Method for determining the presence of disease

Abstract

The invention provides a method for determining presence of a disease, comprising steps of; measuring the levels of expression of transcription products of genes in a biological sample obtained from a subject suspected of having a target disease, wherein the genes comprise at least one gene belonging to each of at least two disease-determining gene families related to the target disease; obtaining values representing deviations by standardizing the levels of the expression based on the levels of expression of transcription products of the corresponding genes in a plurality of healthy subjects; obtaining the average of values representing deviations with respect to the gene belonging to each of the disease-determining gene families; and determining whether or not the subject has the target disease by using the average; as well as a computer program product for determining presence of a disease.

1 . A method for determining presence of a disease, comprising steps of:
 measuring the levels of expression of transcription products of genes in a biological sample obtained from a subject suspected of having a target disease, wherein the genes comprise at least one gene belonging to each of at least two disease-determining gene families related to the target disease;   obtaining values representing deviations by standardizing the levels of the expression based on the levels of expression of transcription products of the corresponding genes in a plurality of healthy subjects;   obtaining the average of values representing deviations with respect to the gene belonging to each of the disease-determining gene families; and   determining, using the average, whether or not the subject has the target disease.   
     
     
         2 . The method according to  claim 1 , wherein the disease-determining gene families in the measuring step are identified by the following steps:
 (a) measuring the levels of expression of transcription products of genes in a biological sample obtained from each of a plurality of patients having the target disease and a plurality of healthy subjects;   (b) standardizing the levels of expression of the gene transcription products in each of the plurality of patients based on the levels of expression of transcription products of the corresponding genes in the plurality of healthy subjects to obtain values representing deviations for each of the plurality of patients;   standardizing the levels of expression of the gene transcription products in each of the plurality of healthy subjects to obtain values representing deviations for each of the plurality of healthy subjects;   (c) classifying the genes, whose expression levels are measured, into at least two gene families using a classification system based on the function of molecules encoded by the genes;   obtaining, as an average for each gene family, the average of values representing deviations for the gene belonging to each of the gene families with respect to each of the plurality of patients and the plurality of healthy subjects;   (d) obtaining a significance probability between the average for each gene family with respect to the plurality of patients and the average for each corresponding gene family with respect to the plurality of healthy subjects; and   (e) identifying the gene family as a disease-determining gene family related to the target disease, when the significance probability for the gene family is 0.05 or less.   
     
     
         3 . The method according to  claim 2 , wherein the classification system based on the function of molecules encoded by the genes is Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), MetaCyc, GenMAPP, BioCarta, KeyMolnet, or Online Mendelian Inheritance in Man (OMIM). 
     
     
         4 . The method according to  claims 1 , wherein the target disease is selected from Crohn's disease, Huntington's disease, and endometriosis. 
     
     
         5 . The method according to  claims 1 , wherein
 the target disease is Crohn's disease, and   the disease-determining gene families are at lease two selected from a G protein-related gene family, a blood coagulation-related gene family, an oxidative stress-related gene family, a phagocytosis-related gene family, and fat oxidation-related gene family.   
     
     
         6 . The method according to  claims 1 , wherein
 the target disease is Huntington's disease, and   the disease-determining gene families are at least two selected from a microtubule-related gene family, a mitochondria-related gene family, and a prostaglandin-related gene family.   
     
     
         7 . The method according to  claims 1 , wherein
 the target disease is endometriosis, and   the disease-determining gene families are at lease two selected from a cytokine synthesis process-related gene family, a cytokine-mediated signaling-related gene family, and an immunoglobulin-mediated immune response-related gene family.   
     
     
         8 . The method according to  claims 1 , wherein the step of measuring the levels of expression of gene transcription products comprises measuring the level of expression of at least one gene belonging to each of at least three disease-determining gene families. 
     
     
         9 . The method according to  claim 5 , wherein
 the G protein-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: GNG3, GNG7, GNA15, GNB5, GNAS, GNG5, GNG11, GNB1, and GNG4,   the blood coagulation-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: GP1BA, GP1BB, ITGB3, GP9, and F13A1,   the oxidative stress-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: GPX1, PTGS1, CLU, and PDLIM1,   the phagocytosis-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: FCER1G, CLEC7A, VAMP7, and FCGR1A, and   the fat oxidation-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: ACOX1, ADIPOR2, ADIPOR1, and ALOX12.   
     
