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Method: High resolution mapping of modified DNA nucleobases using excision repair enzymes
- D. Suzi Bryan,
- Monica Ransom,
- Biniam Adane,
- Kerri York,
- and Jay R. Hesselberth
Genome Res. September 2014 24: 1534-1542; Published in Advance July 11, 2014, doi:10.1101/gr.174052.114
...High resolution mapping of modified DNA nucleobases using excision repair enzymes D. Suzi Bryan 1 , Monica Ransom 1 , Biniam Adane , Kerri York and Jay R. Hesselberth Department of Biochemistry and Molecular Genetics, Program...
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LETTER: Representational Oligonucleotide Microarray Analysis: A High-Resolution Method to Detect Genome Copy Number Variation
- Robert Lucito,
- John Healy,
- Joan Alexander,
- Andrew Reiner,
- Diane Esposito,
- Maoyen Chi,
- Linda Rodgers,
- Amy Brady,
- Jonathan Sebat,
- Jennifer Troge,
- Joseph A. West,
- Seth Rostan,
- Ken C.Q. Nguyen,
- Scott Powers,
- Kenneth Q. Ye,
- Adam Olshen,
- Ennapadam Venkatraman,
- Larry Norton,
- and Michael Wigler
Genome Res. October 2003 13: 2291-2305; Published in Advance January 1, 2003, doi:10.1101/gr.1349003
...'t Veer et al. 2002 ), and three groups, including ours, have adapted microarrays to detect genomic deletions and amplifications in tumors. Pinkel et al. ( 1998 ) have used arrays of BAC DNAs as hybridization probes; Pollack et al. ( 1999 ) have used cDNA fragments as probes; and in our first...
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Methods: High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays
- Jan Oosting,
- Esther H. Lips,
- Ronald van Eijk,
- Paul H.C. Eilers,
- Károly Szuhai,
- Cisca Wijmenga,
- Hans Morreau,
- and Tom van Wezel
Genome Res. March 2007 17: 368-376; Published in Advance January 31, 2007, doi:10.1101/gr.5686107
.... , Butler, A. , West, S. , Grigorova, M. , Jones, K.W. , Wei, W. , Stratton, M.R. , et al. ( 2004 ) High-resolution analysis of DNA copy number using oligonucleotide microarrays . Genome Res. 14 : 287 – 295 . ↵ De Jong, A.E. , van Puijenbroek, M. , Hendriks, Y. , Tops, C. , Wijnen, J. , Ausems, M...
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Resource: High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications
- Tamim H. Shaikh,
- Xiaowu Gai,
- Juan C. Perin,
- Joseph T. Glessner,
- Hongbo Xie,
- Kevin Murphy,
- Ryan O'Hara,
- Tracy Casalunovo,
- Laura K. Conlin,
- Monica D'Arcy,
- Edward C. Frackelton,
- Elizabeth A. Geiger,
- Chad Haldeman-Englert,
- Marcin Imielinski,
- Cecilia E. Kim,
- Livija Medne,
- Kiran Annaiah,
- Jonathan P. Bradfield,
- Elvira Dabaghyan,
- Andrew Eckert,
- Chioma C. Onyiah,
- Svetlana Ostapenko,
- F. George Otieno,
- Erin Santa,
- Julie L. Shaner,
- Robert Skraban,
- Ryan M. Smith,
- Josephine Elia,
- Elizabeth Goldmuntz,
- Nancy B. Spinner,
- Elaine H. Zackai,
- Rosetta M. Chiavacci,
- Robert Grundmeier,
- Eric F. Rappaport,
- Struan F.A. Grant,
- Peter S. White,
- and Hakon Hakonarson
Genome Res. September 2009 19: 1682-1690; Published in Advance July 10, 2009, doi:10.1101/gr.083501.108
...susceptibility, and clinicalmolecular diagnostics. Results Assessment of copy number variation in 2026 healthy individuals DNA samples analyzed in our study were obtained from the whole blood of healthy subjects routinely seen at primary care and well-child clinic practices within the Children’s Hospital...
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Methods: Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion
- Jon Reinders,
- Céline Delucinge Vivier,
- Grégory Theiler,
- Didier Chollet,
- Patrick Descombes,
- and Jerzy Paszkowski
Genome Res. March 2008 18: 469-476; Published in Advance January 24, 2008, doi:10.1101/gr.7073008
...Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion Jon Reinders 1 , 3 , Céline Delucinge Vivier 2 , Grégory Theiler 1 , Didier Chollet 2 , Patrick Descombes 2 , and Jerzy Paszkowski 1...
