Sparse representation and Bayesian detection of genome copy number alterations from microarray data.

Bioinformatics
Roger Pique-RegiShahab Asgharzadeh

Abstract

Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) that are associated with the development and behavior of tumors. Advances in microarray technology have allowed for greater resolution in detection of DNA copy number changes (amplifications or deletions) across the genome. However, the increase in number of measured signals and accompanying noise from the array probes present a challenge in accurate and fast identification of breakpoints that define CNA. This article proposes a novel detection technique that exploits the use of piece wise constant (PWC) vectors to represent genome copy number and sparse Bayesian learning (SBL) to detect CNA breakpoints. First, a compact linear algebra representation for the genome copy number is developed from normalized probe intensities. Second, SBL is applied and optimized to infer locations where copy number changes occur. Third, a backward elimination (BE) procedure is used to rank the inferred breakpoints; and a cut-off point can be efficiently adjusted in this procedure to control for the false discovery rate (FDR). The performance of our algorithm is evaluated using simulated and real genome datasets and compared to other existing techniques. Our appro...Continue Reading

References

Sep 2, 1999·Nature Genetics·J R PollackP O Brown
Aug 19, 2003·Nature Genetics·Donna G AlbertsonJoe W Gray
Sep 24, 2004·Bioinformatics·Philippe HupéEmmanuel Barillot
Oct 12, 2004·Biostatistics·Adam B OlshenMichael Wigler
Feb 12, 2005·BMC Bioinformatics·Franck PicardJean-Jacques Daudin
Sep 15, 2005·Bioinformatics·Hanni Willenbrock, Jane Fridlyand
Mar 15, 2006·Bioinformatics·J C MarioniS Tavaré
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Doron LipsonZohar Yakhini
Jul 29, 2006·Bioinformatics·Sohrab P ShahKevin P Murphy
Nov 24, 2006·Nature·Richard RedonMatthew E Hurles
Jan 20, 2007·Bioinformatics·E S Venkatraman, Adam B Olshen
Jun 26, 2007·PLoS Computational Biology·Oscar M Rueda, Ramón Díaz-Uriarte

❮ Previous
Next ❯

Citations

Jul 7, 2011·European Journal of Human Genetics : EJHG·Sanghoon MoonBong-Jo Kim
Oct 9, 2009·Nature·Donald F ConradMatthew E Hurles
Apr 7, 2010·Nature Genetics·Donald F ConradMatthew E Hurles
Sep 10, 2009·Briefings in Functional Genomics & Proteomics·Laura WinchesterJiannis Ragoussis
Feb 23, 2010·Briefings in Bioinformatics·Mark A van de WielBauke Ylstra
Oct 21, 2010·Bioinformatics·Sandro MorganellaMichele Ceccarelli
Mar 2, 2011·Bioinformatics·Tomas W FitzgeraldRichard Redon
Jul 15, 2011·Bioinformatics·Catherine Stamoulis, Rebecca A Betensky
Jul 27, 2004·Science·Jonathan SebatMichael Wigler
Nov 8, 2012·Physiological Genomics·Wenli Li, Michael Olivier
Oct 27, 2010·EURASIP Journal on Bioinformatics & Systems Biology·Jie ChenHong-Wen Deng
Jul 20, 2010·BMC Bioinformatics·Roger Pique-RegiJuan R González
Aug 18, 2012·BMC Bioinformatics·Zhongyang ZhangChiara Sabatti
Dec 14, 2012·BMC Bioinformatics·Robert B ScharpfIngo Ruczinski
Dec 29, 2012·BMC Bioinformatics·Melissa PronoldShahab Asgharzadeh
May 24, 2013·BMC Bioinformatics·Toby Dylan HockingJean-Philippe Vert
Sep 12, 2012·BMC Genetics·Kyung-Won HongBong-Jo Kim
Oct 26, 2010·BMC Genomics·Yuliaxis Ramayo-CaldasJosep M Folch
Dec 19, 2009·BMC Proceedings·Corina ShtirPaul Marjoram
May 21, 2010·Genome Biology·Andy W PangStephen W Scherer
Jan 7, 2011·PloS One·Debby W TsuangChang-En Yu
Jan 21, 2011·PloS One·Dandan ZhangChunyu Liu
May 6, 2014·Journal of Pediatric Gastroenterology and Nutrition·David T OkouSubra Kugathasan
Dec 22, 2012·Expert Review of Molecular Diagnostics·Geert Vandeweyer, R Frank Kooy

❮ Previous
Next ❯

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.