On the design of clone-based haplotyping

Table 1 Comparison of different clone-based haplotyping protocols

	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 10,000^a	16,377^b	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) = $\frac{nLp}{G}$	7.1	19.2	57.6	14.5	6.0
c_p: Exp(clone coverage per pool) = $\frac{nL}{G}$	0.06	0.07	0.15	0.075	0.25
P_O: 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	411,000^c	358,000	2,640,036

Abbreviations: BAC, Bacterial artificial chromosome; LFR, LFR, Long fragment reads.
^aEstimated given that each pool contains 300 to 600 Mbp and L = 94,000.
^bEstimated by dividing 226 Mbp (number of bases covered in a pool) by L = 13.8 kbp.
^cActual haplotype length for NA20431.

ISSN: 1474-760X