Patent ID: 7711492

Claim:
A method for determining the lymphoma type of a sample X comprising the steps of: a) isolating gene expression product from lymphoma sample X; b) creating one or more lymphoma type pairs, wherein each lymphoma type pair represents a combination of a first lymphoma type and a second lymphoma type; c) for each lymphoma type pair, obtaining gene expression data for a set of genes G in said first lymphoma type and said second lymphoma type; d) calculating a series of scale factors, wherein each scale factor represents a difference in gene expression between said first lymphoma type and said second lymphoma type for one of the genes belonging to said set of genes G; e) identifying a subset of genes g that are differentially expressed between said first lymphoma type and said second lymphoma type; f) generating a series of linear predictor scores for a set of known samples belonging to said first lymphoma type and a set of known samples belonging to said second lymphoma type based on the expression of said subset of genes g identified in step (e); g) contacting the gene expression product from sample X to a plurality of probes to thereby obtain gene expression data for said subset of genes g for sample X; h) generating a linear predictor score for sample X based on the expression of said subset of genes g; i) calculating a probability q that sample X belongs to said first lymphoma type by: q = ϕ ⁡ ( LPS ⁡ ( X ) ; μ ^ 1 , σ ^ 1 ) ϕ ⁡ ( LPS ⁡ ( X ) ; μ ^ 1 , σ ^ 1 ) + ϕ ⁡ ( LPS ⁡ ( X ) ; μ ^ 2 , σ ^ 2 ) wherein LPS(X) is the linear predictor score for sample X, φ(x; μ, σ) is the normal density function with mean μ and standard deviation σ, {circumflex over (μ)} 1 and {circumflex over (σ)} 1 are the mean and variance of the linear predictor scores for said set of known samples belonging to said first lymphoma type, and {circumflex over (μ)} 2 and {circumflex over (σ)} 2 are the mean and variance of the linear predictor scores for said known samples belonging to said second lymphoma type; j) determining whether probability q is a high probability, middle probability, or low probability value, wherein the high probability and the middle probability have an upper cut-off point between 0.5 and 0.99, and the middle probability and the low probability have a lower cut-off point between 0.01 and 0.5; and k) providing probability q to a user, wherein a high probability q indicates that sample X belongs to said first lymphoma type, a low probability q indicates that sample X belongs to said second lymphoma type, and a middle probability q indicates that sample X belongs to neither lymphoma type.