Multigene assay
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.
1. A method of determining the type of fibroepithelial tumor of the breast, in a biological sample obtained from a patient in vitro or a method of managing the treatment of a patient with a fibroepithelial tumor of the breast, comprising:
measuring the expression levels of a combination of genes comprising PRAME, ABCA8, CCL19, FN1, and APOD and obtaining an expression profile of the combination of genes in said sample;
measuring the expression level of one or more normalized genes and obtaining an expression profile of the 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 PRAME, ABCA8, CCL19, FN1 and APOD relative to the control to determine a p-score using a predictive algorithm, wherein the predictive algorithm is:
p
=
e
2.95575
(
Δ
Ct
of
APOD
)
-
0.11934
(
Δ
Ct
of
APOD
⋆
Δ
Ct
of
ABCA
8
)
-
0.43165
(
Δ
Ct
of
PRAME
⋆
Δ
Ct
of
FN
1
)
+
0.08326
(
Δ
Ct
of
PRAME
⋆
Δ
Ct
of
CCL
19
)
1
+
e
2.95575
(
Δ
Ct
of
APOD
)
-
0.11934
(
Δ
Ct
of
APOD
⋆
Δ
Ct
of
ABCA
8
)
-
0.43165
(
Δ
Ct
of
PRAME
⋆
Δ
Ct
of
FN
1
)
+
0.08326
(
Δ
Ct
of
PRAME
⋆
Δ
Ct
of
CCL
19
)
;
determining the presence of a phyllodes tumor in the patient wherein the p-score is 0.5 and above; and
treating patient for a phyllodes tumor.
2. The method of claim 1 , wherein the one or more normalized genes are selected from the group consisting of RMRP, RPL18, RPLP2, SNORA61, and SNORA45.
3. The method of claim 1 , wherein the one or more normalized genes consist of RMRP, RPL18, RPLP2, SNORA61, and SNORA45.
4. The method of claim 1 , wherein the biological sample is selected from the group consisting of an organ, tissue, fraction, and a cell.
5. The method of claim 1 , wherein the biological sample is a malignant tumor sample.
6. The method of claim 1 , wherein the biological sample is a benign tumor sample.
7. The method of claim 5 , wherein the tumor sample is a breast sample.
8. The method of claim 1 , further comprising extracting RNA from the sample for measuring the expression level and obtaining the expression profile of the one or more genes and one or more normalized genes.
9. The method of claim 1 , wherein the expression profile of the one or more genes and one or more normalized genes is obtained from the same biological sample.
10. The method of claim 8 , wherein the expression profile of the one or more genes and one or more normalized genes is obtained by a quantitative PCR method.
11. A kit for determining the type of fibroepithelial tumor of the breast, in a biological sample in vitro, comprising:
a primer pair for amplifying each of the genes in the combination of genes comprising PRAME, ABCA8, CCL19, FN1 and APOD; and
a primer pair for amplifying each of one or more normalized genes selected from the group consisting of RMRP, RPL18, RPLP2, SNORA61, and SNORA45.
12. The kit of claim 11 , wherein the combination of genes further comprises one or more genes selected from the group consisting of TRIM29, and NPTX2.
13. The kit of claim 11 , wherein the one or more normalized genes consists of RMRP, RPL18, RPLP2, SNORA61, and SNORA45.