Patent Publication Number: US-2012040863-A1

Title: Process for tumour characteristic and marker set identification, tumour classification and marker sets for cancer

Description:
FIELD OF THE INVENTION 
     The invention relates to the field of cancer biomarkers, and a process for their identification and use. 
     BACKGROUND TO THE INVENTION 
     The more one knows about a cancer, the more effectively it can be treated. For example, most cancer patients have surgery. However, additional benefits may be possible with additional treatment for some patients. There is not currently a satisfactory approach to determine which patients with cancer would benefit from extra therapy (such as chemotherapy) after surgery. The identification of genes and proteins specific to cancer cells that can be used for prognostic purposes would be helpful in this regard. These genes/proteins which identify tumours associated with a poor prognosis for recovery if treated only by surgery followed by typical standard of care are called poor prognostic biomarkers. These biomarkers can be used as valuable tools for predicting survival after a diagnosis of cancer, for identifying patients for whom the risk of recurrence is sufficiently low that the patient is likely to progress as well or better in the absence of post-surgery chemotherapy and/or radiation treatment or with only typical standard of care treatment post-surgery, and for guiding how oncologists should treat the cancer to obtain the best outcome. 
     Similarly, there are genes expressed in cancers which play a role in drug response. It would be useful to have information on predicted drug response when making clinical decisions. 
     To provide a screening tool with sufficient precision to be of clinical interest, it should preferably consider multiple markers for a type of cancer. A single gene marker does not provide a sufficient level of specificity and sensitivity. By way of example, microarray technology, which can measure more than 25,000 genes at the same time provides a useful tool to find multi-markers. 
     It is an object of the invention to provide sets of markers for use in identifying tumour characteristics of interest and a process for their identification and use. 
     SUMMARY OF THE INVENTION 
     The present invention in one embodiment teaches the usage of gene expression profiles to distinguish ‘good’ and ‘bad’ tumours based on groups of genes. As used herein when referring to predictors and patient survival, the term “good tumour” refers to a tumour which is likely to be cured by surgery and only typical standard of care, without chemotherapy or radiation treatment (even if this is part of the typical standard of care). As used herein, the term “bad tumour” refers to a tumour which is not likely to be cured by surgery and only typical standard of care including chemotherapy or radiation treatment. As used herein, a tumour is “cured” if the patient has not experienced a recurrence of the tumour (or a metastasis of it) within 5 or 10 years of surgery. 
     It is possible to identify sets of genes whose expression profiles are able to distinguish ‘good’ and ‘bad’ tumours. The prior art discloses five such gene expression signal sets and these have been developed as biomarkers for breast cancer samples. Each gene expression signal set was derived from a set of breast tumour samples. However, these five biomarker sets can&#39;t be cross-used. Specifically, the prior art so-called “breast cancer biomarkers” have not been found to be consistently predictive of prognosis when used in another set of breast tumour samples. Biomarkers for other types of cancers have the same problem. Cancer is highly heterogeneous. Frequently for a type of cancer several subtypes can be found. Previously disclosed marker sets are not universal enough for these subtypes. 
     To overcome these problems and the limitation of dataset (sample) availability, a new approach to finding and using sets of biomarkers was developed. 
     In one embodiment of the invention, random training datasets were generated from a published cancer dataset, in which gene expression profiles and clinical information of the patients had been included, to find robust sets of biomarkers&#39;. Gene expression profiles of the random training dataset were correlated with patient survival status and to screening biomarkers. 
     In one embodiment of the invention there is provided a method of identifying biomarkers, said method comprising:
         Generating a random training dataset from currently available datasets (tumour microarray profiling+clinical information of cancer patients)   Screening gene expression signal sets against the random training dataset to identify gene expression signal sets having predictive power for prognosis   Ranking genes based on the frequencies they appeared in the gene expression signal sets which have good predictive power (via screening, last step) and thereby building biomarker sets   Combinatory use of use 3-6 biomarker sets for prediction (i.e., Sample A is predicted by all three biomarker sets as “good tumour”, we will say Sample A is a “good tumour” (low-risk), If all say it is “bad”, we will say it is “bad” (high-risk), otherwise, we say it is intermediate-risk)   Validating the markers using other independent datasets       

     A “gene expression signal” is a tangible indicator of expression of a gene, such as mRNA or protein. 
     In an embodiment of the invention there is provided a process to identify tumour characteristics, said process comprising the following steps:
         1) obtaining three different marker sets each predictive of a characteristic of interest;   2) extracting gene expression signals from tumour cells;   3) correlating the extracted gene expression signals to the three different marker sets;   4) assigning a value to the extracted gene expression signals according to the following rankings:
           a. if the correlation of all three predictive gene expression signal sets predict it to have characteristics of concern, it is designated a bad tumour;   b. if the correlation of all three predictive gene expression signal sets predict it to lack characteristics of concern it is designated a good tumour;   c. if the correlation of all three predictive gene expression signal sets do not provide the same predicted clinical outcome, the tumour is designated as “intermediate.”   
               

     In some cases, the characteristic of concern relates to one or more of: metastisis, inflammation, cell cycle, immunological response genes, drug resistance genes, and multi-drug resistance genes. In some cases the tumour characteristic is responsible to a particular treatment or combination of treatments. 
     In some cases the tumour characteristic is a tendency to lead to poor patient survival post-surgery. 
     In some cases, the tumour characteristic is related to patient survival and step 4 of the process above comprises assigning a value to the extracted gene expression signals according to the following rankings:
         a. if the correlation of all three predictive gene expression signal sets predict it to be a bad tumour, it is designated a bad tumour and more aggressive treatment beyond the typical standard of care would be recommended;   b. if the correlation of all three predictive gene expression signal sets predict it to be a good tumour, no treatment beyond the standard of care would be recommended and no post-surgery chemotherapy or radiation treatment would be recommended;   c. if the correlation of all three predictive gene expression signal sets do not provide the same prognosis, the tumour is designated as “intermediate” and the full typical standard of care treatment, including chemotherapy and/or radiation treatment would be recommended.       

     In cases where the cancer has more than one subtype, it may be desirable to include the preliminary steps of:
         a) identifying the tumour subtype to be examined;   b) selecting marker sets specific to that subtype of tumour.       

     In some cases, the tumour characteristic of interest is the tendency of the tumour to respond to particular treatments, such as chemotherapeutic agents or radiation. In such a case, the gene expression signals are correlated with tumour drug response in the process of developing the training sets. It will be understood that a “good” tumour response to a particular drug would be below-average tumour survival following treatment and a “bad” response would be above-average tumour survival following treatment. Using this approach, and depending on the detail available in the original tumour and clinical data used in developing the training sets, it is possible to develop markers not only for response to individual drugs or treatments, but to combinations of treatments (where there is sufficient data in the original source to permit this). 
     In an embodiment of the invention there is provided a process for determining predictive gene expression signal sets of the type useful in the processes described above comprising the following steps:
         1) obtaining gene expression signal information and patient clinical information for a characteristic of interest for a known tumour population for a cancer of interest;   2) correlating the gene expression signals with clinical patient information regarding the characteristic of interest to identify which genes have predictive power for clinical outcome;   3) creating at least 30 random training datasets from step 1;   4) comparing identified gene expression signals of step 3 to a list of known genes active in cancer;   5) selecting identified gene expression signals which correspond to those on the list of known cancer genes;   6) grouping the selected identified gene expression signals according to their role in biological processes;   7) generating random gene expression signal sets of at least 25 genes from a selected gene expression signals group of step 6;   8) correlating the random gene expression signal sets to the random training datasets of step 3;   9) obtaining a P value for a survival screening from the correlation for each gene expression signal set of step 7;   10) if the P value for a gene expression signal set is less than 0.05 for more than 90% of the random training datasets, keeping the gene expression signal set;   11) ranking the random gene expression signal sets kept in step 10 based on frequency of gene appearances in the set;   12) selecting the top at least 26 genes as potential candidate markers;   13) repeating steps 7 to 12 and producing another, independent, rank set of at least 26 genes;   14) comparing the top genes from step 12 and step 13;   15) if more than 25 of the genes are the same, the top genes are kept as marker sets;   16) twice repeating steps 7 to 15 to obtain three different marker sets;       

     In one embodiment of the invention there is provided a process of identifying patients in need of more or less aggressive treatment than the typical standard of care, said process comprising:
         A “gene expression signal” is a tangible indicator of expression of a gene, such as mRNA (in theory, could one measure protein expression instead if it was technically feasible to do so? Anything else?).   1. An information source comprising tumour and clinical patient information is studied individually. All reported gene expression signals in cells are correlated with patient survival (5 and 10 yrs) in order to identify which genes have predictive power for prognosis within that individual information source. Those gene expression signals found to correlate significantly with patient survival are identified for further examination.   2. Gene expression signals identified in step 1 are compared to a list of known cancer genes and those gene expression signals corresponding to known genes known to have a role in cancer are selected for further analysis. (this will generally give rise to a list of a few hundred to a few thousand gene expression signals)   3. At least 30 (typically between 30 and 40) random training datasets are produced from the information source of step 1. The same individual gene expression signal may appear in multiple random training datasets.   4. Gene expression signals selected in step 2 are grouped according to their role in biological processes (e.g. cell cycle genes, cell death genes, immunological response genes, inflammation genes and so on Go analysis   5. Random gene expression signal sets (typically about a million) are generated, each containing approximately 30 genes randomly selected from a single group produced in step 3.   6. A P value for a survival screening of each random gene expression signal sets of step 4 against each random training datasets is obtained Can you please describe this correlation a bit more?   7. If the P value is less than 0.05 for more than 90% of the random datasets, the random gene set is kept   8. The kept random gene expression signal sets from step 7 are ranked based on the frequencies of the genes appearing in them   9. The top 30 genes (ranked in Step 8) having the highest predictive value as determined in step 8 are selected as potential candidates.   10. Steps 5-9 are repeated, starting from the generation of random gene expression signal sets from each group formed in step 3, and producing another, independent, ranked set of the top 30 genes which are potential candidates.   11 The top 30 genes produced in step 10 are compared to the top 30 genes from step 9. If 25 or more of the 30 are the same, it is called a “stable signature” and is useful in screening patient samples. If fewer than 25/30 are the same, the data is discarded (from both sets of potential candidates). (At least 25 are needed, thus either the first or the second set of potential candidates may be used.   12. Steps 5-11 are repeated twice more for two other groups (of step 3) of gene expression signals. Thus, there will be three sets of stable signatures, each relating to a different group from step 3.   13. Cancer cells from the patient are examined to assess their gene expression activity and its correlation to the gene expression signals in the three stable signatures. Typically, a stable signature will be an indication of likelihood of metastasis and therefore high patient expression matching that signature will indicate a “bad” tumour. However it is possible that a stable signature might indicate protective genes being expressed, such as apoptosis genes, in which case, for that signature, high patient expression of those gene expression signatures would indicate a “good” tumour. In either case, each stable signature is compared to the patient sample and a prediction of “good” or “bad” tumour is made by each stable signature individually. What is the threshold for an indication of “bad” or “good” from a single stable signature? Eg. Is it “bad” if over 50% of the genes found in the signature are expressed in the sample? Is it “bad” if over 50% of the genes found in the signature are expressed above normal basal levels in the corresponding non-cancerous tissue?   14. Combining of the predictions of each of the three sets of gene expression signals as regards the patient sample and assigning a value to the tumour as follows: (a) if all three gene expression signal sets (signatures) predict it to be a bad tumour, it is designated a bad tumour and the patient should be provided more aggressive treatment beyond the typical standard of care; (b) if all three data sets predict it to be a good tumour the patient should receive no treatment beyond the standard of care and should not be subjected to post-surgery chemotherapy or radiation treatment; (c) if all three sets of gene expression products do not provide the same prognosis, the tumour is designated as “intermediate” and the patient should receive the full typical standard of care treatment, including chemotherapy and/or radiation treatment.       

