Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)

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Table 1.

CNV analysis in human patient samples by RQPS

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Table 1.

  • For each sample, an RQPS probe, consisting of an exon fragment (∼50 bp) from within a randomly selected query gene residing within the CNV region fused to a NOTCH2 fragment, was prepared. Both fragments were mutated to contain an SNV. These probes were then used to estimate the copy number of seven loci in a semi-blind test. After RQPS, the results were compared to previously determined array-CGH data. Two discrepancies were found, which were resolved when RQPS was repeated with query sequences matching the CGH probe.

  • aRepeat reaction with RQPS probe matching the CGH probe.

  • bInconsistent result between RQPS probe to a region not covered by a CGH probe and the CGH array.

  • cBoth RQPS and array-CGH data detected amplification; they differ in estimating copy number.

This Article

  1. Published in Advance October 1, 2009, doi: 10.1101/gr.093856.109 Genome Res. 19: 2081-2089

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