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Methods: High-Resolution Analysis of DNA Copy Number Using Oligonucleotide Microarrays
- Graham R. Bignell,
- Jing Huang,
- Joel Greshock,
- Stephen Watt,
- Adam Butler,
- Sofie West,
- Mira Grigorova,
- Keith W. Jones,
- Wen Wei,
- Michael R. Stratton,
- P. Andrew Futreal,
- Barbara Weber,
- Michael H. Shapero,
- and Richard Wooster
Genome Res. February 2004 14: 287-295; doi:10.1101/gr.2012304
...., Esposito, D., Chi, M., Rodgers, L., Brady, A., Sebat, J., Troge, J., et al. 2003 . Representational oligonucleotide microarray analysis: A high-resolution method to detect copy number variation. Genome Res. 13 : 2291 -2305. ↵ Nicholls, R.D., Knoll, J.H., Butler, M.G., Karam, S., and Lalande, M. 1989...
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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
...; Pinkel and Albertson 2005 ). For the detection of these features, different microarray technologies have been used, such as classical CGH, BAC array-based comparative genomic hybridization (array-CGH), cDNA array-CGH, and high-density single-nucleotide polymorphism (SNP) arrays ( Kallioniemi et al. 1993...
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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
...and subsequent PCR creates C-to-T transitions, which can be detected by sequencing, or possibly, on oligonucleotide arrays, analogous to single nucleotide polymorphisms ( Borevitz et al. 2003 ; Singer et al. 2006 ). Indeed, probes derived from bisulfite-converted DNA of a hypermethylated locus in human tumors...
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Method: Biome representational in silico karyotyping
- Valliammai Muthappan,
- Aaron Y. Lee,
- Tamara L. Lamprecht,
- Lakshmi Akileswaran,
- Suzanne M. Dintzis,
- Choli Lee,
- Vincent Magrini,
- Elaine R. Mardis,
- Jay Shendure,
- and Russell N. Van Gelder
Genome Res. April 2011 21: 626-633; Published in Advance February 10, 2011, doi:10.1101/gr.115758.110
...representational in sil ico karyotyping Genome Research 629 www..org and Kurzrock 2004). To determine if BRISK has adequate sensitivity to detect a virally mediated carcinoma, we subjected two fixed, parafin-embeddedmicroscope slides of a nasopharyngeal carcinoma specimen to themethod following phi29 amplification...
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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
...-4086, USA Corresponding author: B.Ylstra@vumc.nl ↵ 12 These authors contributed equally to this work. Abstract Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors...
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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
...Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays Daisuke Komura 1 , 2 , 8 , Fan Shen 3 , 8 , Shumpei Ishikawa 1 , 8 , Karen R. Fitch 3 , Wenwei Chen 3 , Jane Zhang 3...
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Method: Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
- Mark D. Robinson,
- Clare Stirzaker,
- Aaron L. Statham,
- Marcel W. Coolen,
- Jenny Z. Song,
- Shalima S. Nair,
- Dario Strbenac,
- Terence P. Speed,
- and Susan J. Clark
Genome Res. December 2010 20: 1719-1729; Published in Advance November 2, 2010, doi:10.1101/gr.110601.110
...the effect of whole-genome amplification and illustrate that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. By using MBDCap, we compare and contrast microarray- and sequencing-based readouts and highlight the impact that copy number variation (CNV) can make...
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Research: Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
- Elodie Gazave,
- Fleur Darré,
- Carlos Morcillo-Suarez,
- Natalia Petit-Marty,
- Angel Carreño,
- Urko M. Marigorta,
- Oliver A. Ryder,
- Antoine Blancher,
- Mariano Rocchi,
- Elena Bosch,
- Carl Baker,
- Tomàs Marquès-Bonet,
- Evan E. Eichler,
- and Arcadi Navarro
Genome Res. October 2011 21: 1626-1639; Published in Advance August 8, 2011, doi:10.1101/gr.117242.110
...%) can be classified as nonpolymorphic human regions. In order to construct a list of HSNP regions, we proceeded in two steps. First, we surveyed the database of genomic variants (DGV), excluding studies performed with technologies that are known to present increased uncertainty in CNV detection (such...
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REVIEW: Copy number variation: New insights in genome diversity
- Jennifer L. Freeman,
- George H. Perry,
- Lars Feuk,
- Richard Redon,
- Steven A. McCarroll,
- David M. Altshuler,
- Hiroyuki Aburatani,
- Keith W. Jones,
- Chris Tyler-Smith,
- Matthew E. Hurles,
- Nigel P. Carter,
- Stephen W. Scherer,
- and Charles Lee
Genome Res. August 2006 16: 949-961; Published in Advance June 29, 2006, doi:10.1101/gr.3677206
.... 2004 ). This in silico approach has an added advantage over array-based CNV discovery studies in being capable of detecting other structural genomic variants, namely inversions. These would be detected by consistent discrepancies in the aligned orientation of multiple paired end sequences...
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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
...; Mantripragada et al. 2004 ). As the ability to detect small alterations is limited by the spacing and size of the probes on the matrix, there has been a move away from BAC clones to oligonucleotide arrays for experiments where high resolution is required ( Carvalho et al. 2004 ; Ishkanian et al. 2004 ; Sebat et...

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