Array-based comparative genomic hybridization (aCGH) is a powerful tool for chromosomal and genomic studies. With this approach, copy number variations (CNVs) and loss of heterozygosity (LOH) are easily visualized. Copy number variations are DNA alterations resulting in abnormal copies of one or more pieces of DNA (typically large regions of deletion or duplication). Loss of heterozygosity is when the function of one allele is lost when the other allele was already compromised. With easy enumeration of chromosomes, syndromes can be related to aberrant chromosomes or chromosome number.

In Coriell’s Cytogenetics Laboratory, we use the Affymetrix Genome-Wide SNP Array 6.0 for routine analysis of cell lines. We are also equipped to analyze samples using the Affymetrix Cytogenetics Whole-Genome 2.7M Array.

Current parameters for analyses at Coriell, listed below, can be modified to meet other requirements.

Copy Number Variations (CNVs)

• Number of markers = 10;
• Size = 100 kb;
• Confidence = 95%

Loss Of Heterozygosity (LOH)

• Number of markers = 10;
• Size = 5 Mb;
• Confidence = 95%

Karyotype analysis shows an abnormal X chromosome [46,X,dup(X)(p11.3p11.1)].	FISH analysis with probes targeting the X chromosome (DXZ1, green) and the Xp22.32 (Steroid Sulfatase (STS) gene, red) reveal a duplication of the X centromere.
Further investigation using cytogenetic techniques (SNP Array 6.0) confirm these findings (see karyoview and chromosomal view of X chromosome, respectively) at an in-depth level not previously obtained.