Chromosomal imbalances detected via RNA-sequencing in 28 cancers

Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types

(2021) Smruthy Sivakumar et al.   GENETICS

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

Detecting copy number alterations in RNA-Seq using SuperFreq

(2021) Christoffer Flensburg et al.   BIOINFORMATICS

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data

(2020) Akdes Serin Harmanci et al.   Nature Communications

Chromosome arm aneuploidies shape tumour evolution and drug response

(2020) Ankit Shukla et al.   Nature Communications

Pervasive chromosomal instability and karyotype order in tumour evolution

(2020) Thomas B. K. Watkins et al.   NATURE

Aneuploidy drives lethal progression in prostate cancer

(2019) Konrad H. Stopsack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

(2019) Keren Yizhak et al.   SCIENCE

Large-scale analysis of acquired chromosomal alterations in non-tumor samples from patients with cancer

(2019) Y. A. Jakubek et al.   NATURE BIOTECHNOLOGY

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

(2018) Jean Fan et al.   GENOME RESEARCH

Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations

(2018) Po-Ru Loh et al.   NATURE

Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death

(2018) Haley Hieronymus et al.   eLife

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

(2018) Alexandre Coudray et al.   PeerJ

System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows

(2018) Jerry Fowler et al.   GENETIC EPIDEMIOLOGY

Extensive Hidden Genomic Mosaicism Revealed in Normal Tissue

(2016) Selina Vattathil et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Rapid and powerful detection of subtle allelic imbalance from exome sequencing data withhapLOHseq

(2016) F. Anthony San Lucas et al.   BIOINFORMATICS

Copy-number analysis identified new prognostic marker in acute myeloid leukemia

(2016) O Nibourel et al.   LEUKEMIA

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

Somatic gene copy number alterations in colorectal cancer: new quest for cancer drivers and biomarkers

(2015) H Wang et al.   ONCOGENE

Gastric cancer and gene copy number variation: emerging cancer drivers for targeted therapy

(2015) L Liang et al.   ONCOGENE

Large-scale RNA-Seq Transcriptome Analysis of 4043 Cancers and 548 Normal Tissue Controls across 12 TCGA Cancer Types

(2015) Li Peng et al.   Scientific Reports

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Inferring copy number and genotype in tumour exome data

(2014) Kaushalya C Amarasinghe et al.   BMC GENOMICS

Genome-wide copy-number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma

(2013) A. Bouska et al.   BLOOD

Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method

(2013) Joseph D Baugher et al.   BMC GENOMICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

The consequences of chromosomal aneuploidy on the transcriptome of cancer cells

(2012) Thomas Ried et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Haplotype-based profiling of subtle allelic imbalance with SNP arrays

(2012) S. Vattathil et al.   GENOME RESEARCH

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

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

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Whole transcriptome sequencing reveals recurrent NOTCH1 mutations in mantle cell lymphoma

(2011) R. Kridel et al.   BLOOD

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genomic instability — an evolving hallmark of cancer

(2010) Simona Negrini et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2009) Sohrab P. Shah et al.   NATURE

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

(2008) Joshua M Korn et al.   NATURE GENETICS