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A MULTIGENE ASSAY

20180073083 ยท 2018-03-15

    Inventors

    Cpc classification

    International classification

    Abstract

    An in vitro method of determining the type of a fibroepithelial tumour of the breast in a biological sample is provided. The method comprises the steps of obtaining an expression profile of one or more genes selected from the group consisting of PRAME, ADH1 B, CTHRC1, NPTX2, NEFL, ABCA8, DAPL1, TP63_v2, COL17A1, GCNT2, CCL19, MMP3, FN1, TRERF1, TRIM29, TESC, KIF20A, UHRF1, HEPACAM2, APOD, SERHL2. KIF15, HOXD13, GAGE2B, CALML5, C2orf40, ADH1C, CYP1B1, SPAG11B, GRB7, UBE2C, SYNGAP1, TP63_v1, LAMB1, OR5P3, SPC25, SHISA2, SCARA5, LHX2, RORC, DPYSL4, CH25H, and CHST1 in a sample and determining the differential activity of the one or more genes relative to a control; correlating the differential activity of the one or more genes relative to the control to obtain a p-score; and determining the type of fibroepithelial tumour based on the p-score, wherein a p-score of less than 0.5 is indicative of a fibroadenoma and a p-score of 0.5 and above is indicative of phyllodes tumour. Particularly, the said method is exemplified using an expression profile of five genes comprising of PRAME, FN1, CCL19, ABCA8 and APOD. A method for managing the treatment of a subject with a fibroepithelial tumour of the breast is also provided as well as a kit when used in the methods of the present invention.

    Claims

    1-22. (canceled)

    23. A method of determining the type of fibroepithelial tumour of the breast, in a biological sample in vitro, comprising: obtaining an expression profile of a combination of genes comprising PRAME, ABCA8, CCL19, FN1, and APOD in said sample; obtaining an expression profile of one or more normalized genes for use as a control; determining the differential activity of PRAME, ABCA8, CCL19, FN1 and APOD relative to the control based on the expression profile of the one or more genes and one or more normalized genes; correlating the differential activity of PRAME, ABCA8, CCL19, FN1 and APOD relative to the control to obtain a p-score using a predictive algorithm, wherein the predictive algorithm is: p = e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. .Math. CCL .Math. .Math. 19 ) 1 + e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. CCL .Math. .Math. 19 ) ; and determining the type of fibroepithelial tumour based on the p-score, wherein a p-score of less than 0.5 is indicative of a fibroadenoma and a p-score of 0.5 and above is indicative of phyllodes tumour.

    24. The method of claim 23, wherein the combination of genes further comprises one or more genes selected from TRIM29 and NPTX2.

    25. The method of claim 23, wherein the one or more normalized genes are selected from the group consisting of RMRP, RPL18, RPLP2, SNORA61 and SNORA45.

    26. The method of claim 23, wherein the one or more normalized genes consist of RMRP, RPL18, RPLP2, SNORA61 and SNORA45.

    27. The method of claim 23, wherein the biological sample is selected from the group consisting of an organ, tissue, fraction, and a cell.

    28. The method of claim 23, wherein the biological sample is a malignant tumour sample.

    29. The method of claim 23, wherein the biological sample is a benign tumour sample.

    30. The method of claim 28, wherein the tumour sample is a breast sample.

    31. The method of claim 23, further comprising extracting RNA from the sample for obtaining the expression profile of the one or more genes and one or more normalized genes.

    32. The method of claim 23, wherein the expression profile of the one or more genes and one or more normalized genes is obtained from the same biological sample.

    33. The method of claim 31, wherein the expression profile of the one or more genes and one or more normalized genes is obtained by a quantitative PCR method.

    34. A method for managing the treatment of a subject with a fibroepithelial tumour of the breast, comprising: obtaining an expression profile of a combination of genes comprising PRAME, ABCA8, CCL19, FN1 and APOD, in a biological sample obtained from the subject; obtaining an expression profile of one or more normalized genes for use as a control; determining the differential activity of PRAME, ABCA8, CCL19, FN1 and APOD relative to the control based on the expression profile of the one or more genes and one or more normalized genes; correlating the differential activity of PRAME, ABCA8, CCL19, FN1 and APOD relative to the control to obtain a p-score using a predictive algorithm, wherein the predictive algorithm is: p = e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. .Math. CCL .Math. .Math. 19 ) 1 + e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. CCL .Math. .Math. 19 ) ; determining the type of fibroepithelial tumour based on the p-score, wherein a p-score of less than 0.5 is indicative of fibroadenoma and a p-score of 0.5 and above is indicative of phyllodes tumour; and selecting the treatment of the patient based upon the type of fibroepithelial tumour and p-score.

    35. A kit when used in a method of determining the type of fibroepithelial tumour of the breast, in a biological sample in vitro, comprising: obtaining an expression profile of a combination of genes comprising PRAME, ABCA8, CCL19, FN1, and APOD in said sample; obtaining an expression profile of one or more normalized genes for use as a control; determining the differential activity of PRAME, ABCA8, CCL19, FN1 and APOD relative to the control based on the expression profile of the one or more genes and one or more normalized genes; correlating the differential activity of PRAME, ABCA8, CCL19, FN1 and APOD relative to the control to obtain a p-score using a predictive algorithm, wherein the predictive algorithm is: p = e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. .Math. CCL .Math. .Math. 19 ) 1 + e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. CCL .Math. .Math. 19 ) ; and determining the type of fibroepithelial tumour based on the p-score, wherein a p-score of less than 0.5 is indicative of a fibroadenoma and a p-score of 0.5 and above is indicative of phyllodes tumour; wherein the kit comprises: a primer pair for amplifying the combination of genes comprising PRAME, ABCA8, CCL19, FN1 and APOD.

    36. The kit of claim 35, wherein the combination of genes further comprises one or more genes selected from the group consisting of TRIM29 and NPTX2.

    37. The kit of claim 35, further comprising a primer pair for one or more normalized genes selected from the group consisting of RMRP, RPL18, RPLP2, SNORA61 and SNORA45.

    38. The kit of claim 37, wherein the one or more normalized genes consists of RMRP, RPL18, RPLP2, SNORA61 and SNORA45.

    Description

    BRIEF DESCRIPTION OF THE DRAWINGS

    [0027] The invention will be better understood with reference to the detailed description when considered in conjunction with the non-limiting examples and the accompanying drawings, in which:

    [0028] FIG. 1. Expression value of the five genes selected for normalization in 48 samples. Five genes with the least variable expression in 48 samples were selected for normalization. The genes selected were RMRP, RPL18, RPLP2, SNORA61 and SNORA45.

    [0029] FIG. 2. Boxplot of mean decrease in accuracy for 100 RF trees generated for each gene. Ct values of all 23 genes on 46 samples were analysed with Random Forest (RF) classifier algorithm (R version) to rank the importance of genes differentiating fibroadenomas and phyllodes tumours. Mean decrease in accuracy measures the importance of each gene to the classification.

    [0030] FIG. 3. Performance of the algorithm in predicting diagnosis in the independent set of 230 core biopsies. (A) the algorithm has sensitivity of 94.7% and specificity of 82.9%. The positive predictive value (PPV) of the algorithm is 77.3% and the negative predictive value (NPV) of the algorithm is 96.2%. (B) ROC curve of the performance of the algorithm on independent set of 230 core biopsies.

    DETAILED DESCRIPTION OF THE PRESENT INVENTION

    [0031] In a first aspect the present invention refers to a method of method of determining a fibroepithelial tumour of the breast, in a biological sample in vitro. The method may comprise: obtaining an expression profile of one or more genes selected from the group consisting of PRAME, ADH1B, CTHRC1, NPTX2, NEFL, ABCA8, DAPL1, TP63_v2, COL17A1, GCNT2, CCL19, MMP3, FN1, TRERF1, TRIM29, TESC, KIF20A, UHRF1, HEPACAM2, APOD, SERHL2, KIF15, HOXD13, GAGE2B, CALML5, C2orf40, ADH1C, CYP1B1, SPAG11B, GRB7, UBE2C, SYNGAP1, TP63_v1, LAMB1, OR5P3, SPC25, SHISA2, SCARA5, LHX2, RORC, DPYSL4, CH25H, and CHST1, in said sample; obtaining an expression profile of one or more normalized genes for use as a control; determining the differential activity of the one or more genes relative to the control based on the expression profile of the one or more genes and one or more normalized genes; correlating the differential activity of the one or more genes relative to the control to obtain a p-score; and determining the type of fibroepithelial tumour based on the p-score, wherein a p-score of less than 0.5 is indicative of a fibroadenoma and a p-score of 0.5 and higher is indicative of phyllodes tumour.

    [0032] The one or more genes may be selected from the group consisting of PRAME, TRIM29, FN1, CCL19, ABCA8, NPTX2 and APOD. In one embodiment, two, three, four or five or more genes may be selected from the group consisting of PRAME, TRIM29, FN1, CCL19, ABCA8, NPTX2 and APOD. In a preferred embodiment, the one or more genes may consist of PRAME, FN1, CCL19, ABCA8, and APOD.

    [0033] The one or more genes may be compared against one or more reference genes. A reference gene is a gene that is used as a basis of comparison with a gene of interest. It will be understood to one of skill in the art that the expression level of a gene of interest may be normalized against one or more reference genes to obtain an expression level of the gene of interest relative to the reference gene. Normalization of the expression level of a gene of interest against one or more reference genes allows for the comparison of the expression levels of multiple genes of interest within a sample and/or between samples.

    [0034] A reference gene may be a housekeeping gene or a normalized or normalization gene. One or more reference genes may be used alone or in combination. Housekeeping genes are well known in the art and refer to genes that are constitutively expressed in all cells of an organism under normal physiological conditions. Examples of housekeeping genes include but are not limited to -actin, GAPDH and 18S. A normalized gene is one that has whose expression varies minimally across all samples. Normalized genes may be selected based on the smallest value of coefficient of variance (mean/standard deviation). A normalized gene may be a housekeeping gene or any other gene whose expression varies minimally across all samples.

    [0035] In one embodiment, the one or more normalized genes may be selected from the group consisting of RMRP, RPL18, RPLP2, SNORA61 and SNORA45. In a preferred embodiment, the one or more normalized genes may consist of RMRP, RPL18, RPLP2, SNORA61 and SNORA45.

