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/

Aspectos clínicos, morfológicos e imuno-histoquímicos da pitiose gastrintestinal canina

Através de um estudo retrospectivo dos casos de biópsias e necropsias de cães recebidos no Laboratório de Patologia Veterinária da Universidade Federal de Santa Maria, constatou-se a ocorrência de dois casos confirmados e de quatro casos suspeitos de pitiose gastrintestinal canina. Os dois casos diagnosticados e publicados tiveram a etiologia confirmada através da cultura e indução de zoosporogênese ou por nested-PCR. Neste estudo utilizou-se a técnica de imuno-histoquímica com anticorpo policlonal anti-Pythium insidiosum para confirmação da etiologia dos quatro casos suspeitos. A epidemiologia, sinais clínicos, lesões macroscópicas e microscópicas, características histoquímicas e imuno-histoquímicas e diagnósticos diferenciais são relatados e discutidos.<br>Four suspect and two confirmed cases of gastrointestinal pythiosis were found in a retrospective study of biopsy and necropsy cases of dogs received in the Laboratório de Patologia Veterinária at the Universidade Federal de Santa Maria. The two diagnosed and published cases have had the etiology confirmed by culture and zoosporogenesis induction or by nested-PCR. On this study, the etiologic diagnosis of four suspect cases was confirmed by immunohistochemistry using anti-Pythium insidiosum policlonal antibody. Epidemiology, clinical signs, gross and microscopic lesions, histochemistry, immunohistochemistry, and differential diagnoses are reported and discussed