Journal ArticleDOI
Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome
David G. Wang,Jian-Bing Fan,Jian-Bing Fan,Chia-Jen Siao,Chia-Jen Siao,Anthony Berno,Anthony Berno,Peter M. Young,Peter M. Young,Ron Sapolsky,Ron Sapolsky,Ghassan Ghandour,Ghassan Ghandour,Nancy Perkins,Nancy Perkins,Ellen Winchester,Ellen Winchester,Jessica B. Spencer,Jessica B. Spencer,Leonid Kruglyak,Leonid Kruglyak,Lincoln Stein,Lincoln Stein,Linda Hsie,Linda Hsie,Thodoros Topaloglou,Thodoros Topaloglou,Earl Hubbell,Earl Hubbell,Elizabeth M. Robinson,Elizabeth M. Robinson,Michael P. Mittmann,Michael P. Mittmann,Macdonald S. Morris,Macdonald S. Morris,Naiping Shen,Naiping Shen,Dan Kilburn,Dan Kilburn,John D. Rioux,John D. Rioux,Chad Nusbaum,Chad Nusbaum,Steve Rozen,Steve Rozen,Thomas J. Hudson,Thomas J. Hudson,Robert J. Lipshutz,Robert J. Lipshutz,Mark S. Chee,Mark S. Chee,Eric S. Lander,Eric S. Lander +52 more
TLDR
A large-scale survey for SNPs was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips, and a genetic map was constructed showing the location of 2227 candidate SNPs.Abstract:
Single-nucleotide polymorphisms (SNPs) are the most frequent type of variation in the human genome, and they provide powerful tools for a variety of medical genetic studies. In a large-scale survey for SNPs, 2.3 megabases of human genomic DNA was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips. A total of 3241 candidate SNPs were identified. A genetic map was constructed showing the location of 2227 of these SNPs. Prototype genotyping chips were developed that allow simultaneous genotyping of 500 SNPs. The results provide a characterization of human diversity at the nucleotide level and demonstrate the feasibility of large-scale identification of human SNPs.read more
Citations
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Journal ArticleDOI
Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)
TL;DR: Carrying 133 K polymorphic SNPs, this oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput.
Patent
Methods for placing, accepting, and filling orders for products and services
Ryan T. Koehler,Kenneth J. Livak,Junko Stevens,Francisco M. De La Vega,Michael D. Rhodes,Laurent R. Bellon,Janet S. Ziegle,Julie Williams,Dawn Madden,Dennis A. Gilbert,Charles R. Scafe,Hadar Isaac,Yu N. Wang,Eugene G. Spier,Xiaoqing You,Lily Xu,Jeremy Heil,Stephen Glanowski,John Scott,Emily S. Winn-Deen,Ivy McMullen,Lini Wu,Harold Carey Gire,Michael W. Hunkapiller,Susan K. Eddins,Leila G. Smith +25 more
TL;DR: In this paper, methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures and collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet.
Journal ArticleDOI
SNPs by AFLP (SBA): a rapid SNP isolation strategy for non‐model organisms
TL;DR: This work describes a rapid and cost effective method to isolate candidate SNPs in non-model organisms through the direct sequencing of amplified fragment length polymorphism bands.
Journal ArticleDOI
Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.
Sarah E. Munchel,Yen Hoang,Yue Zhao,Joseph Cottrell,Brandy Klotzle,Andrew K. Godwin,Devin C. Koestler,Peter Beyerlein,Jian-Bing Fan,Marina Bibikova,Jeremy Chien +10 more
TL;DR: The results from these studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.
Journal ArticleDOI
Signals of selection in outlier loci in a widely dispersing species across an environmental mosaic.
TL;DR: In this article, the authors test for geographical and sequence-based signals of selection in five putatively adaptive and two putative neutral genes identified in a previous genome scan of the highly dispersing purple sea urchin, Strongylocentrotus purpuratus.
References
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Ann Maria Caviani Pease,Dennis W. Solas,Edward Sullivan,Maureen T. Cronin,Christopher P. Holmes,Stephen P. A. Fodor +5 more
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Journal ArticleDOI
An STS-Based Map of the Human Genome
Thomas J. Hudson,Lincoln D. Stein,Sebastian S. Gerety,Junli Ma,Andrew B. Castle,James Silva,Donna K. Slonim,Rafael Baptista,Leonid Kruglyak,Shu-Hua Xu,Xintong Hu,Angela M. E. Colbert,Carl Rosenberg,Mary Pat Reeve-Daly,Steve Rozen,Lester Hui,Xiaoyun Wu,Christina Vestergaard,Kimberly M. Wilson,Jane S. Bae,Shanak Maitra,Soula Ganiatsas,Cheryl A. Evans,Margaret M. DeAngelis,Kimberly A. Ingalls,Robert Nahf,Lloyd T. Horton,Michele Oskin Anderson,Alville Collymore,Wenjuan Ye,Vardouhie Kouyoumjian,Irena S. Zemsteva,James P. Tam,Richard Devine,Dorothy F. Courtney,Michelle Turner Renaud,Huy Nguyen,Tara J. O'Connor,Cécile Fizames,Sabine Fauré,Gabor Gyapay,Colette Dib,Jean Morissette,James B. Orlin,Bruce W. Birren,Nathan Goodman,Jean Weissenbach,Trevor Hawkins,Simon J. Foote,David C. Page,Eric S. Lander +50 more
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Journal ArticleDOI
Extensive polymorphisms observed in HIV–1 clade B protease gene using high–density oligonucleotide arrays
Michael J. Kozal,Nila Shah,Naiping Shen,Robert Yang,Raymond V. Fucini,Thomas C. Merigan,Douglas D. Richman,Douglas D. Richman,Don Morris,Earl Hubbell,Mark S. Chee,Thomas R. Gingeras +11 more
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Journal ArticleDOI
Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis.
TL;DR: Fourteen of fifteen patient samples with known mutations were accurately diagnosed, and no false positive mutations were identified in 20 control samples, suggesting DNA chip–based assays may provide a valuable new technology for high–throughput cost–efficient detection of genetic alterations.
Journal ArticleDOI
The use of a genetic map of biallelic markers in linkage studies
TL;DR: How polymorphic and densely spaced biallelic markers need to be for extraction of most of the inheritance information from human pedigrees is examined, and a map of 700–900 moderately polymorphic bialLElic markers is concluded to be equivalent to the current 300–400 microsatellite marker sets.
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