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
Detection of CX3CR1 single nucleotide polymorphism and expression on archived eyes with age-related macular degeneration.
TL;DR: The data suggest that the M280 allele, a SNP resulting in aberrant C X3CR1 and CX3CL1 interaction, as well as lowered expression of macular CX 3CR1, may contribute to the development of AMD.
Journal ArticleDOI
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants
Emidio Capriotti,Russ B. Altman +1 more
TL;DR: A Support Vector Machine (SVM) classifier trained on a set of 3163 cancer-causing variants and an equal number of neutral polymorphisms is presented, which results in higher prediction accuracy and correlation coefficient in identifying cancer- Causing variants.
Journal ArticleDOI
The genetics of chronic obstructive pulmonary disease
Alice M. Wood,Robert A. Stockley +1 more
TL;DR: The main methods of genomic research for complex disease traits are described, together with the genes implicated in COPD thus far, their roles in disease causation and the future for this area of investigation.
Journal ArticleDOI
Allelic discrimination by denaturing high-performance liquid chromatography.
TL;DR: Ion-pair reversed-phase high-performance liquid chromatography on alkylated non-porous poly(styrene-divinylbenzene) particles allows the resolution of single-stranded DNA molecules of identical size that differ in a single base.
Journal ArticleDOI
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi.
TL;DR: This study seeks to infer haplotypes, a diploid consensus sequence, from the genome assembly of an organism, Ciona intestinalis, and indicates 97% accuracy in haplotype estimation, based on a simulated data set.
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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