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Method and System for Accurate Construction Of Long Range Haplotype

a technology of haplotype and long-range haplotype, applied in the field of genome analysis methods, can solve the problems of difficult analysis of large-scale datasets and computational intensive phases, and achieve the effect of increasing sample size and increasing accuracy

Pending Publication Date: 2013-11-07
THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIV
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AI Technical Summary

Benefits of technology

The present invention is a modified version of the PHASE model that is more accurate than the FastPHASE model. The modifications include using a parameterization EM algorithm and optimizing haplotypes rather than performing MCMC sampling. The accuracy of the model is believed to be important because the imputed haplotypes are used as hidden states in the HMM. This increase in accuracy is more pronounced with increasing sample size because the PHASE model likelihood produces long, shared haplotypes between pairs of individuals.

Problems solved by technology

When implemented via Markov Chain Monte Carlo algorithms (MCMC), PHASE is computationally intensive where it can be difficult to perform analysis of large-scale datasets, such as those generated in genome-wide association studies (GWAS).

Method used

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  • Method and System for Accurate Construction Of Long Range Haplotype

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Embodiment Construction

[0019]Among other things, the present invention relates to methods, techniques, and algorithms that are intended to be implemented in a digital computer system 100 such as generally shown in FIG. 7. Such a digital computer is well-known in the art and may include the following.

[0020]Computer system 100 may include at least one central processing unit 102 but may include many processors or processing cores. Computer system 100 may further include memory 104 in different forms such as RAM, ROM, hard disk, optical drives, and removable drives that may further include drive controllers and other hardware. Auxiliary storage 112 may also be include that can be similar to memory 104 but may be more remotely incorporated such as in a distributed computer system with distributed memory capabilities.

[0021]Computer system 100 may further include at least one output device 108 such as a display unit, video hardware, or other peripherals (e.g., printer). At least one input device 106 may also be...

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Abstract

In an embodiment of the present invention, a modified version of the PHASE model is implemented that is substantially more accurate than the FastPHASE model. Modifications in an embodiment of the present invention include using a parameterization EM algorithm similar to that of the FastPHASE model, and to perform optimization on haplotypes rather than MCMC sampling. In an embodiment, the imputed haplotypes themselves are used as hidden states in the HMM because this is believed to be important for the PHASE model's accuracy. This increase in accuracy becomes more pronounced with increasing sample size. This difference is attributed to the PHASE model's likelihood which produces long, shared haplotypes between pairs of individuals.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority to U.S. Provisional Application No. 61 / 492,365 filed Jun. 1, 2011, which is hereby incorporated by reference in its entirety for all purposes.STATEMENT OF GOVERNMENT SPONSORED SUPPORT[0002]This invention was made with Government support under contracts GM073059 and HG002357 awarded by the National Institutes of Health. The Government has certain rights in this invention.FIELD OF THE INVENTION[0003]The present invention generally relates to the field of computcr diagnostics. More particularly, the present invention relates to methods for analyzing a genome.BACKGROUND OF THE INVENTION[0004]The term haplotype refers to the combination of alleles at multiple loci along a chromosome. In linkage disequilibrium (LD) mapping, haplotype-based tests are thought to improve power for detecting untyped variants. In population genetics studies of evolutionary histories, haplotype data have been used to detect recombinat...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): G06F19/22G16B30/00G16B20/20G16B20/40G16B40/00
CPCG06F19/22G16B30/00G16B20/00G16B40/00G16B20/20G16B20/40G16H20/10
Inventor JOHNSON, NICHOLASWONG, WING H.TANG, HUA
Owner THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIV
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