23(2): 103–108.

Slavotinek AM (2008) Novel microdeletion syndromes detected by chromosome microarrays. Human Genetics 124(1): 1–17.

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Cheung, Sau Wai, and Pursley, Amber Nolen(Nov 2011) Comparative Genomic Hybridization in the Study of Human Disease. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005955.pub2]