外显子组捕获试剂盒的比较

Comparison of exome capture kits

Agilent HaloPlex Exome Agilent SureSelect All Exon V5.0 NimbleGen SeqCap EZ Human Exome V3.0 Illumina Nextera Rapid Capture Expanded Exome Illumina TruSeq Exome Enrichment
Target size 37 MB 50 MB 64 MB 62 MB 64 MB
Probe size (bases) 161 ± 75 120 55–105 95 95
Number of probes 2.49 million 789 000 2.1 million 347 517 340 427
Number of targeted exons 557 999 335 765 ∼300 000 201 121 201 121
Reads on target (%) ∼80 ∼80 >70 ∼60 >65
(%) target bases covered at ≥10x >90 >90 >95 >97 >97
Recommended DNA input 200 ng 3 mg 3 mg 50 ng 500 ng
Fragmentation method Transposomes Ultrasonication Ultrasonication Transposomes Ultrasonication
Strengths Smallest amounts of DNA required Fewer duplicated reads More uniform coverage Best coverage of UTRs and micro RNAs Best coverage of UTRs and micro RNAs
Better sensitivity for indels Most reads on target Fast
High alignment rate
Weaknesses Variable length target regions Most affected by high GC content Alignment rate less than Agilent High proportion of off target reads High proportion of off-target reads
Variable length target regions Coverage bias in GC-rich regions Variable length target regions
Fewer reads on target compared with NimbleGen Poorest for reads on target

Note . A tabulated comparison of Agilent’s SureSelect and Haloplex capture kits, Illumina’s Nextera and TruSeq kits and NimbleGen’s SeqCap kit.

UTR = untranslated region 

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