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CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data

Qunyuan Zhang, Li Ding, David E. Larson, Daniel C. Koboldt, Michael D. McLellan, Ken Chen, Xiaoqi Shi, Aldi Kraja, Elaine R. Mardis, Richard K. Wilson, Ingrid B. Borecki, Michael A. Province
2009 Computer applications in the biosciences : CABIOS  
Motivation: DNA copy number aberration (CNA) is a hallmark of genomic abnormality in tumor cells.  ...  We propose a population-based approach for RCNA detection with no need of single-sample analysis, which is statistically powerful, computationally efficient and particularly suitable for high-resolution  ...  ACKNOWLEDGEMENTS We wish to thank the TSP and TCGA research networks for providing the real datasets, and thank John Osborne for downloading and organizing the data.  ... 
doi:10.1093/bioinformatics/btp708 pmid:20031968 pmcid:PMC2852218 fatcat:x2tuagxr5rhyvpqejpar4rd54u

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

Benjamin J Raphael, Jason R Dobson, Layla Oesper, Fabio Vandin
2014 Genome Medicine  
First, we describe approaches to detect somatic mutations from high-throughput DNA sequencing data, particularly for tumor samples that comprise heterogeneous populations of cells.  ...  Here, we review computational approaches to identify somatic mutations in cancer genome sequences and to distinguish the driver mutations that are responsible for cancer from random, passenger mutations  ...  Acknowledgements We thank Jason Hu for assistance with the figures. BJR is supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund, an Alfred P.  ... 
doi:10.1186/gm524 pmid:24479672 pmcid:PMC3978567 fatcat:k6p3j2m3mzdnlnkzz76wtfzfv4

Genome-wide identification of significant aberrations in cancer genome

Xiguo Yuan, Guoqiang Yu, Xuchu Hou, Ie-Ming Shih, Robert Clarke, Junying Zhang, Eric P Hoffman, Roger R Wang, Zhen Zhang, Yue Wang
2012 BMC Genomics  
Here we introduce Significant Aberration in Cancer (SAIC), a new method for characterizing and assessing the statistical significance of recurrent CNA units.  ...  Somatic Copy Number Alterations (CNAs) in human genomes are present in almost all human cancers.  ...  Details about the implicated SCAs and full list of genes covered by these SCAs, derived from the glioblastoma data set. Acknowledgements  ... 
doi:10.1186/1471-2164-13-342 pmid:22839576 pmcid:PMC3428679 fatcat:3zcwzrr4rjeyvimkvmmcobkyoy

Detection of recurrent rearrangement breakpoints from copy number data

Anna Ritz, Pamela L Paris, Michael M Ittmann, Colin Collins, Benjamin J Raphael
2011 BMC Bioinformatics  
Comparison of copy number data from multiple individuals reveals recurrent variants. Typically, the interior of a recurrent CNV is examined for genes or other loci associated with a phenotype.  ...  Copy number data from array comparative genome hybridization (aCGH) and next-generation DNA sequencing is widely used to measure copy number variants.  ...  Komen Breast Cancer Foundation. This work was made possible in part with funding from the ADVANCE Program at Brown University, under NSF Grant No. 0548311.  ... 
doi:10.1186/1471-2105-12-114 pmid:21510904 pmcid:PMC3112242 fatcat:yw4cmzkpuzclbj6cvyiakictaa

Expanding the computational toolbox for mining cancer genomes

Li Ding, Michael C. Wendl, Joshua F. McMichael, Benjamin J. Raphael
2014 Nature reviews genetics  
High-throughput DNA sequencing has revolutionized cancer genomics with numerous discoveries relevant to cancer diagnosis and treatment.  ...  The latest sequencing and analysis methods have successfully identified somatic alterations including single nucleotide variants (SNVs), insertions and deletions (indels), structural aberrations, and gene  ...  copy number aberrations, structural aberrations, and gene fusions in cancer genomes are now available.  ... 
doi:10.1038/nrg3767 pmid:25001846 pmcid:PMC4168012 fatcat:wgpspotu3jfp3ahhilcxzz7z5i

Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma

Xiaoyu Wang, Xiaohong Li, Yichen Cheng, Xin Sun, Xibin Sun, Steve Self, Charles Kooperberg, James Y. Dai
2015 Human Genomics  
A high level of somatic copy number alterations (CNAs) accumulates over the decades in the progression from Barrett's esophagus, the precursor lesion, to EA.  ...  First, the recurrent CNAs based on WGS and WES data from 145 EA samples were compared to those found in five previous microarray-based studies.  ...  GISTIC2.0 was used to identify regions with a statistically high frequency of copy number aberrations over background aberrations.  ... 
doi:10.1186/s40246-015-0044-0 pmid:26374103 pmcid:PMC4570720 fatcat:wwuhxrt2araihctnmzwbmhtwpi

Temporal and spatial topography of cell proliferation in cancer [article]

Giorgio Gaglia, Sheheryar Kabraji, Danae Argyropoulou, Yang Dai, Shu Wang, Johann Bergholz, Shannon Coy, Jia-Ren Lin, Rinath Jeselsohn, Otto Metzger, Eric P Winer, Deborah A Dillon (+3 others)
2021 bioRxiv   pre-print
Proliferation is a fundamental trait of cancer cells but is poorly characterized in tumors by classical histologic methods.  ...  Multivariate measures capture clinically significant features of cancer proliferation, a fundamental step in enabling more precise use of anti-cancer therapies.  ...  Ki-67 is a prognostic parameter in breast cancer patients: results of a large 23 population-based cohort of a cancer registry.  ... 
doi:10.1101/2021.05.16.443704 fatcat:43nav545qja2damd5iu67owsgm

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

Michael Krauthammer, Yong Kong, Byung Hak Ha, Perry Evans, Antonella Bacchiocchi, James P McCusker, Elaine Cheng, Matthew J Davis, Gerald Goh, Murim Choi, Stephan Ariyan, Deepak Narayan (+18 others)
2012 Nature Genetics  
Notably, we identified a recurrent UV-signature, an activating mutation in RAC1 in 9.2% of sun-exposed melanomas.  ...  The results identified previously unreported genes and pathways that have a role in melanoma pathogenesis, including effectors for a new gain-of-function mutation that may be amenable to targeted therapy  ...  (a) A plot showing copy number aberrations and high somatic nonsynonymous mutation load.  ... 
doi:10.1038/ng.2359 pmid:22842228 pmcid:PMC3432702 fatcat:voru2anh4jgkdgmtldyuceh24m

A set of duplicons on human chromosome 9 is involved in the origin of a supernumerary marker chromosome

Marianna Paulis, Mirella Bensi, Daniela Moralli, Luigi De Carli, Elena Raimondi
2006 Genomics  
High-resolution FISH coupled to database search demonstrated that a total number of 35 LCR9 paralogs are present in the human genome.  ...  Human chromosome 9 is involved in a number of recurrent structural rearrangements; moreover, its pericentromeric region exhibits a remarkable evolutionary plasticity.  ...  Buzzati Traverso," Università di Pavia, Italy) for helpful suggestions and comments in the preparation of the manuscript.  ... 
doi:10.1016/j.ygeno.2006.02.014 pmid:16597496 fatcat:otiuvcvq7vhitnvhta3hinhfwu

Selection of oncogenic mutant clones in normal human skin varies with body site

Joanna C Fowler, Charlotte King, Christopher Bryant, Michael Hall, Roshan Sood, Swee Hoe Ong, Eleanor Earp, David Fernandez-Antoran, Jonas Koeppel, Stefan C Dentro, David Shorthouse, Amer Durrani (+9 others)
2020 Cancer Discovery  
Skin cancer risk varies substantially across the body, yet how this relates to the mutations found in normal skin is unknown. Here we mapped mutant clones in skin from high and low risk sites.  ...  Fine scale mapping revealed 10% of clones had copy number alterations.  ...  D, Plot summarizing the mutations (VAF ≥ 0.3) and copy-number aberrations for genes identified as being under positive selection in targeted sequencing data for 46 wholegenome punch samples.  ... 
doi:10.1158/2159-8290.cd-20-1092 pmid:33087317 pmcid:PMC7116717 fatcat:ebwrwp3btnegjhqc224leii744

Quantitative PCR identifies a minimal deleted region of 120 kb extending from the Philadelphia chromosome ABL translocation breakpoint in chronic myeloid leukemia with poor outcome

E Kolomietz, P Marrano, K Yee, B Thai, I Braude, A Kolomietz, K Chun, S Minkin, S Kamel-Reid, M Minden, J A Squire
2003 Leukemia  
In contrast, no microdeletion was detected in any of 18 CML samples selected from a group with a more favorable outcome.  ...  Microdeletions were identified by Q-PCR in 25 of 71 patients selected based on less favorable outcome (chronic phase duration of less than 96 months and a survival time of less than 84 months).  ...  EK is a  ... 
doi:10.1038/sj.leu.2402969 pmid:12835719 fatcat:nppyq4vzifdvrljjkrtiswxgtu

Facilitations and Hurdles of Genetic Testing in Neuromuscular Disorders

Andrea Barp, Lorena Mosca, Valeria Ada Sansone
2021 Diagnostics  
Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis  ...  The vast majority of NMDs has a genetic cause, with about 600 genes already identified.  ...  by Sanger enabled DNA reading at base pair resolution.  ... 
doi:10.3390/diagnostics11040701 pmid:33919863 fatcat:pzj6uvmjmrcthjdmf7la3uhbui

The challenges of sequencing by synthesis

Carl W Fuller, Lyle R Middendorf, Steven A Benner, George M Church, Timothy Harris, Xiaohua Huang, Stevan B Jovanovich, John R Nelson, Jeffery A Schloss, David C Schwartz, Dmitri V Vezenov
2009 Nature Biotechnology  
ACKNOWLEDGMENT This work was supported in part by the National Human Genome Research Institute, National Institutes of Health.  ...  Approaches include both single-molecule and ensemble methods requiring features populated with identical copies of DNA fragments.  ...  For ensemble methods the fragments are amplified, providing a collection of identical copies for sequencing. Schemes for SBS.  ... 
doi:10.1038/nbt.1585 pmid:19898456 fatcat:qihs3blj2ffvpcgbrye6vzqgeq

Cytopathology

2009 Modern Pathology  
There was moderate increase of mucopolysaccharide material in the aorta but not CMD. Likewise, the 43 year old female with FBN1 mutation (c.2714G>A) did not show CMD in the aortic specimen.  ...  CMD is a nonspecific finding in ascending aortic aneurysms and dissections and is not always present in those with inheritable connective tissue disorders.  ...  Anal cytologic screening on liquid based prep (LBP), automated PCR-based detection of up to 13 types of high risk HPV DNA (hrHPV) to detect HPV, and high resolution anoscopy (HRA) are used.  ... 
doi:10.1038/modpathol.2008.212 fatcat:xmbakxhx75aspjhrveblxe66ae

Jahrestagung der Deutschen, Österreichischen und Schweizerischen Gesellschaften für Hämatologie und Onkologie. Stuttgart, 19.-23. Oktober 2012, pp 91-181

2012 Onkologie (Basel)  
Abstracts as DNA from the peripheral blood of patients after aHSCT.  ...  Using grafts from Balb/c-TTG chimeras after 40 days for transplantation without anti-human CD4 re-incubation in Balb/c wt mice does not induce any aGvHD development even when higher T-cell numbers are  ...  of fibroblast growth factor receptor 1 (FGFR1) was identified in a large set of sqamous cell carcinomas (SCC) of the lung using high resolution copy number analysis and confirmed by fluorescene in situ  ... 
doi:10.1159/000258182 fatcat:gldg5fqsfree7j7x7tirfuebou
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