Copy Number Variation Detection through the Utilization of Unique Algorithms in the CNV Tool in NextGENe Software
Year: 2013
Type: article
Abstract: One of the most important steps in accurate determination of copy number variants using a case-control comparison is normalizing the coverage level between the different projects. NextGENe's CNV tool uses unique methods for this global normalization and also for log(2) ratio calculation. The global normalization method is based on the median allele coverage of selected heterozygous positions. After normalization, log(2) ratios are calculated by selecting one position in each specified region (based on annotation or amplicon location). The positions are selected if they are adequately representative of the region, and (ideally) if they are heterozygous, so that allele frequency changes can be noted. In this analysis, the tool is used to analyze data from multiple targeted sequencing technologies. A known variant (deletion in the KCNH2 gene) was detected using HaloPlex™ Target Enrichment System Panels. Large chromosomal abnormalities (such as trisomy 21) were detected using Ion AmpliSeq™ Panels.
Source: Europe PMC (PubMed Central)
Authors: N. Shouyong, C.S. Liu, John Mcguigan
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W150790029