Secondly, we are working with .vcf files in GRCh38 build. Is there a way to run ALoFT using this build, or will we need to do a liftover back down to hg19?
Currently, ALOFT cannot be used with build38. We don’t have a plan to upgrade it to HG38. For SNPs, we already provide scores exome wide based on liftover to HG38. However, if you want other annotated features/scores for indels, it cannot be done without doing a liftover back down. While it is not ideal, that will work.
I read Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics and A systematic survey of loss-of-function variants in human protein-coding genes, and interested about the list of ‘LoF-tolerant’ gene category. I would be appreciated if you could provide with it.
Please see below the list of LoF-tolerant genes from the Science paper.
This list is based on the data from Phase 1 of the 1000 Genomes project.
I read with great interest your exciting paper on "Interpretation of genomic variants using a unified biological network approach".
In the last section of the Results, you describe the validation of your logistic regression model using a list of 140 LoF-tolerant genes (McArthur et al 2012) and a list of 115 essential genes (Liao et 2008). Even though I also read both papers, I couldn’t really find the lists of genes mentioned above (e.g. the supplementary table of Liao’s essential genes lists 120 genes and not 115 genes)
So, I was wondering if you’d be so kind and share the list of 140 LoF-tolerant genes and the list of 115 essential genes.
In our plos comp bio paper in Supplementary Table S8 – the genes with significance_score=0 (second column) are LoF-tolerant genes and genes with significance_score=3 are Essential genes. This file contains 140 LoF-tol and 115 essential genes.
I think Liao et al reports 120 essential genes but with gene id conversions we lost 5 of them.