    [0036] In one embodiment, the step of correlating the differential activity of the one or more genes relative to the control to obtain a p-score comprises calculating a Ct (Delta threshold cycle) value for the one or more genes. It will generally be understood that the Ct value is the Ct value for a gene normalized to one or more normalized genes. In one example, the Ct of a gene to be tested may be the Ct value of the gene, normalized to one or more normalized genes. In a preferred example, the Ct of a gene to be tested may be the Ct value of the gene, normalized to the geometric mean (Ct of the five normalized genes) as follows: Ct of test gene=Ct of test genegeometric mean (Ct of five normalization genes)

    [0037] It will generally be understood that one, two, three, four, five or more normalization genes may be used in the Ct calculation.

    [0038] The Ct value may be used to calculate a p-score using a predictive algorithm. For example, a predictive algorithm may be:

    [00001] p = e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. .Math. CCL .Math. .Math. 19 ) 1 + e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. CCL .Math. .Math. 19 )

    [0039] In one embodiment, the biological sample may be selected from the group consisting of an organ, tissue, fraction, and a cell. A tissue sample may be obtained from tumour tissue selected from the group consisting of frozen tissue, tissue biopsies, circulating tumour cells, bodily fluids or other biological sample.

    [0040] The biological sample may be a fresh, frozen, or fixed sample. In one embodiment, the biological sample may be formalin-fixed and paraffin embedded (FFPE).

    [0041] In one embodiment, the bodily fluids may be selected from the group consisting of ascites, effusions, cerebrospinal and urine.

    [0042] In a one embodiment, the biological sample may be a malignant tumour sample. In another embodiment, the biological sample may be a benign tumour sample. In a further preferred embodiment, the tumour sample may be a sample from the breast.

    [0043] In one embodiment, RNA may be extracted from the biological sample in order to obtain the expression profile of the one or more genes and one or more normalized genes. In another embodiment, the expression profile of the one or more genes and one or more normalized genes is obtained from the sample biological sample. In yet another embodiment, the expression profile of the one or more genes and one or more normalized genes may be obtained by a quantitative PCR method.

    [0044] In another aspect, the present invention refers to a method for managing the treatment of a subject with a fibroepithelial tumour of the breast. The method may comprise: obtaining an expression profile of one or more genes selected from the group consisting of PRAME, ADH1B, CTHRC1, NPTX2, NEFL, ABCA8, DAPL1, TP63_v2, COL17A1, GCNT2, CCL19, MMP3, FN1, TRERF1, TRIM29, TESC, KIF20A, UHRF1, HEPACAM2, APOD, SERHL2, KIF15, HOXD13, GAGE2B, CALML5, C2orf40, ADH1C, CYP1B1, SPAG11B, GRB7, UBE2C, SYNGAP1, TP63_v1, LAMB1, OR5P3, SPC25, SHISA2, SCARA5, LHX2, RORC, DPYSL4, CH25H, and CHST1, in a biological sample obtained from the subject; obtaining an expression profile of one or more normalized genes for use as a control; determining the differential activity of the one or more genes relative to the control based on the expression profile of the one or more genes and one or more normalized genes; correlating the differential activity of the one or more genes relative to the control to obtain a p-score; determining the type of fibroepithelial tumour based on the p-score, wherein a p-score of less than 0.5 is indicative of fibroadenoma and a p-score of 0.5 and above is indicative of phyllodes tumour; and selecting the treatment of the patient based upon the type of fibroepithelial tumour and p-score.

    [0045] It will be generally understood that the treatment of a subject with a fibroepithelial tumour of the breast may be tailored based on the indication of a malignant phyllodes tumour or a benign fibroadenoma.

    [0046] In a third aspect, the present invention relates to a kit when used in the method of as described herein. The kit may comprise: a primer pair for amplifying the one or more genes selected from the group consisting of PRAME, ADH1B, CTHRC1, NPTX2, NEFL, ABCA8, DAPL1, TP63_v2, COL17A1, GCNT2, CCL19, MMP3, FN1, TRERF1, TRIM29, TESC, KIF20A, UHRF1, HEPACAM2, APOD, SERHL2, KIF15, HOXD13, GAGE2B, CALML5, C2orf40, ADH1C, CYP1B1, SPAG11B, GRB7, UBE2C, SYNGAP1, TP63_v1, LAMB1, OR5P3, SPC25, SHISA2, SCARA5, LHX2, RORC, DPYSL4, CH25H, and CHST1.

    [0047] In one embodiment, the one or more genes may be selected from the group consisting of PRAME, TRIM29, FN1, CCL19, ABCA8, NPTX2 and APOD. In another embodiment, the one or more genes may consist of PRAME, FN1, CCL19, ABCA8, and APOD.

    [0048] In one embodiment, the kit further comprises a primer pair for one or more normalized genes selected from the group consisting of RMRP, RPL18, RPLP2, SNORA61 and SNORA45. In a preferred embodiment, the one or more normalized genes may consist of RMRP, RPL18, RPLP2, SNORA61 and SNORA45.

    [0049] The invention illustratively described herein may suitably be practiced in the absence of any element or elements, limitation or limitations, not specifically disclosed herein. Thus, for example, the terms comprising, including, containing, etc. shall be read expansively and without limitation. Additionally, the terms and expressions employed herein have been used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the inventions embodied therein herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.

    [0050] The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein.

    [0051] Other embodiments are within the following claims and non-limiting examples. In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group.

    EXPERIMENTAL SECTION

    Example 1

    [0052] Study Population

    [0053] The study received approval from the Institutional Review Board. Forty eight formalin-fixed, paraffin embedded (FFPE) samples of fibroadenomas (FA) and phyllodes tumours (PT) were selected from the database of Department of Pathology, Singapore General Hospital (Table 1). Haematoxylin and eosin (H&E) stained slides were retrieved and reviewed. Diagnoses for the core biopsy samples were confirmed on corresponding excisions.

    TABLE-US-00001 TABLE 1 Clinical features of the training cohort from 38 patients. Fibro- Phyllodes adenomas tumours p- Features (n = 19) (n = 19) value Age Median (range) 35 (17-80) 44 (18-64) 0.09 Size Median (range) 25 (15-50) 65 (25-220) <0.001 Ethnicity, n (%) 0.2 Chinese 13 (68.4) 11 (57.9) Malay 0 (0.0) 4 (21.0) Indian 2 (10.5) 1 (5.3) Others 4 (21.1) 3 (15.8) Histology Simple fibroadenoma 15.sup.a Complex fibroadenoma 4.sup.c Benign phyllodes tumour 13.sup.b Borderline phyllodes tumour 3.sup.c Malignant phyllodes tumour 3.sup.c .sup.a5 paired core biopsies and surgical excisions; .sup.b4 paired core biopsies and surgical excisions; .sup.c1 paired core biopsy and surgical excision

    Example 2

    [0054] Gene Expression Profiling

    [0055] Sample Preparation and RNA Extraction

    [0056] Representative tumour area was identified and marked. 3-7 sections of 10 m sections from the same FFPE tumour block were obtained. Sections were deparaffinised in two changes of xylene for 2 minutes each then in three changes of absolute ethanol for 1 minute each. Macrodissection was performed immediately to retrieve the tumour area. RNA was extracted from the macrodissected tissue using the RNeasy FFPE kit (Qiagen, Germany) according to manufacturer's protocol with slight modifications. Briefly, buffer PKD and proteinase K was added after all ethanol was removed from the tissue. The tissue mixture was incubated overnight at 56 C. instead of 15 minutes as stated in the protocol, then it was incubated at 80 C. for 15 minutes followed by incubation on ice for 3 minutes. DNase I and DNase Booster Buffer was added and incubated in room temperature for 15 minutes after which buffer RBC was added to adjust for binding condition. Absolute ethanol was added and the entire lysate was then passed through a filter cartridge and washed with buffer RPE according to the manufacturer's instructions. Finally, RNA was eluted in 30 l nuclease-free water and stored at 80 C. immediately.

    [0057] Quality Assessment for RNA Extracted

    [0058] RNA extracted was quantified by Nanodrop Spectrophotometer (Thermo Scientific, USA). 100 ng was used for quality assessment by real-time amplification of the RPL13A gene (forward primer, 5-CACTTGGGGACAGCATGAG-3 (SEQ ID NO: 1), and reverse primer, 5-TAACCCCTTGGTTGTGCAT-3 (SEQ ID NO: 2) using the PowerSYBR Green RNA-to-CT 1-Step Kit (Life Technologies, USA) on the CFX96 Real-Time PCR machine (Bio-Rad Laboratories, USA), Samples with threshold cycle (Ct) below 29 passed for subsequent experiments.

    [0059] Expression Profiling by Whole-Genome DASL HT Assay

    [0060] 1 g of RNA were submitted for expression profiling at the Biopolis Shared Facilities, Agency of Science, Technology and Research (A*Star), Singapore. Samples were further subjected to quality assessment on a bioanalyzer before subjected to expression profiling on the Whole-Genome DASL (WG-DASL) HT Assay (Illumina, Inc., USA), The assay interrogates 29,377 features using the HumanHT-12 v4 BeadChip. Quantile-normalized gene expression data pre-analyzed using GenomeStudio was delivered.

    [0061] Selection of Normalization Genes

    [0062] Normalization genes were selected based on the smallest value of coefficient of variance (mean/standard deviation) among all samples. Five genes with the least variable expression were selected. The genes are RMRP, RPL18, RPLP2, SNORA61, and SNORA45 (FIG. 1).

    [0063] Selection of Potential Differentiating Genes

    [0064] Significance Analysis of Microarrays (SAM, R version 3.1.1) was employed to select significant genes that were differentially expressed between phyllodes tumours (PT) and fibroadenomas (FA). Then, genes were filtered based on the following criteria: 1) q-value less than 0.05; 2) mean difference of expression above 500; 3) R-fold above 1.5 (for genes highly expressed in PT) or less than 0.67 (for genes highly expressed in FA). List of genes after criteria applied is shown in Table 2. 43 genes were selected from the list for downstream applications.

