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Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis [article]

Markus Mayrhofer, Bram De Laere, Tom Whitington, Peter Van Oyen, Christophe Ghysel, Jozef Ampe, Piet Ost, Wim Demey, Lucien Hoekx, Dirk Schrijvers, Barbara Brouwers, Willem Lybaert (+20 others)
2018 bioRxiv   pre-print
Comprehensive profiling of the androgen receptor (AR) revealed a continuous increase in the fraction of patients with intra-AR structural variation, from 15.4% during first line mCRPC therapy to 45.2%  ...  However, intronic sequencing of the interrogated tumor suppressors challenge the ubiquitous focus on coding regions and is vital, together with profiling of synchronous white blood cells, to minimize erroneous  ...  This funding bodies had no role in the design, execution or interpretation of the data in this study and did not influence the decision to submit results for publication.  ... 
doi:10.1101/319855 fatcat:asira5wkfbgtpo6cr7oddndgv4

Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer, Bram De Laere, Tom Whitington, Peter Van Oyen, Christophe Ghysel, Jozef Ampe, Piet Ost, Wim Demey, Lucien Hoekx, Dirk Schrijvers, Barbara Brouwers, Willem Lybaert (+20 others)
2018 Genome Medicine  
Comprehensive profiling of the androgen receptor (AR) revealed a continuous increase in the fraction of patients with intra-AR structural variation, from 15. 4% during first-line metastatic castration-resistant  ...  Sequencing of non-repetitive intronic and exonic regions of PTEN, RB1, and TP53 detected biallelic inactivation in 47.5%, 20.3%, and 44.1% of samples with ≥ 0.2 ctDNA fraction, respectively.  ...  Acknowledgements The authors thank all patients for their willingness to participate in this study.  ... 
doi:10.1186/s13073-018-0595-5 pmid:30458854 pmcid:PMC6247769 fatcat:uikki526jng2zbxcf3y3khcygq

XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments

Alberto Magi, Tommaso Pippucci, Carlo Sidore
2017 BMC Genomics  
Results: By using simulated and real datasets we showed that our tool, based on read count approach, is capable to predict the boundaries and the absolute number of DNA copies CNVs/CNAs with high resolutions  ...  We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments  ...  Funding Alberto Magi has been supported by Italian Ministry of Health, Young Investigators Award, Project GR-2011-02352026 Detecting copy number variants from whole-exome sequencing data applied to acute  ... 
doi:10.1186/s12864-017-4137-0 pmid:28934930 pmcid:PMC5609061 fatcat:whstmaggezb53fzlyfpl4wum6q

Long-read single-molecule maps of the functional methylome

Hila Sharim, Assaf Grunwald, Tslil Gabrieli, Yael Michaeli, Sapir Margalit, Dmitry Torchinsky, Rani Arielly, Gil Nifker, Matyas Juhasz, Felix Gularek, Miguel Almalvez, Brandon Dufault (+14 others)
2019 Genome Research  
We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules.  ...  In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spanning hundreds of kilobase pairs.  ...  Gabellini for his kind gift of the CH16-291A23 BAC and K. Glensk for preparing M.TaqI as well as for analyzing M.TaqI labeling efficiency at different CpG methylation levels.  ... 
doi:10.1101/gr.240739.118 pmid:30846530 pmcid:PMC6442387 fatcat:sp4vkjtz3jdf7kflfb5xfpw5fi

Linkage Disequilibrium and Heritability of Copy-Number Polymorphisms within Duplicated Regions of the Human Genome

Devin P. Locke, Andrew J. Sharp, Steven A. McCarroll, Sean D. McGrath, Tera L. Newman, Ze Cheng, Stuart Schwartz, Donna G. Albertson, Daniel Pinkel, David M. Altshuler, Evan E. Eichler
2006 American Journal of Human Genetics  
In an attempt to assess the heritability and LD of copy-number polymorphisms (CNPs) in duplication-rich regions of the genome, we profiled copy-number variation in 130 putative "rearrangement hotspot regions  ...  Studies of copy-number variation and linkage disequilibrium (LD) have typically excluded complex regions of the genome that are rich in duplications and prone to rearrangement.  ...  Web Resources The URLs for data presented herein are as follows:  ... 
doi:10.1086/505653 pmid:16826518 pmcid:PMC1559496 fatcat:kesumt7lgzg5fogmxyncultzsi

