Illumina provides some nice software (called CASAVA) that is typically run at the default settings by Core labs and sequencing outsourcing companies. This software gives high-quality genome alignments and pretty good SNP calls - useful for many purposes. However, real-world research needs are often not satisfied with default automated bioinformatics analysis. Narrowing down hundreds of thousands of SNP calls to the few real disease-related mutations is difficult hands-on work for skilled bioinformaticians. Today in my lab group, we are fighting with false-negatives: SNPs that were present but not called in the germ line sample, leading to false identification of mutations unique to the tumor. It looks like we will have to re-run the SNP detection software many times with small changes in various parameters to optimize specificity vs. sensitivity in each sample. Investigators may sub-contract this type of work to the lab that does the sequencing, they may have skilled bioinformaticians in their lab group, or they may hire bioinformatics consultants. In any case, $1K of sequence data may cost more than $10K for analysis.
PERCEPTION – an AI tool that predicts patient response and resistance to
treatment using single-cell transcriptomics of their tumors
-
[image: rna-seq]
In a proof-of-concept study, researchers at the National Institutes of
Health (NIH) have developed an artificial intelligence (AI) tool t...
1 day ago