SkyMap: High-throughput gene to knowledge mapping through massive integration of public sequencing data

SkyMap: High-throughput gene to knowledge mapping through massive integration of public sequencing data

Here, we introduce Skymap, a standalone database that offers a single, multi-species data matrix incorporating all public sequencing studies. The data matrix contains several omic layers, including expression quantification, allelic read counts, microbes read counts, chip-seq. We reprocessed petabytes of sequencing data to generate the data matrix for each data type.

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MHC-I Genotype Restricts the Oncogenic Mutational Landscape

MHC-I Genotype Restricts the Oncogenic Mutational Landscape

MHC-I molecules expose the intracellular protein content on the cell surface, allowing T cells to detect foreign or mutated peptides. The combination of six MHC-I alleles each individual carries defines the sub-peptidome that can be effectively presented.

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Interaction landscape of inherited polymorphisms with somatic events in cancer

Interaction landscape of inherited polymorphisms with somatic events in cancer

Here, we analyze genomic data for 5954 tumors to reveal and systematically validate 412 genetic interactions between germline polymorphisms and major somatic events, including tumor formation in specific tissues and alteration of specific cancer genes. Among germline-somatic interactions, we find germline variants in RBFOX1 that increase incidence of SF3B1 somatic mutation by eight-fold via functional alterations in RNA splicing.