Comparison of PrASE and Pyrosequencing for SNP Genotyping

Käller, Max; Hultin, Emilie; Holmberg, Kristina; Persson, Marie-Louise; Odeberg, Jacob; Lundeberg, Joakim; Ahmadian, Afshin

doi:10.1186/1471-2164-7-291

Cited by 4 publications

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“… 2005 ), for screening polymorphisms in a multiplex amplification of diagnostic SNP sites for 47 male dingoes, including two of the sequenced samples. The method has been shown to be as accurate as pyrosequencing (Käller et al 2006 ), and the set-up would allow inspection of the whole Y-chr phylogeny previously available (Ding et al . 2011 ).…”

Section: Methodsmentioning

confidence: 99%

Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry

et al. 2012

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The dingo (Canis lupus dingo) is an iconic animal in the native culture of Australia, but archaeological and molecular records indicate a relatively recent history on the continent. Studies of mitochondrial DNA (mtDNA) imply that the current dingo population was founded by a small population of already tamed dogs from Southeast Asia. However, the maternal genetic data might give a unilateral picture, and the gene pool has yet to be screened for paternal ancestry. We sequenced 14,437 bp of the Y-chromosome (Y-chr) from two dingoes and one New Guinea Singing Dog (NGSD). This positioned dingo and NGSD within the domestic dog Y-chr phylogeny, and produced one haplotype not detected before. With this data, we characterized 47 male dingoes in 30 Y-chr single-nucleotide polymorphism sites using protease-mediated allele-specific extension technology. Only two haplotypes, H3 and H60, were found among the dingoes, at frequencies of 68.1 and 31.9 %, respectively, compared to 27 haplotypes previously established in the domestic dog. While H3 is common among Southeast Asian dogs, H60 was specifically found in dingoes and the NGSD, but was related to Southeast Asian dog Y-chr haplotypes. H3 and H60 were observed exclusively in the western and eastern parts of Australia, respectively, but had a common range in Southeast. Thus, the Y-chr diversity was very low, similar to previous observations for d-loop mtDNA. Overall genetic evidence suggests a very restricted introduction of the first dingoes into Australia, possibly from New Guinea. This study further confirms the dingo as an isolated feral dog.Electronic supplementary materialThe online version of this article (doi:10.1007/s10709-012-9658-5) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry

et al. 2012

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Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads

et al. 2008

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Here we present an approach for allelotyping combining the multiplexing features of the trinucleotide threading (TnT) method with pooling of genomic DNA and massively parallel pyrosequencing, enabling reliable allele frequency estimation in large cohorts. The approach offers several benefits as compared to array-based methods and allows undertaking highly complex studies without compromising accuracy, while keeping the workload to a minimum. This proof-of-concept study involves formation of trinucleotide threads, targeting a total of 147 single-nucleotide polymorphisms (SNPs) related to obesity and cancer, for multiplex amplification and allele extraction from a pool of 462 genomes, followed by massively parallel pyrosequencing. Approximately 177k reads were approved, identified, and assigned to SNP-carrying threads rendering representative allele frequencies in the cohort.

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Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues

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Comparison of PrASE and Pyrosequencing for SNP Genotyping

Cited by 4 publications

References 30 publications

Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry

Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry

Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads

Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues

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