Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling

(2015) Timour Baslan et al.   GENOME RESEARCH

Uterine adenosarcomas are mesenchymal neoplasms

(2015) Salvatore Piscuoglio et al.   JOURNAL OF PATHOLOGY

Breast Cancer Genomics From Microarrays to Massively Parallel Sequencing: Paradigms and New Insights

(2015) Charlotte K. Y. Ng et al.   JNCI-Journal of the National Cancer Institute

Massively Parallel Sequencing-Based Clonality Analysis of Synchronous Endometrioid Endometrial and Ovarian Carcinomas

(2015) Anne M. Schultheis et al.   JNCI-Journal of the National Cancer Institute

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

Clinical management of breast cancer heterogeneity

(2015) Dimitrios Zardavas et al.   Nature Reviews Clinical Oncology

Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method

(2015) Lieselot Deleye et al.   Scientific Reports

SNES: single nucleus exome sequencing

(2015) Marco L Leung et al.   GENOME BIOLOGY

Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification

(2015) Charlotte KY Ng et al.   GENOME BIOLOGY

Breast Cancer Genomics From Microarrays to Massively Parallel Sequencing: Paradigms and New Insights

(2015) Charlotte K. Y. Ng et al.   JNCI-Journal of the National Cancer Institute

Massively Parallel Sequencing-Based Clonality Analysis of Synchronous Endometrioid Endometrial and Ovarian Carcinomas

(2015) Anne M. Schultheis et al.   JNCI-Journal of the National Cancer Institute

PI3K Pathway Activation in High-Grade Ductal Carcinoma In Situ--Implications for Progression to Invasive Breast Carcinoma

(2014) R. A. Sakr et al.   CLINICAL CANCER RESEARCH

Prognostic Value of Tumor-Infiltrating Lymphocytes in Triple-Negative Breast Cancers From Two Phase III Randomized Adjuvant Breast Cancer Trials: ECOG 2197 and ECOG 1199

(2014) Sylvia Adams et al.   JOURNAL OF CLINICAL ONCOLOGY

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands

(2014) Ilan Weinreb et al.   NATURE GENETICS

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(2014) Eliezer M Van Allen et al.   NATURE MEDICINE

Anchored multiplex PCR for targeted next-generation sequencing

(2014) Zongli Zheng et al.   NATURE MEDICINE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

PI3K Pathway Dependencies in Endometrioid Endometrial Cancer Cell Lines

(2013) B. Weigelt et al.   CLINICAL CANCER RESEARCH

Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Clinical Practice Guideline Update

(2013) Antonio C. Wolff et al.   JOURNAL OF CLINICAL ONCOLOGY

Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP–CGH analysis

(2013) Abdel Nasser Hosein et al.   LABORATORY INVESTIGATION

The Implications of Clonal Genome Evolution for Cancer Medicine

(2013) Samuel Aparicio et al.   NEW ENGLAND JOURNAL OF MEDICINE

Single-cell paired-end genome sequencing reveals structural variation per cell cycle

(2013) Thierry Voet et al.   NUCLEIC ACIDS RESEARCH

Target inference from collections of genomic intervals

(2013) A. Krasnitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra-tumour genetic heterogeneity and clonal selection

(2012) Lucia Hernandez et al.   JOURNAL OF PATHOLOGY

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

American Society of Clinical Oncology/College of American Pathologists Guideline Recommendations for Immunohistochemical Testing of Estrogen and Progesterone Receptors in Breast Cancer

(2010) M. Elizabeth H. Hammond et al.   JOURNAL OF CLINICAL ONCOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY