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Table 1 Capture probe designs of the compared exome capture kits

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

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%
  1. 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.