A Genotype Filling Method for Constructing Hidden Markov Chains

Abstract

The invention relates to a genotype filling method for constructing a hidden Markov chain, which uses the minority allele types on the rare sites of the sample to preprocess the genotype database; creates a local haplotype cluster model; The nodes of the haplotype cluster model are merged into subsequent similar states; the pathways of the local haplotype cluster model are pruned using the forward-backward algorithm; The pre-probability of the sample diplotype is obtained by balancing and combined with the sequencing likelihood to obtain the posterior probability of the diplotype; the probability of the diplotype is screened by the sample micro-haplotype as an iterative reconstruction of the local haplotype cluster model; loop N times, after obtaining the diploid posterior probability and obtaining the genotype probability of the corresponding locus. The invention constructs local haplotype clusters, generates the posterior probability of diplotypes from the hidden Markov model, filters out the obvious contradictions according to the micro-haplotypes of the samples, and obtains high-accuracy haplotypes after repeated iterations. Judgment type.

Description

technical field [0001] The invention relates to a genotype filling method for constructing hidden Markov chains. Background technique [0002] Gene is the basic unit of heredity, DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) sequence that carries genetic information, passes genetic information to the next generation through replication, and guides protein synthesis to express the genetic information it carries. Thereby controlling the expression of traits of individual organisms. Genetic testing is a technology for detecting DNA through blood, other body fluids, or cells. It is to take the peripheral venous blood or other tissue cells of the tested person, amplify their genetic information, and use specific equipment to detect the DNA molecules in the tested person's cells. It is a method to detect and analyze the gene types and gene defects contained in it and whether its expression function is normal. [0003] In the sequenced gene sequence, some sites are still ...

AI Technical Summary

Problems solved by technology

[0009] So far, some typing methods that are not based on linkage disequilibrium are based on the haplotype data that exist in next-generation sequencing.

Next-generation sequencing has many sites, and many of them are rare sites. At low magnification, the genotype of each site is inaccurate and can only be described by probability

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