    TABLE-US-00002 TABLE 2 Significant genes differentially expressed between fibroadenomas and phyllodes tumours. Accession Fold q- Gene Name Number Change value Mean (FA) Mean (PT) 1 CCL19* NM_006274.2 0.238 0.000 6401.37 1462.00 2 HEPACAM2* NM_198151.1 0.297 0.000 3357.07 1204.56 3 PRAME* NM_206956.1 3.219 0.000 271.22 2356.54 4 ADH1B* NM_000668.3 0.317 0.000 1555.38 361.27 5 LHX2* NM_004789.3 3.017 0.000 192.15 873.55 6 SCGB3A1 NM_052863.2 0.342 0.000 4349.65 1425.53 7 MAGEA4 NM_002362.4 2.622 0.000 98.31 682.85 8 C11orf87 NM_207645.1 2.603 0.000 290.63 1187.03 9 SCARA5* NM_173833.3 0.384 0.000 5991.51 2661.17 10 CALML5* NM_017422.3 0.388 0.000 3366.04 1500.41 11 ABCA8* NM_007168.2 0.394 0.000 5788.98 2538.10 12 C10orf65 NM_138413.2 0.396 0.000 1356.30 476.13 13 OR5P2 NM_153444.1 0.401 0.000 2461.50 931.51 14 HIST2H3C NM_021059.2 2.492 0.000 410.84 1621.87 15 ADAMTS14 NM_139155.2 2.479 0.000 332.15 1041.68 16 ADH1C* NM_000669.3 0.414 0.000 1476.03 496.99 17 DAPL1* NM_001017920.1 0.415 0.000 1533.29 596.97 18 CYP1B1* NM_000104.2 0.416 0.000 3070.42 1223.42 19 RORC* NM_001001523.1 0.416 0.000 3369.06 1315.81 20 INS-IGF2 NM_001042377.1 2.395 0.000 1499.89 5149.56 21 FBLN2 NM_001004019.1 0.420 0.000 1819.30 621.23 22 HMX1 NM_018942.1 2.350 0.000 636.45 2066.76 23 TOX3 NM_001080430.1 0.429 0.000 1554.70 549.13 24 UCN2 NM_033199.3 2.315 0.000 201.58 808.36 25 NPTX2* NM_002523.1 2.307 0.000 534.04 2133.35 26 C1orf116 NM_023938.4 0.450 0.000 6447.65 2744.49 27 SLCO2A1 NM_005630.1 0.451 0.000 2419.34 1179.40 28 SPAG11B* XM_943161.1 2.205 0.000 263.95 1319.11 29 CHST1* NM_003654.2 2.193 0.000 463.73 1758.28 30 GATA4 NM_002052.2 2.170 0.000 420.22 1044.98 31 FOXL2 NM_023067.2 2.163 0.000 298.64 851.84 32 C11orf9 NM_013279.1 2.153 0.000 2178.75 4718.14 33 PTK6 NM_005975.2 0.469 0.000 1625.63 594.36 34 ALDH3A1 NM_000691.3 0.476 0.000 1132.51 473.22 35 SLC6A10P NM_198857.1 2.098 0.000 836.63 2446.74 36 DMD NM_004006.1 0.477 0.000 4006.48 1884.54 37 FOLR1 NM_016724.1 0.480 0.000 3346.14 1464.66 38 COL17A1* NM_130778.1 0.480 0.000 5408.73 2820.70 39 BMPER NM_133468.3 2.078 0.000 442.89 1332.98 40 TP63_v2* NM_001114981.1 0.482 0.000 3334.56 1749.94 41 OR5P3* NM_153445.1 0.483 0.000 3498.35 1615.77 42 CEP55 NM_018131.3 2.068 0.000 620.51 1605.08 43 UBE2C* NM_181800.1 2.037 0.000 1083.86 3086.79 44 RERGL NM_024730.2 0.491 0.000 8754.38 4200.75 45 CHRDL1 NM_145234.2 0.493 0.000 964.70 434.81 46 HIST2H3A NM_001005464.2 2.023 0.000 1125.74 2996.04 47 ARHGAP28 NM_001010000.1 2.016 0.000 402.80 998.87 48 RAB26 NM_014353.4 0.499 0.000 2454.81 1086.37 49 ITPKA NM_002220.1 1.983 0.000 364.95 1256.14 50 PIP5K1B NM_003558.1 0.505 0.000 2060.46 874.85 51 OVOL2 NM_021220.2 0.508 0.000 3404.75 1731.30 52 DPYSL4* NM_006426.1 1.964 0.000 2600.24 6029.72 53 GOLSYN NM_017786.2 0.510 0.000 1196.96 649.42 54 HAO2 NM_016527.2 1.935 0.000 1094.93 2343.37 55 ODF3B NM_001014440.2 0.517 0.000 2348.32 975.50 56 TRIO NM_007118.2 1.931 0.000 983.89 2450.63 57 OMD NM_005014.1 0.518 0.000 2132.70 1094.13 58 CCR6 NM_031409.2 0.518 0.000 4754.45 1956.59 59 TP63_v1* NM_001114979.1 0.519 0.000 2294.56 1109.40 60 SNORD114- NR_003204.1 1.925 0.000 853.71 1982.01 11 61 SCN2A NM_021007.2 0.520 0.000 1381.68 678.87 62 GNAO1 NM_138736.1 0.522 0.000 2558.56 1387.49 63 MYH11 NM_001040114.1 0.524 0.000 10978.83 5947.62 64 NUF2 NM_031423.2 1.906 0.000 502.69 1134.83 65 SORBS2 NM_003603.4 0.525 0.000 2705.25 1260.39 66 DMKN NM_033317.2 0.530 0.000 5553.01 2875.06 67 C2orf40* NM_032411.1 0.533 0.000 7163.03 3881.54 68 SNORD113-2 NR_003230.1 1.860 0.000 2249.67 4955.17 69 ICA1 NM_004968.2 0.539 0.000 4094.35 2054.05 70 TRPV6 NM_018646.2 0.539 0.000 7207.76 3483.60 71 CX3CR1 NM_001337.3 0.543 0.000 2914.17 1294.22 72 TRIM29* NM_058193.1 0.550 0.000 2676.62 1509.53 73 RORC* NM_005060.3 0.550 0.000 1132.56 512.31 74 BNC2 NM_017637.4 1.814 0.000 672.28 1526.15 75 CCL14 NM_032962.2 0.553 0.000 5609.28 2625.91 76 HIST1H2BO NM_003527.4 1.807 0.000 903.41 2227.12 77 BIK NM_001197.3 0.553 0.000 4113.72 2168.46 78 TPD52 NM_005079.2 0.555 0.000 4477.83 2471.86 79 ERBB3 NM_001005915.1 0.557 0.000 2492.09 1233.05 80 CPXM2 NM_198148.1 0.558 0.000 1485.83 730.76 81 KIF15* NM_020242.1 1.771 0.000 845.62 1986.70 82 C9orf61 NM_004816.2 0.567 0.000 6350.94 3483.51 83 CH25H* NM_003956.2 1.758 0.000 3249.49 6596.97 84 LOC387882 NM_207376.1 1.733 0.000 2506.29 5511.78 85 CDC2 NM_033379.2 1.727 0.000 374.19 890.73 86 SPRY4 NM_030964.2 1.727 0.000 682.61 1601.01 87 BCORL1 NM_021946.2 1.711 0.000 578.68 1252.48 88 VASH2 NM_024749.2 1.695 0.000 868.19 1860.94 89 APOD* NM_001647.2 0.597 0.000 27261.88 14662.55 90 SNORD114-2 NR_003194.1 1.654 0.000 941.93 1938.27 91 HIST1H2AB NM_003513.2 1.649 0.000 998.86 2066.51 92 IFIT2 NM_001547.3 0.608 0.000 1615.48 834.68 93 DPP4 NM_001935.3 0.613 0.000 1642.02 867.59 94 DMPK NM_001081563.1 1.624 0.000 544.62 1072.50 95 SV2A NM_014849.2 1.624 0.000 3422.85 6383.33 96 HOXA5 NM_019102.2 0.629 0.000 9540.64 5156.14 97 NTRK2 NM_001018065.1 0.633 0.000 14191.59 8187.81 98 LOC653604 NM_001025303.1 1.568 0.000 2227.40 4100.91 99 UCHL1 NM_004181.3 1.562 0.000 6265.88 11750.85 100 ARSB NM_000046.2 1.561 0.000 738.12 1382.59 101 LAMB1 NM_002291.1 1.555 0.000 2604.77 4853.49 102 CD79A NM_001783.2 0.645 0.000 11756.75 6159.25 103 FN1* NM_212474.1 1.543 0.000 10854.37 19701.55 104 MAGED4 NM_001098800.1 1.535 0.000 3817.08 6777.09 105 COL5A2 NM_000393.2 1.528 0.000 5377.06 9945.28 106 CTAG1B NM_001327.1 3.267 0.005 351.12 2708.49 107 HOXD13* NM_000523.2 2.923 0.005 1228.70 2928.62 108 PRAME* NM_206955.1 2.720 0.005 315.35 1564.15 109 CYTL1 NM_018659.2 2.451 0.005 215.23 1102.61 110 HMGA2 NM_001015886.1 2.388 0.005 338.52 1072.97 111 KRT3 NM_057088.1 2.242 0.005 477.76 1757.73 112 KIF20A* NM_005733.1 2.200 0.005 621.79 1867.56 113 CKAP2L NM_152515.2 2.153 0.005 1131.57 2246.70 114 CHD5 NM_015557.1 2.134 0.005 617.17 2465.83 115 ASPHD1 NM_181718.3 2.052 0.005 653.11 1578.02 116 CDC42 NM_044472.1 2.037 0.005 611.55 1347.53 117 WISP1 NM_003882.2 1.971 0.005 323.17 1120.21 118 TGFB2 NM_003238.1 1.965 0.005 1485.78 3583.24 119 C6orf134 NM_024909.1 1.830 0.005 1976.87 3958.66 120 NECAB2 NM_019065.2 1.826 0.005 320.83 861.02 121 HSP90B3P NR_003130.1 1.785 0.005 2346.80 4540.93 122 MCM4 NM_182746.1 1.776 0.005 740.07 1454.59 123 FAM72D NM_207418.2 1.774 