Genetic Variation in Human DNA Replication Timing

Amnon Koren, Robert E. Handsaker, Nolan Kamitaki, Rosa Karlić, Sulagna Ghosh, Paz Polak, Kevin Eggan, Steven A. McCarroll
2014 Cell  
We used this relationship to analyze variation in replication timing among 161 individuals sequenced by the 1000 Genomes Project.  ...  In genome sequences from proliferating cells, read depth along chromosomes reflected DNA replication activity in those cells.  ...  Research, the Howard Hughes Medical Institute, and the Harvard Stem Cell Institute.  ... 
doi:10.1016/j.cell.2014.10.025 pmid:25416942 pmcid:PMC4359889 fatcat:vltgq256zvgxlmf2u5modeo2r4

Single Cell Multi-Omics Technology: Methodology and Application

Youjin Hu, Qin An, Katherine Sheu, Brandon Trejo, Shuxin Fan, Ying Guo
2018 Frontiers in Cell and Developmental Biology  
In the era of precision medicine, multi-omics approaches enable the integration of data from diverse omics platforms, providing multi-faceted insight into the interrelation of these omics layers on disease  ...  Single cell sequencing technology can dissect the genotypic and phenotypic heterogeneity of bulk tissue and promises to deepen our understanding of the underlying mechanisms governing both health and disease  ...  ACKNOWLEDGMENTS The work was supported by National Key R&D Program of China (2017YFA0104100, 2017YFC1001300), National Natural Science Foundation of China (31700900).  ... 
doi:10.3389/fcell.2018.00028 pmid:29732369 pmcid:PMC5919954 fatcat:d74dfde73vgzxaaxeq6lbzyy4e

Review Computational characterisation of cancer molecular profiles derived using next generation sequencing

Urszula Oleksiewicz, Katarzyna Tomczak, Jakub Woropaj, Monika Markowska, Piotr Stępniak, Parantu K Shah
2015 Contemporary Oncology  
Next generation sequencing (NGS) or deep sequencing platforms are being used to create large catalogues of changes in copy numbers, mutations, structural variations, gene fusions, gene expression, and  ...  However, inferring different types of biological changes from raw reads generated using the sequencing experiments is algorithmically and computationally challenging.  ...  Detecting structural and copy number variations from RNA-Seq data presents similar challenges.  ... 
doi:10.5114/wo.2014.47137 pmid:25691827 pmcid:PMC4322529 fatcat:mpdgbyjgjbfhxbcsxiedb47w44

Recent advances in array comparative genomic hybridization technologies and their applications in human genetics

William W Lockwood, Raj Chari, Bryan Chi, Wan L Lam
2005 European Journal of Human Genetics  
Array comparative genomic hybridization (array CGH) is a method used to detect segmental DNA copy number alterations.  ...  and analytical software programs for computational interpretation of array CGH data.  ...  This work was supported by funds from Genome Canada, NIDCR RO1 DE 015965-01, Lymphoma Research Foundation, CIHR, and NSERC of Canada scholarship to WWL.  ... 
doi:10.1038/sj.ejhg.5201531 pmid:16288307 fatcat:a2dtk3nuszgw7n76o33xfjszyu

Copy Number Variations of Glycoside Hydrolase 45 Genes in Bursaphelenchus xylophilus and Their Impact on the Pathogenesis of Pine Wilt Disease

