Systems and methods for interpreting a human genome using a synthetic reference sequence

Patent metadata

Field	Value
Publication number	US-10127346-B2
Application number	US-201213445923-A
Country	US
Kind code	B2
Filing date	Apr 13, 2012
Priority date	Apr 13, 2011
Publication date	Nov 13, 2018
Grant date	Nov 13, 2018

Abstract

In an embodiment of the present invention, three novel human reference genome sequences were developed based on the most common population-specific DNA sequence (“major allele”). Methods were developed for their integration into interpretation pipelines for highthroughput whole genome sequencing.

First claim

What is claimed is:

1. A method for providing genetic data over a network, comprising:
obtaining reference sequence data describing a synthetic reference genome sequence,
where the synthetic reference genome sequence is a composite sequence comprising a reference sequence substituted using major alleles for an ethnic sub-population,
where major alleles are alleles having estimated allele frequencies of greater than 50% within the ethnic sub-population,
and storing the reference sequence data using a computer system comprising a processor and a memory;

obtaining individual sequence data describing information derived from an individual who is a member of the ethnic sub-population, comprising at least one short sequence read from the individual and storing the individual sequence data using a computer system comprising a processor and a memory;
aligning the obtained at least one short sequence read to the synthetic reference genome sequence using a computer system comprising a processor and a memory;
determining at least one difference between the at least one short sequence read and the synthetic reference genome sequence based on the alignment using a computer system comprising a processor and a memory; and
transmitting the at least one difference to a remote device using a computer system comprising a processor and a memory.

2. The method of claim 1 , wherein determining at least once difference between the at least one short sequence read and the synthetic reference genome sequence is performed for predetermined genomic positions.

3. The method of claim 1 , wherein obtaining reference sequence data comprises generating the synthetic reference genome sequence by:
selecting the ethnic sub-population from HapMap population groups;
determining the major allele at allele positions, where the major allele is an allele estimated to have an allele frequency of greater than 50% in the ethnic sub-population;
substituting the major allele from the ethnic sub-population into the reference sequence.

4. A non-transitory computer-readable medium including instructions that, when executed by a processing unit, cause the processing unit to provide genetic data over a network, by performing the steps comprising:
obtaining reference sequence data describing a synthetic reference genome sequence,
where the synthetic reference genome sequence is a composite sequence comprising a reference sequence substituted using major alleles for an ethnic sub-population,
where major alleles are alleles having estimated allele frequencies of greater than 50% within the ethnic sub-population,
and storing the reference sequence data using a computer system comprising a processor and a memory;

obtaining individual sequence data describing information derived from an individual, wherein the individual's ethnic background includes the ethnic sub-population, comprising at least one short sequence read from the individual and storing the individual sequence data;
aligning the obtained at least one short sequence read to the synthetic reference genome sequence;
determining at least one difference between the at least one short sequence read and the synthetic reference genome sequence based on the alignment; and
transmitting the at least one difference to a remote device.

5. The non-transitory computer-readable medium of claim 4 , wherein determining at least once difference between the at least one short sequence read and the synthetic reference genome sequence is performed for predetermined genomic positions.

6. The non-transitory computer-readable medium of claim 4 , wherein the step for obtaining reference sequence data comprises a step for generating the synthetic reference genome sequence by:
selecting the ethnic sub-population from HapMap population groups;
determining the major allele at allele positions, where the major allele is an allele estimated to have an allele frequency of greater than 50% in the ethnic sub-population;
substituting the major allele from the ethnic sub-population into the reference sequence.

7. A computing device for providing genetic data over a network comprising: a data bus; a memory unit coupled to the data bus; a processing unit coupled to the data bus and configured to
obtain reference sequence data describing a synthetic reference genome sequence,
where the synthetic reference genome sequence is a composite sequence comprising a reference sequence substituted using major alleles for an ethnic sub-population,
where major alleles are alleles having estimated allele frequencies of greater than 50% within the ethnic sub-population,
and store the reference sequence data on a memory;

obtain individual sequence data describing information derived from an individual, wherein the individual's ethnic background includes the ethnic sub-population, comprising at least one short sequence read from the individual and store the individual sequence data on a memory;
align the obtained at least one short sequence read to the synthetic reference genome sequence;
determine at least one difference between the at least one short sequence read and the synthetic reference genome sequence based on the alignment; and
transmit the at least one difference to a remote device.

Assignees

• Dewey Frederick
• Ashley Euan A
• Wheeler Matthew
• Snyder Michael
• Bustamante Carlos
• Univ Leland Stanford Junior

Inventors

• Dewey Frederick
• Ashley Euan A
• Wheeler Matthew
• Snyder Michael
• Bustamante Carlos

Classifications

• G06F19/22

  Physics · mapped topic

• G06N5/02

  Knowledge representation; Symbolic representation · CPC title

• G06F19/18

  Physics · mapped topic

• G06F19/24

  Physics · mapped topic

• G06F19/12 Primary

  Physics · mapped topic