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.

Sulonen et al. Genome Biology 2011 12:R94   doi:10.1186/gb-2011-12-9-r94