Haplotype estimation method
AssigneeNEC Corporation et al
InventorsToshio Furuta, Masao Yanagisawa, Naoyuki Kamatani
Life of this patent
Estimating the term…
Abstract
An EM algorithm and a graph structure are combined so that all haplotype information to be assumed is kept, thus changing a problem into one for searching for a complete graph having a maximum score for haplotype estimation.
Claims30
A method for estimating diplotype configurations of each individual from genotype data with n loci, using a computer system, comprising the steps of:
- representing the diplotype configurations for each individual as an n-locus complete graph structure with multiple permutation genotypes corresponding to vertices;
- taking a weight of each edge of the n-locus complete graph structure as probability of the diplotype configurations estimated by maximum-likelihood estimation from the genotype data;
- selecting a set of vertices of the n-locus complete graph structure using a predetermined score;
- and
- estimating the diplotype configurations of each individual by solving an n-node complete graph having a maximal score.
A method for estimating haplotypes from genotype data with n loci, using a computer system, comprising the steps of:
- representing diplotype configurations for each individual as an n-locus complete graph structure with multiple permutation genotypes corresponding to vertices;
- taking a weight of each edge of the n-locus complete graph structure as probability of the diplotype configurations estimated by maximum-likelihood estimation from the genotype data;
- selecting a set of vertices of the n-locus complete graph structure using a predetermined score;
- estimating the diplotype configurations of each individual by solving an n-node complete graph having a maximal score;
- and
- obtaining haplotype frequency of a population from the diplotype configuration of each individual obtained by the estimation.
A device for estimating diplotype configurations of each individual from genotype data with n loci, said device, comprising:
- means for representing the diplotype configurations for each individual as an n-locus complete graph structure with multiple permutation genotypes corresponding to vertices;
- means for taking the weight of each edge of the n-locus complete graph structure as probability of the diplotype configurations estimated by maximum-likelihood estimation from the genotype data;
- means for selecting a set of vertices of the n-locus complete graph structure using a predetermined score;
- and
- means for estimating the diplotype configurations of each individual by solving an n-node complete graph having a maximal score.
A device for estimating haplotypes from genotype data with n loci, comprising:
- means for representing diplotype configurations for each individual as an n-locus complete graph structure with multiple permutation genotypes corresponding to the vertices;
- means for taking a weight of each edge of the n-locus complete graph structure as probability of diplotype configurations estimated by maximum-likelihood estimation from the genotype data;
- means for selecting a set of vertices of the n-locus complete graph structure using a predetermined score;
- means for estimating the diplotype configurations of each individual by solving an n-node complete graph having a maximal score;
- and
- means for obtaining haplotype frequency of a population from the diplotype configuration of each individual obtained by the estimation.
A program for causing a computer to estimate diplotype configurations of each individual from genotype data with n loci, the program comprising:
- a function for representing the diplotype configurations for each individual as an n-locus complete graph structure with multiple permutation genotypes corresponding to vertices;
- a function for taking a weight of each edge of said n-locus complete graph structure as probability of the diplotype configurations estimated by maximum-likelihood estimation from the genotype data;
- a function for selecting a set of vertices of the n-locus complete graph structure using a predetermined score;
- and
- a function for estimating the diplotype configurations of each individual by solving an n-node complete graph having a maximal score.
A program for causing a computer to estimate haplotypes from genotype data with n loci, the program comprising:
- a function for representing diplotype configurations for each individual as an n-locus complete graph structure with multiple permutation genotypes corresponding to vertices;
- a function for taking a weight of each edge of the n-locus complete graph structure as probability of the diplotype configurations estimated by maximum-likelihood estimation from the genotype data;
- a function for selecting a set of vertices of the n-locus complete graph structure using a predetermined score;
- a function for estimating the diplotype configurations of each individual by solving an n-node complete graph having a maximal score;
- and
- a function for obtaining haplotype frequency of a population from the diplotype configuration of each individual obtained by the estimation.
Dependencies are inferred from the claim text.