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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: Haplotype-based profiling of subtle allelic imbalance with SNP arrays
- Selina Vattathil and
- Paul Scheet
Genome Res. January 2013 23: 152-158; Published in Advance October 1, 2012, doi:10.1101/gr.141374.112
...-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol 2: e41. doi: 10.1371/journal.pcbi.0020041. Chen H, Xing H, Zhang N. 2011. Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays. PLoS Comput Biol 7: e1001060. doi: 10.1371/journal...
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Method: Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
- Gavin Ha,
- Andrew Roth,
- Daniel Lai,
- Ali Bashashati,
- Jiarui Ding,
- Rodrigo Goya,
- Ryan Giuliany,
- Jamie Rosner,
- Arusha Oloumi,
- Karey Shumansky,
- Suet-Feung Chin,
- Gulisa Turashvili,
- Martin Hirst,
- Carlos Caldas,
- Marco A. Marra,
- Samuel Aparicio,
- and Sohrab P. Shah
Genome Res. October 2012 22: 1995-2007; Published in Advance May 25, 2012, doi:10.1101/gr.137570.112
..., the input data representing the observed allelic counts in the tumor DNA are discrete in nature and thus are not well suited to commonly used Gaussian or Student’s-t distributions that are often used for the analogous problem in continuous array data. Third, the allelic count data from the tumor DNAwill...
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LETTER: Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles
- Yoji Kukita,
- Katsuyuki Miyatake,
- Renee Stokowski,
- David Hinds,
- Koichiro Higasa,
- Norio Wake,
- Toshio Hirakawa,
- Hidenori Kato,
- Takao Matsuda,
- Krishna Pant,
- David Cox,
- Tomoko Tahira,
- and Kenshi Hayashi
Genome Res. November 2005 15: 1511-1518; doi:10.1101/gr.4371105
..., C.C. 2004 . Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole amplified DNA. Nucleic Acids Res. 32 : e69 . ↵ Zhang, K., Calabrese, P., Nordborg, M., and Sun, F. 2002a . Haplotype block structure and its applications to association studies: Power...
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METHODS: Arrays of Arrays for High-Throughput Gene Expression Profiling
- Patrick P. Zarrinkar,
- James K. Mainquist,
- Matthew Zamora,
- David Stern,
- John B. Welsh,
- Lisa M. Sapinoso,
- Garret M. Hampton,
- and David J. Lockhart
Genome Res. July 1, 2001 11: 1256-1261; Published in Advance June 12, 2001, doi:10.1101/gr.174801
....K. , Chee M.S. , Reid B.J. , Lockhart D.J. ( 2000 ) Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res. 10 : 1126 – 1137 . ↵ Ross D.T. , Scherf U. , Eisen M.B. , Perou C.M. , Rees C. , Spellman P. , Iyer V. , Jeffrey S.S. , Van de Rijn M. , Waltham M. , et al...
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Method: Copy-number-aware differential analysis of quantitative DNA sequencing data
- Mark D. Robinson,
- Dario Strbenac,
- Clare Stirzaker,
- Aaron L. Statham,
- Jenny Song,
- Terence P. Speed,
- and Susan J. Clark
Genome Res. December 2012 22: 2489-2496; Published in Advance August 9, 2012, doi:10.1101/gr.139055.112
...; this further imbalance can be adjusted through ‘‘normalization’’ (adjustments for depth and diversity) in the statistical modeling. There are now a large number of tools for absolute analysis of qDNA-seq data; methods are available for the detection of short distinct events (e.g., MACS) (Zhang et al. 2008...
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Methods: DNA amplification method tolerant to sample degradation
- Gang Wang,
- Elizabeth Maher,
- Cameron Brennan,
- Lynda Chin,
- Christopher Leo,
- Manjit Kaur,
- Penny Zhu,
- Martha Rook,
- Jia Liu Wolfe,
- and G. Mike Makrigiorgos
Genome Res. November 2004 14: 2357-2366; doi:10.1101/gr.2813404
...or higher) between complex genomes on a genome-wide scale providing highly improved concordance with unamplified material as compared with other amplification methodologies including multiple displacement amplification. Using RCA–RCA, formalin-fixed samples of modest or substantial DNA degradation were...
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METHODS: Genotyping on a Thermal Gradient DNA Chip
- Tomoharu Kajiyama,
- Yuji Miyahara,
- Larry J. Kricka,
- Peter Wilding,
- David J. Graves,
- Saul Surrey,
- and Paolo Fortina
Genome Res. March 1, 2003 13: 467-475; doi:10.1101/gr.790603
.... , Ghandour G. , Patil N. , Wolff R.K. , Chee M.S. , Reid B.J. , Lockhart D.J. ( 2000 ) Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res. 10 : 1126 – 1137 . ↵ Pastinen T. , Raitio M. , Lindroos K. , Tainola P. , Peltonen L. , Syvanen A.C. ( 2000 ) A system...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...to our small sample size, it is also possible that some allele-specific splicing orders result from combinatorial effects of several SNPs, as was shown for variants in DNA that physically interact to regulate gene expression (Corradin et al. 2016). This could be especially relevant if RNA structure...
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Methods: Targeted screening of cis-regulatory variation in human haplotypes
- Dominique J. Verlaan,
- Bing Ge,
- Elin Grundberg,
- Rose Hoberman,
- Kevin C.L. Lam,
- Vonda Koka,
- Joana Dias,
- Scott Gurd,
- Nicolas W. Martin,
- Hans Mallmin,
- Olof Nilsson,
- Eef Harmsen,
- Ken Dewar,
- Tony Kwan,
- and Tomi Pastinen
Genome Res. January 2009 19: 118-127; Published in Advance October 29, 2008, doi:10.1101/gr.084798.108
...to assess AE, which maximizes the information content per gene. Linkage disequilibrium (LD) between the causal variants and intragenic SNPs can lead to AE biased toward one allele. Secondly, we measured allelic expression in pooled DNA and RNA, which allows for the enrichment of heritable variation...

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