Comparison of solution-based exome capture methods for next generation sequencing

Table 1 Capture probe designs of the compared exome capture kits

Exome capture method	Probes	Base pairs covered (kb)	CCDS exons targeted^a	Complete CCDS transcripts targeted^b	miRNAs targeted^c	Mean GC content of the target regions^d	Percentage of base pairs in repeats^e	Percentage of base pairs in CNVs^f
Agilent SureSelect	347 k	37,627	274,264	20,699	646	50.56%	0.2%	34.5%
Agilent SureSelect 50 Mb	635 k	51,647	300,040	23,031	669	50.56%	0.8%	38.3%
NimbleGen SeqCap	2.1 M	33,931	252,479	18,865	559	50.45%	1.3%	33.9%
NimbleGen SeqCap v2.0	2.1 M	44,007	298,304	23,028	686	50.34%	2.1%	35.3%

^aThere are 301,082 exons annotated in total in CCDS from Ensembl v59. ^bAll CCDS annotated exons of a transcript are required to be included in the capture target region. There are 23,634 transcripts in total in CCDS from Ensembl v59. ^cThere are 712 miRNAs in total in miRBase v.15. ^dThe mean GC content for all CCDS annotated exon regions is 52.12%. ^eRepeatMasker, April 2009 freeze. ^fDatabase of Genomic Variants, March 2010 freeze. CNV, copy number variation; M, million.

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