# US 11,028,445 B2 · Molecular prognostic signature for predicting breast cancer metastasis, and uses thereof

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- Number: US 11,028,445 B2
- Document ID: US11028445B2
- Status: Granted
- Kind: B2
- Application number: 16/003,682
- Filed: 2018-06-08
- Published: 2019-05-09
- Granted: 2021-06-08
- Earliest claimed: 2007-01-31
- Assignees: Celera Corporation
- Applicants: Celera Corporation
- Inventors: Kit Lau; Alice Wang
- Web page: https://patentgrep.com/patent/US11028445B2

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/158: Expression markers
- C12Q 2600/16: Primer sets for multiplex assays
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

The present invention is based on the discovery of a unique 14-gene molecular prognostic signature that is useful for predicting breast cancer metastasis. In particular, the present invention relates to methods and reagents for detecting and profiling the expression levels of these genes, and methods of using the expression level information in predicting risk of breast cancer metastasis.

## Claims

### Claim 1

A method of treating a human at risk for breast cancer metastasis, the method comprising:
(a) measuring mRNA expression levels of genes comprising CENPA, PKMYT1, MELK, BUB1, RACGAP1, TK1, UBE2S, DC13, RFC4, PRR11, DIAPH3, and ORC6L in estrogen receptor-positive tumor cells from said human to generate a sum total of said expression levels wherein the mRNA of each of said genes is reverse transcribed and amplified using at least one primer associated with the corresponding gene comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS:1-2, 5-12, and 15-28;
(b) determining said human is at risk for breast cancer metastasis when said sum total exceeds a predefined cutoff threshold; and
(c) administering a breast cancer therapy to said human.

### Claim 2 (depends on 1)

The method of claim 1 in which the expression levels of said genes are normalized against the expression level of at least one control gene, or an average of two or more control genes.

### Claim 3 (depends on 2)

The method of claim 2, wherein the control gene is selected from the group consisting of NUP214, PPIG and SLU7.

### Claim 4 (depends on 3)

The method of claim 3 in which the mRNA of said control gene is reverse transcribed and amplified using at least one primer associated with said control gene comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS:29-34.

### Claim 5 (depends on 1)

The method of claim 1, wherein said predefined cutoff threshold is representative of a higher risk for breast cancer metastasis above said threshold and a lower risk for breast cancer metastasis below said threshold.

### Claim 6 (depends on 1)

The method of claim 1, wherein said expression levels are equally weighted and summed to generate said sum total.

### Claim 7 (depends on 1)

The method of claim 1, wherein said expression levels are differentially weighted and summed to generate said sum total.

### Claim 8 (depends on 1)

The method of claim 1, wherein said sum total is calculated by the following:
-
1
/
12
*
[
∑
i
=
1
12
⁢
Gi
]
wherein Gi=the expression level of each of said genes (i).

### Claim 9 (depends on 1)

The method of claim 1, wherein the method comprises calculating each of said expression levels as a Δ(ΔCt) value.

### Claim 10 (depends on 9)

The method of claim 9, wherein said Δ(ΔCt) value is calculated as follows:
Δ(ΔCt)=(CtGOI−CtEC)test RNA−(CtGOI−CtEC)ref RNA
wherein Ct is the PCR threshold cycle of exponential target amplification, GOI=gene of interest, test RNA=patient sample RNA, ref RNA=reference RNA, and EC=endogenous control.

### Claim 11 (depends on 9)

The method of claim 9, wherein the method comprises multiplying each of said Δ(ΔCt) values by a negative coefficient, or multiplying said sum total by a negative coefficient.

### Claim 12 (depends on 1)

The method of claim 1, wherein said human has no detectable tumor cells in their lymph nodes (node-negative).

### Claim 13 (depends on 1)

The method claim 1, wherein said tumor cells are obtained from a formalin-fixed paraffin-embedded (FFPE) tissue section, a tumor biopsy, or a frozen tumor tissue sample.

### Claim 14 (depends on 1)

The method of claim 1, wherein said breast cancer therapy comprises hormonal therapy or chemotherapy.

### Claim 15 (depends on 1)

The method of claim 1, wherein said breast cancer therapy comprises Tamoxifen.

### Claim 16 (depends on 1)

The method of claim 1, wherein said breast cancer therapy comprises an aromatase inhibitor.