Literature DB >> 11136232

High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

K H Buetow1, M Edmonson, R MacDonald, R Clifford, P Yip, J Kelley, D P Little, R Strausberg, H Koester, C R Cantor, A Braun.   

Abstract

We describe here a system for the rapid identification, assay development, and characterization of gene-based single nucleotide polymorphisms (SNPs). This system couples informatics tools that mine candidate SNPs from public expressed sequence tag resources and automatically designs assay reagents with detection by a chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry platform. As a proof of concept of this system, a genomewide collection of reagents for 9,115 gene-based SNP genetic markers was rapidly developed and validated. These data provide preliminary insights into patterns of polymorphism in a genomewide collection of gene-based polymorphisms.

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Year:  2001        PMID： 11136232      PMCID： PMC14630          DOI： 10.1073/pnas.98.2.581

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  11 in total

1.  Reliable identification of large numbers of candidate SNPs from public EST data.

Authors:  K H Buetow; M N Edmonson; A B Cassidy
Journal:  Nat Genet       Date:  1999-03       Impact factor: 38.330

Review 2.  A gene map of the human genome.

Authors:  G D Schuler; M S Boguski; E A Stewart; L D Stein; G Gyapay; K Rice; R E White; P Rodriguez-Tomé; A Aggarwal; E Bajorek; S Bentolila; B B Birren; A Butler; A B Castle; N Chiannilkulchai; A Chu; C Clee; S Cowles; P J Day; T Dibling; N Drouot; I Dunham; S Duprat; C East; C Edwards; J B Fan; N Fang; C Fizames; C Garrett; L Green; D Hadley; M Harris; P Harrison; S Brady; A Hicks; E Holloway; L Hui; S Hussain; C Louis-Dit-Sully; J Ma; A MacGilvery; C Mader; A Maratukulam; T C Matise; K B McKusick; J Morissette; A Mungall; D Muselet; H C Nusbaum; D C Page; A Peck; S Perkins; M Piercy; F Qin; J Quackenbush; S Ranby; T Reif; S Rozen; C Sanders; X She; J Silva; D K Slonim; C Soderlund; W L Sun; P Tabar; T Thangarajah; N Vega-Czarny; D Vollrath; S Voyticky; T Wilmer; X Wu; M D Adams; C Auffray; N A Walter; R Brandon; A Dehejia; P N Goodfellow; R Houlgatte; J R Hudson; S E Ide; K R Iorio; W Y Lee; N Seki; T Nagase; K Ishikawa; N Nomura; C Phillips; M H Polymeropoulos; M Sandusky; K Schmitt; R Berry; K Swanson; R Torres; J C Venter; J M Sikela; J S Beckmann; J Weissenbach; R M Myers; D R Cox; M R James; D Bentley; P Deloukas; E S Lander; T J Hudson
Journal:  Science       Date:  1996-10-25       Impact factor: 47.728

3.  Centre d'etude du polymorphisme humain (CEPH): collaborative genetic mapping of the human genome.

Authors:  J Dausset; H Cann; D Cohen; M Lathrop; J M Lalouel; R White
Journal:  Genomics       Date:  1990-03       Impact factor: 5.736

Review 4.  Mass spectrometry from miniaturized arrays for full comparative DNA analysis.

Authors:  D P Little; A Braun; M J O'Donnell; H Köster
Journal:  Nat Med       Date:  1997-12       Impact factor: 53.440

5.  Generation and analysis of 280,000 human expressed sequence tags.

Authors:  L D Hillier; G Lennon; M Becker; M F Bonaldo; B Chiapelli; S Chissoe; N Dietrich; T DuBuque; A Favello; W Gish; M Hawkins; M Hultman; T Kucaba; M Lacy; M Le; N Le; E Mardis; B Moore; M Morris; J Parsons; C Prange; L Rifkin; T Rohlfing; K Schellenberg; M Bento Soares; F Tan; J Thierry-Meg; E Trevaskis; K Underwood; P Wohldman; R Waterston; R Wilson; M Marra
Journal:  Genome Res       Date:  1996-09       Impact factor: 9.043

6.  The future of genetic studies of complex human diseases.

Authors:  N Risch; K Merikangas
Journal:  Science       Date:  1996-09-13       Impact factor: 47.728

7.  Accurate mass measurement of oligonucleotides using a time-lag focusing matrix-assisted laser desorption/ionization time-of-flight mass spectrometer.

Authors:  Y Dai; R M Whittal; L Li; S R Weinberger
Journal:  Rapid Commun Mass Spectrom       Date:  1996       Impact factor: 2.419

8.  Identification of apolipoprotein E polymorphisms using temperature cycled primer oligo base extension and mass spectrometry.

