Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens

Somatic mutations in the notch, NF-KB, PIK3CA, and hedgehog pathways in human breast cancers

(2012) Xiang Jiao et al.   GENES CHROMOSOMES & CANCER

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity

(2011) Martin Kerick et al.   BMC Medical Genomics

A computational index derived from whole-genome copy number analysis is a novel tool for prognosis in early stage lung squamous cell carcinoma

(2011) Ornella Belvedere et al.   GENOMICS

KRAS Mutation Detection in Paired Frozen and Formalin-Fixed Paraffin-Embedded (FFPE) Colorectal Cancer Tissues

(2011) Jérome Solassol et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma

(2011) N. J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The uniqueome: a mappability resource for short-tag sequencing

(2010) Ryan Koehler et al.   BIOINFORMATICS

Analyses and interpretation of whole-genome gene expression from formalin-fixed paraffin-embedded tissue: an illustration with breast cancer tissues

(2010) Muhammad G Kibriya et al.   BMC GENOMICS

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

(2010) Henry M. Wood et al.   NUCLEIC ACIDS RESEARCH

The Genetic Landscape of the Childhood Cancer Medulloblastoma

(2010) D. W. Parsons et al.   SCIENCE

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line

(2010) Michael James Clark et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Sensitive Detection of KRAS Mutations in Archived Formalin-Fixed Paraffin-Embedded Tissue Using Mutant-Enriched PCR and Reverse-Hybridization

(2009) Christoph Ausch et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis

(2009) Michal R. Schweiger et al.   PLoS One

Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples

(2009) Craig April et al.   PLoS One

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

RNA expression analysis from formalin fixed paraffin embedded tissues

(2008) Susan M. Farragher et al.   HISTOCHEMISTRY AND CELL BIOLOGY

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE