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Nonreciprocal chromosomal translocations in renal cancer involve multiple DSBs and NHEJ associated with breakpoint inversion but not necessarily with transcription

Hanif Ali, Angelika Daser, Paul Dear, Henry Wood, Pamela Rabbitts, Terence Rabbitts
2013 Genes, Chromosomes and Cancer  
Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59. Brandt VL, Roth DB. 2009. Recent insights into the formation of RAG-induced chromosomal translocations.  ...  end joining or micro-homology end joining.  ...  Neal Copeland for providing a detailed inverse PCR protocol and Prof. Graham Taylor and Ms. Joanne Morgan for NGS facilities.  ... 
doi:10.1002/gcc.22038 pmid:23341332 fatcat:ijapu2u2e5a7do6e6xk2zm6a6q

The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome

Ewa Przybytkowski, Cristiano Ferrario, Mark Basik
2011 BMC Medical Genomics  
Results: DNA from MCF-7 breast cancer cells was analyzed for micro-copy number alterations, defined as measuring less than 1 Mb in genomic length.  ...  The ADM-2 algorithm was used to identify micro-copy number alterations that measured less than 1 Mb in genomic length.  ...  .), the National Cancer Institute of Canada (support to C.F.) and the Quebec Breast Cancer Foundation.  ... 
doi:10.1186/1755-8794-4-16 pmid:21272361 pmcid:PMC3041991 fatcat:6dxta3qeojd33bpff7pja2r2my

The fine-scale architecture of structural variants in 17 mouse genomes

Binnaz Yalcin, Kim Wong, Amarjit Bhomra, Martin Goodson, Thomas M Keane, David J Adams, Jonathan Flint
2012 Genome Biology  
We find considerable complexity in SV formation; about a quarter of SVs in the mouse are composed of a complex mixture of deletion, insertion, inversion and copy number gain.  ...  Accurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact.  ...  DJA is supported by Cancer Research UK.  ... 
doi:10.1186/gb-2012-13-3-r18 pmid:22439878 pmcid:PMC3439969 fatcat:t4zkqrboqfbldbghh323k5w4sm

De novo complex intra chromosomal rearrangement after ICSI: characterisation by BACs micro array-CGH

Serdar Kasakyan, Laurence Lohmann, Azeddine Aboura, Mazin Quimsiyeh, Yves Menezo, Gerard Tachdjian, Moncef Benkhalifa
2008 Molecular Cytogenetics  
studies of the fetus were realized on cultured amniocytes Results: Conventional, molecular cytogenetic and microarray CGH experiments allowed us to conclude that the fetus had a de novo pericentromeric inversion  ...  In routine Assisted Reproductive Technology (ART) men with severe oligozoospermia or azoospermia should be informed about the risk of de novo congenital or chromosomal abnormalities in ICSI program.  ...  Array CGH -DNA microarray analysis We used human genomic micro arrays containing 2600 BAC/PAC clones with an average of 1 MB resolution along the human genome (Human BAC Array-1 MB system, Spectral Genomics  ... 
doi:10.1186/1755-8166-1-27 pmid:19105807 pmcid:PMC2656511 fatcat:sx4pcvfglfbpnf7go7xpqkh2ea

The genomic dynamics during progression of lung adenocarcinomas

Bin Yang, Longhai Luo, Wen Luo, Yong Zhou, Chao Yang, Teng Xiong, Xiangchun Li, Xuan Meng, Lin Li, Xiaopin Zhang, Zhe Wang, Zhixin Wang
2017 Journal of Human Genetics  
To explore the underlying clonal diversity in lung adenocarcinomas, we selected nine individuals with whole-genome sequencing data from primary and matched metastatic tumors as a cohort for study.  ...  Importantly, we found breakage-fusion-bridge (BFB) cycles acting as an important mechanism for underlying cancer gene amplification, such as amplification of CDK4, CDKN3 and FGFR1 in early stage.  ...  We also thank The First Affiliated Hospital of Guangzhou Medical University for sharing the whole-genome data. Author contributions: BY and YZ designed and managed the research.  ... 
doi:10.1038/jhg.2017.40 pmid:28381877 pmcid:PMC5537414 fatcat:jbdoubjgcjbw7b24cycvovfvoq