0.005 672.94 1521.88 124 GLIS1 NM_147193.1 1.773 0.005 1621.56 3544.42 125 ARHGAP28 NM_030672.2 1.723 0.005 405.31 925.08 126 HCFC1R1 NM_001002018.1 1.682 0.005 1110.66 2362.14 127 MEX3A NM_001093725.1 1.682 0.005 502.95 1145.83 128 UHRF1* NM_013282.2 1.679 0.005 1364.77 2768.18 129 SRPX2 NM_014467.1 1.511 0.005 3786.75 6682.12 130 TNFRSF19 NM_148957.2 1.505 0.005 3534.15 6462.72 131 OLFM4 NM_006418.3 0.425 0.006 4922.09 1865.57 132 MYBPC1 NM_002465.2 0.442 0.006 8807.86 4325.10 133 MBP NM_001025100.1 0.450 0.006 2337.70 1170.46 134 ITGB4 NM_001005731.1 0.496 0.006 8161.34 4380.08 135 SEMA3C NM_006379.2 0.499 0.006 1738.78 939.67 136 TNXA NR_001284.1 0.503 0.006 2870.44 1536.83 137 ABCA6 NM_172346.1 0.507 0.006 2887.42 1689.39 138 CDH3 NM_001793.3 0.509 0.006 1727.21 797.36 139 MMP3* NM_002422.3 0.509 0.006 7370.34 3440.73 140 IGJ NM_144646.2 0.525 0.006 11657.95 5536.68 141 MPPED2 NM_001584.1 0.530 0.006 1800.18 855.69 142 ESRP2 NM_024939.2 0.532 0.006 1396.29 806.60 143 KIAA1543 NM_001080429.1 0.533 0.006 7813.91 4351.06 144 LRRC26 XM_939320.1 0.534 0.006 21534.63 11639.52 145 CISH NM_145071.1 0.547 0.006 1111.81 503.47 146 CD300LG NM_145273.2 0.550 0.006 6029.22 3428.30 147 NAAA NM_014435.2 0.554 0.006 2540.54 1383.43 148 NTF5 NM_006179.3 0.559 0.006 1552.44 873.81 149 GCNT2* NM_001491.2 0.565 0.006 1244.85 591.56 150 BEND7 NM_152751.2 0.579 0.006 2081.16 1150.16 151 ADHFE1 NM_001077593.1 0.581 0.006 2700.68 1486.68 152 TMTC1 XM_928461.1 0.599 0.006 1775.89 950.71 153 ZNF683 NM_173574.1 0.602 0.006 1186.86 588.88 154 LAMA3 NM_000227.2 0.603 0.006 3102.16 1699.84 155 SLC44A4 NM_025257.1 0.607 0.006 1634.05 775.09 156 SPNS2 NM_001124758.1 0.608 0.006 2337.54 1176.42 157 C3 XM_941913.1 0.613 0.006 3019.27 1790.95 158 PKIB NM_032471.4 0.615 0.006 9669.95 5673.26 159 RNF39 NM_025236.2 0.617 0.006 6629.28 3876.69 160 ZMAT1 NM_032441.1 0.628 0.006 4823.99 2857.70 161 COL8A2 NM_005202.1 0.656 0.006 1654.50 999.00 162 FAM113B NM_138371.1 0.664 0.006 11107.68 6668.04 163 CTHRC1* NM_138455.2 1.629 0.008 1876.05 4266.54 164 HOXC10 NM_017409.2 1.519 0.008 1145.45 1960.25 165 SERHL2* NM_014509.3 0.469 0.009 3005.44 1304.93 166 IL17RE NM_153480.1 0.481 0.009 1020.90 451.33 167 FAM46C NM_017709.2 0.566 0.009 3404.03 1754.54 168 NTF4 NM_006179.4 0.591 0.009 1681.80 822.32 169 PDZD2 NM_178140.1 0.599 0.009 1892.49 1080.48 170 DST NM_183380.1 0.625 0.009 6094.06 3547.30 171 FAM13AOS NR_002806.2 0.640 0.009 1792.17 1060.99 172 NEFL* NM_006158.1 2.235 0.011 1207.97 3800.96 173 ADAMTS14 NM_139155.1 2.147 0.011 741.49 2476.27 174 GAGE8 NM_012196.1 2.136 0.011 76.18 606.27 175 SEMA7A NM_003612.1 1.679 0.011 466.84 1225.51 176 ADAMTS4 NM_005099.3 1.643 0.011 415.61 1061.23 177 IGDCC4 NM_020962.1 1.615 0.011 1416.17 2674.22 178 ZNF697 NM_001080470.1 1.586 0.011 1769.98 3270.23 179 KIF23 NM_138555.1 1.562 0.011 1592.93 2855.64 180 LMNA NM_005572.2 1.556 0.011 1366.60 2708.40 181 TMEM167A NM_174909.1 1.543 0.011 1034.23 2030.24 182 GPR144 NM_182611.1 0.399 0.012 2233.07 1377.46 183 ANXA8L1 NM_001098845.1 0.443 0.012 2553.16 1366.48 184 FGF12 NM_004113.3 0.481 0.012 3232.40 1532.51 185 PRR22 NM_153359.1 0.505 0.012 1131.53 520.07 186 B3GALT1 NM_020981.2 0.518 0.012 1950.99 987.39 187 SNCG NM_003087.1 0.521 0.012 2253.34 1014.55 188 TJP2 NM_201629.1 0.526 0.012 1240.59 691.40 189 NSUN7 NM_024677.3 0.528 0.012 1867.16 901.46 190 CRB3 NM_139161.2 0.542 0.012 1254.51 648.64 191 GCNT2* NM_145649.2 0.550 0.012 1919.87 908.79 192 SHROOM3 NM_020859.3 0.551 0.012 1795.73 922.72 193 MAL NM_022440.1 0.565 0.012 949.74 390.12 194 DYNLRB2 NM_130897.1 0.569 0.012 4168.95 2474.99 195 MATN2 NM_030583.2 0.574 0.012 10052.44 6120.20 196 SOX10 NM_006941.3 0.584 0.012 9462.89 5634.60 197 PSD4 NM_012455.2 0.586 0.012 8086.61 4639.92 198 ELANE NM_001972.2 0.592 0.012 1889.14 1072.16 199 RASSF6 NM_177532.3 0.601 0.012 4752.91 2773.06 200 IRX1 NM_024337.3 0.602 0.012 2571.54 1439.00 201 C5orf4 NM_016348.1 0.617 0.012 3890.59 2308.86 202 NTRK2 NM_001007097.1 0.619 0.012 11514.66 6827.91 203 NDRG2 NM_201539.1 0.630 0.012 5569.99 3347.51 204 SMOC2 NM_022138.1 0.643 0.012 4976.71 3154.28 205 PGM5 NM_021965.3 0.644 0.012 1755.43 1094.11 206 PDGFD NM_025208.3 0.655 0.012 3886.45 2311.57 207 N4BP2L1 NM_001079691.1 0.660 0.012 6019.26 3611.31 208 EPHA1 NM_005232.3 0.661 0.012 3800.40 2364.55 209 PAGE2B NM_001015038.1 2.368 0.013 673.59 2715.27 210 SULT2B1 NM_177973.1 0.489 0.013 1740.07 753.08 211 DUSP4 NM_001394.5 0.503 0.013 1331.30 773.25 212 FRMPD2 NM_001018071.2 0.518 0.013 1236.62 522.52 213 TSPAN7 NM_004615.2 0.541 0.013 2888.02 1471.26 214 C9orf47 NM_001001938.1 1.819 0.013 548.08 1312.29 215 C6orf134 NM_001031722.1 1.723 0.013 897.08 1932.25 216 COL12A1 NM_080645.1 1.722 0.013 539.58 1451.54 217 NR1D1 NM_021724.1 1.707 0.013 2301.41 4716.38 218 SHANK2 NM_012309.1 0.588 0.013 5854.52 3360.51 219 ABCA6 NM_080284.2 0.608 0.013 3315.73 1790.29 220 LRRC20 NM_018239.2 1.640 0.013 824.08 1772.58 221 REEP4 NM_025232.2 1.616 0.013 2039.11 3741.07 222 ERBB3 NM_001982.2 0.619 0.013 3119.59 1943.86 223 FMO2 NM_001460.2 0.620 0.013 12042.98 6604.46 224 SYNE2 NM_015180.3 0.622 0.013 2511.72 1472.52 225 CDCA4 NM_017955.2 1.592 0.013 3161.08 5549.14 226 CYYR1 NM_052954.2 0.644 0.013 1844.54 1083.32 227 SYNGAP1* NM_006772.1 1.913 0.014 2589.28 4932.32 228 EMILIN1 NM_007046.1 1.776 0.014 3037.94 7187.87 229 STMN1 NM_005563.3 1.743 0.014 451.33 961.24 230 FAM38B NM_022068.1 1.725 0.014 778.49 1721.00 231 RAB23 NM_016277.3 1.635 0.014 1576.94 3283.62 232 HOXA11AS NR_002795.2 1.634 0.014 934.89 1954.07 233 TRERF1* XM_945260.1 1.512 0.014 693.39 1212.20 234 PI16 NM_153370.2 0.448 0.015 12074.86 6681.91 235 HGD NM_000187.2 0.515 0.015 2866.55 1752.37 236 ANXA8L2 NM_001630.2 0.517 0.015 2506.01 1527.62 237 MAPT NM_016841.2 0.517 0.015 1483.95 822.41 238 C11orf92 NM_207429.2 0.523 0.015 1791.35 897.45 239 MIR200A NR_029834.1 0.536 0.015 1228.69 515.17 240 TNFRSF13B NM_012452.2 0.568 0.015 2609.63 1538.91 241 WISP3 NM_003880.2 0.570 0.015 2394.62 1393.60 242 STX19 NM_001001850.1 0.573 0.015 5365.54 2974.33 243 STRC NM_153700.2 0.589 0.015 1667.49 859.88 244 IL20RA NM_014432.2 0.599 0.015 1343.94 768.76 245 GGT6 NM_153338.1 0.600 0.015 2952.64 1700.81 246 WDR17 NM_170710.3 0.617 0.015 1416.91 866.17 247 TSTD1 NM_001113206.1 0.619 0.015 2282.38 1378.68 248 DSC3 NM_024423.1 0.652 0.015 5069.04 3017.29 249 MBP NM_001025101.1 0.654 0.015 1236.99 667.97 250 NET1 NM_005863.2 0.661 0.015 3705.97 2330.58 251 FAM129A NM_022083.1 0.664 0.015 6734.51 4255.89 252 N4BP2L1 NM_052818.1 0.667 0.015 6217.91 3817.98 253 PIP NM_002652.2 0.397 0.016 6718.19 2296.33 254 TP73L NM_003722.3 0.430 0.016 2113.29 1084.30 255 SCGB1D2 NM_006551.3 0.460 0.016 4848.27 1515.54 256 SHISA2* NM_001007538.1 1.949 0.016 958.25 2011.20 257 PCSK1 NM_000439.3 1.914 0.016 98.86 719.27 258 FXYD3 NM_021910.1 0.537 0.016 2357.88 1411.76 259 MARVELD3 NM_052858.3 0.572 0.016 1979.64 1247.22 260 EFEMP1 NM_004105.2 0.600 0.016 3088.12 1602.20 261 KIF11 NM_004523.2 1.658 0.016 681.89 1574.32 262 HIST1H2AJ NM_021066.2 1.650 0.016 1430.62 3077.09 263 PDGFD NM_025208.4 0.614 0.016 3768.43 1961.56 264 SLC44A4 NM_032794.1 0.631 0.016 1673.40 813.44 265 MFSD6 NM_017694.2 0.638 0.016 2501.20 1604.12 266 SLC29A4 NM_001040661.1 1.505 0.016 3231.92 5597.04 267 CASC5 NM_170589.2 1.914 0.017 651.06 1422.31 268 CENPE NM_001813.2 1.634 0.017 500.28 1002.10 269 KDM6B NM_001080424.1 1.622 0.017 1544.49 2639.29 270 BCAT1 NM_005504.4 1.596 0.017 1515.63 3364.82 271 PGAM4 NM_001029891.2 1.592 0.017 2255.10 4830.64 272 PCDH19 NM_020766.1 1.525 0.017 1203.45 2194.59 273 TFCP2L1 NM_014553.1 0.498 0.018 2441.00 1391.77 274 CMTM8 NM_178868.3 0.507 0.018 10265.71 6375.56 275 EDN3 NM_207033.1 0.523 0.018 5356.67 3193.40 276 SULT1A1 NM_177536.1 0.543 0.018 1935.16 1032.19 277 ABCA5 NM_018672.2 0.570 0.018 2016.20 1106.86 278 EPS8L2 NM_022772.2 0.571 0.018 2217.34 1283.15 279 TMTC1 NM_175861.1 0.582 0.018 2098.08 1387.73 280 ROPN1B NM_001012337.1 0.594 0.018 1135.64 607.63 281 ZBTB16 NM_006006.4 0.599 0.018 4783.21 2884.79 282 FLJ25996 NM_001001699.1 0.605 0.018 5190.08 3538.07 283 CYB5R2 NM_016229.2 0.607 0.018 1958.89 1175.93 284 WNT5B NM_030775.2 0.614 0.018 2648.34 1652.66 285 KLC3 NM_145275.1 0.647 0.018 1280.21 696.36 286 CYP2J2 NM_000775.2 0.661 0.018 5849.75 3598.37 287 GAGE2B* NM_001098411.3 2.931 0.019 1195.21 4768.49 288 SNORD113-8 NR_003236.1 1.886 0.019 1751.83 3389.32 289 CAMK2B XM_936314.1 0.536 0.019 1407.32 596.51 290 ZBTB16 NM_001018011.1 0.542 0.019 5137.94 2829.86 291 ATP13A4 NM_032279.2 0.548 0.019 1933.93 1059.11 292 ITIH5 NM_030569.3 0.550 0.019 5602.73 3009.71 293 C9orf152 NM_001012993.1 0.555 0.019 6449.96 3891.87 294 TSPAN18 NM_130783.2 1.803 0.019 932.15 1966.51 295 ASPM NM_018136.2 1.737 0.019 352.06 887.25 296 MUC16 NM_024690.2 0.597 0.019 2027.26 969.68 297 SEMA6B NM_020241.2 1.631 0.019 536.99 1059.44 298 NID2 NM_007361.2 1.577 0.019 1365.27 2905.18 299 HLA-DOA NM_002119.3 0.655 0.019 3773.82 2448.04 300 SAMD3 NM_001017373.2 0.509 0.021 1781.17 1014.57 301 BARX2 NM_003658.3 0.557 0.021 3897.03 2346.09 302 MAMDC2 NM_153267.3 0.583 0.021 2044.78 1282.76 303 LYPLAL1 NM_138794.1 0.591 0.021 3499.07 2176.27 304 TTC22 NM_017904.1 0.593 0.021 2382.69 1426.62 305 HJURP NM_018410.2 1.679 0.021 576.16 1302.81 306 MIR770 NR_030528.1 1.664 0.021 482.61 1022.51 307 ARHGAP8 NM_001017526.1 0.601 0.021 3786.67 2482.97 308 SNORD114-4 NR_003196.1 1.655 0.021 2341.72 4519.16 309 DBI NM_020548.4 0.610 0.021 1515.89 789.03 310 LMX1B NM_002316.1 0.618 0.021 6460.47 4118.79 311 CCNDBP1 NM_037370.1 0.628 0.021 4950.25 3139.22 312 SPDEF NM_012391.1 0.632 0.021 6304.32 4204.84 313 ACSM3 NM_005622.3 0.638 0.021 1450.26 842.78 314 FZD8 NM_031866.1 0.645 0.021 4235.97 2336.29 315 B4GALNT4 NM_178537.3 1.514 0.021 1775.68 3431.11 316 KIT NM_000222.1 0.665 0.021 5842.05 3569.12 317 EFEMP1 NM_001039348.1 0.666 0.021 9176.93 5680.13 318 PIGR NM_002644.2 0.473 0.024 5371.20 3060.51 319 PKIA NM_006823.2 0.526 0.024 2815.33 1840.94 320 CASC5 NM_144508.2 1.783 0.024 495.59 1209.52 321 ITGA10 NM_003637.3 0.569 0.024 5208.86 3166.58 322 KRT8 NM_002273.2 0.572 0.024 4770.01 3155.17 323 EHF NM_012153.3 0.581 0.024 2114.14 1148.85 324 CDCA5 NM_080668.2 1.713 0.024 739.56 1717.33 325 MTL5 NM_001039656.1 0.591 0.024 2604.36 1552.11 326 SPC25* NM_020675.3 1.650 0.024 3789.65 6657.18 327 RNASE4 NM_194431.1 0.611 0.024 1166.43 658.99 328 RNF157 NM_052916.1 1.633 0.024 477.55 1091.62 329 COX6B2 NM_144613.4 0.616 0.024 3268.01 1867.65 330 FAM3B NM_206964.1 0.618 0.024 1426.27 789.44 331 MGC29506 NM_016459.3 0.620 0.024 2898.60 1629.18 332 LRRC50 NM_178452.3 0.624 0.024 1152.82 627.97 333 BNIPL NM_138278.1 0.624 0.024 4963.78 2946.57 334 NTRK2 NM_006180.3 0.633 0.024 2816.20 1784.07 335 LAMA2 NM_000426.3 1.565 0.024 677.43 1352.44 336 SERINC2 NM_178865.3 0.648 0.024 8187.12 5309.52 337 EFNA5 NM_001962.1 0.655 0.024 4359.47 2731.05 338 COL6A2 NM_058175.1 1.523 0.024 1450.53 2881.49 339 MYO5C NM_018728.1 0.660 0.024 8300.77 5500.42 340 THRSP NM_003251.2 0.531 0.026 4300.49 2469.22 341 DLGAP5 NM_014750.3 1.879 0.026 1789.26 4417.65 342 ASTN1 NM_207108.1 1.846 0.026 467.61 1188.01 343 KIAA1984 NM_032874.2 0.548 0.026 7246.09 4458.80 344 JSRP1 NM_144616.2 0.575 0.026 5256.86 3081.64 345 EMID2 NM_133457.2 1.734 0.026 645.89 1485.35 346 MEFV NM_000243.1 0.613 0.026 1857.90 1180.01 347 PKP2 NM_001005242.1 0.614 0.026 2878.62 1781.03 348 TMEM2 NM_013390.1 1.617 0.026 1111.91 1990.57 349 SLC44A3 NM_152369.2 0.631 0.026 3943.79 2664.42 350 C4orf42 NM_052861.2 1.561 0.026 537.87 1416.00 351 ICA1 NM_022308.1 0.651 0.026 5503.17 3489.97 352 SERPINB5 NM_002639.2 0.654 0.026 3795.07 2489.94 353 VIPR1 NM_004624.2 0.663 0.026 44907.00 28943.51 354 DNMT3A NM_153759.2 1.500 0.026 642.00 1219.48 355 CYP4F22 NM_173483.1 0.538 0.027 4583.85 3015.48 356 IFI44L NM_006820.1 0.556 0.027 6717.39 3944.43 357 LY6H NM_002347.2 1.748 0.027 1181.70 3958.99 358 PTPRT NM_007050.4 0.581 0.027 2900.76 1835.73 359 C5orf30 NM_033211.2 0.586 0.027 6103.19 3928.24 360 FAM46B NM_052943.2 0.618 0.027 1406.61 766.40 361 EPCAM NM_002354.2 0.640 0.027 3360.87 2159.08 362 AKAP1 NM_003488.2 0.657 0.027 2219.99 1265.73 363 TCEAL2 NM_080390.3 0.462 0.030 2006.16 644.54 364 CLDN7 NM_001307.3 0.471 0.030 1188.53 451.41 365 HLA-DQB2 NM_182549.1 0.510 0.030 1731.84 508.03 366 PIK3C2G NM_004570.2 0.532 0.030 2463.15 1209.12 367 MAOA NM_000240.2 0.538 0.030 7781.94 3947.87 368 CEACAM1 NM_001024912.1 0.545 0.030 9683.07 5880.37 369 PPP1R1A NM_006741.2 0.547 0.030 949.35 413.73 370 MAGEA9B NM_001080790.1 1.806 0.030 199.68 726.71 371 GRB7* NM_005310.2 0.561 0.030 2054.91 1095.71 372 