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Table 1 Performance of cLPP target capture and sequencing

From: Multiplex target capture with double-stranded DNA probes

(i) Sensitivity; percentage of the target bases that are represented by one or more reads 98.7% of all exons and 97.8% of all target bases at >20× coverage (0.012× mean coverage)
(ii) Specificity; percentage of sequence reads that map to the intended targets (5,471 exons) 98.1% mapped target reads confirming the high on-target specificity of LPP capture
(iii) Accuracy; base calling concordance to known sample SNVs >99% concordance rate for both heterozygous and homozygous SNVs with coverage of 97.9%; sample SNVs at >20× coverage (0.012× mean)
(iv) Uniformity; variability in sequence coverage across target regions 91% of capture products were distributed within a 50-fold range (94% within 100-fold)
(v) Reproducibility; or how closely results obtained from independent samples correlate r = 0.93 rank-order correlation between two different HapMap samples (Figure S8 in Additional file 1); 1.15% SD (P = 0.01) for detecting heterozygous SNV (>20×) in five cLPP capture experiments.
(vi) Cost of LPP target capture $86 per sample for 100 genes in 100 samples or $16.70 per sample for 100 genes in 1,000 samples (Figure S2 in Additional file 1).
(vii) Ease of use and time effort <8 hours target capture and library preparation ('sequencing-ready'), <24 hours MiSeq and approximately 6 hours variant calling (524 genes). Total time: 38 hours
(viii) DNA amount required per experiment >50 ng of genomic DNA
(ix) Multiplexing of candidate genomic targets and of DNA samples Multiplex target capture of 524 genes per sample; sample multiplexing of 7 capture libraries per MiSeq run (#B, Additional file 2).
  1. Performance parameters are adapted from [2] and calculated for cLPPs based on: (i to iv) multiplex targeted sequencing of 524 genes using cLPPs and MiSeq for NA18507 (experiment #7, Additional file 2); (v) comparison of two independent sample preparations (NA18507 and NA12878, experiment #6) and by estimating the standard deviation (SD) across five cLPP capture experiments (experiment #2, 4 to 7, Additional file 2).