[HTML][HTML] Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1

…, V Wang, Y Qi, MD Wilkerson, CR Miller, L Ding… - Cancer cell, 2010 - Elsevier
The Cancer Genome Atlas Network recently cataloged recurrent genomic abnormalities in
glioblastoma multiforme (GBM). We describe a robust gene expression-based molecular
classification of GBM into Proneural, Neural, Classical, and Mesenchymal subtypes and

[HTML][HTML] Somatic mutations affect key pathways in lung adenocarcinoma

L Ding, G Getz, DA Wheeler, ER Mardis, MD McLellan… - Nature, 2008 - ncbi.nlm.nih.gov
Abstract Determining the genetic basis of cancer requires comprehensive analyses of large
collections of histopathologically well-classified primary tumours. Here we report the results
of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas.

[HTML][HTML] Recurring mutations found by sequencing an acute myeloid leukemia genome

ER Mardis, L Ding, DJ Dooling… - … England Journal of …, 2009 - Mass Medical Soc
Background The full complement of DNA mutations that are responsible for the
pathogenesis of acute myeloid leukemia (AML) is not yet known. Methods We used
massively parallel DNA sequencing to obtain a very high level of coverage (approximately

[HTML][HTML] Mutational landscape and significance across 12 major cancer types

…, MC Wendl, TJ Ley, RK Wilson, BJ Raphael, L Ding - Nature, 2013 - ncbi.nlm.nih.gov
Abstract The Cancer Genome Atlas (TCGA) has used the latest sequencing and analysis
methods to identify somatic variants across thousands of tumours. Here we present data and
analytical results for point mutations and small insertions/deletions from 3,281 tumours

[HTML][HTML] Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma

…, DN Hayes, CM Perou, HK Schmidt, L Ding… - Cancer cell, 2010 - Elsevier
We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the
context of The Cancer Genome Atlas (TCGA). We found that a distinct subset of samples
displays concerted hypermethylation at a large number of loci, indicating the existence of a

[HTML][HTML] DNMT3A mutations in acute myeloid leukemia

TJ Ley, L Ding, MJ Walter, MD McLellan… - … England Journal of …, 2010 - Mass Medical Soc
Background The genetic alterations responsible for an adverse outcome in most patients
with acute myeloid leukemia (AML) are unknown. Methods Using massively parallel DNA
sequencing, we identified a somatic mutation in DNMT3A, encoding a DNA

[HTML][HTML] Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing

L Ding, TJ Ley, DE Larson, CA Miller, DC Koboldt… - Nature, 2012 - ncbi.nlm.nih.gov
Summary Most patients with acute myeloid leukemia (AML) die from progressive disease
after relapse, which is associated with clonal evolution at the cytogenetic level 1, 2. To
determine the mutational spectrum associated with relapse, we sequenced the primary

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

…, L Lin, CA Miller, ER Mardis, L Ding… - Genome …, 2012 - genome.cshlp.org
Abstract Cancer is a disease driven by genetic variation and mutation. Exome sequencing
can be utilized for discovering these variants and mutations across hundreds of tumors.
Here we present an analysis tool, VarScan 2, for the detection of somatic mutations and

[HTML][HTML] Comprehensive molecular characterization of gastric adenocarcinoma

…, S Fisher, SB Gabriel, ES Lander, L Ding… - Nature, 2014 - ncbi.nlm.nih.gov
Abstract Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and
clinical characteristics has been complicated by histological and aetiological heterogeneity.
Here we describe a comprehensive molecular evaluation of 295 primary gastric

[HTML][HTML] Genome remodeling in a basal-like breast cancer metastasis and xenograft

LI Ding, MJ Ellis, S Li, DE Larson, K Chen, JW Wallis… - Nature, 2010 - ncbi.nlm.nih.gov
Abstract Massively parallel DNA sequencing technologies provide an unprecedented ability
to screen entire genomes for genetic changes associated with tumor progression. Here we
describe the genomic analyses of four DNA samples from an African-American patient with