Xiaolei Ding, Qingtong Wang, Yunfei Guo, Yulong Li, Sixi Lin, Qingwei Zeng, Feijian Sun, De-Wei Li, Jianren Ye
2021 Forests  
Additionally, tandem repeat variations within coding regions were also detected between different copies of glycoside hydrolase 45 genes that could result in changes in protein sequences and serve as an  ...  Previous studies ignored the possibility of copy number variations of such genes.  ...  Conflicts of Interest: The authors declare no conflict of interest. Forests 2021, 12, 275  ... 
doi:10.3390/f12030275 doaj:ef5d2c55aed04788a561ad9916d0dcb7 fatcat:uhl3xwkyxvev7atddzni3dfofy

Getting Started in Tiling Microarray Analysis

X. Shirley Liu
2007 PLoS Computational Biology  
However, selecting the number of regions could be difficult for big genomes with complex copy number variations.  ...  One method proposes a structural change model to use dynamic programming to segment the genome into a number of regions with different copy numbers; within each region the probe signals (thus genome copy  ... 
doi:10.1371/journal.pcbi.0030183 pmid:17967045 pmcid:PMC2041964 fatcat:jysxfypcr5d4rloj5p3c7jilpm

Germline Predisposition and Copy Number Alteration in Pre-stage Lung Adenocarcinomas Presenting as Ground-Glass Nodules

Yijiu Ren, Shujun Huang, Chenyang Dai, Dong Xie, Larry Zheng, Huikang Xie, Hui Zheng, Yunlang She, Fangyu Zhou, Yue Wang, Pengpeng Li, Ke Fei (+15 others)
2019 Frontiers in Oncology  
These GGNs also bore large segments of copy number gains and/or losses. The CNV segment number tended to be positively correlated with the germline mutations (r = 0.57).  ...  Methods: We investigated single nucleotide variations (SNV), insertions and deletions (INDEL), somatic copy number variations (CNV), and germline mutations of 69 SM-GGN samples collected from 31 patients  ...  Shantanu Banerji for reading the manuscript and for his helpful comments. We thank AME Thoracic Surgery Collaborative Group for their helpful comments.  ... 
doi:10.3389/fonc.2019.00288 pmid:31058088 pmcid:PMC6482264 fatcat:fxkzlxczxberpmvhfl3xpiuv5e

Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles [article]

John S. Sproul, Lindsey M. Barton, David R. Maddison
2020 bioRxiv   pre-print
We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome.  ...  We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution  ...  We thank Anne-Marie Girard-Pohjanpelto for help with fluorescence imaging. We are grateful to Danielle Mendez for her help with library quantitation.  ... 
doi:10.1101/2020.01.03.894527 fatcat:lqf3copyabeixngesyatce4ykq

High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletions

Tianjiao Chu, Suveyda Yeniterzi, Svetlana A. Yatsenko, Mary Dunkel, Patricia A. Shaw, Kimberly D. Bunce, David G. Peters, Maj Hulten
2016 PLoS ONE  
Our goal was to test the hypothesis that inter-individual genomic copy number variation in control samples is a confounding factor in the non-invasive prenatal detection of fetal microdeletions via the  ...  Maternal plasma from two pregnancies affected with a chromosome 5p microdeletion was also sequenced, and analyzed using the GCREM algorithm.  ...  High variance in sequencing read counts amongst normal samples strongly correlates with the frequency of genomic copy number variants We hypothesized that the locus-specific variation of sequence read  ... 
doi:10.1371/journal.pone.0153182 pmid:27249650 pmcid:PMC4889033 fatcat:kyhnmpaoxrfc7fpj7bds3apkdq

Genome structural variation discovery and genotyping

Can Alkan, Bradley P. Coe, Evan E. Eichler
2011 Nature reviews genetics  
None of the four main approaches to discovering structural variation using sequence data is comprehensive.  ...  These data show that the qPCR and read-depth data correlate. Data for part b and the y axis of part c are taken from REF. 75 ; data for the x axis of part c are taken from REF. 116.  ... 
doi:10.1038/nrg2958 pmid:21358748 pmcid:PMC4108431 fatcat:ujvwnpdourethb27w3xvynprhq
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