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Phased Whole Genome Genetic Risk In A Family Quartet

a whole genome and family quartet technology, applied in the field of genomics, can solve the problems of difficulty in assigning, unattractive options, parental origin of genetic variants, etc., and achieve the effect of high throughpu

Inactive Publication Date: 2013-03-28
THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIV
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  • Abstract
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  • Application Information

AI Technical Summary

Problems solved by technology

One of the challenges to the interpretation of massively parallel whole genome sequence data is the assembly and variant calling of sequence reads against the human reference genome.
Although de novo assembly of genome sequences from raw sequence reads represents an alternative approach, computational limitations and the large amount of mapping information encoded in relatively invariant genomic regions make this an unattractive option presently.
One of the upstream challenges to interpretation of this genetic data is the reliance on a human reference genome sequence to 1) identify the genomic location of the billions of short (30 to 500 base pair) sequence reads produced in a massively parallel fashion by high-throughput sequencing, and 2) identify variation in other individuals from this “normal” sequence.
Another barrier to the realization of the goal of genome interpretation pipelines is the difficulty in assigning “phase,” or parental origin of genetic variants, in sequencing studies, because genotypes, not haplotypes, are given at each position.
Another barrier to the realization of the goal of genome interpretation pipelines is the difficulty in assigning risk estimates to the millions of genetic variants present in any individual.

Method used

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  • Phased Whole Genome Genetic Risk In A Family Quartet
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  • Phased Whole Genome Genetic Risk In A Family Quartet

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Embodiment Construction

[0056]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. 40. Such a digital computer or embedded device is well-known in the art and may include the following.

[0057]Computer system 100 may include at least one central processing unit 102 but may include many processors or processing cores. Computer system100 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.

[0058]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 dev...

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Abstract

An embodiment of the present invention is a method for resolving long-range haplotype phase based on family pedigree data, inheritance state determination, and population linkage disequilibrium data. A method according to an embodiment of the present invention provides for the evaluation of genome wide risk using phased haplotype data.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority to U.S. Provisional Application No. 61 / 474,749 filed Apr. 13, 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 HL083914 and OD004613 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 genomics. More particularly, the present invention relates to the field of whole genome sequencing and analysis.BACKGROUND OF THE INVENTION[0004]Whole genome sequencing of related individuals provides opportunities for investigation of human recombination and compound heterozygous loci contributing to Mendelian disease traits as well as error control. The recent publication of low-coverage sequencing data from large numbers of unrelated individuals offers a...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): G06N5/02G16B30/10G16B5/00G16B20/20G16B20/40G16B40/30
CPCG06F19/24G06F19/18G06F19/22G06N5/02G06F19/12G16B20/00G16B30/00G16B30/10G16B40/30G16B5/00G16B20/20G16B20/40G16B40/00
Inventor DEWEY, FREDERICKASHLEY, EUAN A.WHEELER, MATTHEWCORDERO, SERGIOCALESHU, COLLEENORMOND, KELLY
Owner THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIV
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