Digital Sorting of Pure Cell Populations Enables Unambiguous Genetic Analysis of Heterogeneous Formalin-Fixed Paraffin-Embedded Tumors by Next Generation Sequencing

Personalized genomic analyses for cancer mutation discovery and interpretation

(2015) Siân Jones et al.   Science Translational Medicine

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations

(2015) Ankit Malhotra et al.   Genome Medicine

Development and Validation of a Scalable Next-Generation Sequencing System for Assessing Relevant Somatic Variants in Solid Tumors

(2015) Daniel H. Hovelson et al.   NEOPLASIA

A Review of Preanalytical Factors Affecting Molecular, Protein, and Morphological Analysis of Formalin-Fixed, Paraffin-Embedded (FFPE) Tissue: How Well Do You Know Your FFPE Specimen?

(2014) B. Paige Bass et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing

(2014) Stephen Q Wong et al.   BMC Medical Genomics

Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization

(2014) H. Do et al.   CLINICAL CHEMISTRY

Molecular profiling of single circulating tumor cells with diagnostic intention

(2014) B. Polzer et al.   EMBO Molecular Medicine

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

(2014) Ilari Scheinin et al.   GENOME RESEARCH

False Positives in Multiplex PCR-Based Next-Generation Sequencing Have Unique Signatures

(2014) Chad M. McCall et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer

(2014) Cassandra L Hodgkinson et al.   NATURE MEDICINE

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Stars and stripes in pancreatic cancer: role of stellate cells and stroma in cancer progression

(2014) Jeremy S. Wilson et al.   Frontiers in Physiology

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

The proportion of tumor-stroma as a strong prognosticator for stage II and III colon cancer patients: validation in the VICTOR trial

(2012) A. Huijbers et al.   ANNALS OF ONCOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer

(2012) V Abkevich et al.   BRITISH JOURNAL OF CANCER

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

(2011) Arief Gusnanto et al.   BIOINFORMATICS

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Cervical carcinoma-associated fibroblasts are DNA diploid and do not show evidence for somatic genetic alterations

(2011) Willem Ernst Corver et al.   CELLULAR ONCOLOGY

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

(2010) Valentina Boeva et al.   BIOINFORMATICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Genome-wide Allelic State Analysis on Flow-Sorted Tumor Fractions Provides an Accurate Measure of Chromosomal Aberrations

(2008) W. E. Corver et al.   CANCER RESEARCH