Patent Document ID: 8594940
Application ID: 10983405
Patent Flag: 1

Claim One:
1. A system for analyzing the state of a chromosome based on amounts of gene expression, the system comprising one or more processors and a non-transitory computer-readable storage medium encoded with a plurality of computer-executable programs, wherein execution of the programs by the one or more processors causes the system to perform functions of: analyzing a gene expression measurement for each of the plurality of genes; determining a probability distribution (b i ) of an amount of gene expression (e k ) for each of a plurality of genes g k (k=1, 2,. .. , N) sequentially arrayed on the chromosome, wherein the probability distribution is determined by the equation: b i ⁡ ( e k ) = 1 2 ⁢ Πσ i ⁢ exp ⁡ ( - ( e k - μ i ) 2 2 ⁢ σ i 2 ) × Δ ⁢ ⁢ e , wherein the gene expression of at least one of the plurality of chromosomal states is different than the gene expression of another of the plurality of chromosomal states; generating a state transition probability for each of the plurality of genes, wherein the state transition probability indicates a probability that a gene will assume a chromosomal state equal to a chromosomal state of an adjacent gene, wherein the chromosomal state comprises one of a deletion state, an amplification state, and a normal state, the deletion state indicating that the gene is in a deletion region of the chromosome, the amplification state indicating that the gene is in an amplification region thereof, and the normal state indicating that the gene is in a normal region thereof; and detecting the chromosomal state of each of the plurality of genes by: (i) calculating a combination of chromosomal states for the plurality of genes on the chromosome based on the probability distribution obtained via the probability distribution storage unit and the state transition probability, wherein calculating a combination of chromosomal states for the plurality of genes on the chromosome comprises sequentially calculating a probability value δ for each of the plurality of genes and chromosomal states on the chromosome via δ k ⁡ ( j ) = max i ⁢  δ k - 1 ⁡ ( i ) ⁢ q ij ⁡ ( l k )  ⁢ b j ⁡ ( e k ) , wherein k represents position on the chromosome and i represents one of the three chromosomal states, and wherein q ij represents a unit distance transition probability for calculating a vector indicating respective transition probabilities of a position which is a unit distance away from a deletion, amplification, or normal region; and (ii) determining the combination of genes and chromosomal states with the highest probabilities of deletion and/or amplification regions associated with an abnormal region on the chromosome that is indicative of increased disease progression, and outputting at least one abnormal region to a user in a user readable format.