Skip Navigation



Bioinformatics Advance Access published online on November 2, 2005

Bioinformatics, doi:10.1093/bioinformatics/bti741
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
22/1/7    most recent
bti741v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Rabbee, N.
Right arrow Articles by Speed, T. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rabbee, N.
Right arrow Articles by Speed, T. P.
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 26, 2005
Revised September 28, 2005
Accepted October 21, 2005

Article

A genotype calling algorithm for Affymetrix SNP arrays

Nusrat Rabbee 1* and Terence P. Speed 2

1 Department of Statistics, University of California, Berkeley, CA, USA
2 Department of Statistics, University of California, Berkeley, CA, USA; Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

* To whom correspondence should be addressed.
Nusrat Rabbee, E-mail: nrabbee{at}post.harvard.edu


   Abstract

Motivation: A classification algorithm, based on a multi-chip, multi-SNP approach is proposed for Affymetrix SNP arrays. Current procedures for calling genotypes on SNP arrays process all the features associated with one chip and one SNP at a time. Using a large training sample where the genotype labels are known, we develop a supervised learning algorithm to obtain more accurate classification results on new data. The method we propose, RLMM, is based on a robustly fitted, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variance is reduced through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as across thousands of SNPs for accurate classification. In this paper, we apply RLMM to Affymetrix 100K SNP array data, present classification results and compare them to genotype calls obtained from the Affymetrix procedure DM, as well as to the publicly available genotype calls from the HapMap project.

Availability: The RLMM software is implemented in R and is available from Bioconductor or from the first author at.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
BloodHome page
M. E. Sarasquete, R. Garcia-Sanz, L. Marin, M. Alcoceba, M. C. Chillon, A. Balanzategui, C. Santamaria, L. Rosinol, J. de la Rubia, M. T. Hernandez, et al.
Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis
Blood, October 1, 2008; 112(7): 2709 - 2712.
[Abstract] [Full Text] [PDF]


Home page
JNCI J Natl Cancer InstHome page
P. Liu, H. G. Vikis, D. Wang, Y. Lu, Y. Wang, A. G. Schwartz, S. M. Pinney, P. Yang, M. de Andrade, G. M. Petersen, et al.
Familial Aggregation of Common Sequence Variants on 15q24-25.1 in Lung Cancer
J Natl Cancer Inst, September 17, 2008; 100(18): 1326 - 1330.
[Abstract] [Full Text] [PDF]


Home page
Hum Mol GenetHome page
Y.-J. Liu, X.-G. Liu, L. Wang, C. Dina, H. Yan, J.-F. Liu, S. Levy, C. J. Papasian, B. M. Drees, J. J. Hamilton, et al.
Genome-wide association scans identified CTNNBL1 as a novel gene for obesity
Hum. Mol. Genet., June 15, 2008; 17(12): 1803 - 1813.
[Abstract] [Full Text] [PDF]


Home page
NEJMHome page
C. Ober, Z. Tan, Y. Sun, J. D. Possick, L. Pan, R. Nicolae, S. Radford, R. R. Parry, A. Heinzmann, K. A. Deichmann, et al.
Effect of Variation in CHI3L1 on Serum YKL-40 Level, Risk of Asthma, and Lung Function
N. Engl. J. Med., April 17, 2008; 358(16): 1682 - 1691.
[Abstract] [Full Text] [PDF]


Home page
Molecular Cancer TherapeuticsHome page
J. Greshock, J. Cheng, D. Rusnak, A. M. Martin, R. Wooster, T. Gilmer, K. Lee, B. L. Weber, and T. Zaks
Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines
Mol. Cancer Ther., April 1, 2008; 7(4): 935 - 943.
[Abstract] [Full Text] [PDF]


Home page
Arch NeurolHome page
H. Li, S. Wetten, L. Li, P. L. St. Jean, R. Upmanyu, L. Surh, D. Hosford, M. R. Barnes, J. D. Briley, M. Borrie, et al.
Candidate Single-Nucleotide Polymorphisms From a Genomewide Association Study of Alzheimer Disease
Arch Neurol, January 1, 2008; 65(1): 45 - 53.
[Abstract] [Full Text] [PDF]


Home page
DiabetesHome page
M. G. Hayes, A. Pluzhnikov, K. Miyake, Y. Sun, M. C.Y. Ng, C. A. Roe, J. E. Below, R. I. Nicolae, A. Konkashbaev, G. I. Bell, et al.
Identification of Type 2 Diabetes Genes in Mexican Americans Through Genome-Wide Association Studies
Diabetes, December 1, 2007; 56(12): 3033 - 3044.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
Y. Xiao, M. R. Segal, Y.H. Yang, and R.-F. Yeh
A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays
Bioinformatics, June 15, 2007; 23(12): 1459 - 1467.
[Abstract] [Full Text] [PDF]


Home page
BiostatisticsHome page
B. Carvalho, H. Bengtsson, T. P. Speed, and R. A. Irizarry
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
Biostat., April 1, 2007; 8(2): 485 - 499.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
J. Hua, D. W. Craig, M. Brun, J. Webster, V. Zismann, W. Tembe, K. Joshipura, M. J. Huentelman, E. R. Dougherty, and D. A. Stephan
SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays
Bioinformatics, January 1, 2007; 23(1): 57 - 63.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
G. Hu, H.-Y. Wang, D. M. Greenawalt, M. A. Azaro, M. Luo, I. V. Tereshchenko, X. Cui, Q. Yang, R. Gao, L. Shen, et al.
AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays
Nucleic Acids Res., October 18, 2006; 34(17): e116 - e116.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
P. Lamy, C. L. Andersen, F. P. Wikman, and C. Wiuf
Genotyping and annotation of Affymetrix SNP arrays
Nucleic Acids Res., September 1, 2006; 34(14): e100 - e100.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
D. L. Nicolae, X. Wu, K. Miyake, and N. J. Cox
GEL: a novel genotype calling algorithm using empirical likelihood
Bioinformatics, August 15, 2006; 22(16): 1942 - 1947.
[Abstract] [Full Text] [PDF]



Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.