Apr 3
CS Bits & Bytes Hosts Jaime Davila
CS Bits and Bytes hosts a research talk by Jaime Davila titled "Faster Detection of Microsatellite Instability in Cancer Transcriptomics using k-mers"
Abstract: Endometrial and colorectal cancers are frequently caused by high microsatellite instability (MSI-H). MSI-H samples contain an excess amount of insertions and deletions (indels) in mononucleotide repeats, regions of the genome where the same nucleotide repeats itself. The detection of MSI-H in DNA sequencing is commonplace and existing bioinformatic approaches require mapping the sequencing reads to the human reference genome, a computationally intensive task that takes hours. It is increasingly recognized that MSI-H can be detected in the transcriptome, which motivates us to design a fast method to detect MSI-H cases by considering a small fraction of the sequencing reads.
We tested our method using 35 paired tumor/normal transcriptomes with a median number of 50 million reads, which were filtered down to under 2,500 k-mers per case. Our method’s median processing time is less than 2 minutes, which compares favorably when approaches that require mapping which take over 3 hours. Our method has a specificity/sensitivity of 86% and AUC score of 93%.
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from Computer Science