PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing.
With the advance of next-generation sequencing (NGS) technologies, increasingly ambitious applications are becoming feasible. A particularly powerful one is the sequencing of polymorphic, pooled samples. The pool can be naturally occurring, as in the case of multiple pathogen strains in a blood sample, multiple types of cells in a cancerous tissue sample, or multiple isoforms of mRNA in a cell. In these cases, it's difficult or impossible to partition the subtypes experimentally before sequencing, and those subtype frequencies must hence be inferred. In addition, investigators may occasionally want to artificially pool the sample of a large number of individuals for reasons of cost-efficiency, e.g., when carrying out genetic mapping using bulked segregant analysis. Here we describe PoolHap, a computational tool for inferring haplotype frequencies from pooled samples when haplotypes are known. The key insight into why PoolHap works is that the large number of SNPs that come with genome-wide coverage can compensate for the uneven coverage across the genome. The performance of PoolHap is illustrated and discussed using simulated and real data. We show that PoolHap is able to accurately estimate the proportions of haplotypes with less than 2% error for 34-strain mixtures with 2X total coverage Arabidopsis thaliana whole genome polymorphism data. This method should facilitate greater biological insight into heterogeneous samples that are difficult or impossible to isolate experimentally. Software and users manual are freely available at http://arabidopsis.gmi.oeaw.ac.at/quan/poolhap/.
Gregor Mendel Institute, Vienna, Austria. quan.long@gmi.oeaw.ac.at
Quan
Q
Long
Daniel C
DC
Jeffares
Qingrun
Q
Zhang
Kai
K
Ye
Viktoria
V
Nizhynska
Zemin
Z
Ning
Chris
C
Tyler-Smith
Magnus
M
Nordborg
D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology; D005787:Gene Frequency; D016678:Genome; D006239:Haplotypes; D020407:Internet; D008722:Methods; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
Bioinformatics. 2009 Jul 15;25(14):1754-60
19451168
Bioinformatics. 2009 Apr 15;25(8):1026-32
19244387
Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3983-8
12629218
Med Mycol. 2008 Feb;46(1):41-52
17885956
Am J Hum Genet. 2001 Apr;68(4):978-89
11254454
Dev Comp Immunol. 2010 Jul;34(7):741-8
20153768
PLoS One. 2008 Aug 06;3(8):e2882
18682730
Trends Genet. 2009 Feb;25(2):91-8
19110336
Nat Genet. 2010 Mar;42(3):260-3
20101244
Bioinformatics. 2009 Aug 15;25(16):2078-9
19505943
Cancer Res. 1989 Apr 15;49(8):2147-56
2702656
Nat Methods. 2009 Nov;6(11 Suppl):S13-20
19844226
Anal Biochem. 2002 Sep 15;308(2):401-4
12419357
J Mol Recognit. 1995 Jan-Apr;8(1-2):77-84
7598955
Nucleic Acids Res. 1998 Apr 15;26(8):2031-3
9518500