Thyroid cancer staging and genomics

Ashok R. Shaha, R. Michael Tuttle
2019 Annals of Translational Medicine  
The updated AJCC/TNM staging system for papillary thyroid cancer (8th Edition): from the perspective of genomic analysis. World J Surg 2018;42:3624-31.  ...  Genomic analysis has become quite popular in various human cancers such as prostate, pancreas, and melanoma.  ...  Even though we have made major progress in genomic analysis of several human cancers, it appears that we are still in the early stages of our experience.  ... 
doi:10.21037/atm.2019.03.11 pmid:31032328 pmcid:PMC6462588 fatcat:xjkrsip7ajfy3dr3im7rw6nqwe

Analysis of Micro-Rearrangements in 25 Eukaryotic Species Pairs by SyntenyMapper

Stefanie Kaufmann, Dmitrij Frishman, Shoba Ranganathan
2014 PLoS ONE  
High-quality mapping of genomic regions and genes between two organisms is an indispensable prerequisite for evolutionary analyses and comparative genomics.  ...  On the other hand, the size of rearranged regions remains relatively constant regardless of the evolutionary distance between the organisms, implying a length constraint in the rearrangement process.  ...  In human, all genes lie on the forward strand, implying that an inversion occurred in mouse. Our approach recognizes this inversion of multiple genes and redefines it as a new syntenic region.  ... 
doi:10.1371/journal.pone.0112341 pmid:25375783 pmcid:PMC4223023 fatcat:266d5awhjjh4tm7xhwrijqxvjy

Computational proteogenomic identification and functional interpretation of translated fusions and micro structural variations in cancer [article]

Yen-Yi Lin, Alexander Gawronski, Faraz Hach, Sujun Li, Ibrahim Numanagic, Iman Sarrafi, Swati Mishra, Andrew William McPherson, Colin C Collins, Milan Radovich, Haixu Tang, S. Cenk Sahinalp
2017 bioRxiv   pre-print
We have applied our framework to all The Cancer Genome Atlas (TCGA) breast cancer Whole Genome Sequencing (WGS) and/or RNA-Seq data sets, spanning all four major subtypes, for which proteomics data from  ...  normal and disease conditions.Our framework includes MiStrVar, an algorithmic method we developed to identify micro structural variants (microSVs) on genomic HTS data.  ...  .), and the NSERC Discovery Frontiers Grant on the Cancer Genome Collaboratory (C.S.) for funding this research.  ... 
doi:10.1101/168377 fatcat:5nucafpn5veqth2jcyvh32auym

Circular DNA intermediates in the generation of large human segmental duplications

Javier U. Chicote, Marcos López-Sánchez, Tomàs Marquès-Bonet, José Callizo, Luis A. Pérez-Jurado, Antonio García-España
2020 BMC Genomics  
Duplications of large genomic segments provide genetic diversity in genome evolution.  ...  Here we provide evidence of the participation of circular DNA intermediates in the single generation of some large human segmental duplications.  ...  in cancer genomes.  ... 
doi:10.1186/s12864-020-06998-w pmid:32847497 fatcat:zrazc6j6f5fdza7cghgneigmv4

Application of long-read sequencing to the detection of structural variants in human cancer genomes

Yoshitaka Sakamoto, Suzuko Zaha, Yutaka Suzuki, Masahide Seki, Ayako Suzuki
2021 Computational and Structural Biotechnology Journal  
Among the various research fields in which long-read sequencing has been applied, cancer genomics has shown the most remarkable advances.  ...  Therefore, by complementing the current short-read sequencing analysis, long-read sequencing should reveal the complex nature of human genomes in their healthy and disease states, which will open a new  ...  CLCLs are complicated SVs combining local tandem duplication, inversion, and/or micro deletions.  ... 
doi:10.1016/j.csbj.2021.07.030 pmid:34527193 pmcid:PMC8350331 fatcat:tbfihovjkregnhg5zri6pk3eva

