De novo mutations in human genetic disease

JA Veltman, HG Brunner - Nature Reviews Genetics, 2012 - nature.com
New mutations have long been known to cause genetic disease, but their true contribution to
the disease burden can only now be determined using family-based whole-genome or …

Advances in understanding cancer genomes through second-generation sequencing

M Meyerson, S Gabriel, G Getz - Nature Reviews Genetics, 2010 - nature.com
Cancers are caused by the accumulation of genomic alterations. Therefore, analyses of
cancer genome sequences and structures provide insights for understanding cancer …

Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes

R Malik, G Chauhan, M Traylor, M Sargurupremraj… - Nature …, 2018 - nature.com
Stroke has multiple etiologies, but the underlying genes and pathways are largely unknown.
We conducted a multiancestry genome-wide-association meta-analysis in 521,612 …

Dynamic and adaptive cancer stem cell population admixture in colorectal neoplasia

EG Vazquez, N Nasreddin, GN Valbuena… - Cell Stem Cell, 2022 - cell.com
Intestinal homeostasis is underpinned by LGR5+ve crypt-base columnar stem cells (CBCs),
but following injury, dedifferentiation results in the emergence of LGR5− ve regenerative …

Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations

R Bueno, EW Stawiski, LD Goldstein, S Durinck… - Nature …, 2016 - nature.com
Abstract We analyzed transcriptomes (n= 211), whole exomes (n= 99) and targeted exomes
(n= 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we …

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations

J Bendl, J Stourac, O Salanda, A Pavelka… - PLoS computational …, 2014 - journals.plos.org
Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the
coding regions are frequently associated with the development of various genetic diseases …

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models

HA Shihab, J Gough, DN Cooper, PD Stenson… - Human …, 2013 - Wiley Online Library
The rate at which nonsynonymous single nucleotide polymorphisms (ns SNP s) are being
identified in the human genome is increasing dramatically owing to advances in whole …

Rare-variant association testing for sequencing data with the sequence kernel association test

MC Wu, S Lee, T Cai, Y Li, M Boehnke, X Lin - The American Journal of …, 2011 - cell.com
Sequencing studies are increasingly being conducted to identify rare variants associated
with complex traits. The limited power of classical single-marker association analysis for rare …

Predicting the functional impact of protein mutations: application to cancer genomics

B Reva, Y Antipin, C Sander - Nucleic acids research, 2011 - academic.oup.com
As large-scale re-sequencing of genomes reveals many protein mutations, especially in
human cancer tissues, prediction of their likely functional impact becomes important …

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer

CM Rudin, S Durinck, EW Stawiski, JT Poirier… - Nature …, 2012 - nature.com
Small-cell lung cancer (SCLC) is an exceptionally aggressive disease with poor prognosis.
Here, we obtained exome, transcriptome and copy-number alteration data from …