     In some cases, for this process it will be desirable to group the selected identified gene expression signals according to their role in biological process using Gene Ontology analysis. 
     Preferably between 30 and 50 random training sets are created. More preferably, between 30 and 40 training sets are created. 
     It will sometimes be desirable to select the genes know to be active in cancer from the groups of genes responsible for metastasis, cell proliferation, tumour vascularisation, and drug response. 
     In some embodiments of the invention involving the process described above, in step 7, between about 750,000 and 1,250,000, or between about 900,000 and 1,100,000 or about a million random gene expression signal sets are generated. In some embodiments of the invention as described in the process above, in step 7, the random gene expression signal sets generated contain between about 25 and 50, or 28-32 or about 30 genes. 
     In an embodiment of the invention as described in the process above, in step 12 the top 26-50, or 28-32 or about 30 genes are selected. 
     In some cases when considering tumour characteristics relating to patient survival, it will be desirable to employ at least one cancer biomarker set selected from the list consisting essentially of NRC-1, NRC-2, NRC-3, NRC-4, NRC-5, NRC-6, NRC-7, NRC-8, and NRC-9. 
     In an embodiment of the invention there is provided a kit comprising at least three marker sets and instructions to carry out the process described above in order to identify a tumour characteristic of interest. In some cases, the kit will comprise at least 10 gene expression signals listed in Table 1A or 1 B. In some cases, the kit will comprise at least 30 nucleic acid biomarkers identified according to the process described above. 
     In an embodiment of the invention there is provided the use of any of the gene expression signals in Table 1A or 1B in identifying one or more tumour characteristics of interest. In some cases, at least different three markers sets are used in some cases at least 1, 2, or 3 of the marker sets including at least 1, 5, 10, 20, or 25 of the gene expression signals found in Table 1A or 1 B. In some cases each marker set contains at least 1, 5, 10, 20 or 25 of the gene expression signals found in Table 1A or 1 B. 
     In an embodiment of the invention, the cancer biomarkers are breast cancer biomarkers and the first subtype of sample is an ER+ sample. 
     In an embodiment of the invention, in the process described above, the random training sets are generated by randomly picking samples while maintaining the same ratio of “good” and “bad” tumours as that in the set from which they are chosen. 
     In some cases, the tumour characteristic(s) of interest will relate to patient survival (for example, following surgery and typical standard of care) and in such cases, the method may be used to identify patients in need of more or less aggressive treatment than the typical standard of care. (Chemotherapy and radiation treatment are, in themselves, hazardous. Thus, it is best to avoid providing such treatment to patients who do not need them.) 
     In some cases, it will be desirable to study tumour tissue for a patient by extracting gene expression signals (e.g. mRNA, protein) and assaying the presence (and in some cases level) of gene expression signals of interest using a reporter specific for the gene expression signal of interest. This may be done in a micro-array format permitting examination of multiple gene expression signals essentially simultaneously. A reporter may be a probe which binds to a nucleic acid sequence of interest, an antibody specific to a protein of interest, or any other such material (many such reporters are known in the art and used routinely). The reporter effects a change in the sample permitting assessment of the gene expression signal of interest. In some cases the change effected may be a change in an optical aspect of the sample, in other cases the change may be a change in another assayable aspect of the sample such as its radioactive or fluorescent properties. 
     In situations where a particular type of cancer has more than one subtype (eg. ER+ and ER− breast cancers), it will be preferable to classify the patient&#39;s cancer by subtype initially, and then use markers developed in relation to that subtype. 
     In some cases, the tumour characteristic(s) of interest will relate to tumour response to particular treatment(s) and in such cases, the method may be used to identify promising treatment approaches (one or more chemotherapeutics or combinations of treatments) for the patient having the tumour. 
     As used herein “tumour” includes any cancer cell which it is desirable to destroy or neutralize in a patient. For example, it may include cancer cells found in solid tumours, myelomas, lymphomas and leukemias. 
     Tumours will generally be mammalian or bird tumours and may be tumours of: human, ape, cat, dog, pig, cattle, sheep, goat, rabbit, mouse, rat, guinea pig, hamster, gerbil, chicken, duck, or goose. 
     It will be apparent that the combinatorial use of three independent sets of gene expression signals is not limited to gene expression signals produced according to the approach described herein, but may also be applied to cancer biomarker datasets sold commercially or reported in the literature. (Although the reliability of the final screening result will depend to some extend on the robustness of the sets used and therefore it is recommended to use cancer biomarker datasets which are robust). In some instances it will be desirable to select cancer biomarker datasets comprising genes involved in different biological processes (E.g. one dataset might relate to inflammation, another to cell cycle and the third to metastasis.) 
     The process is general and may be applied to any type of cancer. For example it is useful in relation to those cancer types listed in Table 4. 
     In an embodiment of the invention, the process is applied to determine how aggressively a breast cancer patient should be treated post-surgery. 
     One embodiment of the process is provided below, in parallel with a description of Example 1:
         Step 1: developing an automatic survival screening method using cancer cell gene microarray data and survival information of the tumour patients. (By way of non-limiting example, surface and secreted proteins were identified from the microarray data of JM01 cell line (mouse breast cancer cell line, in-house cell line and data), to screen a public breast cancer dataset (295 samples, Chang et al., PNAS 102:3738, 2005). The term “survival screening” is defined as examination of the statistical significance of the correlation between each single gene expression value and patient survival status (“good” or “bad”) by performed Kaplan-Meier analysis by implementing the Cox-Mantel log-rank test (Cui et al., Molecular Systems Biology, 3:152, 2007). From this screening, seven proteins were obtained, which can individually distinguish ‘good’ and ‘bad’ tumours. By way of example, in a portion of Example 1, the protein (MMP9) was selected to be validated experimentally in the original cell line. When applying MMP9 antibody to the cell line, the epithelial to mesenchymal transition in cancer progression was blocked. This result indicates that the method is suitable to find metastasis related genes.   Step 2 conducting a genome-wide survival screening of genes whose expression values are correlated with breast cancer patient survivals was conducted. (In Example 1, two training datasets, defined as Dataset 1 (78 samples, van&#39;t Veer et al., Nature, 2002), and Dataset 2 (286 samples, Wang et al., Lancet, 365:671, 2005), were used.) The resulting gene expression signal lists are called S1, and S2, respectively. The total genes of these two lists are called St gene expression signal list (St=S1+S2).   Step 3: Where the cancer of interest has more than one sub-type, markers for a first sub-type are generated. (For example, in Example 1, ER+ and ER− markers were generated.) In Example 1, ER+ tumour markers were generated by extracting all the ER+ samples from above datasets and defined as S1-ER+ (extracted from Dataset 1) and S2-ER+ sets (extracted from Dataset 2), respectively. 35 random-training-sets are generated by randomly picking up N samples (N=60) from S2-ER+ sets. The ratio of “good” and “bad” tumours is preserved essentially the same as that in S2-ER+ sets. 36 training-sets are obtained by adding S1-ER+ to the 35 random-training-sets mentioned above.   Step 4: obtaining a gene expression signal list (in Example 1, St-ER+ gene expression signal list) by genome-wide survival screening, which involves repeating Step 2 but using subsets for the first tumour subtype, eg. datasets, S1-ER+ and S2-ER+ sets in Example 1. Using the St-ER+ gene expression signal list, Gene Ontology (GO) analysis (using GO annotation software, David, http://david.abcc.ncifcrf.gov/) is performed, only the genes which belong to GO terms that are known to be associated with cancer, such as cell cycle, cell death and so on are used for further marker screening.   Step 5: 1 million distinct random-gene-sets (each random-gene-set contains 30 genes) are generated from each selected GO term annotated genes (normally around 60-80 genes per GO term by randomly picking up 30 genes from one GO term annotated genes.   Steps 6 and 7: Further survival screening is conducted, preferably using 1 million random-gene-sets against all the first tumour subtype training sets (eg. In Example 1, 36 ER+ training sets) (generated in Step 3). For each training set, the statistical significance of the correlation between the expression values of each random-gene-set (30 genes) and patient survival status (“good” or “bad”) is examined, for example by performed Kaplan-Meier analysis by implementing the Cox-Mantel log-rank test. If the P value is less than 0.05 for a survival screening using one random-gene-set against one training set, it is said that that random-gene-set passed that training set.   Step 7: When all the first subtype (eg. 36 ER+) training sets have more than 2,000 random-gene-sets passed, or a P value of more than 0.05 has been obtained for more than 90% of the randon training datasets, these passed random-gene-sets are kept.   Step 8: The genes in the kept random-gene-sets of claim  7  are ranked based on the frequencies appearance in the passed random-gene-sets.   Step 9: The top 30 genes (defined as potential marker set) are chosen as a potential-marker-set. It should be noted that, while 30 genes are preferred, between 20 and 40 may be used, more preferably between 25 and 35 or more preferably 27-33. In some instances, 25-30 individual gene expression signals are desired in each set used for screening purposes, thus various input numbers may be used to produce this output.   Step 10: Step 5 is repeated using the same GO term used initially in Step 5 and another 1 million distinct random-gene-sets are generated, which are used to repeat Steps 6 and 7.   Step 11: If the gene members for the top 30 are substantially the same as those in the potential-marker-set (step 9), it means the potential-marker-set is stable and can be used as a real cancer biomarker set. This potential-marker-set is designated as a marker set (this one can be used for patients now), If the gene expression signals for the two potential marker sets are not substantially the same it is an indication that these GO term genes are unsuitable for finding a biomarker set and the potential marker sets are dropped from further analysis. In some cases it will be desirable to have at least 25 of the 30 gene expression signals the same in the two potential marker sets before designating it as a marker set. In some cases it will be desirable to have 26, 27, 28, 29, or 30 of the gene expression signals the same in the two potential marker sets.   Step 12: Steps 5-11 are repeated twice more for two other groups (of step 3) of gene expression signals. Thus, there will be three sets of stable signatures, each relating to a different group from step 3.   In example 1, 3 sets of markers (called NRC-1, -2 and -3, respectively, each set contains 30 genes, see Table 1) were obtained and tested in ER+training sets (S1-ER+ and S2-ER+). The testing process is illustrated. The samples in each training set can be divided into three groups: low-risk, intermediate-risk and high-risk groups.
           Optional step 12 b: as an optional step, which was carried out in Example 1, it can be useful to further analyze biomarker sets to further stratify the high-risk group. This step involves taking the samples from high-risk group (which in Example 1 was stratified by NRC-1, -2 and -3, of the training set, S2-ER+) and repeating Steps 3, 4, 5, 6, 7, and 8.   
           In Example 1, another 3 sets of markers (called NRC-4, -5 and -6, respectively were obtained. Each set contained 30 genes (see Table 1). These sets were targeted for the high-risk group which was stratified by NRC-1, -2 and -3.
           Step 12 c: as an optional step, conducted in Experiment 1, to get biomarkers for a second sub-type of tumours (in example 1,ER− tumours) all second subtype samples in datasets 1 and 2 are extracted (eg. the ER− samples from Datasets 1 and 2, respectively, and defined as S1-ER− (extracted from Dataset 1) and S2-ER− (extracted from Dataset 2) sets, respectively). 35 random-training-sets are generated by randomly picking up N samples (N=40) from dataset 2, subtype two sets (eg. S2-ER− sets). The ratio of “good” and “bad” tumours is maintained as that in the overall dataset 2, subtype 2 sets (S2-ER− sets). Training-sets are obtained (36 in Example 1) by adding dataset 1, type 2 (eg. S1-ER−) to the 35 random-training-sets mentioned above. Step 4 is repeated using dataset 1, subtype 2 (eg.S1-ER−) and dataset 2, subtype 2 (eg. S2-ER−) sets to obtain a combined dataset, subtype 2 (eg. St-ER−) gene expression signal list, and then GO analysis is performed. Steps 5, 6, 7, and 8 are then repeated.   
               

     In Example 1, another 3 sets of markers (called NRC-7, -8 and -9, respectively. Each set contains 30 genes, see Table 1) were obtained. These sets were used for ER− samples. 
     Testing Process 
     General Overview 
    
    
     EXAMPLE 1 
     In example 1, for each marker set, nearest shrunken centroid classification and leave-one-out methods were employed. We then combinatory used 3 marker sets together for predicting the recurrence of each sample. 
     For a given dataset, which contains n samples, the test process used in Example 1 was the following (step by step):
         Step 13: For a targeted testing sample, we extracted the gene expression profile of the marker set. For each gene expression value, we multiply its marker-factor and get the modified gene expression profile of the testing sample. We computed the standardized centroids for both “good” and “bad” classes from the n−1 samples for the marker set using PAM method (Tibshirani et al., PNAS, 99:6567, 2002). Multiply the marker-factor of each gene to the class centroids and get the modified class centroids of the marker set.       

     For predicting the recurrence of the targeted testing sample using the marker set: we compare the modified gene expression profile of the sample to each of these modified class centroids. The class whose centroid that it is closest to, in squared distance, is the predicted class for that sample. If the sample is predicted as “good” tumour, it is denoted as 0, otherwise, it is denoted as 1.
         Step 14: For ER+ samples, if a sample has predicted as 0 for all 3 marker sets, we assign it in low-risk group; If a sample has predicted as 1 for all 3 marker sets, we assign it in a high-risk group; If a sample is not assigned in low-risk group neither high-risk group, we assign it in intermediate-risk group. For ER− samples, a sample has predicted as 0 for all 3 marker sets, we assign it into low-risk group, otherwise, we assign it into high-risk group. This is a modification of the usual practice of assigning ambiguous samples to an intermediate group. In the case of highly aggressive cancer subtypes, it may be desirable to classify all cancers which are not clearly low-risk as high risk and treat them aggressively, beyond the ordinary standard of care.       

