Recurrent repeat expansions in human cancer genomes

[1]  R. Yuen,et al.  Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences , 2021, Genome research.

[2]  Patricia A. Castruita,et al.  p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR) , 2021, Cell.

[3]  A. Hannan.  Repeat DNA expands our understanding of autism spectrum disorder , 2021, Nature.

[4]  M. Gymrek,et al.  Patterns of de novo tandem repeat mutations and their role in autism , 2020, Nature.

[5]  K. Garimella,et al.  Repeat expansions confer WRN dependence in microsatellite-unstable cancers , 2020, Nature.

[6]  Jian Zhang,et al.  Crosstalk Between the MSI Status and Tumor Microenvironment in Colorectal Cancer , 2020, Frontiers in Immunology.

[7]  S. Scherer,et al.  Genome-wide detection of tandem DNA repeats that are expanded in autism , 2020, Nature.

[8]  Michael J. Purcaro,et al.  Expanded encyclopaedias of DNA elements in the human and mouse genomes , 2020, Nature.

[9]  David M. Thomas,et al.  The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly , 2020, Nature Communications.

[10]  E. Eichler,et al.  Slipped-CAG DNA binding small molecule induces trinucleotide repeat contractions in vivo , 2020, Nature Genetics.

[11]  Snædis Kristmundsdottir,et al.  popSTR2 enables clinical and population-scale genotyping of microsatellites , 2019, Bioinform..

[12]  Wyeth W. Wasserman,et al.  ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data , 2019, Genome Biology.

[13]  Ryan E. Mills,et al.  Structural variation in the sequencing era , 2019, Nature Reviews Genetics.

[14]  A. Bardelli,et al.  Adaptive mutability of colorectal cancers in response to targeted therapies , 2019, Science.

[15]  Howard Y. Chang,et al.  Circular ecDNA promotes accessible chromatin and high oncogene expression , 2019, Nature.

[16]  M. Gymrek,et al.  The impact of short tandem repeat variation on gene expression , 2019, Nature Genetics.

[17]  E. Koonin,et al.  Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues , 2019, Proceedings of the National Academy of Sciences.

[18]  Katherine R. Smith,et al.  Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS , 2019, American journal of human genetics.

[19]  Evan E. Eichler,et al.  Characterizing the Major Structural Variant Alleles of the Human Genome , 2019, Cell.

[20]  Melanie Bahlo,et al.  Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data. , 2018, American journal of human genetics.

[21]  Satoru Miyano,et al.  Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types , 2018, bioRxiv.

[22]  Guocheng Yuan,et al.  Quantitative integration of epigenomic variation and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator at gene promoters , 2018, Cell Discovery.

[23]  Nima Mousavi,et al.  Profiling the genome-wide landscape of tandem repeat expansions , 2018, bioRxiv.

[24]  K. D. Sørensen,et al.  Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci , 2018, Nature Genetics.

[25]  Ville Mustonen,et al.  The repertoire of mutational signatures in human cancer , 2018, Nature.

[26]  A. Hannan,et al.  Tandem repeats mediating genetic plasticity in health and disease , 2018, Nature Reviews Genetics.

[27]  Mousheng Xu,et al.  Synthetic transcription elongation factors license transcription across repressive chromatin , 2017, Science.

[28]  David Heckerman,et al.  Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes , 2017, American journal of human genetics.

[29]  R. Nolley,et al.  Cabozantinib inhibits tumor growth and metastasis of a patient-derived xenograft model of papillary renal cell carcinoma with MET mutation , 2017, Cancer biology & therapy.

[30]  Icgc,et al.  Pan-cancer analysis of whole genomes , 2017, bioRxiv.

[31]  D. MacArthur,et al.  STRetch: detecting and discovering pathogenic short tandem repeat expansions , 2017, bioRxiv.

[32]  Maureen A. Sartor,et al.  annotatr: Genomic regions in context , 2016, bioRxiv.

[33]  Chris Shaw,et al.  Detection of long repeat expansions from PCR-free whole-genome sequence data , 2016, bioRxiv.

[34]  R. Stewart,et al.  Synthetic genome readers target clustered binding sites across diverse chromatin states , 2016, Proceedings of the National Academy of Sciences.

[35]  P. Park,et al.  A molecular portrait of microsatellite instability across multiple cancers , 2016, Nature Communications.

[36]  Jay Shendure,et al.  Classification and characterization of microsatellite instability across 18 cancer types , 2016, Nature Medicine.

[37]  C. Guillemette,et al.  Divergent Expression and Metabolic Functions of Human Glucuronosyltransferases through Alternative Splicing. , 2016, Cell reports.

[38]  S. Chanock,et al.  Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite , 2015, Nature Genetics.

[39]  Yves Pommier,et al.  Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. , 2015, Cell reports.

[40]  Janos X. Binder,et al.  DISEASES: Text mining and data integration of disease–gene associations , 2014, bioRxiv.

[41]  N. Hacohen,et al.  Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity , 2015, Cell.

[42]  S. Mirkin,et al.  The balancing act of DNA repeat expansions. , 2013, Current opinion in genetics & development.

[43]  E. Chen,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[44]  M. Pook,et al.  Epigenetics in Friedreich's Ataxia: Challenges and Opportunities for Therapy , 2013, Genetics research international.

[45]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[46]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[47]  C. Freudenreich,et al.  Expanded CAG/CTG Repeat DNA Induces a Checkpoint Response That Impacts Cell Proliferation in Saccharomyces cerevisiae , 2011, PLoS genetics.

[48]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[49]  A. Hannan.  Tandem repeat polymorphisms: modulators of disease susceptibility and candidates for 'missing heritability'. , 2010, Trends in genetics : TIG.

[50]  M. Finel,et al.  Substrate specificity of the human UDP‐glucuronosyltransferase UGT2B4 and UGT2B7 , 2007, The FEBS journal.

[51]  S. Snyder,et al.  p53 Mediates Cellular Dysfunction and Behavioral Abnormalities in Huntington’s Disease , 2005, Neuron.

[52]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[53]  J Isola,et al.  Molecular cytogenetics of primary breast cancer by CGH , 1998, Genes, chromosomes & cancer.

[54]  P. Kantoff,et al.  The CAG repeat within the androgen receptor gene and its relationship to prostate cancer. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[55]  A. Berchuck,et al.  Genetic instability of microsatellites in endometrial carcinoma. , 1993, Cancer research.

[56]  Y. Nakamura,et al.  Genetic instability in pancreatic cancer and poorly differentiated type of gastric cancer. , 1993, Cancer research.

[57]  Darryl Shibata,et al.  Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis , 1993, Nature.

[58]  K. Kinzler,et al.  Clues to the pathogenesis of familial colorectal cancer. , 1993, Science.

[59]  S N Thibodeau,et al.  Microsatellite instability in cancer of the proximal colon. , 1993, Science.

[60]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[61]  Skipper Seabold,et al.  Statsmodels: Econometric and Statistical Modeling with Python , 2010, SciPy.

[62]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[63]  C. Caskey,et al.  Unstable triplet repeat sequences: A source of cancer mutations? , 1995, Stem cells.

[64]  M. Stratton,et al.  Instability of short tandem repeats (microsatellites) in human cancers , 1994, Nature Genetics.