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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 one-half 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. Sex-matched 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 sex-mismatched 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.

SUBMITTER: Yatsenko SA 

PROVIDER: S-EPMC2671340 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature

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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.

Yatsenko Svetlana A SA   Shaw Chad A CA   Ou Zhishuo Z   Pursley Amber N AN   Patel Ankita A   Bi Weimin W   Cheung Sau Wai SW   Lupski James R JR   Chinault A Craig AC   Beaudet Arthur L AL  

The Journal of molecular diagnostics : JMD 20090326 3


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, d  ...[more]

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