Identification of [872] sig. mutated regions across #cancer types http://www.nature.com/ng/journal/v48/n2/full/ng.3471.html ranges from noncoding annotations to 3D structure
#Chromatin…shapes the mutational landscape of cancer
http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Low DNase correlates w/ high SNVs in melanoma. True generally?
Pooled association tests for rare variants in exon-resequencing http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032073 Simulation shows advantage of mult. rarity thresholds
Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ,
Sunyaev SR. Pooled association tests for rare variants in
exon-resequencing studies. American Journal of Human Genetics (2010)
86: 832-838.
SUMMARY
Multiple studies indicate strong association between rare variants and
resulting phenotype. This paper describes a population-genetics
simulation framework to study the influence of variant allele
frequency on the corresponding phenotype. In a prior study, causal
relationship between variants and phenotype was resolved by performing
association test on set of variants having allele frequency below a
fixed threshold. However, here it is observed that simulation
frameworks based on a variable allele frequency threshold provide
higher accuracy in association test compared to the fixed allele
frequency model. In addition, inclusion of predicted functional
effects of variants (Polyphen-2 scores) increases the accuracy of the
variable frequency threshold model. Overall, this paper describes a novel methodology, which can be
used to explore the association between rare variants and various
diseases.
Analysis of noncoding somatic mutations &…expression alterations http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html 505 WGS variants w. RNAseq, #TCGA as of Mar ’14
all of what’s in TCGA as of spring ’14
505 TCGA WGS Somatic mutations, Expression Calls, CNA
via
https://www.synapse.org/#!Synapse:syn2882200
Orthogonal to PCAWG-607 (Alexandrov et al + 100 "public" stomach cancers)