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[Detection of a copy number mutation on chromosome 7q36 using the Affymetrix SNP Array 6.0].

OBJECTIVE
To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndactyly syndrome and syndactyly type IV using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR).


METHODS
Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3.0. The qPCR assay was carried out using the DeltaDeltaCT method to validate the duplication.


RESULTS
With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387 kb.


CONCLUSION
Screening with the Affymetrix Genome-Wide Human SNP Array 6.0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.