     Validation of the Marker Sets in Three Testing Datasets 
     To test the robustness and predicting accuracy of the marker sets, we tested the marker sets in three independent breast cancer datasets from these publications (Koe et al., Cancer Cell, 2006; Chang et al., PNAS 102:3738, 2005 and Sotiriou C, et al., J. Natl Cancer Inst, 98:262, 2006), In total, 644 samples were tested. 
     For ER+ samples, in each dataset, we first used NRC-1, -2 and -3 marker sets (from the three breast cancer datasets mentioned above) to stratify the samples into low (LG), intermediate (MG) and high (HG)-risk groups. If the high-risk group had less than 10 samples, we merged MG and HG groups and called it intermediate-risk group. Otherwise, we used NRC-4, -5 and -6 marker sets to stratify the HG group into three new groups: low (NLG), intermediate (NMG) and high (NHG)-risk groups. We merged NLG and MG and called it intermediate-risk group, and merged NMG and NHG and called it a high-risk group. The LG is low-risk group. We obtained very good results with high predictability accuracy (−90% for non-recurrence patients) for the low-risk group and classified three groups nicely in all the 3 testing datasets (See table 2). 
     For ER− samples, in each dataset, we used NRC-7, -8 and -9 marker sets to stratify the samples into low (LG-) and high (HG-)-risk groups. We also obtained very good results with high predicting accuracy (˜92-100% for non-recurrence patients) for the low-risk group and classified two groups nicely in all the 3 testing datasets (See table 2). 
     Combinatory Usage of the Marker Sets Improve Predicting Accuracy 
     For ER+ samples, when NRC-1, NRC-2 and NRC-3 are all in agreement to predict the sample as “good” tumour, the accuracy was significantly improved than using a single marker set, such as NRC-1, NRC-2 or NRC-3 (Table 3). The same results were obtained when NRC-7, NRC-8 and NRC-9 are all in agreement to predict the sample as “good” tumour for ER− samples (Table 3). In general, it is found that the integrative usage of 3 marker sets improves predictive accuracy over using a single set. In one embodiment of the invention accuracy was improved from about 70% to about 90%. In one embodiment of the invention, accuracy is at least 90%. In another embodiment it is at lease 95%. 
     Thus, there is provided herein robust sets of biomarkers and uses thereof. 
     It will be understood that, depending on the type of cancer, and the condition of the patient, different gene profiles may be considered “bad”. Metastasis is generally considered to be a significant factor in the decision about how to treat a patient with cancer and sets of biomarker sets, such as those disclosed herein, are useful for that purpose. In addition, biomarker sets can be used to identify cancer cell types which are likely to respond well (or poorly) to one or more particular drugs. Regardless of the exact factors being considered as “good” or “bad”, it will usually be desirable to begin the process with training sets S1 and S2 containing both “good” and “bad” genes. Level of gene expression may be considered when identifying good drug targets since highly-expressed targets frequently make good drug targets. 
     In general, the low-risk group (having “good prognostic signature”) will not go to treatment, but high-risk group (having “poor prognostic signature”) should receive treatment in addition to surgery. Generally, the intermediate-risk group will do so as well; however, this will depend on the typical standard of care for that type of tumour. 
     While each of the biomarker sets disclosed herein is, individually, useful in predicting the need for additional treatment, overall prediction accuracy can be markedly improved by the use of multiple biomarker sets. 
     For example, if a patient sample is screened against NRC — 1, NRC — 2 and NRC — 3 and all three sets indicate “good” prognosis, the patient is considered to be low risk. If all indicate “bad” prognosis, the sample is considered to be high risk. If one or two sets say “bad” and the other(s) says “good”, the cancer is considered to be intermediate risk. 
     In an embodiment of the invention, in order to determine if a patient sample is “good” or “bad” in relation to any one biomarker set (e.g. NRC — 1), the biomarker set is used to independently screen two banks of cancer cells representing samples from a large number of patients. The first bank represents “good” cancer cells (with a known clinical history of not exhibiting the behaviour or characteristic of concern, such as metastasis) and the second bank represents “bad” cancer cells (with a known clinical history of exhibiting the behaviour or characteristic of concern). Each of the “good” and “bad” banks will produce a gene expression signature (standard “good” and “bad” gene expression signatures for “good” and “bad” tumours), respectively, for each biomarker set. For a patient sample, the gene expression signature of a biomarker set of the patient sample is compared to the standard “good” and “bad” gene expression signatures of that biomarker set. Those patient samples which most closely resemble the standard “bad” signature of that biomarker set are considered “bad” and those which most closely resemble the standard “good” signature of that biomarker set are considered “good.” 
     The method may in some cases involve the combinatory using of one or more of the following cancer biomarker sets: NRC-1, NRC-2, NRC-3, NRC-4, NRC-5, NRC-6, NRC-7, NRC-8, NRC-9. 
     Example of one possible approach to using the process when a subtype has been identified (for this example ER+/ER−)−:
         ER status is determined for the tumour sample of cancer cells. (this is often done in clinical setting)   For ER+ samples, if a sample has predicted as “good” for all 3 marker sets (NRC-1, -2, and -3), it is assigned into low-risk group; If a sample has predicted as “bad” for all 3 marker sets, it is assigned into a high-risk group; If a sample is not assigned into low-risk group neither high-risk group, it is assigned into intermediate-risk group.   For the ER+ high-risk group, which is defined by the marker sets (NRC-1, -2, and -3), is predicted again using the marker sets (NRC-4, -5, and -6). If a sample has predicted as “bad” for all 3 marker sets, it is assigned into a high-risk group. Otherwise, it is assigned into the intermediate-risk group, which is defined by NRC-1, -2, and -3.   For ER− samples, a sample has predicted as “good” for all 3 marker sets (NRC-7, -8, and -9), it is assigned into low-risk group, otherwise, it is assigned into high-risk group.       

     In an embodiment of the invention there is provided a method of assessing the likelihood of a patient benefiting form additional cancer treatment in addition to surgery, said method comprising:
         printing gene probes of the marker sets onto a microarray gene chip   extracting message RNAs from the tumour sample.   hybridizing the message RNA onto the microarray gene chip.   scanning the hybridized microarray chip to get all the readouts of marker genes for the sample.   normalizing the readouts   constructing the gene expression profiles of each marker set for the sample   correlating the gene expression profiles of each marker set to those of the standard (known as “good” and “bad”) tumour samples to make predictions.       

     Detailed information for making microarray gene chip, scanning and normalization of array data can be found at Agilent company website: 
     http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/default.aspx. and in the publicly available literature. 
     
       
         
           
               
             
               
                 TABLE 1A 
               
             
            
               
                   
               
               
                 Lists of NRC biomarker gene signatures for ER+ and ER− breast cancer patients: 
               
            
           
           
               
               
               
            
               
                 EntrezGene ID 
                 Gene Name 
                 Description 
               
               
                   
               
            
           
           
               
            
               
                 NRC_1 (immune) 
               
            
           
           
               
               
               
            
               
                 730 
                 C7 
                 Complement component 7 
               
               
                 6401 
                 SELE 
                 Selectin E (endothelial adhesion molecule 1) 
               
               
                 939 
                 CD27 
                 CD27 molecule 
               
               
                 2152 
                 F3 
                 Coagulation factor III (thromboplastin, tissue factor) 
               
               
                 51561 
                 IL23A 
                 Interleukin 23, alpha subunit p19 
               
               
                 9607 
                 CARTPT 
                 CART prepropeptide 
               
               
                 6696 
                 SPP1 
                 Secreted phosphoprotein 1 (osteopontin, bone sialoprot   
               
               
                   
                   
                 I, early T-lymphocyte activation 1) 
               
               
                 7138 
                 TNNT1 
                 Troponin T type 1 (skeletal, slow) 
               
               
                 784 
                 CACNB3 
                 Calcium channel, voltage-dependent, beta 3 subunit 
               
               
                 729 
                 C6 
                 Complement component 6 
               
               
                 2165 
                 F13B 
                 Coagulation factor XIII, B polypeptide 
               
               
                 6403 
                 SELP 
                 Selectin P (granule membrane protein 140 kDa, antigen 
               
               
                   
                   
                 CD62) 
               
               
                 5452 
                 POU2F2 
                 POU class 2 homeobox 2 
               
               
                 6774 
                 STAT3 
                 Signal transducer and activator of transcription 3 (acute- 
               
               
                   
                   
                 phase response factor) 
               
               
                 5265 
                 SERPINA1 
                 Serpin peptidase inhibitor, clade A (alpha-1 antiproteina   
               
               
                   
                   
                 antitrypsin), member 1 
               
               
                 8074 
                 FGF23 
                 Fibroblast growth factor 23 
               
               
                 4607 
                 MYBPC3 
                 Myosin binding protein C, cardiac 
               
               
                 7940 
                 LST1 
                 Leukocyte specific transcript 1 
               
               
                 3952 
                 LEP 
                 Leptin (obesity homolog, mouse) 
               
               
                 6776 
                 STAT5A 
                 Signal transducer and activator of transcription 5A 
               
               
                 259 
                 AMBP 
                 Alpha-1-microglobulin/bikunin precursor 
               
               
                 7125 
                 TNNC2 
                 Troponin C type 2 (fast) 
               
               
                 6331 
                 SCN5A 
                 Sodium channel, voltage-gated, type V, alpha subunit 
               
               
                 857 
                 CAV1 
                 Caveolin 1, caveolae protein, 22 kDa 
               
               
                 5936 
                 RBM4 
                 RNA binding motif protein 4 
               
               
                 641 
                 BLM 
                 Bloom syndrome 
               
               
                 2534 
                 FYN 
                 FYN oncogene related to SRC, FGR, YES 
               
               
                 604 
                 BCL6 
                 B-cell CLL/lymphoma 6 (zinc finger protein 51) 
               
               
                 10874 
                 NMU 
                 Neuromedin U 
               
               
                 3240 
                 HP 
                 Haptoglobin 
               
            
           
           
               
            
               
                 NRC_2 (cell cycle) 
               
            
           
           
               
               
               
            
               
                 5933 
                 RBL1 
                 Retinoblastoma-like 1 (p107) 
               
               
                 6790 
                 AURKA 
                 Aurora kinase A 
               
               
                 898 
                 CCNE1 
                 Cyclin E1 
               
               
                 332 
                 BIRC5 
                 Baculoviral IAP repeat-containing 5 (survivin) 
               
               
                 4830 
                 NME1 
                 Non-metastatic cells 1, protein (NM23A) expressed in 
               
               
                 259266 
                 ASPM 
                 Asp (abnormal spindle) homolog, microcephaly associat 
               
               
                   
                   
                 ( Drosophila ) 
               
               
                 3070 
                 HELLS 
                 Helicase, lymphoid-specific 
               
               
                 10628 
                 TXNIP 
                 Thioredoxin interacting protein 
               
               
                 3981 
                 LIG4 
                 Ligase IV, DNA, ATP-dependent 
               
               
                 10051 
                 SMC4 
                 Structural maintenance of chromosomes 4 
               
               
                 4175 
                 MCM6 
                 Minichromosome maintenance complex component 6 
               
               
                 1063 
                 CENPF 
                 Centromere protein F, 350/400ka (mitosin) 
               
               
                 11186 
                 RASSF1 
                 Ras association (RalGDS/AF-6) domain family 1 
               
               
                 51053 
                 GMNN 
                 Geminin, DNA replication inhibitor 
               
               
                 9787 
                 DLG7 
                 Discs, large homolog 7 ( Drosophila ) 
               
               
                 11145 
                 HRASLS3 
                 HRAS-like suppressor 3 
               
               
                 274 
                 BIN1 
                 Bridging integrator 1 
               
               
                 4013 
                 LOH11CR2A 
                 Loss of heterozygosity, 11, chromosomal region 2, gene 
               
               
                 5501 
                 PPP1CC 
                 Protein phosphatase 1, catalytic subunit, gamma isoforn 
               
               
                 8099 
                 CDK2AP1 
                 CDK2-associated protein 1 
               
               
                 10615 
                 SPAG5 
                 Sperm associated antigen 5 
               
               
                 4750 
                 NEK1 
                 NIMA (never in mitosis gene a)-related kinase 1 
               
               
                 22924 
                 MAPRE3 
                 Microtubule-associated protein, RP/EB family, member; 
               
               
                 1163 
                 CKS1B 
                 CDC28 protein kinase regulatory subunit 1B 
               
               
                 5598 
                 MAPK7 
                 Mitogen-activated protein kinase 7 
               
               
                 26060 
                 APPL1 
                 Adaptor protein, phosphotyrosine interaction, PH domai   
               
               
                   
                   
                 and leucine zipper containing 1 
               
               
                 11011 
                 TLK2 
                 Tousled-like kinase 2 
               
               
                 22933 
                 SIRT2 
                 Sirtuin (silent mating type information regulation 2 
               
               
                   
                   
                 homolog) 2 ( S. cerevisiae ) 
               
               
                 22919 
                 MAPRE1 
                 Microtubule-associated protein, RP/EB family, member 
               
               
                 5884 
                 RAD17 
                 RAD17 homolog ( S. pombe ) 
               
            
           
           
               
            
               
                 NRC_3 (apoptosis) 
               
            
           
           
               
               
               
            
               
                 4982 
                 TNFRSF11B 
                 Tumour necrosis factor receptor superfamily, member 1 
               
               
                   
                   
                 (osteoprotegerin) 
               
               
                 7704 
                 ZBTB16 
                 Zinc finger and BTB domain containing 16 
               
               
                 333 
                 APLP1 
                 Amyloid beta (A4) precursor-like protein 1 
               
               
                 27250 
                 PDCD4 
                 Programmed cell death 4 (neoplastic transformation 
               
               
                   
                   
                 inhibitor) 
               
               
                 9459 
                 ARHGEF6 
                 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 
               
               
                 8835 
                 SOCS2 
                 Suppressor of cytokine signaling 2 
               
               
                 332 
                 BIRC5 
                 Baculoviral IAP repeat-containing 5 (survivin) 
               
               
                 983 
                 CDC2 
                 Cell division cycle 2, G1 to S and G2 to M 
               
               
                 9700 
                 ESPL1 
                 Extra spindle pole bodies homolog 1 ( S. cerevisiae ) 
               
               
                 7262 
                 PHLDA2 
                 Pleckstrin homology-like domain, family A, member 2 
               
               
                 26586 
                 CKAP2 
                 Cytoskeleton associated protein 2 
               
               
                 9135 
                 RABEP1 
                 Rabaptin, RAB GTPase binding effector protein 1 
               
               
                 4893 
                 NRAS 
                 Neuroblastoma RAS viral (v-ras) oncogene homolog 
               
               
                 4830 
                 NME1 
                 Non-metastatic cells 1, protein (NM23A) expressed in 
               
               
                 1191 
                 CLU 
                 Clusterin 
               
               
                 6776 
                 STAT5A 
                 Signal transducer and activator of transcription 5A 
               
               
                 596 
                 BCL2 
                 B-cell CLL/lymphoma 2 
               
               
                 54205 
                 CYCS 
                 Cytochrome c, somatic 
               
               
                 3605 
                 IL17A 
                 Interleukin 17A 
               
               
                 4255 
                 MGMT 
                 O-6-methylguanine-DNA methyltransferase 
               
               
                 10553 
                 HTATIP2 
                 HIV-1 Tat interactive protein 2, 30 kDa 
               
               
                 55367 
                 LRDD 
                 Leucine-rich repeats and death domain containing 
               
               
                 1434 
                 CSE1L 
                 CSE1 chromosome segregation 1-like (yeast) 
               
               
                 3981 
                 LIG4 
                 Ligase IV, DNA, ATP-dependent 
               
               
                 8717 
                 TRADD 
                 TNFRSF1A-associated via death domain 
               
               
                 694 
                 BTG1 
                 B-cell translocation gene 1, anti-proliferative 
               
               
                 2730 
                 GCLM 
                 Glutamate-cysteine ligase, modifier subunit 
               
               
                 4790 
                 NFKB1 
                 Nuclear factor of kappa light polypeptide gene enhancer 
               
               
                   
                   
                 B-cells 1 (p105) 
               
               
                 5519 
                 PPP2R1B 
                 Protein phosphatase 2 (formerly 2A), regulatory subunit 
               
               
                   
                   
                 beta isoform 
               
               
                 5618 
                 PRLR 
                 Prolactin receptor 
               
            
           
           
               
            
               
                 NRC_4 (cell motility) 
               
            
           
           
               
               
               
            
               
