Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

By Ekta Khurana, Yao Fu, V. Colonna, X. Mu, Hyun Min Kang, Tuuli Lappalainen, A. Sboner, L. Lochovsky, Jieming Chen, A. Harmanci and 38 more. Science, 2013

370 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d7bb9e840c5b3668c671dc4dbc3673b3fbfb62b6

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In Molecular Biology

Citations in the corpus

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios (2021, methodology): “The 1kGP resources have been collectively cited over 16,000 times to date and have been utilized for foundational applications such as genotype imputation, eQTL mapping, variant pathogenicity prioritization, population history, and evolutionary genetics studies (Almeida et al., 2014; Hara et al., 20”
Improved exome prioritization of disease genes through cross-species phenotype comparison (2014, methodology): “The methodology thus represents a powerful approach toward the prioritization of variants in noncoding regions (Khurana et al. 2013).”
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma (2017, result): “Compared to approaches used in previous cancer genome studies (32,33), FIREFLY differs in three important respects.”
The human splicing code reveals new insights into the genetic determinants of disease (2014, methodology): “use functional annotations of the genome (2, 8, 47), tools that are trained using existing disease annotations and thus suffer from overfitting to known mutations or severe selection bias (7–9, 48, 49); GWAS (50, 51); and expressionbased quantitative trait loci (QTL) (16, 52).”
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer (2014, methodology): “Through analyzing the variation patterns of natural polymorphisms, we have published a prototype approach (FunSeq) to identify potential noncoding drivers [26].”
The molecular taxonomy of primary prostate cancer (2015, background): “Interestingly, no occult driver abnormalities or highly recurrent regulatory mutations were identified, such as the TERT promoter mutation common to many other tumor types (Khurana et al., 2013).”