AYRRIS™ / BIO – NGS ANALYTICS
Ayrris / BIO employs analytical pipelines specifically designed to automate Exome, Whole Genome and RNA-SEQ analysis and data management. Their purpose is to ingest a set of data, act on it in massively parallel executions and produce a result that can then be exported for further analysis, publishing, etc.
Exome analysis is the most cost-effective way to analyze the few percent of the genome that codes for genes. Complete annotation of the aligned sequence including indels, rare variants, SNPs, quality scores, genotype of the sample, SNP rs numbers, RefSeq IDs, CCDS IDs and variant gene functional effects is provided. Files of the summary data are also delivered in formats compatible with the UCSC Genome Browser or the Integrative Genomics Viewer (IGV) so that it can be viewed at a higher level. All major exome capture kits are supported including both versions of Agilent SureSelect, Illumina TruSeq, Invitrogen TargetSeq and Roche NimbleGen SeqCap EZ.
Medium Appliance Performance
The sequencing of the whole genome is the only technique to determine the polymorphisms, genetic disease associations and genetic defects of an entire individual or organism. The alignment of the read sequences can be performed with Bowtie, BWA and other commercial third party aligners depending on customer preference. This analysis results in a BAM file as well as Excel sheets summarizing all SNPs, rare variants, and indels. The functional effects of the coding indels and SNPs and the genetic disease associations from the Genetic Association Database (GAD) are also provided. In addition, all of these results can be visualized with the Integrative Genomics Viewer (IGV).
Medium Appliance Performance
Using Samples From the 1000 Genomes Project
The analysis of RNA-SEQ data yields valuable information on the prevalent transcripts and novel splice forms in the tissue of interest. In addition, the expression levels of each transcript are determined. This data can be utilized in personal medicine approaches such the Connectivity Map (Lamb et al., 2006) to develop individualized therapies. SNP, rare variant and indel are also ascertained which provide information on possible disease causing genetic defects and susceptibilities. All of this data is delivered in a format that can be visualized by the Integrative Genomics Browser (IGV) and UCSC Genome Browser tools.
Performance on Mini Appliance
Lamb, J., Crawford, E.D., Peck, D., Modell, J.W., Blat, I.C., Wrobel, M.J., Lerner, J., Brunet, J.P., Subramanian, A., Ross, K.N., Reich, M., Hieronymus, H., Wei, G., Armstrong, S.A., Haggarty, S.J., Clemons, P.A., Wei, R., Carr, S.A., Lander, E.S., Golub, T.R. (2006). The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science, 313, 1929-1935.
DE NOVO ASSEMBLY
In the case of organisms for which no reference sequence exists, a de novo assembly must be done. This can be accomplished at either the transcriptome or genomic level depending on the source of the sequence data. The assembled contigs and annotations of the top Blast gene hits for each contig is provided in a summary sheet.