Whole Exome Sequencing (WES) analysis is now available for several research purposes. A frequently updated pipeline, WEP, is used to call variants, both SNPs and indels. Variants are then filtered with many public databases including dbSNP, the 1000 Genomes project, HapMap exomes and more. Variant prioritization is obtained by comparing disease and healthy controls and performing their functional annotation (e.g. the functional relevance of a protein variant is assessed by SITF software). Moreover, for family-based samples, the advanced analysis of haplotype phasing and complex heterozygous or homologous mutations detection is available as well.
A new sequencing platform, the MiSeq Illumina sequencer, allows to identify known causative mutations by producing a Ultra-Deep coverage on a selected list of Targeted genomic regions Sequencing (UDT-Seq). UDT-Seq is becoming particularly suitable for clinical diagnostic applications since it implies full coverage of sequenced regions and guarantees that no other mutation was lost by the analysis. COVACS is a new automated high-performance bioinformatics web platform, developed for targeting genes at high coverage through deep sequencing with the maximum usability, and focused on rational diagnosis of targeted therapies. It identifies Single Nucleotide Variants (SNVs) and Deletion/Insertion Variants (DIVs) classified by different useful scores (e.g. depth coverage).