TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Circulating MicroRNA Biomarker Studies: Pitfalls and Potential Solutions

(2014) K. W. Witwer   CLINICAL CHEMISTRY

Comparative genomic hybridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicentre, prospective trial (SAFIR01/UNICANCER)

(2014) Fabrice André et al.   LANCET ONCOLOGY

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies

(2014) C. Bettegowda et al.   Science Translational Medicine

Comparing somatic mutation-callers: beyond Venn diagrams

(2013) Su Kim et al.   BMC BIOINFORMATICS

Inferring primary tumor sites from mutation spectra: a meta-analysis of histology-specific aberrations in cancer-derived cell lines

(2013) Felix Dietlein et al.   HUMAN MOLECULAR GENETICS

Massively-parallel sequencing assists the diagnosis and guided treatment of cancers of unknown primary

(2013) Richard W Tothill et al.   JOURNAL OF PATHOLOGY

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Cancer of unknown primary site

(2012) Nicholas Pavlidis et al.   LANCET

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA

(2012) T. Forshew et al.   Science Translational Medicine

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Blood Cell Origin of Circulating MicroRNAs: A Cautionary Note for Cancer Biomarker Studies

(2011) C. C. Pritchard et al.   Cancer Prevention Research

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

Cancer metastasis networks and the prediction of progression patterns

(2009) L L Chen et al.   BRITISH JOURNAL OF CANCER

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Pathologic Evaluation of Unknown Primary Cancer

(2009) Karin A. Oien   SEMINARS IN ONCOLOGY

MicroRNAs accurately identify cancer tissue origin

(2008) Nitzan Rosenfeld et al.   NATURE BIOTECHNOLOGY