Classification of patients having diffuse large B-cell lymphoma based upon gene expression

• US 7,332,280 B2
• Filed: 03/03/2004
• Issued: 02/19/2008
• Est. Priority Date: 10/14/2003
• Status: Active Grant

• Current Assignee: Ash A. Alizadeh, David Botstein, Izidore S. Lossos, Mark A. Wechser, Robert J. Tibshirani, Ronald Levy
• Original Assignee: Ash A. Alizadeh, David Botstein, Izidore S. Lossos, Mark A. Wechser, Robert J. Tibshirani, Ronald Levy
• Inventors: Wechser, Mark A., Botstein, David, Levy, Ronald, Tibshirani, Robert J., Lossos, Izidore S., Alizadeh, Ash A.
• Primary Examiner(s): Foley; Shanon
• Assistant Examiner(s): Yao; Lei
• Application Number:
  US10/792,374
• Publication Number:
  US 20050079513A1
• Time in Patent Office: 1,448 Days
• Field of Search: 435/7.23, 435/6, 536/23.1
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 33/57426 leukemia

Abstract

Methods and kits for classifying patients having diffuse large B-cell lymphoma (DLBCL) based upon expression of a plurality of genes are disclosed. Real-time quantitative RT-PCR can be used to measure expression values. Correlating expression values of the plurality of genes in a tumor sample from the patient to reference expression values obtained from DLBCL patients can stratify patients in the classification groups. The methods and kits can be used to predict overall patient survival.

Claims

1. A method for classifying a patient having diffuse large B-cell lymphoma (DLBCL), the method comprising:

measuring expression of a plurality of genes in a tumor sample from the patient to produce measured expression values;

normalizing said measured expression values to produce normalized expression values;

correlating said normalized expression values to normalized reference expression values obtained for said plurality of genes from DLBCL patients grouped into survival groups; and

classifying the patient into one of said survival groups based upon weighed predictor Z in formula;

Z=(A×

LMO2)+(B×

BCL6)+(C×

FN1)+(D×

CCND2)+(E×

SCYA3)+(F×

BCL2)

wherein A is −

0.03, B is −

0.2, C is −

0.2, D is 0.03, E is 0.2, and F is 0.6 and wherein LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2 are log base 2 of normalized expression values for genes LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2, respectively.

2. The method according to claim 1 wherein a Z value of less than −

0.06 indicates high probability of survival, a Z value of from −

0.06 to 0.09 indicates medium probability of survival and a Z value of greater than 0.09 indicates low probability of survival.

3. The method according to claim 1, further comprising:

predicting survival of the patient wherein said plurality of genes are predictive of probability of survival and wherein said survival groups comprise groups of said DLBCL patients having known overall probability of survival.

4. The method according to claim 3 wherein said known overall probability of survival comprises overall probability of survival after anthracycline-based chemotherapy.

5. The method according to claim 1 wherein said normalized expression values comprise ratios of measured expression values obtained from said plurality of genes to expression values of a housekeeping gene.

6. The method according to claim 5 wherein the housekeeping gene is PGK1 or GAPDH.

7. The method according to claim 1 wherein said measuring expression of said plurality of genes in said tumor sample from the patient comprises performing real time RT-PCR on a portion of said tumor sample from the patient.

8. The method according to claim 1, further comprising:

determining whether said normalized expression values are similar to said normalized reference expression values obtained for said plurality of genes grouped into said survival groups selected from low, medium and high overall probability of survival after anthracycline-based chemotherapy.

9. The method according to claim 1 wherein said plurality of genes is selected from the group consisting of LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2.

10. The method according to claim 1 wherein said plurality of genes comprises LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2.

11. The method according to claim 1 wherein said measuring expression of a plurality of genes comprises:

hybridizing a plurality of primers to said plurality of genes, said plurality of primers being selected from a group consisting of SEQ. ID. NO. 11, SEQ. ID. NO. 12, SEQ. ID. NO. 20, SEQ. ID. NO. 21, SEQ. ID. NO. 26, SEQ. ID. NO. 27, SEQ. ID. NO. 50, SEQ. ID. NO. 51, SEQ. ID. NO. 62, SEQ. ID. NO. 63, SEQ. ID. NO. 104, and SEQ. ID. NO. 105.