FOXJ1 NM_001454.2 1.754 0.030 229.46 780.35 373 NETO1 NM_138966.2 1.700 0.030 1067.26 1959.71 374 TESC* NM_017899.1 0.598 0.030 2449.50 1573.30 375 NRG1 NM_013961.1 0.599 0.030 2300.46 1365.91 376 MGST1 NM_020300.3 0.608 0.030 3726.89 2315.80 377 LAMB3 NM_000228.2 0.610 0.030 6255.97 3475.73 378 MANEAL NM_001031740.1 0.613 0.030 3173.76 1923.89 379 CASZ1 NM_017766.2 0.622 0.030 6722.05 4295.98 380 FSD1 NM_024333.1 1.580 0.030 678.13 1489.33 381 HLF NM_002126.3 0.639 0.030 5116.98 3500.22 382 MNDA NM_002432.1 0.639 0.030 2792.82 1720.02 383 PTTG1 NM_004219.2 1.563 0.030 1212.25 2590.68 384 MFI2 NM_005929.3 0.653 0.030 2075.84 1210.85 385 FAM180A NM_205855.2 0.658 0.030 2096.69 1318.29 386 RASSF5 NM_182664.1 0.664 0.030 1721.08 1041.90 387 VAV3 NM_006113.4 0.402 0.033 8116.96 5195.56 388 ZNF365 NM_199451.1 2.203 0.033 1153.31 2682.04 389 SCRG1 NM_007281.1 0.506 0.033 1859.99 735.93 390 SLC15A3 NM_016582.1 0.534 0.033 3705.00 2429.71 391 SNORD113-3 NR_003231.1 1.834 0.033 1276.34 2584.28 392 RASL10B NM_033315.2 1.788 0.033 791.38 1563.66 393 TRIM36 NM_001017397.1 0.560 0.033 2257.09 1326.39 394 ARSI NM_001012301.1 1.749 0.033 454.78 1071.58 395 LIMK2 NM_001031801.1 0.577 0.033 3360.60 2217.09 396 MIR758 NR_030406.1 1.707 0.033 966.82 1948.64 397 FAM19A3 NM_182759.2 0.588 0.033 2991.35 1697.30 398 EMILIN2 NM_032048.2 1.669 0.033 861.14 1650.57 399 MPL NM_005373.1 0.614 0.033 4382.76 2621.58 400 NCRNA00086 NR_024359.1 0.624 0.033 4452.01 2848.11 401 MAP7 NM_003980.3 0.627 0.033 3641.58 2247.45 402 PTPN14 NM_005401.3 0.629 0.033 2264.16 1485.96 403 C1orf210 NM_182517.1 0.633 0.033 1642.61 993.86 404 OGFRL1 NM_024576.3 0.636 0.033 2972.37 2001.70 405 UHRF1* NM_013282.3 1.567 0.033 1799.98 3710.71 406 FKBP5 NM_004117.2 0.638 0.033 5802.11 3205.01 407 MARVELD2 NM_001038603.1 0.647 0.033 1859.90 1222.49 408 AP3B2 NM_004644.3 0.650 0.033 2544.13 1846.27 409 LOXL1 NM_005576.2 1.537 0.033 1546.19 3043.68 410 SEMA6D XM_932857.1 0.658 0.033 7387.83 4338.46 411 LIMK2 NM_016733.2 0.660 0.033 3146.77 2118.91 412 WISP1 NM_080838.1 1.507 0.033 595.66 1293.80 413 PATE2 NM_212555.1 2.069 0.034 723.49 1495.55 414 GHR NM_000163.2 0.547 0.034 5916.34 3780.11 415 RIMS3 NM_014747.2 0.557 0.034 2868.29 1445.12 416 NCAM2 NM_004540.2 1.745 0.034 568.60 1146.17 417 IRF5 NM_002200.3 0.574 0.034 6314.57 3417.46 418 TNXB NM_019105.5 0.578 0.034 4307.63 2506.85 419 ESM1 NM_007036.2 1.695 0.034 419.83 1125.72 420 BCAM NM_005581.3 0.592 0.034 4008.67 2717.16 421 AGAP2 NM_014770.2 1.678 0.034 597.65 1349.29 422 FAM70A NM_017938.2 0.599 0.034 1124.51 582.97 423 KRTCAP3 NM_173853.2 0.607 0.034 2644.96 1708.37 424 SSTR2 NM_001050.2 1.635 0.034 511.65 1311.88 425 HISPPD2A NM_014659.3 0.612 0.034 3479.15 2356.67 426 NEBL NM_213569.1 0.613 0.034 1967.93 1448.98 427 EPHB2 NM_017449.2 1.616 0.034 576.57 1112.69 428 ARHGEF6 NM_004840.2 0.626 0.034 4110.98 2539.33 429 NDP NM_000266.1 0.639 0.034 4433.51 2980.29 430 RDH13 NM_138412.2 0.641 0.034 2995.10 1913.10 431 IL33 NM_033439.2 0.649 0.034 2375.01 1504.68 432 FBP1 NM_000507.2 0.660 0.034 4784.64 2871.86 433 CD52 NM_001803.2 0.664 0.034 1743.20 1066.91 434 COL4A3 NM_000091.3 0.483 0.036 1440.44 719.66 435 HAO2 NM_001005783.1 1.840 0.036 700.28 1772.14 436 DSC2 NM_004949.2 0.615 0.036 1580.48 1016.66 437 FLJ35220 NM_173627.2 0.635 0.036 5574.31 3487.78 438 TUBA4A NM_006000.1 0.637 0.036 3251.36 2077.71 439 RGS4 NM_005613.3 1.567 0.036 2900.10 5683.53 440 ALOX12P2 NR_002710.2 0.660 0.036 2633.27 1640.38 441 KLHL13 NM_033495.2 0.661 0.036 3417.06 2333.31 442 CBX2 NM_032647.2 1.510 0.036 774.71 1569.19 443 STARD13 NM_178007.1 1.502 0.036 1304.35 2397.16 444 PAX3 NM_181457.1 2.324 0.039 597.99 2629.24 445 ELF5 NM_198381.1 0.507 0.039 3148.49 2175.22 446 RASL10A NM_001007279.1 0.565 0.039 8881.16 5468.29 447 TUBB3 NM_006086.2 1.706 0.039 4462.77 11205.60 448 NCAPG NM_022346.3 1.627 0.039 1297.34 3067.78 449 STGC3 NM_001006608.1 1.527 0.039 1036.13 1730.31 450 MARVELD3 NM_001017967.2 0.656 0.039 5956.64 3727.05 451 PLCH2 NM_014638.2 0.656 0.039 4228.64 2330.33 452 SCGB2A1 NM_002407.1 0.478 0.042 6748.52 2718.14 453 MAG NM_002361.2 0.483 0.042 3992.14 1543.57 454 TNFRSF19 NM_018647.2 1.857 0.042 487.79 1122.24 455 PIWIL4 NM_152431.1 1.722 0.042 926.50 1753.34 456 THY1 NM_006288.2 1.679 0.042 1530.80 3262.60 457 ARL4A NM_005738.2 0.597 0.042 1309.67 715.34 458 C10orf81 NM_024889.3 0.601 0.042 6115.98 3386.63 459 ZYX NM_003461.4 1.638 0.042 3139.48 5732.50 460 ALPK1 NM_025144.2 0.617 0.042 4443.17 2971.44 461 TAC1 NM_013996.1 1.613 0.042 750.93 1586.43 462 FLJ41170 NM_001004332.1 1.589 0.042 1979.78 3648.73 463 NCF4 NM_000631.3 0.630 0.042 4176.33 2724.81 464 TSPAN13 NM_014399.3 0.632 0.042 3535.54 2399.95 465 JUP NM_021991.1 0.658 0.042 1698.53 1040.23 466 ZCCHC2 NM_017742.3 0.665 0.042 5162.55 3490.08 467 CIDEC NM_022094.2 0.463 0.046 2205.13 941.07 468 GAGE7 NM_021123.1 2.110 0.046 575.07 5033.76 469 C12orf64 NM_173591.1 0.550 0.046 1211.27 462.96 470 PLA2G4F NM_213600.2 0.554 0.046 2543.44 1380.16 471 UBE2T NM_014176.1 1.591 0.046 1266.30 2904.94 472 HBB NM_000518.4 0.637 0.046 3566.15 1765.02 473 TMEM100 NM_018286.1 1.537 0.046 256.03 836.57 474 RPS6KA2 NM_021135.4 0.655 0.046 8247.86 5568.94 475 HAS2 NM_005328.1 1.517 0.046 1035.99 2001.11 476 GABPAP XM_938298.1 1.506 0.046 598.04 1098.78 477 PAX3 NM_013942.2 2.142 0.049 537.16 2262.60 478 SLC26A3 NM_000111.1 0.482 0.049 4880.16 2852.26 479 GAGE5 NM_001475.1 2.062 0.049 759.23 5996.04 480 SALL1 NM_002968.1 1.951 0.049 1058.12 2064.68 481 MCART6 NM_001012755.1 1.882 0.049 945.35 1766.50 482 BAPX1 NM_001189.2 1.812 0.049 403.09 1134.67 483 ST6GAL2 NM_032528.1 1.780 0.049 831.75 2110.68 484 PRODH NM_016335.2 0.569 0.049 1709.93 1160.31 485 CHST6 NM_021615.3 1.752 0.049 658.88 1500.16 486 SHOX2 NM_006884.1 1.711 0.049 720.36 1506.59 487 LY6H XM_937329.1 1.685 0.049 1172.31 3856.24 488 SNORD78 NR_003944.1 1.657 0.049 520.12 1195.82 489 ANGPT2 NM_001118887.1 1.647 0.049 854.48 1785.14 490 SLC5A1 NM_000343.1 0.614 0.049 3000.44 1985.11 491 PGLYRP2 NM_052890.3 0.628 0.049 3602.18 2424.65 492 MEG8 NR_024149.1 1.586 0.049 1089.55 1969.35 493 FGF1 NM_033136.1 0.649 0.049 2508.60 1660.88 494 DKK2 NM_014421.2 0.650 0.049 1471.40 804.08 495 TCIRG1 NM_006053.2 1.522 0.049 1172.05 1991.77 *genes with primers successfully designed for qPCR assays

