Prognostic gene expression signature for non small cell lung cancer patients
The invention relates to a method of typing non-small cell lung cancer by determining RNA levels for a set of genes. The typing can be used for determining a metastasizing potential of the cancer cells. The invention further relates to a set of probes and a set of primers for typing non-small cell cancer cells.
1. A method for typing a sample of a human individual suffering from stage I or stage II non-small cell lung cancer (NSCLC) as indicating a low risk or high risk of recurrence of NSCLC within three years from identification of said NSCLC in said individual, the method comprising
a) providing a lung tissue sample from said individual comprising non-small cell lung cancer cells or suspected to comprise non-small cell lung cancer cells;
b) preparing RNA from said tissue sample;
c) determining RNA levels for a set of genes in said RNA; and
d typing said sample as indicating a low risk or high risk of recurrence of NSCLC within three years from identification of said NSCLC in said individual on the basis of the levels of RNA determined for said set of genes, wherein said set of genes comprises at least two of the genes indicated by SEQ ID NOS. 1-216 and 218-237 in Table 3.
2. The method according to claim 1 , wherein typing said samples on the basis of the RNA levels determined for said set of genes comprises comparing the RNA levels of the genes indicated by SEQ ID NOS: 1-216 and 218-237 to the RNA levels of said genes in a reference sample.
3. The method according to claim 1 , whereby one of said genes indicated by SEQ ID NOS: 1-216 and 218-237 is induced in a low risk NSCLC sample, compared to the average level of expression of said gene in a reference sample, while a second gene from said genes indicated by SEQ ID NOS: 1-216 and 218-237 is repressed in a low risk NSCLC sample compared to the average level of expression of said gene in a reference sample.
4. The method according to claim 1 , whereby said set of genes comprises SEQ ID NOS: 1-72.
5. The method according to claim 1 , further comprising normalizing the determined RNA levels of said set of genes in said sample.
6. A method of classifying a sample from a human individual suffering from non-small cell lung cancer (NSCLC), comprising
classifying a sample as derived from a human individual having a low risk of recurrence of NSCLC within three years from indentification of said NSCLC in said individual, or as derived from an individual having a high risk of recurrence of NSCLC within three years from identification of said NSCLC in said individual by a method comprising
providing a lung tissue sample from said individual, wherein the sample comprises stage I or stage II NSCLC cells or is suspected to comprise stage I or stage II NSCLC cells;
determining a level of RNA for a set of genes comprising at least two of the genes indicated by SEQ ID NOS: 1-216 and 218-237 in Table 3 in said sample;
determining a similarity value for the level of RNA in said sample and a level of RNA for said set of genes in a patient having a low risk of recurrence of NSCLC within three years from identification of said NSCLC in said individual; and
classifying said individual as having a low risk of recurrence of NSCLC within three years from identification of said NSCLC in said individual if said similarity value exceeds a first similarity threshold value, and classifying said individual as having a high risk of recurrence of NSCLC within three years of identification of said NSCLC in said individual if said similarity value is below said first similarity threshold value.
7. The method according to claim 3 , wherein the one gene listed in Table 3 is C3orf41 indicated by SEQ ID NO: 1, while the second gene listed in Table 3 is C1orf24, indicated by SEQ ID NO: 2.