Project description:SNP genotyping was used to determine if the free living Highland Wild dogs of Papua, Indonesia are the ansestors of captive New Guinea Singing Dogs.
Project description:Comparison of SNP profiles of the Patagonain Sheepdog with European breeds confirms Scottish origin and position basal to modern herding breeds.
Project description:Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification.
Project description:Proteomic genotyping is the use of genetically variant peptides (GVPs), detected in a forensic protein sample, to infer the genotype of corresponding non-synonymous SNP alleles in the donor’s genome. This process does not depend on the presence of accessible or useable DNA in a sample. This makes proteomic genotyping an attractive alternative for analysis of problematic forensic samples, such as hair shafts, degraded bones or teeth, fingermarks, or sexual assault evidence. To demonstrate the concept in hair shafts, we developed an optimized sample processing protocol that could be used with high effectiveness on single hairs. This allows us to determine if the detected profiles of genetically variant peptides are robust and result in a consistent profile of inferred SNP alleles regardless of the chemical or biological history of the sample. Several real world scenarios have been evaluated. Here we include a study of four European subjects that had both pigmented and non-pigmented (or gray and non-gray) hair shafts. We tested whether (a) protein profiles change as a result of the loss of pigmentation and (b) these changes were reflected in the inferred genotype derived from detection of genetically variant peptides. Using this information, we can determine whether the resulting GVP profiles are more dependent on the biological context of pigmentation status or the underlying genotype.
Project description:Purpose: The purpose of this study was to evaluate SNP genotyping methodology as a means to detect chromosomal abnormalities previously diagnosed by G-band karyotype or fluorescence in situ hybridization (FISH) analysis and to determine the frequency of sub-microscopic (cryptic) chromosomal alterations in these subjects. Methods: We used the Illumina HumanHap Beadchip platform to genotype 40 individuals having previously detected chromosomal anomalies (by G-banded and/or FISH analysis). The resulting data were analyzed for signal intensity (log R ratio) and allelic composition (B allele frequency). Results: SNP array analysis detected 100% of previously identified cytogenetic abnormalities. Changes or clarifications of the ISCN karyotype designation assigned by conventional cytogenetic and/or FISH analysis were made in 82 % of the cases (32 of 39). Nine of the 39 cases (23%) involved a reassignment of an abnormal band while an additional 9 of the 39 (23%) resulted in a clarification of a sub-band assignment. In 8 more of the 39 cases (21%) the previously reported alterations were confirmed, however the SNP analysis also identified related cryptic alterations. SNP analysis not only confirmed FISH-detected abnormalities but also more precisely mapped the breakpoints of 6/6 patients. Investigations into the origin of de novo abnormalities in 15 trio families established that 12 /15 occurred on the paternal chromosome. Conclusions: SNP genotyping array analysis, confirmed all previously detected structural chromosomal abnormalities and provided additional, clinically-relevant genomic information in 82% of these alterations.
Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background.