Variant detection sensitivity and biases in whole genome and exome sequencing

BMC Bioinformatics

Table 1 Cost of sequencing to achieve a given level of heterozygous SNV detection sensitivity

Method	Lane usage	Mean on-target depth	Sensitivity	Cost
Whole genome	1 lane/sample	11X	94.0%	4.60
Whole genome	2 lanes/sample	22X	98.5%	8.79
Exome	16 samples/lane	22X	91.1%	1.00
	12 samples/lane	29X	93.4%	1.09
	8 samples/lane	44X	95.9%	1.28
	6 samples/lane	58X	96.9%	1.46
	4 samples/lane	88X	98.1%	1.63

All costs have been normalised against the cheapest exome sequencing (16 samples per lane). Estimated costs include library preparation, exome capture and multiplexing where applicable, and paired-end sequencing on Illumina HiSeq.

ISSN: 1471-2105