                 57045 
                 TWSG1 
                 Twisted gastrulation homolog 1 ( Drosophila ) 
               
               
                 3730 
                 KAL1 
                 Kallmann syndrome 1 sequence 
               
               
                 283 
                 ANG 
                 Angiogenin, ribonuclease, RNase A family, 5 
               
               
                 2549 
                 GAB1 
                 GRB2-associated binding protein 1 
               
               
                 6352 
                 CCL5 
                 Chemokine (C-C motif) ligand 5 
               
               
                 6402 
                 SELL 
                 Selectin L (lymphocyte adhesion molecule 1) 
               
               
                 643 
                 BLR1 
                 Burkitt lymphoma receptor 1, GTP binding protein 
               
               
                   
                   
                 (chemokine (C—X—C motif) receptor 5) 
               
               
                 3576 
                 IL8 
                 Interleukin 8 
               
               
                 9542 
                 NRG2 
                 Neuregulin 2 
               
               
                 6662 
                 SOX9 
                 SRY (sex determining region Y)-box 9 (campomelic 
               
               
                   
                   
                 dysplasia, autosomal sex-reversal) 
               
               
                 9027 
                 NAT8 
                 N-acetyltransferase 8 
               
               
                 7852 
                 CXCR4 
                 Chemokine (C—X—C motif) receptor 4 
               
               
                 55591 
                 VEZT 
                 Vezatin, adherens junctions transmembrane protein 
               
               
                 55704 
                 CCDC88A 
                 Coiled-coil domain containing 88A 
               
               
                 2028 
                 ENPEP 
                 Glutamyl aminopeptidase (aminopeptidase A) 
               
               
                 3912 
                 LAMB1 
                 Laminin, beta 1 
               
               
                 2304 
                 FOXE1 
                 Forkhead box E1 (thyroid transcription factor 2) 
               
               
                 7059 
                 THBS3 
                 Thrombospondin 3 
               
               
                 3915 
                 LAMC1 
                 Laminin, gamma 1 (formerly LAMB2) 
               
               
                 7043 
                 TGFB3 
                 Transforming growth factor, beta 3 
               
               
                 23129 
                 PLXND1 
                 Plexin D1 
               
               
                 8611 
                 PPAP2A 
                 Phosphatidic acid phosphatase type 2A 
               
               
                 5921 
                 RASA1 
                 RAS p21 protein activator (GTPase activating protein) 1 
               
               
                 6376 
                 CX3CL1 
                 Chemokine (C—X3—C motif) ligand 1 
               
               
                 3087 
                 HHEX 
                 Hematopoietically expressed homeobox 
               
               
                 9464 
                 HAND2 
                 Heart and neural crest derivatives expressed 2 
               
               
                 4991 
                 OR1D2 
                 Olfactory receptor, family 1, subfamily D, member 2 
               
               
                 6885 
                 MAP3K7 
                 Mitogen-activated protein kinase kinase kinase 7 
               
               
                 7019 
                 TFAM 
                 Transcription factor A, mitochondrial 
               
               
                 4692 
                 NDN 
                 Necdin homolog (mouse) 
               
            
           
           
               
            
               
                 NRC_5 (cell proliferation) 
               
            
           
           
               
               
               
            
               
                 283 
                 ANG 
                 Angiogenin, ribonuclease, RNase A family, 5 
               
               
                 2919 
                 CXCL1 
                 Chemokine (C—X—C motif) ligand 1 (melanoma growth 
               
               
                   
                   
                 stimulating activity, alpha) 
               
               
                 2549 
                 GAB1 
                 GRB2-associated binding protein 1 
               
               
                 3507 
                 IGHM 
               
               
                 7045 
                 TGFBI 
                 Transforming growth factor, beta-induced, 68 kDa 
               
               
                 3576 
                 IL8 
                 Interleukin 8 
               
               
                 973 
                 CD79A 
                 CD79a molecule, immunoglobulin-associated alpha 
               
               
                 10220 
                 GDF11 
                 Growth differentiation factor 11 
               
               
                 6662 
                 SOX9 
                 SRY (sex determining region Y)-box 9 (campomelic 
               
               
                   
                   
                 dysplasia, autosomal sex-reversal) 
               
               
                 1032 
                 CDKN2D 
                 Cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK   
               
               
                 11040 
                 PIM2 
                 Pim-2 oncogene 
               
               
                 10428 
                 CFDP1 
                 Craniofacial development protein 1 
               
               
                 3600 
                 IL15 
                 Interleukin 15 
               
               
                 5473 
                 PPBP 
                 Pro-platelet basic protein (chemokine (C—X—C motif) liga   
               
               
                   
                   
                 7) 
               
               
                 8451 
                 CUL4A 
                 Cullin 4A 
               
               
                 5376 
                 PMP22 
                 Peripheral myelin protein 22 
               
               
                 50810 
                 HDGFRP3 
                 Hepatoma-derived growth factor, related protein 3 
               
               
                 4067 
                 LYN 
                 V-yes-1 Yamaguchi sarcoma viral related oncogene 
               
               
                   
                   
                 homolog 
               
               
                 7188 
                 TRAF5 
                 TNF receptor-associated factor 5 
               
               
                 7453 
                 WARS 
                 Tryptophanyl-tRNA synthetase 
               
               
                 3601 
                 IL15RA 
                 Interleukin 15 receptor, alpha 
               
               
                 2028 
                 ENPEP 
                 Glutamyl aminopeptidase (aminopeptidase A) 
               
               
                 5511 
                 PPP1R8 
                 Protein phosphatase 1, regulatory (inhibitor) subunit 8 
               
               
                 55704 
                 CCDC88A 
                 Coiled-coil domain containing 88A 
               
               
                 7041 
                 TGFB1I1 
                 Transforming growth factor beta 1 induced transcript 1 
               
               
                 706 
                 TSPO 
                 Translocator protein (18 kDa) 
               
               
                 8611 
                 PPAP2A 
                 Phosphatidic acid phosphatase type 2A 
               
               
                 8850 
                 PCAF 
                 P300/CBP-associated factor 
               
               
                 8914 
                 TIMELESS 
                 Timeless homolog ( Drosophila ) 
               
               
                 23705 
                 CADM1 
                 Cell adhesion molecule 1 
               
            
           
           
               
            
               
                 NRC_6 (sex) 
               
            
           
           
               
               
               
            
               
                 939 
                 CD27 
                 CD27 molecule 
               
               
                 5680 
                 PSG11 
                 Pregnancy specific beta-1-glycoprotein 11 
               
               
                 283 
                 ANG 
                 Angiogenin, ribonuclease, RNase A family, 5 
               
               
                 6662 
                 SOX9 
                 SRY (sex determining region Y)-box 9 (campomelic 
               
               
                   
                   
                 dysplasia, autosomal sex-reversal) 
               
               
                 6715 
                 SRD5A1 
                 Steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 
               
               
                   
                   
                 alpha-steroid delta 4-dehydrogenase alpha 1) 
               
               
                 8863 
                 PER3 
                 Period homolog 3 ( Drosophila ) 
               
               
                 3620 
                 INDO 
                 Indoleamine-pyrrole 2,3 dioxygenase 
               
               
                 668 
                 FOXL2 
                 Forkhead box L2 
               
               
                 5079 
                 PAX5 
                 Paired box 5 
               
               
                 23198 
                 PSME4 
                 Proteasome (prosome, macropain) activator subunit 4 
               
               
                 54466 
                 SPIN2A 
                 Spindlin family, member 2A 
               
               
                 7852 
                 CXCR4 
                 Chemokine (C—X—C motif) receptor 4 
               
               
                 6347 
                 CCL2 
                 Chemokine (C-C motif) ligand 2 
               
               
                 5818 
                 PVRL1 
                 Poliovirus receptor-related 1 (herpesvirus entry mediato   
               
               
                 3576 
                 IL8 
                 Interleukin 8 
               
               
                 4986 
                 OPRK1 
                 Opioid receptor, kappa 1 
               
               
                 7707 
                 ZNF148 
                 Zinc finger protein 148 
               
               
                 10670 
                 RRAGA 
                 Ras-related GTP binding A 
               
               
                 1816 
                 DRD5 
                 Dopamine receptor D5 
               
               
                 83737 
                 ITCH 
                 Itchy homolog E3 ubiquitin protein ligase (mouse) 
               
               
                 1984 
                 EIF5A 
                 Eukaryotic translation initiation factor 5A 
               
               
                 3416 
                 IDE 
                 Insulin-degrading enzyme 
               
               
                 4184 
                 SMCP 
                 Sperm mitochondria-associated cysteine-rich protein 
               
               
                 1628 
                 DBP 
                 D site of albumin promoter (albumin D-box) binding prot   
               
               
                 3295 
                 HSD17B4 
                 Hydroxysteroid (17-beta) dehydrogenase 4 
               
               
                 8239 
                 USP9X 
                 Ubiquitin specific peptidase 9, X-linked 
               
               
                 51665 
                 ASB1 
                 Ankyrin repeat and SOCS box-containing 1 
               
               
                 3014 
                 H2AFX 
                 H2A histone family, member X 
               
               
                 3624 
                 INHBA 
                 Inhibin, beta A 
               
               
                 6019 
                 RLN2 
                 Relaxin 2 
               
            
           
           
               
            
               
                 NRC_7 (apoptosis) 
               
            
           
           
               
               
               
            
               
                 1012 
                 CDH13 
                 Cadherin 13, H-cadherin (heart) 
               
               
                 57823 
                 SLAMF7 
                 SLAM family member 7 
               
               
                 51129 
                 ANGPTL4 
                 Angiopoietin-like 4 
               
               
                 23213 
                 SULF1 
                 Sulfatase 1 
               
               
                 2697 
                 GJA1 
                 Gap junction protein, alpha 1, 43 kDa 
               
               
                 4583 
                 MUC2 
                 Mucin 2, oligomeric mucus/gel-forming 
               
               
                 3304 
                 HSPA1B 
                 Heat shock 70 kDa protein 1B 
               
               
                 79370 
                 BCL2L14 
                 BCL2-like 14 (apoptosis facilitator) 
               
               
                 9994 
                 CASP8AP2 
                 CASP8 associated protein 2 
               
               
                 2185 
                 PTK2B 
                 PTK2B protein tyrosine kinase 2 beta 
               
               
                 3981 
                 LIG4 
                 Ligase IV, DNA, ATP-dependent 
               
               
                 2765 
                 GML 
                 GPI anchored molecule like protein 
               
               
                 27250 
                 PDCD4 
                 Programmed cell death 4 (neoplastic transformation 
               
               
                   
                   
                 inhibitor) 
               
               
                 28986 
                 MAGEH1 
                 Melanoma antigen family H, 1 
               
               
                 355 
                 FAS 
                 Fas (TNF receptor superfamily, member 6) 
               
               
                 308 
                 ANXA5 
                 Annexin A5 
               
               
                 2914 
                 GRM4 
                 Glutamate receptor, metabotropic 4 
               
               
                 57099 
                 AVEN 
                 Apoptosis, caspase activation inhibitor 
               
               
                 842 
                 CASP9 
                 Caspase 9, apoptosis-related cysteine peptidase 
               
               
                 1409 
                 CRYAA 
                 Crystallin, alpha A 
               
               
                 4792 
                 NFKBIA 
                 Nuclear factor of kappa light polypeptide gene enhancer 
               
               
                   
                   
                 B-cells inhibitor, alpha 
               
               
                 6788 
                 STK3 
                 Serine/threonine kinase 3 (STE20 homolog, yeast) 
               
               
                 5516 
                 PPP2CB 
                 Protein phosphatase 2 (formerly 2A), catalytic subunit, b 
               
               
                   
                   
                 isoform 
               
               
                 57019 
                 CIAPIN1 
                 Cytokine induced apoptosis inhibitor 1 
               
               
                 8682 
                 PEA15 
                 Phosphoprotein enriched in astrocytes 15 
               
               
                 7042 
                 TGFB2 
                 Transforming growth factor, beta 2 
               
               
                 1870 
                 E2F2 
                 E2F transcription factor 2 
               
               
                 2898 
                 GRIK2 
                 Glutamate receptor, ionotropic, kainate 2 
               
               
                 972 
                 CD74 
                 CD74 molecule, major histocompatibility complex, class 
               
               
                   
                   
                 invariant chain 
               
               
                 7189 
                 TRAF6 
                 TNF receptor-associated factor 6 
               
            
           
           
               
            
               
                 NRC_8 (cell adhesion) 
               
            
           
           
               
               
               
            
               
                 57823 
                 SLAMF7 
                 SLAM family member 7 
               
               
                 1012 
                 CDH13 
                 Cadherin 13, H-cadherin (heart) 
               
               
                 3547 
                 IGSF1 
                 Immunoglobulin superfamily, member 1 
               
               
                 7045 
                 TGFBI 
                 Transforming growth factor, beta-induced, 68 kDa 
               
               
                 1404 
                 HAPLN1 
                 Hyaluronan and proteoglycan link protein 1 
               
               
                 80144 
                 FRAS1 
                 Fraser syndrome 1 
               
               
                 10666 
                 CD226 
                 CD226 molecule 
               
               
                 26032 
                 SUSD5 
                 Sushi domain containing 5 
               
               
                 10979 
                 PLEKHC1 
                 Pleckstrin homology domain containing, family C (with 
               
               
                   
                   
                 FERM domain) member 1 
               
               
                 9620 
                 CELSR1 
                 Cadherin, EGF LAG seven-pass G-type receptor 1 
               
               
                   
                   
                 (flamingo homolog,  Drosophila ) 
               
               
                 4815 
                 NINJ2 
                 Ninjurin 2 
               
               
                 3684 
                 ITGAM 
                 Integrin, alpha M (complement component 3 receptor 3 
               
               
                   
                   
                 subunit) 
               
