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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
...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 1 , 2 , 12 , Daoud Sie 1 , 12 , Henrik Bengtsson 3...
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Research: Whole genome sequencing of matched primary and metastatic acral melanomas
- Samra Turajlic,
- Simon J. Furney,
- Maryou B. Lambros,
- Costas Mitsopoulos,
- Iwanka Kozarewa,
- Felipe C. Geyer,
- Alan MacKay,
- Jarle Hakas,
- Marketa Zvelebil,
- Christopher J. Lord,
- Alan Ashworth,
- Meirion Thomas,
- Gordon Stamp,
- James Larkin,
- Jorge S. Reis-Filho,
- and Richard Marais
Genome Res. February 2012 22: 196-207; Published in Advance December 19, 2011, doi:10.1101/gr.125591.111
...and Olshen 2007). Microarray comparative genomic hybridization Themicroarray comparative genomic hybridization platform used for this study was constructed at the Breakthrough Breast Cancer ResearchCenter and comprises;32,000 BAC clones tiled across the . DNA labeling, array hybridizations, and image...
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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 Collins 2000 ; Hanahan and Weinberg 2000 ; Albertson and Pinkel 2003 ; Albertson et al. 2003 ). CGH has been used widely to characterize DNA copy changes in tumors. Originally this technique was implemented using metaphase chromosomal spreads but has been adapted to array-CGH using BAC, cDNA...
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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
..., are differentially labeled and hybridized to a representative arrayed on a matrix. Over the past several years a number of different array platforms have been utilized for CGH from bacteria artificial chromosomes (BACs) and cosmids to cDNA clones and oligonucleotides ( Solinas-Toldo et al. 1997 ; Pinkel et al. 1998...
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METHODS: Whole Genome Analysis of Genetic Alterations in Small DNA Samples Using Hyperbranched Strand Displacement Amplification and Array–CGH
- José M. Lage,
- John H. Leamon,
- Tanja Pejovic,
- Stefan Hamann,
- Michelle Lacey,
- Deborah Dillon,
- Richard Segraves,
- Bettina Vossbrinck,
- Antonio González,
- Daniel Pinkel,
- Donna G. Albertson,
- Jose Costa,
- and Paul M. Lizardi
Genome Res. February 1, 2003 13: 294-307; doi:10.1101/gr.377203
...: In this window In a new window Figure 8. Analysis of breast cancer cell line MCF7 using BAC clones located in Chromosome 20. The graph on the top shows the copy-number variation for the array–CGH experiment corresponding to the hybridization of genomic DNA from the cell line MCF7 against female DNA. The graph...
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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: Two Methods of Whole-Genome Amplification Enable Accurate Genotyping Across a 2320-SNP Linkage Panel
- David L. Barker,
- Mark S.T. Hansen,
- A. Fawad Faruqi,
- Diane Giannola,
- Orlando R. Irsula,
- Roger S. Lasken,
- Martin Latterich,
- Vladimir Makarov,
- Arnold Oliphant,
- Jonathon H. Pinter,
- Richard Shen,
- Irina Sleptsova,
- William Ziehler,
- and Eric Lai
Genome Res. May 2004 14: 901-907; doi:10.1101/gr.1949704
...-resistant primers in an isothermal amplification reaction ( Dean et al. 2002 ). This method is based on strand-displacement synthesis ( Lizardi et al. 1998 ; Lage et al. 2003 ), and was originally developed for amplifying large circular DNA templates such as plasmids and BAC DNAs ( Dean et al. 2001 ). MDA...
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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
...number changes in tumor samples, where DNA from the same individual can be used as a reference, the use of matched samples is not possible for CNV detection in normal individuals. Similarly, the use of a single reference, as is often used in BAC-array CGH, is limited by the inability to determine whether...
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Research: Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution
- Martin Völker,
- Niclas Backström,
- Benjamin M. Skinner,
- Elizabeth J. Langley,
- Sydney K. Bunzey,
- Hans Ellegren,
- and Darren K. Griffin
Genome Res. April 2010 20: 503-511; Published in Advance March 31, 2010, doi:10.1101/gr.103663.109
...genomic hybridization (CGH) with zebra finch genomic DNA samples on a chicken whole- tiling path microarray. In the Discussion and Methods sections, we have outlined the caveats pertaining to how sequence divergence between the two species may lead us to call an apparent loss in copy number...
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Research: Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
- Ruth A. Swanson-Wagner,
- Steven R. Eichten,
- Sunita Kumari,
- Peter Tiffin,
- Joshua C. Stein,
- Doreen Ware,
- and Nathan M. Springer
Genome Res. December 2010 20: 1689-1699; Published in Advance October 29, 2010, doi:10.1101/gr.109165.110
.... Comparative genomic hybridization (CGH) of DNA samples to microarrays can be used to detect both CNV and PAV. A custom long oligonucleotide microarray was designed using the reference sequence of the B73 maize genotype (Schnable et al. 2009) andwasused to perform CGH analyses of 32,487 maize genes (see...

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