Table 1

Capture probe designs of the compared exome capture kits

Exome capture method

Probes

Base pairs covered (kb)

CCDS exons targeteda

Complete CCDS transcripts targetedb

miRNAs targetedc

Mean GC content of the target regionsd

Percentage of base pairs in repeatse

Percentage of base pairs in CNVsf


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

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