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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