     
         10 . The method according to  claim 6 , wherein
 the microtubule-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: DYNC1LI1, DYNLL1, DYNLT1, and DYNLT3,   the mitochondria-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: ATP5F1, ATP5J, ATP5L, ATP5C1, ATP5O, COX6A1, COX7A2, CYCS, MRPL18, MRPS35, NDUFA4, NDUFA9, NDUFB1, NDUFB3, NDUFB5, NDUFC1, NDUFS4, TIMM17A, TIMM8B, TOMM20, TOMM7, UQCRH, UQCR, and UQCRQ, and   the prostaglandin-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: PTGER2, PTGER4, and PTGES3.   
     
     
         11 . The method according to  claim 7 , wherein
 the cytokine synthesis process-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: CEBPE and CD28,   the cytokine-mediated signaling-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: EREG, STAT3, STAT5A, STAT5B, SOCS1, SOCS5, RELA, CEBPA, DUOX2, DUOX1, STAT4, ZNF675, IL2RB, IRAK3, KIT, LRP8, TNFRSF1A, PLP2, TNFRSF1B, TGM2, CCR1, CCR2, PF4, CX3CL1, IL1R1, CSF2RB, CLCF1, and NUP85, and   the immunoglobulin-mediated immune response-related gene family contains at least one gene selected from the group consisting of genes represented by the following gene symbols: IGHG3, IGHM, CD74, FCER1G, BCL10, PRKCD, CD27, MYD88, and TLR8.   
     
     
         12 . The method according to  claims 1 , wherein the biological sample is blood. 
     
     
         13 . The method according to  claims 1 , wherein the determination is made by inputting, to a determination formula, the average obtained from the subject suspected of having the target disease, wherein the determination formula is obtained based on: averages previously obtained in the same manner as in the measuring step and the obtaining step using biological samples collected from healthy subjects; and averages previously obtained in the same manner as in the measuring step and the obtaining step using biological samples collected from patients having the target disease. 
     
     
         14 . The method according to  claim 13 , wherein the determination formula is prepared using a discriminant analysis method. 
     
     
         15 . The method according to  claim 14 , wherein the discriminant analysis method is a support vector machine, a linear discriminant analysis, a neural network, a k-neighborhood discriminator, a decision tree, or a random forest. 
     
     
         16 . A computer program product, comprising:
 a computer readable medium; and   software instructions, on the computer readable medium, for enabling a computer to perform operations comprising:   receiving the levels of expression of transcription products of genes in a biological sample obtained from a subject suspected of having a target disease, wherein the genes comprise at least one gene belonging to each of at least two disease-determining gene families related to the target disease;   obtaining values representing deviations by standardizing the levels of the expression based on the levels of expression of transcription products of the corresponding genes in a plurality of healthy subjects;   obtaining the average of values representing deviations with respect to the gene belonging to each of the disease-determining gene families;   determining whether or not the subject has the target disease by using the average; and   outputting the result of the determination.   
     
     
         17 . The computer program product according to  claim 16 , wherein the operations further comprises:
 receiving the levels of expression of transcription products of genes in a biological sample obtained from each of a plurality of patients having the target disease and a plurality of healthy subjects;   standardizing the levels of expression of the gene transcription products in each of the plurality of patients based on the levels of expression of the transcription products of the corresponding genes in the plurality of healthy subjects to obtain values representing deviations for each of the plurality of patients;   standardizing the levels of expression of the gene transcription products in each of the plurality of healthy subjects to obtain values representing deviations for each of the plurality of healthy subjects;   classifying the genes, whose expression levels are measured, into at least two gene families according to a classification system based on the function of molecules encoded by the genes;   obtaining, as an average for each gene family, the average of values representing deviations for the gene belonging to each of the gene families with respect to each of the plurality of patients and the plurality of healthy subjects;   obtaining a significance probability between the average for each gene family with respect to the plurality of patients and the average for each corresponding gene family with respect to the plurality of healthy subjects; and   identifying the gene family as a disease-determining gene family related to the target disease, when the significance probability for the gene family is 0.05 or less.   
     
     
         18 . The computer program product according to  claim 16 , wherein the determination comprises a discriminant analysis method.