SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species

Abstract

BackgroundIn recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements in terms of genotyping cost, manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species: ranging from one for goats to more than ten for cattle, and the number of arrays available is increasing rapidly. However, there is limited or no effort to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. past and current assemblies) SNP information.ResultsHere we present SNPchiMp v.3, a solution to these issues for the six major livestock species (cow, pig, horse, sheep, goat and chicken). Original data was collected directly from SNP array producers and specific international genome consortia, and stored in a MySQL database. The database was then linked to an open-access web tool and to public databases. SNPchiMp v.3 ensures fast access to the database (retrieving within/across SNP array data) and the possibility of annotating SNP array data in a user-friendly fashion.ConclusionsThis platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines. In recognition of the open-access use of Ensembl resources, SNPchiMp v.3 was officially credited as an Ensembl E!mpowered tool. Availability at http://bioinformatics.tecnoparco.org/SNPchimp.

The major histocompatibility complex homozygous inbred Babraham pig as a resource for veterinary and translational medicine

“…In addition, structurally variable haplotypes often confound the mapping of second‐generation sequencing technologies that produce relatively short reads used to design the SNP chip. Indeed, using SNPchimp to search the Illumina 60 k SNP array showed only two SNPs present in the vicinity of the classical MHC class I loci (ie, within the interval of Sscrofa10.2, chr 7:24 600 000‐24 765 000). Confirming that the Babraham MHC is homozygous would add significant value to this animal line as both a veterinary and biomedical model.…”

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

“…Genepop was also used to estimate population relatedness using pairwise estimates of F st among breeds. The reduced panel was analysed using SNPchiMp (Nicolazzi et al, 2015) to obtain information on the genomic distribution of SNPs.…”

Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations

“…Several SNP-chips are available in cattle, with different marker densities and costs (see [46]). In this work, an overall very high accuracy of prediction was achieved using the BovineSNP50 v2 Illumina BeadChip, which contains 54 609 SNPs.…”