    Example 3

    [0065] Validation of Selected Genes by Quantitative Polymerase Chain Reaction (qPCR) Assay

    [0066] Primers Design

    [0067] Primers were designed using Primer-BLAST (NCBI) with accession number listed in Table 3. Criteria for qPCR primers designed were as follows: 1) amplicon size of 50 to 80 basepair (bp); 2) at least one primer spanning across an exon-exon boundary; 3) At least 7 bases must anneal to the 5 and 3 side of the junction. List of primers designed is as shown in Table 3.

    TABLE-US-00003 TABLE3 Primersdesignedforpotentialdifferentiatinggenesand normalizationgenes. Accession Accession Number number provided usedfor Ampl- Gene byWG- primer ForwardPrimer ReversePrimer icon Name DASL design Sequence Sequence size ABCA8 NM_ NM_ CCTGGCGGACAG GAAGAGCCC 57 007168.2 007168.2 GAAAGTATT GCGCACTTT (SEQIDNO:3) AG (SEQIDNO:4) ADH1B NM_ NM_ TCGCATTAAGAT CCACGTGGT 50 000668.3 000668.5 GGTGGCTGT CATCTGTGT (SEQIDNO:5) GA (SEQIDNO:6) ADH1C NM_ NM_ GTTCGCATTAAG GTTGCCACT 63 000669.3 000669.3 ATGGTGGCTG AACCACATG (SEQIDNO:7) CT (SEQIDNO:8) APOD NM_ NM_ CTGCATCCAGGC GTTCCATCA 78 001647.2 001647.3 CAACTACTC GCTCTCAAC (SEQIDNO:9) TCCT (SEQIDNO:10) C2orf40 NM_ NM_ AACGAGAAGCAC GCTTTATTC 55 032411.1 032411.2 CTGTTCCAA TCATCAACG (SEQIDNO:11) GCCA (SEQIDNO:12) CALML5 NM_ NM_ GGCCCAGCTAAG CTCCTGGAA 67 017422.3 017422.4 GAAACTCAT GCTGATTTCGC (SEQIDNO:13) (SEQIDNO:14) CCL19 NM_ NM_ ACCTCAGCCAAG CCTCTGCAC 51 006274.2 006274.2 ATGAAGCG GGTCATAGG (SEQIDNO:15) TT (SEQIDNO:16) CH25H NM_ NM_ ATGGAGTTCTTC CTTGTGGAA 66 003956.2 003956.3 GTGTGGCA GGTGCGGTA (SEQIDNO:17) CA (SEQIDNO:18) CHST1 NM_ NM_ CTCTTTGACCTC TTCCAGGAA 66 003654.2 003654.5 ACCCCTTGG CATTGCATG (SEQIDNO:19) GC (SEQIDNO:20) COL17A NM_ NM_ CTTGCCGGGAAC AATTCAGAC 54 1 130778.1 000494.3 CTCCTATG CCTCGCAGC (SEQIDNO:21) AA (SEQIDNO:22) CTHRC1 NM_ NM_ GGTGGTGGACCT GTCTCGACC 61 138455.2 138455.3 GTATAATGGA AGGCACTCCT (SEQIDNO:23) (SEQIDNO:24) CYP1B1 NM_ NM_ CTTCACCAGGTA CATACAAGG 82 000104.2 000104.3 TCCTGATGTGC CAGACGGTC (SEQIDNO:25) CC (SEQIDNO:26) DAPL1 NM_ NM_ CGCACTGGAGAA GGGTTTTTG 61 001017920.1 001017920.2 GCTCAACTA ATGCGCCAT (SEQIDNO:27) GT (SEQIDNO:28) DPYSL4 NM_ NM_ GGATCACGAGTG TCGTCATTC 52 006426.1 006426.2 ACCGCCTT ACGATCCTC (SEQIDNO:29) CC (SEQIDNO:30) FN1 NM_ NM_ TCGCAGCTTCGA GACGCTTGT 70 212474.1 054034.2 GATCAGTG GGAATGTGT (SEQIDNO:31) CG (SEQIDNO:32) GAGE2B NM_ NM_ TCATCTGTGTGA GGCTCTACG 71 001098411.3 001098411.3 AATATGAGTTGGC TAGCGTCTT (SEQIDNO:33) GG (SEQIDNO:34) GCNT2 NM_ NM_ CTGCCACGGCCA CCAGCCACT 62 145649.2 001491.2 CTATGTA TTAAGTCTC (SEQIDNO:35) CGT (SEQIDNO:36) GRB7 NM_ NM_ ACCTCTAAGGAT ACCACGTAC 65 005310.2 001030002.2 CCGAGGCA ACGTTGGAC (SEQIDNO:37) TC (SEQIDNO:38) HEPACA NM_ NM_ TTCCAGGATTCC GCAAATCTT 59 M2 198151.1 198151.1 AAGCAGGT GCCCCGATA (SEQIDNO:39) CAC (SEQIDNO:40) HOXD13 NM_ NM_ CTTCCTTTCCAG CCCTCTTCG 59 000523.2 000523.3 GGGATGTGG GTAGACGCAC (SEQIDNO:41) (SEQIDNO:42) KIF15 NM_ NM_ ATCTCAGGTTAG TAGGAATCC 58 020242.1 020242.2 AAAACGAAAAGC TGTAGGCAG (SEQIDNO:43) GC (SEQIDNO:44) KIF20A NM_ NM_ ACGATTCAAGGT ATTGAAGAT 63 005733.1 005733.2 ACCATCAAGGA CAGCGCCAG (SEQIDNO:45) GG (SEQIDNO:46) LAMB1 NM_ NM_ GCTTTCAGTTTC CGCAGCCGT 70 002291.1 002291.2 TTAGCCCTGTG AGCTGAACT (SEQIDNO:47) (SEQIDNO:48) LHX2 NM_ NM_ AGTCGGAGCTCA AGAGAAGCG 71 004789.3 004789.3 CCTGTTTC CCTGTAGTA (SEQIDNO:49) GTC (SEQIDNO:50) MMP3 NM_ NM_ TGCAGTTAGAGA AGGCATGGG 65 002422.3 002422.3 ACATGGAGACTT CCAAAACAT (SEQIDNO:51) TTC (SEQIDNO:52) NEFL NM_ NM_ TTGCAGCTTACA CTGGTGAAA 55 006158.1 006158.4 GGAAACTCTTG CTGAGTCGG (SEQIDNO:53) GT (SEQIDNO:54) NPTX2 NM_ NM_ CTGGAGCGAGGC GTGGGAGGG 58 002523.1 002523.2 AATAGCG ACACCTTGA (SEQIDNO:55) AC (SEQIDNO:56) OR5P3 NM_ NM_ ATGGGGACTGGA ATCCTCAGA 60 153445.1 153445.1 AATGACACC TAACCCCAA (SEQIDNO:57) AAGAGT (SEQIDNO:58) PRAME NM_ NM_ TCCAGAGACAAC CCACGCACG 75 206956.1 206955.1 TTCGCGG TCTGAGAGT (SEQIDNO:59) AATA (SEQIDNO:60) RORC NM_ NM_ CCTGACAGAGAT CCCTGTAGG 50 001001523.1 005060.3 AGAGCACCTG ACTTGCAGA (SEQIDNO:61) CG (SEQIDNO:62) SCARA5 NM_ NM_ TTCATCTTAGCA GTTCACATT 69 173833.3 173833.5 GTGTCCAGGC GCGAGTCAG (SEQIDNO:63) GG (SEQIDNO:64) SERHL2 NM_ NM_ CCTCTTCTCCCG CTGTAATGG 71 014509.3 014509.4 CAAGACTTTTA GACGAGAGC (SEQIDNO:65) CC (SEQIDNO:66) SHISA2 NM_ NM_ TCGGCAGTGCCC ACAAACACG 50 001007538.1 001007538.1 ATCTACG GAGCCAACA (SEQIDNO:67) ATG (SEQIDNO:68) SPAG11 XM_ NM_ TACCAAGTGCAC AGGCCCTAA 72 B 943161.1 016512.3 ATCTCTCACC AAAGTCCAC (SEQIDNO:69) ACA (SEQIDNO:70) SPC25 NM_ NM_ CCTGCCTGCGAA TCGAAAAGT 56 020675.3 020675.3 GCATTGTC GCCAGTTCG (SEQIDNO:71) TCC (SEQIDNO:72) SYNGAP NM_ NM_ GCCCCCTTCAGA ACGTATTGG 50 1 006772.1 006772.2 GATGTACG GTTCGGTGC (SEQIDNO:73) AT (SEQIDNO:74) TESC NM_ NM_ TGTTCCACATGT GCTCCTCGA 72 017899.1 017899.3 ACGACTCGG CCACATTTC (SEQIDNO:75) GAT (SEQIDNO:76) TP63_ NM_ NM_ AGCAGCAAGTTT CGAAACGGG 55 v1* 001114979.1 001114979.1 CGGACAGT CGCTTCGTA (SEQIDNO:77) (SEQIDNO:78) TP63_ NM_ NM_ ATTGCAGCATTG GATCGCATG 61 v2* 001114981.1 001114981.1 TCAGGATCTGG TCGAAATTG (SEQIDNO:79) CTCA (SEQIDNO:80) TRERF1 NM_ NM_ AGGAGTGTGGCA CTCCTGCTG 71 033502.1 033502.2 AAGTCTTCTT CCTGTGAGTTT (SEQIDNO:81) (SEQIDNO:82) TRIM29 NM_ NM_ AAGCAGACTATG ATCCCGTTG 56 012101.2 012101.3 CTGTCTCACT CCTTTGTTGAC (SEQIDNO:83) (SEQIDNO:84) UBE2C NM_ NM_ GGCAAAAGGCTA TCAGGGAAG 71 181800.1 007019.3 CAGCAGGA GCAGAAATC (SEQIDNO:85) CC (SEQIDNO:86) UHRF1 NM_ NM_ TACGACGACTAC GGACGTCCC 52 013282.2 013282.3 CCGGAGAA TGGAGTTCA (SEQIDNO:87) TC (SEQIDNO:88) RMRP.sup. NR_ NR_ CAGAGAGTGCCA TACGCTTCT 70 003051.2 003051.3 CGTGCATA TGGCGGACT (SEQIDNO:89) TT (SEQIDNO:90) RPL18.sup. NM_ NM_ AGAGGTGTACCG GTAGGGTTT 61 000979.2 000979.3 GCATTTCG GGTGTGGCT (SEQIDNO:91) GT (SEQIDNO:92) RPLP2.sup. NM_ NM_ ACCGGCTCAACA CTGGGCAAT 62 001004.2 001004.3 AGGTTATCA GACGTCTTC (SEQIDNO:93) AA (SEQIDNO:94) SNORA6 NR_ NR_ TCCTGATCCCTT TCCTCCTTT 57 1.sup. 002987.1 002987.1 TCCCATCG TACGACCAC (SEQIDNO:95) CA (SEQIDNO:96) SNORA4 NR_ NR_ CTTGTCCTGGTG CCCCCACCA 61 5.sup. 002977.1 002977.1 TGCTAGAGT GTGAATCAA (SEQIDNO:97) GA (SEQIDNO:98) *refers to different variants of the same gene .sup.normalization genes

    [0068] Synthesis of cDNA and qPCR Assay

    [0069] cDNA was synthesized from 1 g of RNA using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Life Technologies, USA) on a thermal cycler according to manufacturer's protocol. cDNA was then diluted 10-fold for subsequent qPCR assays.