Authors:  D P Little; A Braun; B Darnhofer-Demar; H Köster
Journal:  Eur J Clin Chem Clin Biochem       Date:  1997-07

9.  Polymorphisms in the coagulation factor VII gene and the risk of myocardial infarction.

Authors:  L Iacoviello; A Di Castelnuovo; P De Knijff; A D'Orazio; C Amore; R Arboretti; C Kluft; M Benedetta Donati
Journal:  N Engl J Med       Date:  1998-01-08       Impact factor: 91.245

10.  A physical map of 30,000 human genes.

Authors:  P Deloukas; G D Schuler; G Gyapay; E M Beasley; C Soderlund; P Rodriguez-Tomé; L Hui; T C Matise; K B McKusick; J S Beckmann; S Bentolila; M Bihoreau; B B Birren; J Browne; A Butler; A B Castle; N Chiannilkulchai; C Clee; P J Day; A Dehejia; T Dibling; N Drouot; S Duprat; C Fizames; S Fox; S Gelling; L Green; P Harrison; R Hocking; E Holloway; S Hunt; S Keil; P Lijnzaad; C Louis-Dit-Sully; J Ma; A Mendis; J Miller; J Morissette; D Muselet; H C Nusbaum; A Peck; S Rozen; D Simon; D K Slonim; R Staples; L D Stein; E A Stewart; M A Suchard; T Thangarajah; N Vega-Czarny; C Webber; X Wu; J Hudson; C Auffray; N Nomura; J M Sikela; M H Polymeropoulos; M R James; E S Lander; T J Hudson; R M Myers; D R Cox; J Weissenbach; M S Boguski; D R Bentley
Journal:  Science       Date:  1998-10-23       Impact factor: 47.728
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  145 in total

1.  Hierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometry.

Authors:  Silvia Paracchini; Barbara Arredi; Rod Chalk; Chris Tyler-Smith
Journal:  Nucleic Acids Res       Date:  2002-03-15       Impact factor: 16.971

2.  Quantitative mutant analysis of viral quasispecies by chip-based matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry.

Authors:  G Amexis; P Oeth; K Abel; A Ivshina; F Pelloquin; C R Cantor; A Braun; K Chumakov; A Brau
Journal:  Proc Natl Acad Sci U S A       Date:  2001-10-02       Impact factor: 11.205

3.  RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis.

Authors:  Ralf Hartmer; Niels Storm; Sebastian Boecker; Charles P Rodi; Franz Hillenkamp; Christian Jurinke; Dirk van den Boom
Journal:  Nucleic Acids Res       Date:  2003-05-01       Impact factor: 16.971

4.  Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry.

Authors:  Jörg Tost; Philipp Schatz; Matthias Schuster; Kurt Berlin; Ivo Glynne Gut
Journal:  Nucleic Acids Res       Date:  2003-05-01       Impact factor: 16.971

5.  High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools.

Authors:  Karen L Mohlke; Michael R Erdos; Laura J Scott; Tasha E Fingerlin; Anne U Jackson; Kaisa Silander; Pablo Hollstein; Michael Boehnke; Francis S Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2002-12-13       Impact factor: 11.205

6.  Genetic covariance between gamma-glutamyl transpeptidase and fatty liver risk factors: role of beta2-adrenergic receptor genetic variation in twins.

Authors:  Rohit Loomba; Fangwen Rao; Lian Zhang; Srikrishna Khandrika; Michael G Ziegler; David A Brenner; Daniel T O'Connor
Journal:  Gastroenterology       Date:  2010-06-09       Impact factor: 22.682

7.  Re-sequencing of multiple single nucleotide polymorphisms by liquid chromatography-electrospray ionization mass spectrometry.

Authors:  H Oberacher; P J Oefner; G Hölzl; A Premstaller; K Davis; C G Huber
Journal:  Nucleic Acids Res       Date:  2002-07-15       Impact factor: 16.971

Review 8.  MALDI-TOF mass spectrometry: a versatile tool for high-performance DNA analysis.

Authors:  Christian Jurinke; Paul Oeth; Dirk van den Boom
Journal:  Mol Biotechnol       Date:  2004-02       Impact factor: 2.695

9.  A genotyping strategy based on incorporation and cleavage of chemically modified nucleotides.

Authors:  Jia Liu Wolfe; Tomohiko Kawate; David A Sarracino; Martin Zillmann; Jeffrey Olson; Vincent P Stanton; Gregory L Verdine
Journal:  Proc Natl Acad Sci U S A       Date:  2002-08-08       Impact factor: 11.205

10.  Amino acid variant in the kinase binding domain of dual-specific A kinase-anchoring protein 2: a disease susceptibility polymorphism.

Authors:  Stefan Kammerer; Lora L Burns-Hamuro; Yuliang Ma; Sara C Hamon; Jaume M Canaves; Michael M Shi; Matthew R Nelson; Charles F Sing; Charles R Cantor; Susan S Taylor; Andreas Braun
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-19       Impact factor: 11.205
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