SoftGenetics NextGENe versions

v2.3 [May 7, 2013]
- The CNV detection tool of NextGENe version 2.3.4 and forward, has added a sophisticated new coverage-based algorithm developed for NGS sequencing data from instruments such as Illumina, Roche, and Ion Torrent sequencing platforms. This includes whole exome and targeted sequencing panels such as Ion Torrent AmpliSeq panels or the HaloPlex Target Enrichment System from Agilent Technologies. Copy number variations can now be detected in NGS sequencing data using dispersion measurements and a novel Hidden Markov Model (HMM) not found in other programs such as Partek Genomics Suite. Specified regions of a “sample” project and a “control” project are used to determine a coverage ratio measured in RPKM for every region (sample divided by sample plus control). CNV calls are made on the basis of changes in coverage, utilizing automatic measurement of noise (dispersion) and a novel Hidden Markov Model. Additionally, each called region receives phred-scaled scores describing the probability of "Deletion", "Duplication", and "Normal" CNV states. Results are available in a table and graphical view.
- In addition to a novel HMM method, NextGENe also features a proprietary SNP-based normalization method which utilizes a unique method for normalizing coverage between two samples. A list of heterozygous SNPs with allele percentages close to 50% is generated for each sample, and the median coverage for these alleles is used to normalize the samples on a global level. After normalization, a representative position for each region is selected and used to calculate a log2 ratio.