Circulating concentrations of micro-nutrients and risk of breast cancer: A Mendelian randomization study [article]

N. Papadimitriou, N. Dimou, D. Gill, I. Tzoulaki, N. Murphy, E. Riboli, S. J. Lewis, R. M. Martin, M. J. Gunter, K. K. Tsilidis
2019 bioRxiv   pre-print
authors are identified as personnel of the International Agency for Research on Cancer / World Health Organization, the authors alone are responsible for the views expressed in this article and they do  ...  AbstractBackgroundThe epidemiological literature reports inconsistent associations between consumption or circulating concentrations of micro-nutrients and breast cancer risk.  ...  Acknowledgements The breast cancer genome-wide association analyses were supported by the  ... 
doi:10.1101/668186 fatcat:ntvq7divc5h3zgbst3ss2cze7e

Genome-wide copy number aberrations and HER2 and FGFR1 alterations in primary breast cancer by molecular inversion probe microarray

Hui Chen, Rajesh R. Singh, Xinyan Lu, Lei Huo, Hui Yao, Kenneth Aldape, Ronald Abraham, Shumaila Virani, Meenakshi Mehrotra, Bal Mukund Mishra, Alex Bousamra, Constance Albarracin (+9 others)
2017 OncoTarget  
To identify novel prognostic biomarkers in breast cancer, we used molecular inversion probe (MIP) microarray to explore genome-wide copy number aberrations (CNA) and breast cancer-related gene alterations  ...  Chromothripsis, a catastrophic genome rearrangement, has been described recently in various cancer genomes and affects cancer progression and prognosis.  ...  GRANT SUPPORT RRB is supported in part by the National Institutes of Health Specialized Program of Research Excellence in Uterine Cancer (NIH 2P50 CA098258-08).  ... 
doi:10.18632/oncotarget.14802 pmid:28125801 pmcid:PMC5355228 fatcat:krhidkyobbe2la47rojpi5sjma

Microsatellite Instability in Human Non-Melanoma and Melanoma Skin Cancer

Anthony G. Quinn, Eugene Healy, Ishtiaq Rehman, Stephen Sikkink, Jonathan L. Rees
1995 Journal of Investigative Dermatology  
DISCUSSION In this study, we investigated the importance of genomic instability as evidenced by micro satellite electrophoretic mobility shifts in a large series of human skin cancers.  ...  in the development of some human cancers.  ... 
doi:10.1111/1523-1747.ep12664612 pmid:7860992 fatcat:gcqhppzsjra75li24pjirccxju

Micro-RNAs and copy number changes: New levels of gene regulation in acute myeloid leukemia

Richard A. Larson
2010 Chemico-Biological Interactions  
Fewer CNAs have been detected in AML than in pediatric ALL. Micro-RNAs (miRs) are non-coding small RNA molecules containing about 22 nucleotides that are typically encoded within introns.  ...  Distinctive genome-wide miR expression profiles have been associated with different subsets of AML.  ...  Le Beau at the University of Chicago for helpful discussions and his many other colleagues in the CALGB for their collaborative translational research on AML.  ... 
doi:10.1016/j.cbi.2009.10.002 pmid:19822134 pmcid:PMC2846194 fatcat:3ught7mtyzf5xjhuvf3tqxid5a

Long read sequencing reveals sequential complex rearrangements driven by Hepatitis B virus integration [article]

Songbo Wang, Jiadong Lin, Xiaofei Yang, Zihang Li, Tun Xu, Peng Jia, Tingjie Wang, Bo Wang, Liangshuo Hu, Kai Ye
2021 bioRxiv   pre-print
Integration of Hepatitis B (HBV) virus into human genome disrupts genetic structures and cellular functions.  ...  Overall, our long read based analysis reveals a novel sequential rearrangement progress driven by HBV integration, hinting the structural and functional implications on human genomes.  ...  It has been reported that chr4q-LOH presented in 11% of ovarian cancer 17 .  ... 
doi:10.1101/2021.12.09.471697 fatcat:7jmr6iny3nhthhh2wc2w55iy6q
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