SNP calling by sequencing pooled samples
Perez-Enciso, Miguel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Esteve-Codina, Anna (Centre de Recerca en Agrigenòmica)
Ferretti, Luca (Centre de Recerca en Agrigenòmica)
Raineri, Emanuele (Centre Nacional d'Anàlisi Genòmica)
Nevado, Bruno (University of Oxford. Department of Plant Sciences)
Heath, Simon (Centre Nacional d'Anàlisi Genòmica)

Data:	2012
Resum:	Performing high throughput sequencing on samples pooled from different individuals is a strategy to characterize genetic variability at a small fraction of the cost required for individual sequencing. In certain circumstances some variability estimators have even lower variance than those obtained with individual sequencing. SNP calling and estimating the frequency of the minor allele from pooled samples, though, is a subtle exercise for at least three reasons. First, sequencing errors may have a much larger relevance than in individual SNP calling: while their impact in individual sequencing can be reduced by setting a restriction on a minimum number of reads per allele, this would have a strong and undesired effect in pools because it is unlikely that alleles at low frequency in the pool will be read many times. Second, the prior allele frequency for heterozygous sites in individuals is usually 0. 5 (assuming one is not analyzing sequences coming from, e. g. cancer tissues), but this is not true in pools: in fact, under the standard neutral model, singletons (i. e. alleles of minimum frequency) are the most common class of variants because P(f) ∝ 1/f and they occur more often as the sample size increases. Third, an allele appearing only once in the reads from a pool does not necessarily correspond to a singleton in the set of individuals making up the pool, and vice versa, there can be more than one read - or, more likely, none - from a true singleton.
Ajuts:	Ministerio de Economía y Competitividad AGL 2010-14822
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Bioinformàtica
Publicat a:	BMC bioinformatics, Vol. 13 (2012) , ISSN 1471-2105

DOI: 10.1186/1471-2105-13-239
PMID: 22992255

8 p, 426.0 KB

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