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Team Shares Low-Cost Copy Number Profiling Approach

For a paper in BMC Genomics, investigators at the University of Cambridge and elsewhere present a probabilistic approach and corresponding tool known as conliga — designed for interrogating copy number patterns in a low-cost manner using FAST-SeqS assay data. "The use of FAST-SeqS data, until now, has largely been limited to the detection of whole chromosome gains and entire chromosome arm gains and losses," they explain, noting that the conliga approach "uses a fully probabilistic approach to infer relative copy number (RCN) alterations at each locus from FAST-SeqS data." Among other comparisons, the team found that conliga unearthed copy number patterns comparable to those found with high-coverage whole-genome sequencing in 11 esophageal adenocarcinoma samples at a fraction of the cost. The authors suggest that the strategy is particularly amenable to profiling copy number patterns in tumor samples with low purity. "We show that conliga provides high-resolution SCNA profiles using a convenient, low-cost assay," they report. "We believe that conliga makes FAST-SeqS a more clinically valuable assay as well as a useful research tool, enabling inexpensive and fast copy number profiling of pre-malignant and cancer samples.

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