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According to the present invention, in order to enhance biomarker searching and discovering power, continuous variables used when defining nucleotide polymorphism are used to select and rank disease variation markers based on comparative analysis methods (allele square value difference, allele depth tangent difference, allele absolute value difference, geometric allele difference, statistical allele difference, and allele imbalance proportion), the weighted value with respect to the locus function, or the like, followed by reverse classification, thereby improving the sensitivity of discovering genome biomarkers corresponding various cancers, drug resistance of cancers, rare diseases, chronic diseases, and disease risks and phenotypes of normal persons, when compared with existing methods.(AA) Normal/disease genome comparison & ranking(BB) Raw information : Allelic Depth, Allelic imbalance, Signal intensity, and Quality Score(CC) Conventional method (normal/disease genome comparison)(DD) Novel method (normal/disease genome comparison)(EE, SS) Mutation definition(FF) Raw information-based genome comparison(GG) Method difference(HH) Mutation information-based genome comparison(II) SNP mutation comparison(JJ) CNV mutation comparison(K1, K2) Normal(L1, L2) Patient(M1, M2) Candidate marker(N1) Allelic Depth Diff D(N2) Geometry Diff G(N3) Chi-Square Dev C(N4) Imbalance Diff R(N5) Allele Quality score Q+(OO) Variant Diffscore SUM(PP, RR) Disease mutation marker candidate list(QQ) Sensitivity(TT, WW) SNP, SNA, INDEL, and CNV(UU) Conventional(VV) Novel(XX) Manual Inspection (all are correct answers)COPYRIGHT KIPO 2015