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US 10,540,324 B2Granted
Human haplotyping system and method
AssigneeSyntekabio Co., Ltd.
InventorsJongsun Jung, Sunho Lee, Sojeong Ka, Jonghui Hong, Yangrae Cho
Life of this patent
Estimating the term…
Abstract
Disclosed is a human haplotyping method. The method includes: collecting a sequence of a gene to be analyzed; matching and aligning reads of the collected sequence to a reference stored in a database; electing candidate alleles from among alleles of the reference; and selecting a final allele from among the candidate alleles.
Claims17
A human haplotyping method comprising:
- a sequence read collection step of collecting a sequence of a gene to be analyzed;
- a sequence read alignment step of matching and aligning reads of the collected sequence to a reference stored in a database, comprising steps of aligning the sequence leads to the reference stored in the database and filtering the aligned sequence reads depending on an absolute value of matching with the reference alleles;
- an allele selection step of selecting candidate alleles from among alleles of the reference by selecting the candidate alleles depending on a distribution of the aligned sequence reads as a tiling array pattern, wherein determination of the distribution of the aligned sequence reads comprises converting the distribution of the aligned reads into a score, and determining that the alleles are false alleles, when the score is lower than a threshold value;
- and
- an allele determination step of selecting a final allele from among the candidate alleles,
- wherein the score is calculated by the following equation:
- score
- =
- ∑
- j
- =
- 1
- m
-
- (
-
- noreadj
-
- c
- )
- 4
- wherein m is a value determined depending on the length of the alleles;
- C is a constant;
- and noread is a constant determined for a region to which the sequence reads are not aligned.
21 more elements
A human haplotyping system configured to:
- match and align sequence reads, collected from a gene to be analyzed, to reference alleles stored in a database;
- select candidate alleles from among the reference alleles by selecting the candidate alleles depending on a distribution of the aligned sequence reads as a tiling array pattern, wherein determination of the distribution of the aligned sequence reads comprises converting the distribution of the aligned reads into a score, and determining that the alleles are false alleles, when the score is lower than a threshold value;
- and
- select two final alleles from among the candidate alleles,
- wherein the aligning of the sequence reads is performed by aligning the sequence reads to the reference stored in the database, and then filtering the aligned sequence reads depending on an absolute value of matching with the reference alleles, and
- wherein the score is calculated by the following equation:
- score
- =
- ∑
- j
- =
- 1
- m
-
- (
-
- noreadj
-
- c
- )
- 4
- wherein m is a value determined depending on the length of the alleles;
- C is a constant;
- and noread is a constant determined for a region to which the sequence reads are not aligned.
21 more elements
Dependencies are inferred from the claim text.