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
Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium.
TL;DR: It is shown that the ascertainment scheme has a large effect on the estimation of linkage disequilibrium and recombination, and some methods of correcting for ascertainment biases when estimating recombination rates from SNP data are described.
Journal ArticleDOI
Insertion-deletion polymorphisms in 3' regions of maize genes occur frequently and can be used as highly informative genetic markers.
Dinakar Bhattramakki,Maureen Dolan,Mike Hanafey,Robin Wineland,Dave Vaske,James C. Register,Scott V. Tingey,Antoni Rafalski +7 more
TL;DR: This paper clearly demonstrates that the resequencing of 3′ EST sequence and the discovery and mapping of indel markers will position corresponding expressed genes on the genetic map.
Journal ArticleDOI
Flow cytometry-based minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring.
Hong Cai,P. Scott White,David C. Torney,Alina Deshpande,Zaolin Wang,Babetta L. Marrone,John P. Nolan +6 more
TL;DR: This work has developed a sensitive and rapid flow cytometry-based assay for the multiplexed analysis of SNPs based on polymerase-mediated primer extension, or minisequencing, using microspheres as solid supports, and genomic analysis using multiplexing microsphere arrays (GAMMArrays), enables the simultaneous analysis of dozens, and potentially hundreds ofSNPs per sample.
Journal ArticleDOI
Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: Lessons from Ladakh
Thierry Wirth,Xiaoyan Wang,Bodo Linz,Richard P. Novick,J. Koji Lum,Martin J. Blaser,Giovanna Morelli,Daniel Falush,Mark Achtman +8 more
TL;DR: It is shown that DNA sequences from Helicobacter pylori, a bacterium that colonizes the stomachs of most humans and is usually transmitted within families, can distinguish between closely related human populations and are superior in this respect to classical human genetic markers.
Journal ArticleDOI
Surface plasmon resonance applications in clinical analysis
Stefano Mariani,Maria Minunni +1 more
TL;DR: The state of the art of clinical target detection with SPR-based biosensors in complex matrices as well as in standard solution when innovative approaches or advanced instrumentations were employed for improved detection are reported.
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.
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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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