Open Access Database

SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock

Ezequiel Luis Nicolazzi1*, Matteo Picciolini1, Francesco Strozzi1, Robert David Schnabel2, Cindy Lawley3, Ali Pirani4, Fiona Brew5 and Alessandra Stella16

Author Affiliations

1 Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi 26900, Italy

2 University of Missouri, Columbia, MO 65203, USA

3 Illumina Inc, 5200 Illumina Way, San Diego, CA 92121, USA

4 Affymetrix Inc, 3420 Central Expressway, Santa Clara, CA 95051, USA

5 Affymetrix UK Ltd, Mercury Park, Wycombe Lane, High Wycombe HP10 0HH, UK

6 Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi 26900, Italy

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BMC Genomics 2014, 15:123  doi:10.1186/1471-2164-15-123

Published: 11 February 2014

Abstract

Background

Currently, six commercial whole-genome SNP chips are available for cattle genotyping, produced by two different genotyping platforms. Technical issues need to be addressed to combine data that originates from the different platforms, or different versions of the same array generated by the manufacturer. For example: i) genome coordinates for SNPs may refer to different genome assemblies; ii) reference genome sequences are updated over time changing the positions, or even removing sequences which contain SNPs; iii) not all commercial SNP ID’s are searchable within public databases; iv) SNPs can be coded using different formats and referencing different strands (e.g. A/B or A/C/T/G alleles, referencing forward/reverse, top/bottom or plus/minus strand); v) Due to new information being discovered, higher density chips do not necessarily include all the SNPs present in the lower density chips; and, vi) SNP IDs may not be consistent across chips and platforms. Most researchers and breed associations manage SNP data in real-time and thus require tools to standardise data in a user-friendly manner.

Description

Here we present SNPchiMp, a MySQL database linked to an open access web-based interface. Features of this interface include, but are not limited to, the following functions: 1) referencing the SNP mapping information to the latest genome assembly, 2) extraction of information contained in dbSNP for SNPs present in all commercially available bovine chips, and 3) identification of SNPs in common between two or more bovine chips (e.g. for SNP imputation from lower to higher density). In addition, SNPchiMp can retrieve this information on subsets of SNPs, accessing such data either via physical position on a supported assembly, or by a list of SNP IDs, rs or ss identifiers.

Conclusions

This tool combines many different sources of information, that otherwise are time consuming to obtain and difficult to integrate. The SNPchiMp not only provides the information in a user-friendly format, but also enables researchers to perform a large number of operations with a few clicks of the mouse. This significantly reduces the time needed to execute the large number of operations required to manage SNP data.

Keywords:
SNP chip; SNP data; Relational database; Assembly; Imputation; GWAS; Bovine livestock