A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy

(2017) Teresa Davoli et al.   SCIENCE

Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy

(2016) Weiguo Zhang et al.   Nature Communications

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

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A Decision Support Framework for Genomically Informed Investigational Cancer Therapy

(2015) Funda Meric-Bernstam et al.   JNCI-Journal of the National Cancer Institute

A Decision Support Framework for Genomically Informed Investigational Cancer Therapy

(2015) Funda Meric-Bernstam et al.   JNCI-Journal of the National Cancer Institute

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

(2014) Yi Li et al.   BIOINFORMATICS

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

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

(2014) Cassandra L Hodgkinson et al.   NATURE MEDICINE

Reliable Single Cell Array CGH for Clinical Samples

(2014) Zbigniew T. Czyż et al.   PLoS One

Copy number alteration burden predicts prostate cancer relapse

(2014) H. Hieronymus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

(2013) Nora Rieber et al.   PLoS One

A Robust Method to Analyze Copy Number Alterations of Less than 100 kb in Single Cells Using Oligonucleotide Array CGH

(2013) Birte Möhlendick et al.   PLoS One

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

Copy number alterations of c-MYC and PTEN are prognostic factors for relapse after prostate cancer radiotherapy

(2012) Gaetano Zafarana et al.   CANCER

Clonal evolution in cancer

(2012) Mel Greaves 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

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

(2012) C. Zong et al.   SCIENCE

The Causes and Consequences of Polyploidy in Normal Development and Cancer

(2011) Teresa Davoli et al.   Annual Review of Cell and Developmental Biology

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

Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies

(2010) David T. Miller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) Valentina Boeva et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Architecture Characterizes Tumor Progression Paths and Fate in Breast Cancer Patients

(2010) H. G. Russnes et al.   Science Translational Medicine

Comparison of Whole Genome Amplification Methods for Further Quantitative Analysis with Microarray-based Comparative Genomic Hybridization

(2008) Yun-Shien Lee et al.   Taiwanese Journal of Obstetrics & Gynecology