SNP detection

Loïck Le Dantec, Olivier Cantin

This project originated from fruitful meetings of the INRA biodiversity working group (DGAP) concerning the obtention and management of genetic variability data. genetic variability is shown by polymorphous markers. Markers data combined to phenotypic data give the opportunity to discover genotype/phenotype associations which in turn can be used in genetic improvement programs and in biodiversity management. SNPs (Single Nucleotide Polymorphisms) are the more numerous genetic markers with a relatively homogeneous distribution and hence are very good markers. High-throughput sequencing and ESTs programs provides most of the data within which it is possible to identify candidate SNPs. To date, there is no publicly available automated system for SNP detection.

In order to provide such a system, we initialised the development of a SNP detection pipe-line. This system permits the detection via two different strategies :

  • SNP detection in EST databases 
  • SNP detection in sequences produced by direct DNA sequencing.

Both strategies provide data different in terms of quality. EST data are poor-quality and as such require a probabilistic approach for SNP detection.

In the case of DNA direct sequencing, superior quality is obtained but arises the problem of heterozygote detection. 

As can be seen in Figure 1, the pipe-line relies on the same architecture for both strategies as far as base-calling (Phred), clustering (Phrap) and visualisation/validation (Consed) steps are concerned. However, SNP detection is performed through Polybayes for EST data and through PolyPhred for genomic data. Analysis results are inserted within a SNP database with web access for the user. All softwares have been integrated with the Pise system(C. Letondal - Pasteur Institute). The system is presently partly under working condition but more software developments are underway before allowing public access.


Figure 1 : architecture of the SNP detection pipe-line

 

 

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