Enrichment of sequencing targets from the human genome by solution hybridization

Table 3 Variant detection rate and concordance¹

		Microarray SNPs²		Variant detection rate (%)		Variant concordance³ (%)		Number of discordant SNPs
Sample	Replicate	On target	On or near target	On target	On or near target	On target	On or near target	On target	On or near target
NA15510	Capture 1	4,062	6,682	93.5	76.4	99.7	99.6	10	20
NA15510	Capture 2	4,062	6,682	93.7	75.2	99.8	99.8	8	10
HE00069	Capture 1	4,055	6,675	93.0	77.7	99.5	99.5	19	27
HE00069	Capture 2	4,055	6,675	93.4	77.4	99.6	99.6	14	22
	Average	4,059	6,679	93.4	76.7	99.7	99.6	13	20

¹Only variant bases with an MAQ quality score of 30 or greater are included in this table.
²Number of microarray genotypes in the on-target sequences or in the on or near (target ± 150 bp) target sequences.
³Number of genotypes that match between sequence and microarray genotype divided by total comparisons.

ISSN: 1474-760X