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Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group.

Publication ,  Journal Article
Ghosh, S; Karanjawala, ZE; Hauser, ER; Ally, D; Knapp, JI; Rayman, JB; Musick, A; Tannenbaum, J; Te, C; Shapiro, S; Eldridge, W; Musick, T ...
Published in: Genome Res
February 1997

Large-scale genotyping is required to generate dense identity-by-descent maps to map genes for human complex disease. In some studies the number of genotypes needed can approach or even exceed 1 million. Generally, linkage and linkage disequilibrium analyses depend on clear allele identification and subsequent allele frequency estimation. Accurate grouping or categorization of each allele in the sample (allele calling or binning) is therefore an absolute requirement. Hence, a genotyping system that can reliably achieve this is necessary. In the case of affected sib-pair analysis without parents, the need for accurate allele calling is even more critical. We describe methods that permit precise sizing of alleles across multiple gels using the fluorescence-based, Applied Biosystems (ABI) genotyping technology and discuss ways to reduce genotyping error rates. Using database utilities, we show how to minimize intergel allele size variation, to combine data effectively from different models of ABI sequencing machines, and automatically bin alleles. The final data can then be converted into a format ready for analysis by statistical genetic packages such as MENDEL.

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Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

February 1997

Volume

7

Issue

2

Start / End Page

165 / 178

Location

United States

Related Subject Headings

  • Taq Polymerase
  • Quality Control
  • Polymerase Chain Reaction
  • Humans
  • Genotype
  • Genetic Techniques
  • Genetic Markers
  • Genetic Linkage
  • Electrophoresis, Polyacrylamide Gel
  • Electronic Data Processing
 

Citation

APA
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MLA
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Ghosh, S., Karanjawala, Z. E., Hauser, E. R., Ally, D., Knapp, J. I., Rayman, J. B., … Collins, F. S. (1997). Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group. Genome Res, 7(2), 165–178. https://doi.org/10.1101/gr.7.2.165
Ghosh, S., Z. E. Karanjawala, E. R. Hauser, D. Ally, J. I. Knapp, J. B. Rayman, A. Musick, et al. “Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group.Genome Res 7, no. 2 (February 1997): 165–78. https://doi.org/10.1101/gr.7.2.165.
Ghosh S, Karanjawala ZE, Hauser ER, Ally D, Knapp JI, Rayman JB, Musick A, Tannenbaum J, Te C, Shapiro S, Eldridge W, Musick T, Martin C, Smith JR, Carpten JD, Brownstein MJ, Powell JI, Whiten R, Chines P, Nylund SJ, Magnuson VL, Boehnke M, Collins FS. Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group. Genome Res. 1997 Feb;7(2):165–178.

Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

February 1997

Volume

7

Issue

2

Start / End Page

165 / 178

Location

United States

Related Subject Headings

  • Taq Polymerase
  • Quality Control
  • Polymerase Chain Reaction
  • Humans
  • Genotype
  • Genetic Techniques
  • Genetic Markers
  • Genetic Linkage
  • Electrophoresis, Polyacrylamide Gel
  • Electronic Data Processing