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
Overlapping pools for high-throughput targeted resequencing
Snehit Prabhu,Itsik Pe'er +1 more
TL;DR: This work presents a framework for overlapping pool design, where each individual sample is resequenced in several pools (many individuals to many pools), and guarantees high probability of unambiguous singleton carrier identification while maintaining the features of naïve pools in terms of sensitivity, specificity, and the ability to estimate allele frequencies.
Patent
Method and apparatus for performing large numbers of reactions using array assembly with releasable primers
TL;DR: In this article, a method and apparatus for performing a large number of chemical and biological reactions by bringing two arrays into close position and allowing reactants on the surfaces of two arrays to come into contact is described.
Journal ArticleDOI
Joint linkage and linkage disequilibrium mapping in natural populations.
Rongling Wu,Zhao-Bang Zeng +1 more
TL;DR: Simulation studies indicate that the statistical method implemented by the Fisher-scoring algorithm can provide accurate and precise estimates for the allele frequencies, recombination fractions, and linkage disequilibria between different markers.
Journal ArticleDOI
Genetics of coronary heart disease: current knowledge and research principles.
Bernhard R. Winkelmann,Joerg Hager,William E. Kraus,Piera Merlini,Bernard Keavney,Peter J. Grant,Joseph B. Muhlestein,Christopher B. Granger +7 more
Journal ArticleDOI
Psychiatric genetics: back to the future
TL;DR: It seems timely to consider the state of the field and to consider carefully how it might advance, the problems to be faced and the resources required.
References
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Journal ArticleDOI
Light-generated oligonucleotide arrays for rapid DNA sequence analysis
Ann Maria Caviani Pease,Dennis W. Solas,Edward Sullivan,Maureen T. Cronin,Christopher P. Holmes,Stephen P. A. Fodor +5 more
TL;DR: It is reported here how modern photolithographic techniques can be used to facilitate sequence analysis by generating miniaturized arrays of densely packed oligonucleotide probes, which can then be applied to parallel DNA hybridization analysis, directly yielding sequence information.
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
TL;DR: A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases, anchored by the radiation hybrid and genetic maps.
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
TL;DR: In the first clinical application of high–density oligonucleotide arraysequencing, the sequences of 167 viral isolates from 102 patients have been determined and the DNA sequence of USA HIV–1 clade B proteases was found to be extremely variable.
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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