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METHODS: Loss of Heterozygosity Assay for Molecular Detection of Cancer Using Energy-transfer Primers and Capillary Array Electrophoresis
- Igor L. Medintz,
- Chyi-Chia Richard Lee,
- Wendy W. Wong,
- Kristin Pirkola,
- David Sidransky,
- and Richard A. Mathies
Genome Res. August 1, 2000 10: 1211-1218; doi:10.1101/gr.10.8.1211
...G.P. , Galipeau P.C. , Reid B.J. ( 1999 ) Loss of heterozygosity analysis using whole amplification, cell sorting, and fluorescence-based PCR. Genome Res. 9 : 482 – 491 . ↵ Sidransky D. ( 1997 ) Nucleic acid-based methods for the detection of cancer. Science 278 : 1054 – 1058 . ↵ Steiner G...
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Resource: The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine
- Leslie G. Biesecker,
- James C. Mullikin,
- Flavia M. Facio,
- Clesson Turner,
- Praveen F. Cherukuri,
- Robert W. Blakesley,
- Gerard G. Bouffard,
- Peter S. Chines,
- Pedro Cruz,
- Nancy F. Hansen,
- Jamie K. Teer,
- Baishali Maskeri,
- Alice C. Young,
- NISC Comparative Sequencing Program,
- Teri A. Manolio,
- Alexander F. Wilson,
- Toren Finkel,
- Paul Hwang,
- Andrew Arai,
- Alan T. Remaley,
- Vandana Sachdev,
- Robert Shamburek,
- Richard O. Cannon,
- and Eric D. Green
Genome Res. September 2009 19: 1665-1674; Published in Advance July 14, 2009, doi:10.1101/gr.092841.109
...amplification, PCR products are sequenced using 3730XL instruments (Applied Biosystems). Quality control We have implemented a number of steps for the quality control of ClinSeq-generated sequence data. For example, to ensure that a particular DNA sample being sequenced is, in fact, the sameDNA sample analyzed...
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ARTICLE: Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays
- Rui Mei,
- Patricia C. Galipeau,
- Cynthia Prass,
- Anthony Berno,
- Ghassan Ghandour,
- Nila Patil,
- Roger K. Wolff,
- Mark S. Chee,
- Brian J. Reid,
- and David J. Lockhart
Genome Res. August 1, 2000 10: 1126-1137; doi:10.1101/gr.10.8.1126
....4 or &gt;2.5 (depending on which allele was lost) were considered to be indicative of allelic imbalance. Amplification and Hybridization of SNPs SNP-containing loci were amplified by allele-specific multiplex PCR from both tumor and normal genomic DNA. The multiplex PCR was performed by use of 46 PCR...
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ARTICLE: Pattern of Sequence Variation Across 213 Environmental Response Genes
- Robert J. Livingston,
- Andrew von Niederhausern,
- Anil G. Jegga,
- Dana C. Crawford,
- Christopher S. Carlson,
- Mark J. Rieder,
- Sivakumar Gowrisankar,
- Bruce J. Aronow,
- Robert B. Weiss,
- and Deborah A. Nickerson
Genome Res. October 2004 14: 1821-1831; Published in Advance September 13, 2004, doi:10.1101/gr.2730004
...software (PCR-overlap, http://droog.mbt.washington.edu/PCR-Overlap.html ). All exons, genomic sequences conserved in mouse, and &gt;1 kb of 5′ and 3′ flanking regions were targeted. For genes &lt;30 kb, the entire genomic sequence for the candidate was targeted for resequencing. For genes &gt;30 kb, all...
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
.../Crl, F344/Crl, SHR/N; outbred: SD/Crl, SD/A, SD/Hsd, WIST/Crl) as well as two wild rat isolates. The genomic context of each candidate SNP was obtained from rat assembly using the corresponding position field in the CASCAD database. Primers for PCR amplification and sequencing of the genomic region were...
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LETTER: High-Resolution Physical Map and Transcript Identification of a Prostate Cancer Deletion Interval on 8p22
- Zarema H. Arbieva,
- Kumarika Banerjee,
- Su Young Kim,
- Seby L. Edassery,
- Vasilios S. Maniatis,
- Stephen K. Horrigan,
- and Carol A. Westbrook
Genome Res. February 1, 2000 10: 244-257; doi:10.1101/gr.10.2.244
...evaluated for their expression profile by Northern blot analysis. Inserts from the exon amplification-isolated clones 20B08e1, 20B08e4, and 20B08e5 were gel-purified and labeled using random hexamer priming. For the remaining three ESTs, PCR amplification products of genomic DNA with EST primers were used...
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METHODS: Mining SNPs From EST Databases
- Leslie Picoult-Newberg,
- Trey E. Ideker,
- Mark G. Pohl,
- Scott L. Taylor,
- Miriam A. Donaldson,
- Deborah A. Nickerson,
- and Michael Boyce-Jacino
Genome Res. February 1, 1999 9: 167-174; doi:10.1101/gr.9.2.167
...different contigs were tested. Primers for PCR amplification of the candidate SNP sites were designed based on the contig data for each site. Seventeen of the 88 sites were analyzed initially by fluorescence-based DNA sequencing of PCR products. An example of two common but silent base substitutions...

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