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Table 1 Comparison of different clone-based haplotyping protocols

From: On the design of clone-based haplotyping

  Kitzman et al. [11](fosmid) Suk et al. [12](fosmid) Peters et al. [13](LFR) Kaper et al.[14] Lo et al. [16](BAC)
n: Number of clones per pool 5,000 5,000 5,000 to 10,000a 16,377b 5,000
L: Exp(clone length), kbp 37 40 60 13.8 140
p: Number of pools 115 288 384 192 24
c: Exp(clone coverage) = nLp G 7.1 19.2 57.6 14.5 6.0
c p : Exp(clone coverage per pool) = nL G 0.06 0.07 0.15 0.075 0.25
PO: overlap probability = 1 - e - c p , % 11.31 13.06 25.92 13.93 39.35
Exp(haplotype length), bp 2.05 × 107 4.37 × 1010 5.30 × 1016 4.89 × 109 3.42 × 105
Simulated haplotype length, bp 825,046 2,486,692 8,585,663 300,336 2,210,343
Actual haplotype length, bp 386,000 959,175 411,000c 358,000 2,640,036
  1. Abbreviations: BAC, Bacterial artificial chromosome; LFR, LFR, Long fragment reads.
  2. aEstimated given that each pool contains 300 to 600 Mbp and L = 94,000.
  3. bEstimated by dividing 226 Mbp (number of bases covered in a pool) by L = 13.8 kbp.
  4. cActual haplotype length for NA20431.