{"search_session":{},"preferences":{"l":"ar","queryLanguage":"ar"},"patentId":"EP_2299377_A1","frontPageModel":{"patentViewModel":{"ref":{"entityRefType":"PATENT","entityRefId":"163-463-241-896-162"},"entityMetadata":{"linkedIds":{"empty":true},"tags":[],"collections":[{"id":8907,"type":"PATENT","title":"Univ College London Patent Portfolio","description":"","access":"OPEN_ACCESS","displayAvatar":true,"attested":false,"itemCount":4836,"tags":[],"user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"notes":[{"id":8222,"type":"COLLECTION","user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"text":"
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b) generating a first linear predictor score for sample X based on the expression of genes in the subset of genes G1 in the sample and a second linear predictor score for sample X based on the expression of genes in the subset of genes G2 in the sample;
c) calculating a first probability q1 that sample X belongs to the first lymphoma type by: q 1 = ϕ LPS X 1 ; μ ^ 1 , σ ^ 1 ϕ LPS X 1 ; μ ^ 1 , σ ^ 1 + ϕ LPS X 1 ; μ ^ 2 , σ ^ 2 wherein (i) LPS(X)1 is the first linear predictor score for sample X, (ii) φ(x; µ, σ) is the normal density function with mean µ and standard deviation σ , (iii) µ̂1, and σ̂1 are the mean and variance of linear predictor scores based on expression of the subset of genes G1 in known samples of the first lymphoma type, and (iv) µ̂2 and σ̂2 are the mean and variance of linear predictor scores based on expression of the subset of genes G1 in known samples of the second lymphoma type; and
d) calculating a second probability q2 that sample X belongs to the first lymphoma type by: q 2 = ϕ LPS X 2 ; μ ^ 1 , σ ^ 1 ϕ LPS X 2 ; μ ^ 1 , σ ^ 1 + ϕ LPS X 2 ; μ ^ 2 , σ ^ 2 wherein (i) LPS(X)2 is the second linear predictor score for sample X, (ii) φ(x; µ, σ) is the normal density function with mean µ and standard deviation σ, (iii) µ̂1 and σ̂1 are the mean and variance of the linear predictor scores based on expression of the subset of genes G2 in known samples belonging to the first lymphoma type, and (iv) µ̂2 and σ̂2 are the mean and variance of the linear predictor scores based on expression of the subset of genes G2 in known samples belonging to the second lymphoma type;
e) providing probability q1 and q2 to a user, wherein sample X is classified as BL if q1 and q2 are both greater than 90%."],"number":1,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1, wherein the method further comprises
1) identifying the subset of genes corresponding to G1 and G2 by(i) creating the series of lymphoma type pairs, wherein each lymphoma type pair represents a combination of a first lymphoma type and a second lymphoma type, and wherein the first lymphoma type is BL;(ii) for each lymphoma type pair, obtaining gene expression data for the set of genes G in the first lymphoma type and the second lymphoma type;(iii) calculating the series of scale factors, wherein each scale factor represents a difference in gene expression between the first lymphoma type and the second lymphoma type for one of the genes belonging to the set of genes G; and(iv) dividing the set of genes G into two gene subsets G1 and G2, wherein G1 consists of c-myc and c-myc target genes and G2 consists of z genes from the set of genes G with the largest scale factors, and wherein G2 does not include any genes falling into G1; and
2) generating the first and second series of linear predictor scores for a set of known samples belonging to the first lymphoma type and a set of known samples belonging to the second lymphoma type, wherein the first series of linear predictor scores are based on expression of the subset of genes G1 and the second series of linear predictor scores are based on expression of the subset of genes G2."],"number":2,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 or 2, wherein z is 100."],"number":3,"annotation":false,"title":false,"claim":true},{"lines":["The method of any one of claims 1-3, wherein the scale factors are t-statistics."],"number":4,"annotation":false,"title":false,"claim":true},{"lines":["The method of any one of claims 1-4, wherein the linear predictor scores are calculated by: LPS S = ∑ j t j S j , wherein Sj is the expression of gene j in a sample S and tj is the scale factor representing the difference in expression of gene j between a first lymphoma type and a second lymphoma type."],"number":5,"annotation":false,"title":false,"claim":true},{"lines":["The method of any one of claims 1-5, wherein the second lymphoma subtype is activated B cell-like (ABC), germinal center B cell-like (GCB), or primary mediastinal B cell lymphoma (PMBL)."],"number":6,"annotation":false,"title":false,"claim":true},{"lines":["The method of any one of claims 1-5, wherein the wherein the second lymphoma subtype is DLBCL."],"number":7,"annotation":false,"title":false,"claim":true}]}},"filters":{"npl":[],"notNpl":[],"applicant":[],"notApplicant":[],"inventor":[],"notInventor":[],"owner":[],"notOwner":[],"tags":[],"dates":[],"types":[],"notTypes":[],"j":[],"notJ":[],"fj":[],"notFj":[],"classIpcr":[],"notClassIpcr":[],"classNat":[],"notClassNat":[],"classCpc":[],"notClassCpc":[],"so":[],"notSo":[],"sat":[]},"sequenceFilters":{"s":"SEQIDNO","d":"ASCENDING","p":0,"n":10,"sp":[],"si":[],"len":[],"t":[],"loc":[]}}