Microarray-Based Comparative Genomic Hybridization Using Sex-Matched Reference DNA Provides Greater Sensitivity for Detection of Sex Chromosome Imbalances than Array-Comparative Genomic Hybridization with Sex-Mismatched Reference DNA

Abstract

In array-comparative genomic hybridization (array-CGH) experiments, the measurement of DNA copy number of sex chromosomal regions depends on the sex of the patient and the reference DNAs used. We evaluated the ability of bacterial artificial chromosomes/P1-derived artificial and oligonucleotide array-CGH analyses to detect constitutional sex chromosome imbalances using sex-mismatched reference DNAs. Twenty-two samples with imbalances involving either the X or Y chromosome, including deletions, duplications, triplications, derivative or isodicentric chromosomes, and aneuploidy, were analyzed. Although concordant results were obtained for approximately onehalf of the samples when using sex-mismatched and sex-matched reference DNAs, array-CGH analyses with sex-mismatched reference DNAs did not detect genomic imbalances that were detected using sex-matched reference DNAs in 6 of 22 patients. Small duplications and deletions of the X chromosome were most difficult to detect in female and male patients, respectively, when sex-mismatched reference DNAs were used. Sexmatched reference DNAs in array-CGH analyses provides optimal sensitivity and enables an automated statistical evaluation for the detection of sex chromosome imbalances when compared with an experimental design using sex-mismatched reference DNAs. Using sexmismatched reference DNAs in array-CGH analyses may generate false-negative, false-positive, and ambiguous results for sex chromosome-specific probes, thus masking potential pathogenic genomic imbalances. Therefore, to optimize both detection of clinically relevant sex chromosome imbalances and ensure proper experimental performance, we suggest that alternative internal controls be developed and used instead of using sex-mismatched reference DNAs.

Human subtelomeric copy number gains suggest a DNA replication mechanism for formation: beyond breakage–fusion–bridge for telomere stabilization

“…The size, extent, and genomic content of each rearrangement were determined to 0.5–3 kb resolution. Gender-matched reference DNAs were obtained from either a normal male or female individual (Yatsenko et al 2009b). The same reference DNA has been used for all patients studied by whole genome as well as custom 9q34 microarray.…”

Recombinant chromosome 7 in a mosaic 45,X/47,XXX patient

“…The array used in our case is not quantitative to assess how many copies of the X chromosome were gained. The detection of an extra X chromosome in patients with 47,XXX is obscured when sex‐mismatched reference DNA is used and it becomes even more problematic in patients with mosaicism for trisomy [Yatsenko et al, 2009]. In our opinion, conventional chromosome and FISH analysis provide a much more accurate picture of mosaic sex chromosome imbalances.…”

Enhancer Chip: Detecting Human Copy Number Variations in Regulatory Elements

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