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Research: Identification of copy number variants in horses
- Ryan Doan,
- Noah Cohen,
- Jessica Harrington,
- Kylee Veazy,
- Rytis Juras,
- Gus Cothran,
- Molly E. McCue,
- Loren Skow,
- and Scott V. Dindot
Genome Res. May 2012 22: 899-907; Published in Advance March 1, 2012, doi:10.1101/gr.128991.111
...(Guryev et al. 2008; Chen et al. 2009; Nicholas et al. 2009; Zhang et al. 2009; Conrad et al. 2010; DeBolt 2010; Fadista et al. 2010; Mills et al. 2011; Nicholas et al. 2011). CNVs are typically defined as segments of DNA at least 1000 base pairs (1000 bp or 1 kb) in length that vary in copy number...
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Methods: Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
- Daisuke Komura,
- Fan Shen,
- Shumpei Ishikawa,
- Karen R. Fitch,
- Wenwei Chen,
- Jane Zhang,
- Guoying Liu,
- Sigeo Ihara,
- Hiroshi Nakamura,
- Matthew E. Hurles,
- Charles Lee,
- Stephen W. Scherer,
- Keith W. Jones,
- Michael H. Shapero,
- Jing Huang,
- and Hiroyuki Aburatani
Genome Res. December 2006 16: 1575-1584; Published in Advance November 22, 2006, doi:10.1101/gr.5629106
....W. , Wei, W. , Stratton, M.R. , et al. ( 2004 ) High-resolution analysis of DNA copy number using oligonucleotide microarrays . Genome Res. 14 : 287 – 295 . ↵ Conrad, D.F. , Andrews, T.D. , Carter, N.P. , Hurles, M.E. , Pritchard, J.K. ( 2006 ) A high-resolution survey of deletion polymorphism in the human...
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Methods: Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization
- Jason S. Maydan,
- Stephane Flibotte,
- Mark L. Edgley,
- Joanne Lau,
- Rebecca R. Selzer,
- Todd A. Richmond,
- Nathan J. Pofahl,
- James H. Thomas,
- and Donald G. Moerman
Genome Res. March 2007 17: 337-347; Published in Advance January 31, 2007, doi:10.1101/gr.5690307
...an oligonucleotide-based approach with a high-density array format (∼385,000 unique probes) is already leading to widespread adoption of this method for high-resolution mapping of DNA breakpoints for larger sized chromosomal rearrangements in tumors and microdeletion syndromes in humans ( Pollack et al. 2002...
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Methods: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
- Daniel A. Peiffer,
- Jennie M. Le,
- Frank J. Steemers,
- Weihua Chang,
- Tony Jenniges,
- Francisco Garcia,
- Kirt Haden,
- Jiangzhen Li,
- Chad A. Shaw,
- John Belmont,
- Sau Wai Cheung,
- Richard M. Shen,
- David L. Barker,
- and Kevin L. Gunderson
Genome Res. September 2006 16: 1136-1148; Published in Advance August 9, 2006, doi:10.1101/gr.5402306
...) and cancer (acquired aberration) ( Albertson and Pinkel 2003 ). Many of these aberrations are characterized by rearrangements in genomic DNA or changes in copy number such as deletions, duplications, and amplifications ( Kallioniemi et al. 1992 , 1994 , 1996 ; Hayashizaki et al. 1993 ; Wang et al. 2002...
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Method: DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly
- Ilari Scheinin,
- Daoud Sie,
- Henrik Bengtsson,
- Mark A. van de Wiel,
- Adam B. Olshen,
- Hinke F. van Thuijl,
- Hendrik F. van Essen,
- Paul P. Eijk,
- François Rustenburg,
- Gerrit A. Meijer,
- Jaap C. Reijneveld,
- Pieter Wesseling,
- Daniel Pinkel,
- Donna G. Albertson,
- and Bauke Ylstra
Genome Res. December 2014 24: 2022-2032; Published in Advance September 18, 2014, doi:10.1101/gr.175141.114
...an alternative to microarrays for many analysis applications, including copy number detection. Several methods have been developed to estimate DNA copy number from WGS data. They can be grouped into the following four categories, each of which has its own set of requirements, strengths, and weaknesses (Teo et al...
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