Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing

Table 1 Summary of the results.

	Primers	Single strand separation	Double Hyb	Specificity	Exons with reads*	Bases Covered*
Baseline	-	-	-	35%	98%	75%
Single Strand	-	Yes	-	54%	99%	92%
Primer Block	Yes	-	-	62% (63%^†)	99% (99%^†)	88% (94%^†)
Double Hybridization	Yes	-	Yes	90% (82%^†)	98% (98%^†)	84% (89%^†)

* Not considering flanking regions
† Results from replication using the tumor genomic DNA.
4 μg of genomic library was used for all experiments. The hybridization mix contained 50 μg of Human Cot-1, 52 μl of Agilent 10× Blocking agent and 260 μl of Agilent 2× hybridization buffer. Specificity is calculated by dividing sequence counts within the targeted region by total sequence counts mapable to the human genome uniquely for each run. Targeted region is defined as the targeted exon +/- 100 bp.