Month: October 2017

Hypermutation in Cancer

[PMID: 29056344] [Cell]

Comprehensive Analysis of Hypermutation in Human Cancer

“an extensive assessment of mutation burden through sequencing analysis of >81,000 tumors from pediatric and adult patients” “Mutation burden analysis reveals new drivers of hypermutation in POLE and POLD1.” “Replication repair deficiency was a major contributing factor. ” “Unbiased clustering, based on mutational context, revealed clinically relevant subgroups regardless of the tumors’ tissue of origin, highlighting similarities in evolutionary dynamics leading to hypermutation.” “The order of mutational signatures identified previous treatment and germline replication repair deficiency”


Selection of Somatic Mutations

[PMID: 29056346] [Cell]

Universal Patterns of Selection in Cancer and Somatic Tissues

“Nearly all (∼99%) coding mutations are tolerated and escape negative selection. Half of the coding driver mutations occur outside of known cancer genes.” Another great work from Sanger Institute.


[PMID: 29036324] [Nucleic Acids Research]

PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types

“Using the genotype and expression data of 9196 tumor samples in 33 cancer types from The Cancer Genome Atlas (TCGA), we identified 5 606 570 eQTL-gene pairs in the cis-eQTL analysis and 231 210 eQTL-gene pairs in the trans-eQTL analysis.” “We developed PancanQTL, a user-friendly database, to store cis-eQTLs, trans-eQTLs, survival-associated eQTLs and GWAS-related eQTLs to enable searching, browsing and downloading.”



[PMID: 28977528] [Nucleic Acids Research]

MAPPIN: a method for annotating, predicting pathogenicity and mode of inheritance for nonsynonymous variants

“a prediction method which utilizes a random forest algorithm to distinguish between nsSNVs with dominant, recessive, and benign effects.” “MAPPIN outperforms CADD and Eigen in predicting disease inheritance modes for all validation datasets. “


Bi-allelic Variants and HRD

[PMID: 29021619] [Nature Communications]

Pan-cancer analysis of bi-allelic alterations in homologous recombination DNA repair genes

“over 5% of all cancers harbor bi-allelic pathogenic mutations in HR-related genes” “bi-allelic alterations in HR DNA repair-related genes occur across cancer types, are mutually exclusive, and are associated with genomics features consistent with lack of competent HR DNA repair” mono-allelic alterations are not associated with HDR.


Review of Sequencing

[PMID: 29019985] [Nature]

DNA sequencing at 40: past, present and future

“This review commemorates the 40th anniversary of DNA sequencing”



[PMID: 28974235] [Genome Biology]

Alignment-free sequence comparison: benefits, applications, and tools

A review of Alignment-free sequence analyses tools.