Cancer Genome Research

Cancer genome research with RTG Investigator applies accurate variant analysis software with support for Indel and SNP calling that integrates short read sequence data from Illumina and Complete Genomics instruments.  The accurate identification of known genetic variants and the discovery of ‘private’ variants in previously unsequenced individuals are prerequisites for personalized medicine and genome-based diagnostics.  For cancer diagnostics, the major goals are to identify medically relevant and actionable disease-associated mutations such as single nucleotide polymorphisms (SNPs), copy number variants (CNVs) and chromosomal aberrations, as well as produce an accurate picture of an individual’s genome structure under normal and disease conditions.

Real Time Genomics has developed a robust analytical pipeline for detection and discovery of novel and disease-causing variants from human genome sequence data.  Cancer genomics can benefit from the sensitive, robust pipeline to help identify causal mutations or be used to confirm consensus variants in combination with existing data.

RTG is developing an alternative variant caller to assist analysis when researchers employ the pioneering tumor/normal experimental paradigm, developed at The Genome Institute at Washington University. The new software (coming soon) will process alignment data and take into consideration sample heterogeneity (normal cells present in tumor sample) and loss of heterozygosity in SNP calling.

This pipeline includes the map and cgmap commands for read mapping and alignment of Illumina, 454 and Complete Genomics data, basic utilities for managing nucleotide sequence data, the snp command to call sequence variants, coverage for reporting coverage depth, and the cnv command for reporting copy number variation ratios statistics.

Multi-platform SNP

Combining reads from different sequence technologies delivers higher variant call accuracy.  The RTG snp command can apply platform-specific base quality information from both Illumina and Complete Genomics sequencing platforms to adjust variant call scoring.  In a test with NA19240 reads, plotting true positive vs false positive variant calls at progressively higher posterior scores shows variant calls with the combined CG + Illumina read data to be more accurate than with either CG or Illumina data alone.

Coverage

Observing and comparing read depths across genomic loci supports experimental quality assurance.  The RTG coverage command measures coverage depth at each base pair and reports in industry standard BED format.  Sensitivity tuning parameters allow an investigator to identify the most appropriate set of alignments for downstream analysis.

Copy Number Variation

Comparing two genomes against a reference across loci shows large scale duplications and deletions, particularly useful in cancer genomics.  The RTG cnv command calculates the ratio of coverage at each loci between a test genome and a base genome.  Bucket size can be adjusted for data smoothing.  Filter settings allow different analytical comparisons with the same alignments.

Through their Early Access Program (EAP), Real Time Genomics enabled VIB to independently assess and validate the results from Complete Genomics.  Looking forward, RTG software gives us the flexibility to perform novel bioinformatics analysis with existing and new Complete Genomics read data. - Diether Lambrecht, Group leader of Complex Genetics