Nature Genetics

Nature Genetics Advance Online Publication

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  • doi:10.1038/ng.3987

    This study presents a probabilistic framework for inferring negative and positive selection in human cancers that addresses the problem of mutation rate variation. Applying the model to sequencing data from 17 cancer types identifies new significantly mutated genes and detects significant signals of negative selection in many cancer types.' );return false" > Bayesian inference of negative and positive selection in human cancers
  • doi:10.1038/ng.3991

    This analysis of cancer sequencing data identifies a reduced somatic mutation rate in exons and shows that this phenomenon is due to higher mismatch-repair activity in exons as compared to introns. These findings have implications for the understanding of mutational and DNA repair processes and for studying the evolution of both tumors and species.' );return false" > Reduced mutation rate in exons due to differential mismatch repair
  • doi:10.1038/ng.3990

    Analysis of a large cohort of EGFR-mutant lung cancer cell-free DNA samples along with longitudinal samples from a patient with EGFR-mutant lung cancer identifies pathways that inhibit EGFR-inhibitor response. Co-occurring genetic alterations influence clinical outcomes and underscore the need for combination therapies.' );return false" > Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers
  • doi:10.1038/ng.3988

    RNA Capture Long Seq (CLS) is a new method for transcript annotation that combines targeted RNA capture with long-read sequencing. CLS reannotates GENCODE lncRNAs and increases the number of validated splice junctions and transcript models for targeted loci.' );return false" > High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
  • doi:10.1038/ng.3978

    A meta-analysis of exome-wide association studies for blood lipid levels in East Asian populations identifies a novel coding variant. Exome array data from the Global Lipids Genetics Consortium were integrated and led to the discovery of novel and population-specific variants associated with cholesterol and triglycerides.' );return false" > Exome chip meta-analysis identifies novel loci and East Asian–specific coding variants that contribute to lipid levels and coronary artery disease
  • doi:10.1038/ng.3985

    This large-scale genome-wide association analysis of subjects with asthma, hay fever or eczema provides insights into the shared genetic basis of these allergic diseases. The findings suggest that these diseases partly co-occur because they share many genetic risk variants that dysregulate the expression of immune-related genes.' );return false" > Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology
  • doi:10.1038/ng.3980

    Analysis of whole-genome sequencing data from 163 vervet monkeys from Africa and the Caribbean shows high diversity among taxa and identifies signatures of selection. Selection signals affect viral processes, and genes that show response to SIV in vervets but not macaques have elevated selection scores.' );return false" > Ancient hybridization and strong adaptation to viruses across African vervet monkey populations
  • doi:10.1038/ng.3984

    CERES is a new computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for copy number effects and variable sgRNA activity. Applying CERES to new genome-scale CRISPR–Cas9 essentiality screen data from 342 cancer cell lines and other published data sets shows that CERES decreases false-positive results and provides consistent estimates of sgRNA activity.' );return false" > Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells
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