               
                 2909 
                 GRLF1 
                 Glucocorticoid receptor DNA binding factor 1 
               
               
                 54798 
                 DCHS2 
                 Dachsous 2 ( Drosophila ) 
               
               
                 2811 
                 GP1BA 
                 Glycoprotein Ib (platelet), alpha polypeptide 
               
               
                 7414 
                 VCL 
                 Vinculin 
               
               
                 6404 
                 SELPLG 
                 Selectin P ligand 
               
               
                 2185 
                 PTK2B 
                 PTK2B protein tyrosine kinase 2 beta 
               
               
                 4771 
                 NF2 
                 Neurofibromin 2 (bilateral acoustic neuroma) 
               
               
                 950 
                 SCARB2 
                 Scavenger receptor class B, member 2 
               
               
                 101 
                 ADAM8 
                 ADAM metallopeptidase domain 8 
               
               
                 3491 
                 CYR61 
                 Cysteine-rich, angiogenic inducer, 61 
               
               
                 22795 
                 NID2 
                 Nidogen 2 (osteonidogen) 
               
               
                 55591 
                 VEZT 
                 Vezatin, adherens junctions transmembrane protein 
               
               
                 4586 
                 MUC5AC 
                 Mucin 5AC, oligomeric mucus/gel-forming 
               
               
                 3636 
                 INPPL1 
                 Inositol polyphosphate phosphatase-like 1 
               
               
                 2833 
                 CXCR3 
                 Chemokine (C—X—C motif) receptor 3 
               
               
                 261734 
                 NPHP4 
                 Nephronophthisis 4 
               
               
                 10418 
                 SPON1 
                 Spondin 1, extracellular matrix protein 
               
               
                 8500 
                 PPFIA1 
                 Protein tyrosine phosphatase, receptor type, f polypepti   
               
               
                   
                   
                 (PTPRF), interacting protein (liprin), alpha 1 
               
            
           
           
               
            
               
                 NRC_9 (cell growth) 
               
            
           
           
               
               
               
            
               
                 23418 
                 CRB1 
                 Crumbs homolog 1 ( Drosophila ) 
               
               
                 3488 
                 IGFBP5 
                 Insulin-like growth factor binding protein 5 
               
               
                 2620 
                 GAS2 
               
               
                 5654 
                 HTRA1 
                 HtrA serine peptidase 1 
               
               
                 27113 
                 BBC3 
                 BCL2 binding component 3 
               
               
                 2697 
                 GJA1 
                 Gap junction protein, alpha 1, 43 kDa 
               
               
                 348 
                 APOE 
                 Apolipoprotein E 
               
               
                 4881 
                 NPR1 
                 Natriuretic peptide receptor A/guanylate cyclase A 
               
               
                   
                   
                 (atrionatriuretic peptide receptor A) 
               
               
                 575 
                 BAI1 
                 Brain-specific angiogenesis inhibitor 1 
               
               
                 9837 
                 GINS1 
                 GINS complex subunit 1 (Psf1 homolog) 
               
               
                 51466 
                 EVL 
                 Enah/Vasp-like 
               
               
                 357 
                 SHROOM2 
                 Shroom family member 2 
               
               
                 207 
                 AKT1 
                 V-akt murine thymoma viral oncogene homolog 1 
               
               
                 2027 
                 ENO3 
                 Enolase 3 (beta, muscle) 
               
               
                 6531 
                 SLC6A3 
                 Solute carrier family 6 (neurotransmitter transporter, 
               
               
                   
                   
                 dopamine), member 3 
               
               
                 8089 
                 YEATS4 
                 YEATS domain containing 4 
               
               
                 6905 
                 TBCE 
                 Tubulin folding cofactor E 
               
               
                 3490 
                 IGFBP7 
                 Insulin-like growth factor binding protein 7 
               
               
                 6665 
                 SOX15 
                 SRY (sex determining region Y)-box 15 
               
               
                 55785 
                 FGD6 
                 FYVE, RhoGEF and PH domain containing 6 
               
               
                 5925 
                 RB1 
                 Retinoblastoma 1 (including osteosarcoma) 
               
               
                 55558 
                 PLXNA3 
                 Plexin A3 
               
               
                 7251 
                 TSG101 
                 Tumour susceptibility gene 101 
               
               
                 978 
                 CDA 
                 Cytidine deaminase 
               
               
                 3912 
                 LAMB1 
                 Laminin, beta 1 
               
               
                 7042 
                 TGFB2 
                 Transforming growth factor, beta 2 
               
               
                 56288 
                 PARD3 
                 Par-3 partitioning defective 3 homolog ( C. elegans ) 
               
               
                 7486 
                 WRN 
                 Werner syndrome 
               
               
                 2054 
                 STX2 
                 Syntaxin 2 
               
               
                 5516 
                 PPP2CB 
                 Protein phosphatase 2 (formerly 2A), catalytic subunit, b 
               
               
                   
                   
                 isoform 
               
               
                   
               
               
                 Note: 
               
               
                 The message RNA sequences for each gene listed in this table have been attached at the end of this document. All message RNA sequences for each gene in Table 1 are extracted from National Center for Biotechnology Information (NCBI), a public database. 
               
               
                     indicates data missing or illegible when filed 
               
            
           
         
       
     
     The format of sequences is a FASTA format. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (“&gt;”) symbol in the first column. 
     An example sequence in FASTA: 
     
       
         
           
               
               
            
               
                 &gt;6019|NM_005059 
                   
               
               
                 ATGCCTCGCCTGTTTTTTTTCCACCTGCTAGGAGTCTGTTTACTACTGAACCAATTTTCCAGAGCAGTCG 
               
               
                   
               
               
                 CGGACTCATGGATGGAGGAAGTTATTAAATTATGCGGCCGCGAATTAGTTCGCGCGCAGATTGCCATTTG 
               
               
                   
               
               
                 CGGCATGAGCACCTGGAGCAAAAGGTCTCTGAGCCAGGAAGATGCTCCTCAGACACCTAGACCAGTGGCA 
               
               
                   
               
               
                 GGTGATTTTATTCAAACAGTCTCACTGGGAATCTCACCGGACGGAGGGAAAGCACTGAGAACAGGAAGCT 
               
               
                   
               
               
                 GCTTCACCCGAGAGTTCCTTGGTGCCCTTTCCAAATTGTGCCATCCTTCATCAACAAAGATACAGAAACC 
               
               
                   
               
               
                 ATAAATATGATGTCAGAATTTGTTGCTAATTTGCCACAGGAGCTGAAGTTAACCCTGTCTGAGATGCAGC 
               
               
                   
               
               
                 CAGCATTACCACAGCTACAACAACATGTACCTGTATTAAAAGATTCCAGTCTTCTCTTTGAAGAATTTAA 
               
               
                   
               
               
                 GAAACTTATTCGCAATAGACAAAGTGAAGCCGCAGACAGCAGTCCTTCAGAATTAAAATACTTAGGCTTG 
               
               
                   
               
               
                 GATACTCATTCTCGAAAAAAGAGACAACTCTACAGTGCATTGGCTAATAAATGTTGCCATGTTGGTTGTA 
               
               
                   
               
               
                 CCAAAAGATCTCTTGCTAGATTTTGCTGAGATGAAGCTAATTGTGCACATCTCGTATAATATTCACACAT 
               
               
                   
               
               
                 ATTCTTAATGACATTTCACTGATGCTTCTATCAGGTCCCATCAATTCTTAGAATATCTAAGAATCTTTGT 
               
               
                   
               
               
                 TAGATATTAGGTCCCATCAATTCTTAGAATATCTAAACATCTTTGTTGATGTTTAGATTTTTTTATTTGA 
               
               
                   
               
               
                 TGTGTAAGAAAATGTTCTTTGTGTGATTAAATGACACATTTTTTTGCTG 
               
            
           
         
       
     
     In the description line, the first item, 6019 is NCBI EntrezGene ID, which is the ID in the first column of Table 1; another item after the symbol (“|”) is the NCBI reference message RNA sequence ID. It should be noted that one EntrezGene ID may have several reference message RNA sequences. In this case, all the message RNA sequences for one EntrezGene ID are listed. Each sequence represents one reference message RNA sequence. 
     
       
         
           
               
             
               
                 TABLE 1B 
               
             
            
               
                   
               
               
                 Gene expression signal list of NRC gene signatures 
               
            
           
           
               
               
               
            
               
                 Gene Name 
                 EntrezGene ID 
                 Gene Description 
               
               
                   
               
            
           
           
               
            
               
                 NRC-1 (Cell Cycle) 
               
            
           
           
               
               
               
            
               
                 RBL1 
                 5933 
                 Retinoblastoma-like 1 (p107) 
               
               
                 CCNF 
                 899 
                 Cyclin F 
               
               
                 NME1 
                 4830 
                 Non-metastatic cells 1, protein (NM23A) expressed 
               
               
                   
                   
                 in 
               
               
                 CDK2AP1 
                 8099 
                 CDK2-associated protein 1 
               
               
                 BIRC5 
                 332 
                 Baculoviral IAP repeat-containing 5 (survivin) 
               
               
                 TLK2 
                 11011 
                 Tousled-like kinase 2 
               
               
                 SMC4 
                 10051 
                 Structural maintenance of chromosomes 4 
               
               
                 CCNE1 
                 898 
                 Cyclin 
               
               
                   
                   
                 E1 
               
               
                 APPL1 
                 26060 
                 Adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper 
               
               
                 LOH11CR2A 
                 4013 
                 Loss of heterozygosity, 11, chromosomal region 2, gene A 
               
               
                 MAPRE1 
                 22919 
                 Microtubule-associated protein, RP/EB family, member 1 
               
               
                 HRASLS3 
                 11145 
                 HRAS-like suppressor 3 
               
               
                 GADD45A 
                 1647 
                 Growth arrest and DNA-damage-inducible, alpha 
               
               
                 HELLS 
                 3070 
                 Helicase, lymphoid-specific 
               
               
                 PPP1CC 
                 5501 
                 Protein phosphatase 1, catalytic subunit, gamma isoform 
               
               
                 GMNN 
                 51053 
                 Geminin, DNA replication inhibitor 
               
               
                 EPHB2 
                 2048 
                 EPH receptor B2 
               
               
                 RAD17 
                 5884 
                 RAD17 homolog ( S. pombe ) 
               
               
                 AURKA 
                 6790 
                 Aurora kinase A 
               
               
                 NEK1 
                 4750 
                 NIMA (never in mitosis gene a)-related kinase 1 
               
               
                 RASSF1 
                 11186 
                 Ras association (RalGDS/AF-6) domain family 1 
               
               
                 VASH1 
                 22846 
                 Vasohibin 1 
               
               
                 MAPRE3 
                 22924 
                 Microtubule-associated protein, RP/EB family, member 3 
               
               
                 CDCA8 
                 55143 
                 Cell division cycle associated 8 
               
               
                 CDC73 
                 79577 
                 Cell division cycle 73, Paf1/RNA polymerase II complex component, homolo   
               
               
                 SIRT2 
                 22933 
                 Sirtuin (silent mating type information regulation 2 homolog) 2 ( S. cerevisiae ) 
               
               
                 MAPK7 
                 5598 
                 Mitogen-activated protein kinase 7 
               
               
                 MKI67 
                 4288 
                 Antigen identified by monoclonal antibody Ki-67 
               
               
                 TFDP1 
                 7027 
                 Transcription factor Dp-1 
               
               
                 DMBT1 
                 1755 
                 Deleted in malignant brain tumours 1 
               
            
           
           
               
            
               
                 NRC-2(immune) 
               
            
           
           
               
               
               
            
               
                 C7 
                 730 
                 Complement component 7 
               
               
                 SELE 
                 6401 
                 Selectin E (endothelial adhesion molecule 1) 
               
               
                 CD27 
                 939 
                 CD27 molecule 
               
               
                 F3 
                 2152 
                 Coagulation factor III (thromboplastin, tissue factor) 
               
               
                 IL23A 
                 51561 
                 Interleukin 23, alpha subunit 
               
               
                   
                   
                 p19 
               
               
                 CARTPT 
                 9607 
                 CART 
               
               
                   
                   
                 prepropeptide 
               
               
                 SPP1 
                 6696 
                 Secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphc   
               
               
                 TNNT1 
                 7138 
                 Troponin T type 1 (skeletal, slow) 
               
               
                 CACNB3 
                 784 
                 Calcium channel, voltage-dependent, beta 3 subunit 
               
               
                 C6 
                 729 
                 Complement component 6 
               
               
                 F13B 
                 2165 
                 Coagulation factor XIII, B polypeptide 
               
               
                 SELP 
                 6403 
                 Selectin P (granule membrane protein 140 kDa, antigen CD62) 
               
               
                 POU2F2 
                 5452 
                 POU class 2 homeobox 2 
               
               
                 STAT3 
                 6774 
                 Signal transducer and activator of transcription 3 (acute-phase response fac   
               
               
                 SERPINA1 
                 5265 
                 Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), men   
               
               
                 FGF23 
                 8074 
                 Fibroblast growth factor 23 
               
               
                 MYBPC3 
                 4607 
                 Myosin binding protein C, cardiac 
               
               
                 LST1 
                 7940 
                 Leukocyte specific transcript 1 
               
               
                 LEP 
                 3952 
                 Leptin (obesity homolog, mouse) 
               
               
                 STAT5A 
                 6776 
                 Signal transducer and activator of transcription 5A 
               
               
                 AMBP 
                 259 
                 Alpha-1-microglobulin/bikunin precursor 
               
               
                 TNNC2 
                 7125 
                 Troponin C type 2 (fast) 
               
               
                 SCN5A 
                 6331 
                 Sodium channel, voltage-gated, type V, alpha 
               
               
                   
                   
                 subunit 
               
               
                 CAV1 
                 857 
                 Caveolin 1, caveolae protein, 22 kDa 
               
               
                 RBM4 
                 5936 
                 RNA binding motif protein 4 
               
               
                 BLM 
                 641 
                 Bloom syndrome 
               
               
                 FYN 
                 2534 
                 FYN oncogene related to SRC, FGR, 
               
               
                   
                   
                 YES 
               
               
                 BCL6 
                 604 
                 B-cell CLL/lymphoma 6 (zinc finger protein 51) 
               
               
                 NMU 
                 10874 
                 Neuromedin U 
               
               
                 HP 
                 3240 
                 Haptoglobin 
               
            
           
