Pacific biosciences sequencing technology for genotyping and variation discovery in human data

BMC Genomics

Table 1 Validation calls for Pacific Biosciences and Illumina MiSeq

	Pacific Biosciences RS	Pacific Biosciences RS	Illumina MiSeq	Illumina MiSeq
	called Poly	called Mono	called Poly	called Mono
Confirmed	37	1	38	0
*de novo* SNP
Confirmed	1	59	5	55
artifact

Number of sites called polymorphic and monomorphic by Pacific Biosciences RS and Illumina MiSeq in the validation experiment. Datasets were sequenced from the same amplicons and were downsampled to 70x average coverage for comparison. Pacific Biosciences shows good accuracy with consistently high percentages in all metrics and making only 2 out 98 wrong calls, while MiSeq shows excellent sensitivity and negative predictive value but lower specificity and positive predictive value and 5 out of 98 wrong calls, all of the same class.
Poly = polymorphic site; Mono = monomorphic site.

ISSN: 1471-2164