[HTML][HTML] Accurate whole human genome sequencing using reversible terminator chemistry

…, JM Boutell, J Bryant, RJ Carter, RK Cheetham… - nature, 2008 - ncbi.nlm.nih.gov
Abstract DNA sequence information underpins genetic research, enabling discoveries of
important biological or medical benefit. Sequencing projects have traditionally employed
long (400–800 bp) reads, but the existence of reference sequences for the human and many

[HTML][HTML] A comprehensive catalogue of somatic mutations from a human cancer genome

ED Pleasance, RK Cheetham, PJ Stephens… - Nature, 2010 - ncbi.nlm.nih.gov
Abstract All cancers carry somatic mutations. A subset of these somatic alterations, termed
driver mutations, confer selective growth advantage and are implicated in cancer
development, whereas the remainder are passengers. Here we have sequenced the

[HTML][HTML] Mapping copy number variation by population scale genome sequencing

…, C Alkan, A Abyzov, SC Yoon, K Ye, RK Cheetham… - Nature, 2011 - ncbi.nlm.nih.gov
Summary Genomic structural variants (SVs) are abundant in humans, differing from other
variation classes in extent, origin, and functional impact. Despite progress in SV
characterization, the nucleotide resolution architecture of most SVs remains unknown. We

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

…, S Swamy, J Becq, LJ Murray, RK Cheetham - …, 2012 - academic.oup.com
Abstract Motivation: Whole genome and exome sequencing of matched tumor–normal
sample pairs is becoming routine in cancer research. The consequent increased demand for
somatic variant analysis of paired samples requires methods specialized to model this

Demographic history and rare allele sharing among human populations

…, D Wheeler, J Li, M Jian, G Li, R Li… - Proceedings of the …, 2011 - National Acad Sciences
Abstract High-throughput sequencing technology enables population-level surveys of
human genomic variation. Here, we examine the joint allele frequency distributions across
continental human populations and present an approach for combining complementary

[HTML][HTML] Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer

…, S White, A Alsop, J Becq, GR Bignell, RK Cheetham… - Cell, 2012 - Elsevier
The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered
due to a transmissible facial cancer spread by direct transfer of living cancer cells through
biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil

[HTML][HTML] Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints

…, S Homolka, H Bignell, RJ Carter, RK Cheetham… - PloS one, 2009 - journals.plos.org
Background Mycobacterium tuberculosis complex (MTBC), the causative agent of
tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of
the classical examples of a genetically monomorphic pathogen. Because of this limited DNA

CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data

…, T Royce, AJ Cox, DJ Evers, RK Cheetham… - …, 2010 - academic.oup.com
Abstract Motivation: Copy number abnormalities (CNAs) represent an important type of
genetic mutation that can lead to abnormal cell growth and proliferation. New high-
throughput sequencing technologies promise comprehensive characterization of CNAs. In

APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma

…, M Bibikova, RK Cheetham, JB Fan, R Grocock… - Cancer research, 2013 - AACR
Abstract Ovarian cancer is a clinically and molecularly heterogeneous disease. The driving
forces behind this variability are unknown. Here, we report wide variation in the expression
of the DNA cytosine deaminase APOBEC3B, with elevated expression in the majority of

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma

CS Ross-Innes, J Becq, A Warren, RK Cheetham… - Nature …, 2015 - nature.com
The molecular genetic relationship between esophageal adenocarcinoma (EAC) and its
precursor lesion, Barrett's esophagus, is poorly understood. Using whole-genome
sequencing on 23 paired Barrett's esophagus and EAC samples, together with one in-depth