    [0070] qPCR assays were performed on the CFX96 machine. Each qPCR reaction consisted of 1 Power SYBR Green PCR Master Mix (Life Technologies, USA), 0.5 M of forward and reverse primer each and 1 l of the diluted cDNA as template in a final total volume of 10 l. Non-template control acted as a negative control. Specificity of the amplicons was checked with meltcurve analysis.

    [0071] To validate the expression observed on the WG-DASL Array, six representative samples were used as a pilot run for each potential gene tested.

    [0072] Data Analysis

    [0073] Expression data from qPCR assays was obtained in terms of threshold cycle (Ct). Ct above 40 was deemed as below limit of detection and is converted to 40. Delta Ct (Ct) was quantified as follows:


    Ct of test gene=Ctgeometric mean (Ct of five normalization genes)

    [0074] Ct data was transformed to 2.sup.Ct as a positive linear scale for comparison with expression value of DASL. Significance of correlation was analyzed with Pearson's correlation test. Table 4 shows the results of the pilot run. Genes with good correlation value (r0.6) were subjected to testing on remaining 40 samples. Two samples had no sufficient RNA for the qPCR assays after characterization on WG-DASL and hence were not included in the analysis.

    TABLE-US-00004 TABLE 4 Correlation of expression value on WG- DASL and qPCR results for genes selected. Gene Name Pearson's r p-value PRAME* 0.991 <0.001 ADH1B* 0.976 0.001 CTHRC1* 0.968 0.002 NPTX2* 0.965 0.002 NEFL* 0.961 0.002 ABCA8* 0.931 0.007 DAPL1* 0.915 0.011 TP63_v2* 0.901 0.014 COL17A1* 0.896 0.016 GCNT2* 0.880 0.021 CCL19* 0.870 0.024 MMP3* 0.855 0.030 FN1* 0.835 0.039 TRERF1* 0.798 0.057 TRIM29* 0.794 0.059 TESC* 0.777 0.069 KIF20A* 0.776 0.070 UHRF1* 0.739 0.093 HEPACAM2* 0.714 0.111 APOD* 0.713 0.112 SERHL2* 0.671 0.145 KIF15* 0.659 0.154 HOXD13* 0.625 0.185 GAGE2B 0.557 0.251 CALML5 0.548 0.260 C2orf40 0.545 0.263 ADH1C 0.487 0.327 CYP1B1 0.442 0.380 SPAG11B 0.438 0.385 GRB7 0.411 0.418 UBE2C 0.336 0.580 SYNGAP1 0.330 0.524 TP63_v1 0.220 0.676 LAMB1 0.188 0.762 OR5P3 0.082 0.877 SPC25 0.056 0.928 SHISA2 0.006 0.991 SCARA5 0.052 0.922 LHX2 0.103 0.846 RORC 0.157 0.766 DPYSL4 0.201 0.703 CH25H 0.298 0.566 CHST1 0.844 0.072 *genes selected for full-scale run on 40 samples

    Example 4

    [0075] Development of an Algorithm Model Based on qPCR Assay Results on 46 Samples

    [0076] Variable Selection Using Random Forest

    [0077] Ct values of all 23 genes on 46 samples were analyzed with Random Forest (RF) classifier algorithm (R version) to rank importance of genes differentiating fibroadenomas and phyllodes tumours. Results are as shown in FIG. 2 for 100 RF trees generated.

    [0078] Development of an Algorithm Model Using Logistic Regression

    [0079] Top seven genes (TRIM29, FN1, CCL19, ABCA8, NPTX2, APOD, PRAME) were used for logistic regression modeling. All possible models were screened to find the best model using the glmulti package (R version) including the interactions terms. The best model was selected based on the lowest AIC (Akaike information criteria) value. The coefficient of the best model generated is as shown in Table 5. The AIC for the model was 14.2.

    TABLE-US-00005 TABLE 5 Coefficients of the best model in predicting diagnosis in the 46-sample set. Genes Coefficients APOD 2.95575 APOD: ABCA8 0.11934 PRAME: FN1 0.43165 PRAME: CCL19 0.08326

    Example 5

    [0080] Validation of the Predicting Algorithm on an Independent Set

    [0081] An independent set of 230 core biopsy samples (189 fibroadenomas and 41 phyllodes tumours) was employed to evaluate the performance of the algorithm. RNA was extracted and cDNA synthesized as per the protocol above. Ct values were obtained as per the protocols above. Probability (p) of each sample whether it is a fibroadenoma or phyllodes tumours are calculated in the following manner:

    [00002] p = e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. .Math. CCL .Math. .Math. 19 ) 1 + e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. CCL .Math. .Math. 19 )

    [0082] A sample is predicted as a phyllodes tumour when p is 0.5 and above. Otherwise, the sample is predicted as a fibroadenoma. The outcome of the multigene assay was compared against the final diagnosis on the corresponding surgical excisions. Cases without subsequent surgical excisions were free from progression for at least two years and diagnosis made based on the initial core biopsy was used as the reference instead. The five-gene assay has an overall accuracy of 92.6% (FIG. 3), with a sensitivity of 82.9% and specificity of 94.7%. The positive predictive value (PPV) and negative predictive value (NPV) are 77.3% and 96.2%.

    Example 6

    [0083] Protocol for a Multigene Assay Classifying Breast Fibroepithelial Lesion

    [0084] Equipment [0085] 1. Real-time PCR machine [0086] 2. Nanodrop Spectrophotometer [0087] 3. Heat block/Water bath/Thermomixer [0088] 4. Microtome

    [0089] Materials [0090] 1. RNeasy FFPE Kit (Qiagen, Catalogue No. 73504) [0091] 2. Power SYBRGreen RNA-to-CT 1-Step Kit (Applied Biosystems, Catalog No. 4389986) [0092] 3. Xylene [0093] 4. Absolute ethanol

    [0094] Consumables [0095] 1. 1.5 ml and 2.0 ml microtubes [0096] 2. Glass slides [0097] 3. Sterile scalpels

    [0098] Protocol [0099] 1. Identification of tumour area by a pathologist. Fish 5 sections of 10 m of tissue onto 5 glass slides respectively. [0100] 2. Deparaffinise tissue in two changes of xylene and 3 changes of absolute ethanol. Scrape tumour area with a sterile scalpel and transfer tissue into a 1.5 ml microtube containing 500 l absolute ethanol. Perform RNA extraction using Qiagen RNeasy FFPE Kit. [0101] 3. Quantify RNA with a Nanodrop Spectrophotometer. [0102] 4. For each well, prepare a 10 l reaction as follows in Table 6 (table modified from Power SYBR Green RNA-to-CT 1-Step Kit protocol). For non-template control (NTC), RNA template should be replaced by RNase-free water. Primer sequences are shown in Table 8. [0103] 5. Real-time PCR machine is set up as follows in Table 7 (table modified from Power SYBR Green RNA-to-CT 1-Step Kit Protocol). [0104] 6. Check the meltcurve temperature (refer to Table 8) to ensure the desired product is amplified. Read Ct for each well for ABCA8, APOD, CCL19, FN1 and FRAME. Perform quantification for each well as follows:


    Ct of each gene=Ctgeometric mean (Ct of RMRP, RPL18, RPLP2, SNORA45 and SNORA61) [0105] 7. Perform calculation as follow to work out a probability score.

    [00003] p = e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. .Math. CCL .Math. .Math. 19 ) 1 + e 2.95575 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD ) - 0.11934 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. APOD .Math. .Math. Ct .Math. .Math. of .Math. .Math. ABCA .Math. .Math. 8 ) - 0.43165 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. FN .Math. .Math. 1 ) + 0.08326 .Math. ( .Math. .Math. Ct .Math. .Math. of .Math. .Math. PRAME .Math. .Math. Ct .Math. .Math. of .Math. .Math. CCL .Math. .Math. 19 ) [0106] 8. If p is 0.5 and above, the outcome of the test is a phyllodes tumour. If p is less than 0.5, the outcome of the test is a fibroadenoma.

    TABLE-US-00006 TABLE 6 PCR reaction components Component Volume (l) Power Sybr Green RT-PCR Mix (2x) 5 Forward and Reverse Primers* (200 nM) 2 RT Enzyme Mix (125x) 0.08 RNase-free water Variable RNA template (100 ng) Variable

    TABLE-US-00007 TABLE 7 Thermal cycling conditions for real-time PCR. Temperature Step ( C.) Time Step Reverse 48 30 minutes Reverse Transcription Transcription Activation of DNA 95 10 minutes Activation of DNA polymerase polymerase Cycling (40 cycles) Cycling (40 cycles) Denature 95 15 seconds Denature Anneal/Extend 60 60 seconds Anneal/Extend

    TABLE-US-00008 TABLE8 Primersequencesandmeltcurvetemperature. Meltcurve Temperature Name ForwardsSequence ReverseSequence ( C.) ABCA8 CCTGGCGGACAGGAA GAAGAGCCCGCGCAC 77.5 AGTATT TTTAG (SEQIDNO:3) (SEQIDNO:4) APOD CTGCATCCAGGCCAA GTTCCATCAGCTCTC 75.5 CTACTC AACTCCT (SEQIDNO:9) (SEQIDNO:10) CCL19 ACCTCAGCCAAGATG CCTCTGCACGGTCAT 77.5 AAGCG AGGTT (SEQIDNO:15) (SEQIDNO:16) FN1 TCGCAGCTTCGAGAT GACGCTTGTGGAATG 76 CAGTG TGTCG (SEQIDNO:31) (SEQIDNO:32) PRAME TCCAGAGACAACTTC CCACGCACGTCTGAG 75.5 GCGG AGTAATA (SEQIDNO:59) (SEQIDNO:60) RMRP CAGAGAGTGCCACGT TACGCTTCTTGGCGG 80 GCATA ACTTT (SEQIDNO:89) (SEQIDNO:90) RPL18 AGAGGTGTACCGGCA GTAGGGTTTGGTGTG 81 TTTCG GCTGT (SEQIDNO:91) (SEQIDNO:92) RPLP2 ACCGGCTCAACAAGG CTGGGCAATGACGTC 75 TTATCA TTCAA (SEQIDNO:93) (SEQIDNO:94) SNORA45 CTTGTCCTGGTGTGCTAG CCCCCACCAGTGAAT 76 AGT CAAGA (SEQIDNO:97) (SEQIDNO:98) SNORA61 TCCTGATCCCTTTCCCAT TCCTCCTTTTACGAC 75.5 CG CACCA (SEQIDNO:95) (SEQIDNO:96)