           
               
            
               
                 NRC-3 (apoptosis) 
               
            
           
           
               
               
               
            
               
                 ZBTB16 
                 7704 
                 Zinc finger and BTB domain containing 16 
               
               
                 ARHGEF6 
                 9459 
                 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 
               
               
                 PHLDA2 
                 7262 
                 Pleckstrin homology-like domain, family A, member 2 
               
               
                 TNFRSF11B 
                 4982 
                 Tumour necrosis factor receptor superfamily, member 11b 
               
               
                   
                   
                 (osteoprotegerin) 
               
               
                 CYCS 
                 54205 
                 Cytochrome c, somatic 
               
               
                 TRADD 
                 8717 
                 TNFRSF1A-associated via death domain 
               
               
                 BIRC5 
                 332 
                 Baculoviral IAP repeat-containing 5 (survivin) 
               
               
                 PDCD4 
                 27250 
                 Programmed cell death 4 (neoplastic transformation inhibitor) 
               
               
                 SOCS2 
                 8835 
                 Suppressor of cytokine signaling 2 
               
               
                 PPP2R1B 
                 5519 
                 Protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform 
               
               
                 MGMT 
                 4255 
                 O-6-methylguanine-DNA 
               
               
                   
                   
                 methyltransferase 
               
               
                 IKBKG 
                 8517 
                 Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase 
               
               
                   
                   
                 gamma 
               
               
                 BTG1 
                 694 
                 B-cell translocation gene 1, anti- 
               
               
                   
                   
                 proliferative 
               
               
                 NRAS 
                 4893 
                 Neuroblastoma RAS viral (v-ras) oncogene homolog 
               
               
                 ESPL1 
                 9700 
                 Extra spindle pole bodies homolog 1 ( S. cerevisiae ) 
               
               
                 CDC2 
                 983 
                 Cell division cycle 2, G1 to S and G2 to M 
               
               
                 APLP1 
                 333 
                 Amyloid beta (A4) precursor-like protein 1 
               
               
                 TCTN3 
                 26123 
                 Tectonic family member 3 
               
               
                 NME1 
                 4830 
                 Non-metastatic cells 1, protein (NM23A) expressed 
               
               
                   
                   
                 in 
               
               
                 STAT5A 
                 6776 
                 Signal transducer and activator of transcription 5A 
               
               
                 CLU 
                 1191 
                 Clusterin 
               
               
                 BCL2 
                 596 
                 B-cell CLL/lymphoma 2 
               
               
                 HTATIP2 
                 10553 
                 HIV-1 Tat interactive protein 2, 30 kDa 
               
               
                 EEF1A2 
                 1917 
                 Eukaryotic translation elongation factor 1 alpha 2 
               
               
                 INHA 
                 3623 
                 Inhibin, alpha 
               
               
                 TNFSF9 
                 8744 
                 Tumour necrosis factor (ligand) superfamily, member 9 
               
               
                 LRDD 
                 55367 
                 Leucine-rich repeats and death domain containing 
               
               
                 FADD 
                 8772 
                 Fas (TNFRSF6)-associated via death domain 
               
               
                 IL19 
                 29949 
                 Interleukin 19 
               
               
                 KIAA0367 
                 23273 
               
            
           
           
               
            
               
                 NRC_4 (cell adhesion) 
               
            
           
           
               
               
               
            
               
                 CHL1 
                 10752 
                 Cell adhesion molecule with homology to L1CAM (close homolog of L1) 
               
               
                 COL15A1 
                 1306 
                 Collagen, type XV, alpha 1 
               
               
                 CRNN 
                 49860 
                 Cornulin 
               
               
                 KAL1 
                 3730 
                 Kallmann syndrome 1 
               
               
                   
                   
                 sequence 
               
               
                 SOX9 
                 6662 
                 SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal s   
               
               
                   
                   
                 reversal) 
               
               
                 PTPRF 
                 5792 
                 Protein tyrosine phosphatase, receptor type, F 
               
               
                 ITGA7 
                 3679 
                 Integrin, alpha 7 
               
               
                 MFAP4 
                 4239 
                 Microfibrillar-associated protein 4 
               
               
                 EDG1 
                 1901 
                 Endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 
               
               
                 ZEB2 
                 9839 
                 Zinc finger E-box binding homeobox 2 
               
               
                 PDZD2 
                 23037 
                 PDZ domain containing 2 
               
               
                 ROBO1 
                 6091 
                 Roundabout, axon guidance receptor, homolog 1 ( Drosophila ) 
               
               
                 FBN2 
                 2201 
                 Fibrillin 2 (congenital contractural arachnodactyly) 
               
               
                 POSTN 
                 10631 
                 Periostin, osteoblast specific factor 
               
               
                 CDH5 
                 1003 
                 Cadherin 5, type 2, VE-cadherin (vascular 
               
               
                   
                   
                 epithelium) 
               
               
                 PKD1 
                 5310 
                 Polycystic kidney disease 1 (autosomal dominant) 
               
               
                 TGFB1I1 
                 7041 
                 Transforming growth factor beta 1 induced transcript 1 
               
               
                 ITGA5 
                 3678 
                 Integrin, alpha 5 (fibronectin receptor, alpha polypeptide) 
               
               
                 RASA1 
                 5921 
                 RAS p21 protein activator (GTPase activating protein) 1 
               
               
                 COL11A2 
                 1302 
                 Collagen, type XI, alpha 2 
               
               
                 VEZT 
                 55591 
                 Vezatin, adherens junctions transmembrane protein 
               
               
                 CLDN4 
                 1364 
                 Claudin 4 
               
               
                 BCL6 
                 604 
                 B-cell CLL/lymphoma 6 (zinc finger protein 51) 
               
               
                 AMIGO2 
                 347902 
                 Adhesion molecule with Ig-like domain 2 
               
               
                 ECM2 
                 1842 
                 Extracellular matrix protein 2, female organ and adipocyte specific 
               
               
                 FAF1 
                 11124 
                 Fas (TNFRSF6) associated factor 1 
               
               
                 ITGB8 
                 3696 
                 Integrin, beta 8 
               
               
                 PRPH2 
                 5961 
                 Peripherin 2 (retinal degeneration, slow) 
               
               
                 CEACAM1 
                 634 
                 Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycopro 
               
               
                 THY1 
                 7070 
                 Thy-1 cell surface antigen 
               
            
           
           
               
            
               
                 NRC_5 (cell cycle) 
               
            
           
           
               
               
               
            
               
                 NDN 
                 4692 
                 Necdin homolog (mouse) 
               
               
                 CDCA8 
                 55143 
                 Cell division cycle associated 8 
               
               
                 CHEK2 
                 11200 
                 CHK2 checkpoint homolog ( S. pombe ) 
               
               
                 CDC45L 
                 8318 
                 CDC45 cell division cycle 45-like ( S. cerevisiae ) 
               
               
                 STRN3 
                 29966 
                 Striatin, calmodulin binding protein 3 
               
               
                 PYCARD 
                 29108 
                 PYD and CARD domain containing 
               
               
                 HERC5 
                 51191 
                 Hect domain and RLD 5 
               
               
                 MN1 
                 4330 
                 Meningioma (disrupted in balanced translocation) 1 
               
               
                 XRCC2 
                 7516 
                 X-ray repair complementing defective repair in Chinese hamster cells 2 
               
               
                 NOLC1 
                 9221 
                 Nucleolar and coiled-body phosphoprotein 1 
               
               
                 CHFR 
                 55743 
                 Checkpoint with forkhead and ring finger domains 
               
               
                 NHP2L1 
                 4809 
                 NHP2 non-histone chromosome protein 2-like 1 ( S. cerevisiae ) 
               
               
                 MCM7 
                 4176 
                 Minichromosome maintenance complex component 7 
               
               
                 PIM2 
                 11040 
                 Pim-2 oncogene 
               
               
                 INHBA 
                 3624 
                 Inhibin, beta A 
               
               
                 ACPP 
                 55 
                 Acid phosphatase, prostate 
               
               
                 CETN3 
                 1070 
                 Centrin, EF-hand protein, 3 (CDC31 homolog, yeast) 
               
               
                 MIS12 
                 79003 
                 MIS12, MIND kinetochore complex component, homolog (yeast) 
               
               
                 PCAF 
                 8850 
                 P300/CBP-associated factor 
               
               
                 PTMA 
                 5757 
                 Prothymosin, alpha (gene sequence 28) 
               
               
                 AXL 
                 558 
                 AXL receptor tyrosine kinase 
               
               
                 Sep-11 
                 55752 
                 Septin 
               
               
                   
                   
                 11 
               
               
                 LTBP2 
                 4053 
                 Latent transforming growth factor beta binding protein 2 
               
               
                 SUPT5H 
                 6829 
                 Suppressor of Ty 5 homolog ( S. cerevisiae ) 
               
               
                 TOB2 
                 10766 
                 Transducer of ERBB2, 2 
               
               
                 CDK5R1 
                 8851 
                 Cyclin-dependent kinase 5, regulatory subunit 1 
               
               
                   
                   
                 (p35) 
               
               
                 ILF3 
                 3609 
                 Interleukin enhancer binding factor 3, 90 kDa 
               
               
                 POLD1 
                 5424 
                 Polymerase (DNA directed), delta 1, catalytic subunit 125 kDa 
               
               
                 GADD45B 
                 4616 
                 Growth arrest and DNA-damage-inducible, beta 
               
               
                 CDT1 
                 81620 
                 Chromatin licensing and DNA replication factor 1 
               
            
           
           
               
            
               
                 NRC_6 (cell motility) 
               
            
           
           
               
               
               
            
               
                 KAL1 
                 3730 
                 Kallmann syndrome 1 
               
               
                   
                   
                 sequence 
               
               
                 PRSS3 
                 5646 
                 Protease, serine, 3 (mesotrypsin) 
               
               
                 CHL1 
                 10752 
                 Cell adhesion molecule with homology to L1CAM (close homolog of L1) 
               
               
                 ROBO1 
                 6091 
                 Roundabout, axon guidance receptor, homolog 1 ( Drosophila ) 
               
               
                 ZEB2 
                 9839 
                 Zinc finger E-box binding homeobox 2 
               
               
                 EDG1 
                 1901 
                 Endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 
               
               
                 CDA 
                 978 
                 Cytidine deaminase 
               
               
                 ATP1A3 
                 478 
                 ATPase, Na+/K+ transporting, alpha 3 polypeptide 
               
               
                 IGFBP7 
                 3490 
                 Insulin-like growth factor binding protein 7 
               
               
                 INHBA 
                 3624 
                 Inhibin, beta A 
               
               
                 CSPG4 
                 1464 
                 Chondroitin sulfate proteoglycan 4 
               
               
                 WFDC1 
                 58189 
                 WAP four-disulfide core domain 1 
               
               
                 PF4 
                 5196 
                 Platelet factor 4 (chemokine (C—X—C motif) ligand 4) 
               
               
                 ALOX12 
                 239 
                 Arachidonate 12-lipoxygenase 
               
               
                 NDN 
                 4692 
                 Necdin homolog (mouse) 
               
               
                 CCDC88A 
                 55704 
                 Coiled-coil domain containing 88A 
               
               
                 CEACAM1 
                 634 
                 Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycopro 
               
               
                 ARPC3 
                 10094 
                 Actin related protein 2/3 complex, subunit 3, 21 kDa 
               
               
                 BCL6 
                 604 
                 B-cell CLL/lymphoma 6 (zinc finger protein 51) 
               
               
                 PPAP2B 
                 8613 
                 Phosphatidic acid phosphatase type 2B 
               
               
                 LAMB1 
                 3912 
                 Laminin, beta 1 
               
               
                 DNAH2 
                 146754 
                 Dynein, axonemal, heavy chain 2 
               
               
                 SLIT3 
                 6586 
                 Slit homolog 3 ( Drosophila ) 
               
               
                 CDK5R1 
                 8851 
                 Cyclin-dependent kinase 5, regulatory subunit 1 
               
               
                   
                   
                 (p35) 
               
               
                 ADRA2A 
                 150 
                 Adrenergic, alpha-2A-, 
               
               
                   
                   
                 receptor 
               
               
                 AMOT 
                 154796 
                 Angiomotin 
               
               
                 ACTG1 
                 71 
                 Actin, gamma 1 
               
               
                 TGFB3 
                 7043 
                 Transforming growth factor, beta 3 
               
               
                 KDR 
                 3791 
                 Kinase insert domain receptor (a type III receptor tyrosine 
               
               
                   
                   
                 kinase) 
               
               
                 ABI3 
                 51225 
                 ABI gene family, member 3 
               
            
           
           
               
            
               
                 NRC-7 (apoptosis) 
               
            
           
           
               
               
               
            
               
                 CDH13 
                 1012 
                 Cadherin 13, H-cadherin 
               
               
                   
                   
                 (heart) 
               
               
                 SLAMF7 
                 57823 
                 SLAM family member 7 
               
               
                 ANGPTL4 
                 51129 
                 Angiopoietin-like 4 
               
               
                 SULF1 
                 23213 
                 Sulfatase 1 
               
               
                 GJA1 
                 2697 
                 Gap junction protein, alpha 1, 43 kDa 
               
               
                 MUC2 
                 4583 
                 Mucin 2, oligomeric mucus/gel-forming 
               
               
                 INPP5D 
                 3635 
                 Inositol polyphosphate-5-phosphatase, 145 kDa 
               
               
                 BCL2L14 
                 79370 
                 BCL2-like 14 (apoptosis facilitator) 
               
               
                 CASP8AP2 
                 9994 
                 CASP8 associated protein 2 
               
               
                 PTK2B 
                 2185 
                 PTK2B protein tyrosine kinase 2 beta 
               
               
                 LIG4 
                 3981 
                 Ligase IV, DNA, ATP- 
               
               
                   
                   
                 dependent 
               
               
                 GML 
                 2765 
                 GPI anchored molecule like protein 
               
               
                 PDCD4 
                 27250 
                 Programmed cell death 4 (neoplastic transformation inhibitor) 
               
               
                 MAGEH1 
                 28986 
                 Melanoma antigen family H, 1 
               
               
                 FAS 
                 355 
                 Fas (TNF receptor superfamily, member 6) 
               
               
                 ANXA5 
                 308 
                 Annexin A5 
               
               
                 GRM4 
                 2914 
                 Glutamate receptor, metabotropic 4 
               
               
                 AVEN 
                 57099 
                 Apoptosis, caspase activation inhibitor 
               
               
                 CASP9 
                 842 
                 Caspase 9, apoptosis-related cysteine peptidase 
               
               
                 CRYAA 
                 1409 
                 Crystallin, alpha A 
               
               
                 NFKBIA 
                 4792 
                 Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, 
               
               
                 STK3 
                 6788 
                 Serine/threonine kinase 3 (STE20 homolog, yeast) 
               
               
                 PPP2CB 
                 5516 
                 Protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform 
               
               
                 CIAPIN1 
                 57019 
                 Cytokine induced apoptosis inhibitor 1 
               
               
                 PEA15 
                 8682 
                 Phosphoprotein enriched in astrocytes 15 
               
               
                 TGFB2 
                 7042 
                 Transforming growth factor, beta 2 
               
               
                 OLFR@ 
                 4972 
                 olfactory receptor cluster 
               
               
                 MGC29506 
                 51237 
                 Hypothetical protein 
               
               
                   
                   
                 MGC29506 
               
               
                 CD74 
                 972 
                 CD74 molecule, major histocompatibility complex, class II invariant chain 
               
               
                 TRAF6 
                 7189 
                 TNF receptor-associated factor 6 
               
            
           
           
               
            
               
                 NRC-8 (cell adhesion) 
               
            
           
           
               
               
               
            
               
                 SLAMF7 
                 57823 
                 SLAM family member 7 
               
               
                 CDH13 
                 1012 
                 Cadherin 13, H-cadherin 
               
               
                   
                   
                 (heart) 
               
               
                 IGSF1 
                 3547 
                 Immunoglobulin superfamily, member 1 
               
               
                 TGFBI 
                 7045 
                 Transforming growth factor, beta-induced, 68 kDa 
               
               
                 HAPLN1 
                 1404 
                 Hyaluronan and proteoglycan link protein 1 
               
               
                 FRAS1 
                 80144 
                 Fraser syndrome 1 
               
               
                 PLEKHC1 
                 10979 
                 Pleckstrin homology domain containing, family C (with FERM domain) mem   
               
               
                 CD226 
                 10666 
                 CD226 molecule 
               
               
                 SUSD5 
                 26032 
                 Sushi domain containing 5 
               
               
                 CELSR1 
                 9620 
                 Cadherin, EGF LAG seven-pass G-type receptor 1 (flamingo homolog, Dros 
               
               
                 GRLF1 
                 2909 
                 Glucocorticoid receptor DNA binding factor 1 
               
               
                 NID2 
                 22795 
                 Nidogen 2 (osteonidogen) 
               
               
                 DDR1 
                 780 
                 Discoidin domain receptor family, member 1 
               
               
                 NINJ2 
                 4815 
                 Ninjurin 2 
               
               
                 DCHS2 
                 54798 
                 Dachsous 2 ( Drosophila ) 
               
               
                 ITGAM 
                 3684 
                 Integrin, alpha M (complement component 3 receptor 3 subunit) 
               
               
                 SCARB2 
                 950 
                 Scavenger receptor class B, member 2 
               
               
                 CYR61 
                 3491 
                 Cysteine-rich, angiogenic inducer, 61 
               
               
                 PVRL2 
                 5819 
                 Poliovirus receptor-related 2 (herpesvirus entry mediator B) 
               
               
                 PTK2B 
                 2185 
                 PTK2B protein tyrosine kinase 2 beta 
               
               
                 SELPLG 
                 6404 
                 Selectin P ligand 
               
               
                 GP1BA 
                 2811 
                 Glycoprotein Ib (platelet), alpha 
               
               
                   
                   
                 polypeptide 
               
               
                 VCL 
                 7414 
                 Vinculin 
               
               
                 CXCR3 
                 2833 
                 Chemokine (C—X—C motif) receptor 3 
               
               
                 WFDC1 
                 58189 
                 WAP four-disulfide core domain 1 
               
               
                 DLG1 
                 1739 
                 Discs, large homolog 1 ( Drosophila ) 
               
               
                 ENTPD1 
                 953 
                 Ectonucleoside triphosphate diphosphohydrolase 1 
               
               
                 CTNNA3 
                 29119 
                 Catenin (cadherin-associated protein), alpha 3 
               
               
                 PPFIA1 
                 8500 
                 Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacl 
               
               
                 NF2 
                 4771 
                 Neurofibromin 2 (bilateral acoustic neuroma) 
               
            
           
           
               
            
               
                 NRC-9 (cell growth) 
               
            
           
           
               
               
               
            
               
                 WFDC1 
                 58189 
                 WAP four-disulfide core domain 1 
               
               
                 CDH13 
                 1012 
                 Cadherin 13, H-cadherin 
               
               
                   
                   
                 (heart) 
               
               
                 ETV4 
                 2118 
                 Ets variant gene 4 (E1A enhancer binding protein, E1AF) 
               
               
                 DDR1 
                 780 
                 Discoidin domain receptor family, member 1 
               
               
                 PLEKHC1 
                 10979 
                 Pleckstrin homology domain containing, family C (with FERM domain) mem   
               
               
                 SELPLG 
                 6404 
                 Selectin P ligand 
               
               
                 CYR61 
                 3491 
                 Cysteine-rich, angiogenic inducer, 61 
               
               
                 TKT 
                 7086 
                 Transketolase (Wernicke-Korsakoff syndrome) 
               
               
                 VAX2 
                 25806 
                 Ventral anterior homeobox 2 
               
               
                 RAI1 
                 10743 
                 Retinoic acid induced 1 
               
               
                 SEMA6A 
                 57556 
                 Sema domain, transmembrane domain (TM), and cytoplasmic domain, (serr   
               
               
                   
                   
                 6A 
               
               
                 DLG1 
                 1739 
                 Discs, large homolog 1 ( Drosophila ) 
               
               
                 BTG1 
                 694 
                 B-cell translocation gene 1, anti- 
               
               
                   
                   
                 proliferative 
               
               
                 PTCH1 
                 5727 
                 Patched homolog 1 
               
               
                   
                   
                 ( Drosophila ) 
               
               
                 FGF20 
                 26281 
                 Fibroblast growth factor 20 
               
               
                 OGFR 
                 11054 
                 Opioid growth factor receptor 
               
               
                 NINJ2 
                 4815 
                 Ninjurin 2 
               
               
                 MORF4L2 
                 9643 
                 Mortality factor 4 like 2 
               
               
                 VCL 
                 7414 
                 Vinculin 
               
               
                 ESR2 
                 2100 
                 Estrogen receptor 2 (ER beta) 
               
               
                 OPHN1 
                 4983 
                 Oligophrenin 1 
               
               
                 NTRK3 
                 4916 
                 Neurotrophic tyrosine kinase, receptor, type 3 
               
               
                 CDKN2C 
                 1031 
                 Cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) 
               
               
                 CDK5R1 
                 8851 
                 Cyclin-dependent kinase 5, regulatory subunit 1 
               
               
                   
                   
                 (p35) 
               
               
                 TOP2B 
                 7155 
                 Topoisomerase (DNA) II beta 180 kDa 
               
               
                 PPT1 
                 5538 
                 Palmitoyl-protein thioesterase 1 (ceroid-lipofuscinosis, neuronal 1, infantile) 
               
               
                 GDF2 
                 2658 
                 Growth differentiation factor 2 
               
               
                 GFRA3 
                 2676 
                 GDNF family receptor alpha 3 
               
               
                 GP1BA 
                 2811 
                 Glycoprotein Ib (platelet), alpha 
               
               
                   
                   
                 polypeptide 
               
               
                 PPP2CB 
                 5516 
                 Protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform 
               
               
                   
               
               
                     indicates data missing or illegible when filed 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
               
                   
               
               
                 Performance of the validation of the marker sets in 3 testing datasets 
               
               
                   
               
             
            
               
                 ER+ sample 
               
            
           
           
               
               
               
               
            
               
                 Group 
                 Test set 1 (173 samples)* 
                 Test set 2 (74 samples) 
                 Test set 3 (201 samples) 
               
               
                   
               
               
                 Low-risk 
                 N = 99, R = 57.2%, 
                 N = 22, R = 29.7%, 
                 N = 87, R = 43.3%, 
               
               
                   
                 R1 = 93.9% 
                 R1 = 90.9% 
                 R1 = 86.8% 
               
               
                 Intermediate 
                 N = 34, R = 19.6%, 
                 N = 52, R = 70.3%, 
                 N = 78, R = 38.8%, R1 = 69.2% 
               
               
                   
                 R1 = 82.4% 
                 R1 = 79.7% 
               
               
                 High-risk 
                 N = 40, R = 23.1%, 
                 — 
                 N = 36, R = 17.9%, R2 = 33.3% 
               
               
                   
                 R2 = 42.5% 
               
               
                   
               
            
           
           
               
            
               
                 ER− sample 
               
            
           
           
               
               
               
               
            
               
                 Group 
                 Test set 1 (46 samples)* 
                 Test set 2 (43 samples) 
                 Test set 3 (31 samples) 
               
               
                   
               
               
                 Low-risk 
                 N = 9, R = 19.6%, 
                 N = 13, R = 30.2%, 
                 N = 14, R = 45.2%, R1 = 100% 
               
               
                   
                 R1 = 100% 
                 R1 = 92.3% 
               
               
                 High-risk 
                 N = 37, R = 80.4%, 
                 N = 30, R = 69.8%, 
                 N = 17, R = 54.8%, R2 = 35.3% 
               
               
                   
                 R2 = 51.4% 
                 R2 = 40% 
               
               
                   
               
               
                 Notes: 
               
               
                 *There are 295 samples in the original Test set 1. However, it includes 76 samples, which are from van&#39;t Veer et al., Nature, 415: 530, 2002. Because we used van&#39;t Veer dataset (van&#39;t Veer et al., Nature, 415: 530, 2002) as a training set, we then removed these 76 samples from the 295 samples. Therefore, Test set 1 contains 219 samples. 
               
               
                 1. N represents sample number 
               
               
                 2. R represents the ratio of the sample number in the group to the total sample number of test set 
               
               
                 3. R1 represents the percentage of the samples having non-recurrence (accuracy) 
               
               
                 4. R2 represents the percentage of the samples having recurrence (accuracy) 
               
               
                 5. Test set 1 is from Chang et al., PNAS, 2005 
               
               
                 6. Test set 2 is from Koe et al., Cancer Cell, 2006 
               
               
                 7. Test set 3 is from Sotiriou et al., J. Natl Cancer Inst, 98: 262, 2006 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Comparisons of combinatory usage of marker sets and each 
               
               
                 individual marker set for predicting low-risk group samples 
               
            
           
           
               
               
               
            
               
                   
                 Marker set 
                 Accuracy (in low-risk group) 
               
               
                   
                   
               
               
                   
                   
                 Test set 1 (173 samples) 
               
               
                   
                 NRC-1 
                 92.80% 
               
               
                   
                 NRC-2 
                 91.80% 
               
               
                   
                 NRC-3 
                 92.20% 
               
               
                   
                 NRC-1, 2, 3 
                   94% 
               
               
                   
                   
                 Test set 2 (74 samples) 
               
               
                   
                 NRC-1 
                 86.80% 
               
               
                   
                 NRC-2 
                 88.90% 
               
               
                   
                 NRC-3 
                 78.30% 
               
               
                   
                 NRC-1, 2, 3 
                   91% 
               
               
                   
                   
                 Test set 3 (201 samples) 
               
               
                   
                 NRC-1 
                 83.10% 
               
               
                   
                 NRC-2 
                 80.50% 
               
               
                   
                 NRC-3 
                 79.50% 
               
               
                   
                 NRC-1, 2, 3 
                   87% 
               
            
           
           
               
            
               
                 ER− samples 
               
            
           
           
               
               
               
            
               
                   
                   
                 Test set 1 (46 samples)* 
               
               
                   
                 NRC-7 
                   76% 
               
               
                   
                 NRC-8 
                 72.70% 
               
               
                   
                 NRC-9 
                 56.50% 
               
               
                   
                 NRC-7, 8, 9 
                   100% 
               
               
                   
                   
                 Test set 2 (43 samples) 
               
               
                   
                 NRC-7 
                   85% 
               
               
                   
                 NRC-8 
                 84.20% 
               
               
                   
                 NRC-9 
                 73.10% 
               
               
                   
                 NRC-7, 8, 9 
                 92.30% 
               
               
                   
                   
                 Test set 3 (31 samples) 
               
               
                   
                 NRC-7 
                   91% 
               
               
                   
                 NRC-8 
                   100% 
               
               
                   
                 NRC-9 
                 86.40% 
               
               
                   
                 NRC-7, 8, 9 
                   100% 
               
               
                   
                   
               
               
                   
                 Note: 
               
               
                   
                 The datasets used are the same as those in Table 2. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
               
                   
               
               
                 List of Cancers 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                   
                 Acute Lymphoblastic Leukemia, Adult 
               
               
                   
                 Acute Lymphoblastic Leukemia, Childhood 
               
               
                   
                 Acute Myeloid Leukemia, Adult 
               
               
                   
                 Acute Myeloid Leukemia, Childhood 
               
               
                   
                 Adrenocortical Carcinoma 
               
               
                   
                 Adrenocortical Carcinoma, Childhood 
               
               
                   
                 AIDS-Related Cancers 
               
               
                   
                 AIDS-Related Lymphoma 
               
               
                   
                 Anal Cancer 
               
               
                   
                 Appendix Cancer 
               
               
                   
                 Astrocytomas, Childhood) 
               
               
                   
                 Atypical Teratoid/Rhabdoid Tumor, Childhood, Central 
               
               
                   
                 Nervous System 
               
               
                   
                 Basal Cell Carcinoma, see Skin Cancer 
               
               
                   
                 (Nonmelanoma) 
               
               
                   
                 Bile Duct Cancer, Extrahepatic 
               
               
                   
                 Bladder Cancer 
               
               
                   
                 Bladder Cancer, Childhood 
               
               
                   
                 Bone Cancer, Osteosarcoma and Malignant Fibrous 
               
               
                   
                 Histiocytoma 
               
               
                   
                 Brain Stem Glioma, Childhood 
               
               
                   
                 Brain Tumor, Adult 
               
               
                   
                 Brain Tumor, Brain Stem Glioma, Childhood 
               
               
                   
                 Brain Tumor, Central Nervous System Atypical 
               
               
                   
                 Teratoid/Rhabdoid Tumor, Childhood 
               
               
                   
                 Brain Tumor, Central Nervous System Embryonal 
               
               
                   
                 Tumors, Childhood 
               
               
                   
                 Brain Tumor, Craniopharyngioma, Childhood 
               
               
                   
                 Brain Tumor, Ependymoblastoma, Childhood 
               
               
                   
                 Brain Tumor, Ependymoma, Childhood 
               
               
                   
                 Brain Tumor, Medulloblastoma, Childhood 
               
               
                   
                 Brain Tumor, Medulloepithelioma, Childhood 
               
               
                   
                 Brain Tumor, Pineal Parenchymal Tumors of 
               
               
                   
                 Intermediate Differentiation, Childhood) 
               
               
                   
                 Brain Tumor, Supratentorial Primitive Neuroectodermal 
               
               
                   
                 Tumors and Pineoblastoma, Childhood 
               
               
                   
                 Brain and Spinal Cord Tumors, Childhood (Other) 
               
               
                   
                 Breast Cancer 
               
               
                   
                 Breast Cancer and Pregnancy 
               
               
                   
                 Breast Cancer, Childhood 
               
               
                   
                 Breast Cancer, Male 
               
               
                   
                 Bronchial Tumors, Childhood 
               
               
                   
                 Burkitt Lymphoma 
               
               
                   
                 Carcinoid Tumor, Childhood 
               
               
                   
                 Carcinoid Tumor, Gastrointestinal 
               
               
                   
                 Carcinoma of Unknown Primary 
               
               
                   
                 Central Nervous System Atypical Teratoid/Rhabdoid 
               
               
                   
                 Tumor, Childhood 
               
               
                   
                 Central Nervous System Embryonal Tumors, Childhood 
               
               
                   
                 Central Nervous System Lymphoma, Primary 
               
               
                   
                 Cervical Cancer 
               
               
                   
                 Cervical Cancer, Childhood 
               
               
                   
                 Childhood Cancers 
               
               
                   
                 Chordoma, Childhood 
               
               
                   
                 Chronic Lymphocytic Leukemia 
               
               
                   
                 Chronic Myelogenous Leukemia 
               
               
                   
                 Chronic Myeloproliferative Disorders 
               
               
                   
                 Colon Cancer 
               
               
                   
                 Colorectal Cancer, Childhood 
               
               
                   
                 Craniopharyngioma, Childhood 
               
               
                   
                 Cutaneous T-Cell Lymphoma, see Mycosis Fungoides 
               
               
                   
                 and Sézary Syndrome 
               
               
                   
                 Embryonal Tumors, Central Nervous System, 
               
               
                   
                 Childhood 
               
               
                   
                 Endometrial Cancer 
               
               
                   
                 Ependymoblastoma, Childhood 
               
               
                   
                 Ependymoma, Childhood 
               
               
                   
                 Esophageal Cancer 
               
               
                   
                 Esophageal Cancer, Childhood 
               
               
                   
                 Ewing Sarcoma Family of Tumors 
               
               
                   
                 Extracranial Germ Cell Tumor, Childhood 
               
               
                   
                 Extragonadal Germ Cell Tumor 
               
               
                   
                 Extrahepatic Bile Duct Cancer 
               
               
                   
                 Eye Cancer, Intraocular Melanoma 
               
               
                   
                 Eye Cancer, Retinoblastoma 
               
               
                   
                 Gallbladder Cancer 
               
               
                   
                 Gastric (Stomach) Cancer 
               
               
                   
                 Gastric (Stomach) Cancer, Childhood 
               
               
                   
                 Gastrointestinal Carcinoid Tumor 
               
               
                   
                 Gastrointestinal Stromal Tumor (GIST) 
               
               
                   
                 Gastrointestinal Stromal Cell Tumor, Childhood 
               
               
                   
                 Germ Cell Tumor, Extracranial, Childhood 
               
               
                   
                 Germ Cell Tumor, Extragonadal 
               
               
                   
                 Germ Cell Tumor, Ovarian 
               
               
                   
                 Gestational Trophoblastic Tumor 
               
               
                   
                 Glioma, Adult 
               
               
                   
                 Glioma, Childhood Brain Stem 
               
               
                   
                 Hairy Cell Leukemia 
               
               
                   
                 Head and Neck Cancer 
               
               
                   
                 Hepatocellular (Liver) Cancer, Adult (Primary) 
               
               
                   
                 Hepatocellular (Liver) Cancer, Childhood (Primary) 
               
               
                   
                 Histiocytosis, Langerhans Cell 
               
               
                   
                 Hodgkin Lymphoma, Adult 
               
               
                   
                 Hodgkin Lymphoma, Childhood 
               
               
                   
                 Hypopharyngeal Cancer 
               
               
                   
                 Intraocular Melanoma 
               
               
                   
                 Islet Cell Tumors (Endocrine Pancreas) 
               
               
                   
                 Kaposi Sarcoma 
               
               
                   
                 Kidney (Renal Cell) Cancer 
               
               
                   
                 Kidney Cancer, Childhood 
               
               
                   
                 Langerhans Cell Histiocytosis 
               
               
                   
                 Laryngeal Cancer 
               
               
                   
                 Laryngeal Cancer, Childhood 
               
               
                   
                 Leukemia, Acute Lymphoblastic, Adult 
               
               
                   
                 Leukemia, Acute Lymphoblastic, Childhood 
               
               
                   
                 Leukemia, Acute Myeloid, Adult 
               
               
                   
                 Leukemia, Acute Myeloid, Childhood 
               
               
                   
                 Leukemia, Chronic Lymphocytic 
               
               
                   
                 Leukemia, Chronic Myelogenous 
               
               
                   
                 Leukemia, Hairy Cell 
               
               
                   
                 Lip and Oral Cavity Cancer 
               
               
                   
                 Liver Cancer, Adult (Primary) 
               
               
                   
                 Liver Cancer, Childhood (Primary 
               
               
                   
                 Lung Cancer, Non-Small Cell 
               
               
                   
                 Lung Cancer, Small Cell 
               
               
                   
                 Lymphoma, AIDS-Related 
               
               
                   
                 Lymphoma, Burkitt 
               
               
                   
                 Lymphoma, Cutaneous T-Cell, see Mycosis Fungoides 
               
               
                   
                 and Sezary Syndrome 
               
               
                   
                 Lymphoma, Hodgkin, Adult 
               
               
                   
                 Lymphoma, Hodgkin, Childhood 
               
               
                   
                 Lymphoma, Non-Hodgkin, Adult 
               
               
                   
                 Lymphoma, Non-Hodgkin, Childhood 
               
               
                   
                 Lymphoma, Primary Central Nervous System 
               
               
                   
                 Macroglobulinemia, Waldenstrom 
               
               
                   
                 Malignant Fibrous Histiocytoma of Bone and 
               
               
                   
                 Osteosarcoma 
               
               
                   
                 Medulloblastoma, Childhood 
               
               
                   
                 Medulloepithelioma, Childhood 
               
               
                   
                 Melanoma 
               
               
                   
                 Melanoma, Intraocular (Eye) 
               
               
                   
                 Merkel Cell Carcinoma 
               
               
                   
                 Mesothelioma, Adult Malignant 
               
               
                   
                 Mesothelioma, Childhood 
               
               
                   
                 Metastatic Squamous Neck Cancer with Occult Primary 
               
               
                   
                 Mouth Cancer 
               
               
                   
                 Multiple Endocrine Neoplasia Syndrome, Childhood 
               
               
                   
                 Multiple Myeloma/Plasma Cell Neoplasm 
               
               
                   
                 Mycosis Fungoides 
               
               
                   
                 Myelodysplastic Syndromes 
               
               
                   
                 Myelodysplastic/Myeloproliferative Neoplasms 
               
               
                   
                 Myelogenous Leukemia, Chronic 
               
               
                   
                 Myeloid Leukemia, Adult Acute 
               
               
                   
                 Myeloid Leukemia, Childhood Acute 
               
               
                   
                 Myeloma, Multiple 
               
               
                   
                 Myeloproliferative Disorders, Chronic 
               
               
                   
                 Nasal Cavity and Paranasal Sinus Cancer 
               
               
                   
                 Nasopharyngeal Cancer 
               
               
                   
                 Nasopharyngeal Cancer, Childhood 
               
               
                   
                 Neuroblastoma 
               
               
                   
                 Non-Hodgkin Lymphoma, Adult 
               
               
                   
                 Non-Hodgkin Lymphoma, Childhood 
               
               
                   
                 Non-Small Cell Lung Cancer 
               
               
                   
                 Oral Cancer, Childhood 
               
               
                   
                 Oral Cavity Cancer, Lip and 
               
               
                   
                 Oropharyngeal Cancer 
               
               
                   
                 Osteosarcoma and Malignant Fibrous Histiocytoma of 
               
               
                   
                 Bone 
               
               
                   
                 Ovarian Cancer, Childhood 
               
               
                   
                 Ovarian Epithelial Cancer 
               
               
                   
                 Ovarian Germ Cell Tumor 
               
               
                   
                 Ovarian Low Malignant Potential Tumor 
               
               
                   
                 Pancreatic Cancer 
               
               
                   
                 Pancreatic Cancer, Childhood 
               
               
                   
                 Pancreatic Cancer, Islet Cell Tumors 
               
               
                   
                 Papillomatosis, Childhood 
               
               
                   
                 Paranasal Sinus and Nasal Cavity Cancer 
               
               
                   
                 Parathyroid Cancer 
               
               
                   
                 Penile Cancer 
               
               
                   
                 Pharyngeal Cancer 
               
               
                   
                 Pineal Parenchymal Tumors of Intermediate 
               
               
                   
                 Differentiation, Childhood 
               
               
                   
                 Pineoblastoma and Supratentorial Primitive 
               
               
                   
                 Neuroectodermal Tumors, Childhood 
               
               
                   
                 Pituitary Tumor 
               
               
                   
                 Plasma Cell Neoplasm/Multiple Myeloma 
               
               
                   
                 Pleuropulmonary Blastoma 
               
               
                   
                 Pregnancy and Breast Cancer 
               
               
                   
                 Primary Central Nervous System Lymphoma 
               
               
                   
                 Prostate Cancer 
               
               
                   
                 Rectal Cancer 
               
               
                   
                 Renal Cell (Kidney) Cancer 
               
               
                   
                 Renal Cell (Kidney) Cancer, Childhood 
               
               
                   
                 Renal Pelvis and Ureter, Transitional Cell Cancer 
               
               
                   
                 Respiratory Tract Carcinoma Involving the NUT Gene 
               
               
                   
                 on Chromosome 15 
               
               
                   
                 Retinoblastoma 
               
               
                   
                 Rhabdomyosarcoma, Childhood 
               
               
                   
                 Salivary Gland Cancer 
               
               
                   
                 Salivary Gland Cancer, Childhood 
               
               
                   
                 Sarcoma, Ewing Sarcoma Family of Tumors 
               
               
                   
                 Sarcoma, Kaposi 
               
               
                   
                 Sarcoma, Soft Tissue, Adult 
               
               
                   
                 Sarcoma, Soft Tissue, Childhood 
               
               
                   
                 Sarcoma, Uterine 
               
               
                   
                 Sezary Syndrome 
               
               
                   
                 Skin Cancer (Nonmelanoma) 
               
               
                   
                 Skin Cancer, Childhood 
               
               
                   
                 Skin Cancer (Melanoma) 
               
               
                   
                 Skin Carcinoma, Merkel Cell 
               
               
                   
                 Small Cell Lung Cancer 
               
               
                   
                 Small Intestine Cancer 
               
               
                   
                 Soft Tissue Sarcoma, Adult 
               
               
                   
                 Soft Tissue Sarcoma, Childhood 
               
               
                   
                 Squamous Cell Carcinoma, see Skin Cancer 
               
               
                   
                 (Nonmelanoma) 
               
               
                   
                 Squamous Neck Cancer with Occult Primary, 
               
               
                   
                 Metastatic 
               
               
                   
                 Stomach (Gastric) Cancer 
               
               
                   
                 Stomach (Gastric) Cancer, Childhood 
               
               
                   
                 Supratentorial Primitive Neuroectodermal Tumors, 
               
               
                   
                 Childhood 
               
               
                   
                 T-Cell Lymphoma, Cutaneous, 
               
               
                   
                 Testicular Cancer 
               
               
                   
                 Throat Cancer 
               
               
                   
                 Thymoma and Thymic Carcinoma 
               
               
                   
                 Thymoma and Thymic Carcinoma, Childhood 
               
               
                   
                 Thyroid Cancer 
               
               
                   
                 Thyroid Cancer, Childhood 
               
               
                   
                 Transitional Cell Cancer of the Renal Pelvis and Ureter 
               
               
                   
                 Trophoblastic Tumor, Gestational 
               
               
                   
                 Ureter and Renal Pelvis, Transitional Cell Cancer 
               
               
                   
                 Urethral Cancer 
               
               
                   
                 Uterine Cancer, Endometrial 
               
               
                   
                 Uterine Sarcoma 
               
               
                   
                 Vaginal Cancer 
               
               
                   
                 Vaginal Cancer, Childhood 
               
               
                   
                 Vulvar Cancer 
               
               
                   
                 Waldenström Macroglobulinemia 
               
               
                   
                 Wilms Tumor