Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity

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The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

(2020) Yiqun Zhang et al.   Nature Communications

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Targeted genomic profiling of acral melanoma

(2019) Iwei Yeh et al.   JNCI-Journal of the National Cancer Institute

Genomic Heterogeneity and Branched Evolution of Early Stage Primary Acral Melanoma Shown by Multiregional Microdissection Sequencing

(2019) Xiannian Zhang et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways

(2019) Christopher D. Steele et al.   CANCER CELL

Association of Patient Characteristics and Tumor Genomics With Clinical Outcomes Among Patients With Non–Small Cell Lung Cancer Using a Clinicogenomic Database

(2019) Gaurav Singal et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Distinct Genomic Features in a Retrospective Cohort of Mucosal, Acral and Vulvovaginal Melanomas

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Germline variants in oculocutaneous albinism genes and predisposition to familial cutaneous melanoma

(2019) Vaishnavi Nathan et al.   Pigment Cell & Melanoma Research

Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets

(2019) Felicity Newell et al.   Nature Communications

Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

Translational pathology, genomics and the development of systemic therapies for acral melanoma

(2019) Yian Ann Chen et al.   SEMINARS IN CANCER BIOLOGY

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

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Genome doubling shapes the evolution and prognosis of advanced cancers

(2018) Craig M. Bielski et al.   NATURE GENETICS

The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature

(2018) Gareth J. Inman et al.   Nature Communications

SEdb: a comprehensive human super-enhancer database

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Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy

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Human tumor genomics and zebrafish modeling identify SPRED1 loss as a driver of mucosal melanoma

(2018) Julien Ablain et al.   SCIENCE

Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma

(2017) Winnie S. Liang et al.   GENOME RESEARCH

Unexpected UVR and non-UVR mutation burden in some acral and cutaneous melanomas

(2017) Robert V Rawson et al.   LABORATORY INVESTIGATION

Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers

(2017) Aaron M. Goodman et al.   MOLECULAR CANCER THERAPEUTICS

Whole-genome landscapes of major melanoma subtypes

(2017) Nicholas K. Hayward et al.   NATURE

A non-coding function of TYRP1 mRNA promotes melanoma growth

(2017) David Gilot et al.   NATURE CELL BIOLOGY

The efficacy of anti-PD-1 agents in acral and mucosal melanoma

(2016) Alexander N. Shoushtari et al.   CANCER

Initial misdiagnosis of melanoma located on the foot is associated with poorer prognosis

(2016) Wiebke Sondermann et al.   MEDICINE

Molecular profiling, including TERT promoter mutations, of acral lentiginous melanomas

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Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Evaluating the evaluation of cancer driver genes

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pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

(2016) Jasreet Hundal et al.   Genome Medicine

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

(2015) Linda J Valentijn et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer

(2015) Joaquin Mateo et al.   NEW ENGLAND JOURNAL OF MEDICINE

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(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

The mutational burden of acral melanoma revealed by whole-genome sequencing and comparative analysis

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Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution

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Prognosis of Acral Melanoma: A Series of 281 Patients

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Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Two Distinct Categories of Focal Deletions in Cancer Genomes

(2013) Megha Rajaram et al.   PLoS One

Somatic Point Mutation Calling in Low Cellularity Tumors

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Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

RNA-SeQC: RNA-seq metrics for quality control and process optimization

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STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

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

(2012) Pablo Cingolani et al.   FLY

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

(2012) Ethan Cerami et al.   Cancer Discovery

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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Whole genome sequencing of matched primary and metastatic acral melanomas

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Tyrosinase related protein 1 (TYRP1/gp75) in human cutaneous melanoma

(2011) Ghanem Ghanem et al.   Molecular Oncology

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

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Acral Lentiginous Melanoma

(2009) Porcia T. Bradford et al.   ARCHIVES OF DERMATOLOGY

The Sequence Alignment/Map format and SAMtools

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

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Fifteen-year quest for microphthalmia-associated transcription factor target genes

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NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS