# US 2020/0399707 A1 · Methods for screening a subject for a cancer

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- Number: US 2020/0399707 A1
- Document ID: US20200399707A1
- Status: Published application
- Kind: A1
- Application number: 16/908,822
- Filed: 2020-06-23
- Published: 2020-12-24
- Earliest claimed: 2014-10-20
- Assignees: Inserm (Institut National De La Sante Et De La Recherche Medicale); Institut Regional Du Cancer De Montpellier; Universite De Montpellier
- Applicants: Inserm (Institut National De La Santé Et De La Recherche MéDicale); Institut Regional Du Cancer De Montpellier; Universite De Montpellier
- Inventors: Alain THIERRY; Safia EL MESSAOUDI
- Web page: https://patentgrep.com/patent/US20200399707A1

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C12Q 2600/112: Disease subtyping, staging or classification
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/158: Expression markers
- 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 relates to methods for screening a subject for a cancer. In particular, the present invention relates to a method (A) for screening a subject for a cancer comprising the steps of i) extracting the cell free nucleic acids from a sample obtained from the subject, ii) determining the total concentration of mitochondrial cell free nucleic acids, ii) determining the total concentration of nuclear cell free nucleic acids iv) calculating the ratio of the level determined at step ii) to the concentration determined at step iii), v) comparing ratio determined at step iv) with a predetermined corresponding reference value and vi) concluding that the subject suffers from a cancer when the ratio determined at step iv) is lower than the predetermined corresponding reference value or concluding that the subject does not suffer from a cancer when the ratio determined at step iv) is higher than the predetermined corresponding reference value.

## Claims

### Claim 1

A method for treating a subject for a cancer comprising the steps of
i) extracting cell free nucleic acids from a sample obtained from the subject,
ii) determining a total concentration of mitochondrial cell free nucleic acids,
iii) determining a total concentration of nuclear cell free nucleic acids,
iv) calculating a ratio (CmCn content ratio) of the total concentration of mitochondrial cell free nucleic acids determined at step ii) to the total concentration of nuclear cell free nucleic acids determined at step iii),
v) comparing the ratio determined at step iv) with a predetermined corresponding reference value
vi) determining that the subject suffers from a cancer when the ratio determined at step iv) is lower than the predetermined corresponding reference value, and
vii) administering an anti-cancer treatment to the subject determined to suffer from a cancer,
wherein the cancer is not colorectal cancer.

### Claim 2 (depends on 1)

The method of claim 1 wherein the cell free nucleic acids are cell free DNA nucleic acids (ccfDNA).

### Claim 3 (depends on 1)

The method of claim 1 wherein the total concentration of cell free nucleic acids is determined by Q-PCR.

### Claim 4 (depends on 1)

The method of claim 1 further comprising the steps of a) amplifying and quantifying a nuclear target nucleic acid sequence and b) amplifying and quantifying a mitochondrial target nucleic acid sequence.

### Claim 5 (depends on 4)

The method of claim 4 wherein one or both of the nuclear target nucleic acid sequence and the mitochondrial target nucleic acid sequence is part of a coding or non-coding sequence.

### Claim 6 (depends on 4)

The method of claim 4 wherein the mitochondrial target nucleic acid sequence is comprised in a mitochondrial gene selected from the group consisting of ND1; ND2; COX1; COX2; ATPS; ATP6; COX3; ND3; ND4L; ND4; ND5; ND6; CYTB; TRNF; TRND; RNR1 TRNV; TRNK; RNR2 TRNL1; TRNS1; TRNI; TRNP; TRNQ; TRNE; TRNM; TRNT TRNW; TRNL2 TRNA; TRNS2; TRNN; TRNR; TRNA; TRNG; TRNN; TRNC; and TRNY.

### Claim 7 (depends on 4)

The method of claim 4 wherein the mitochondrial target nucleic acid sequence is comprised in a non-coding region of the mitochondrial genome.

### Claim 8 (depends on 4)

The method of claim 4 wherein the mitochondrial target nucleic acid sequence and the target nuclear nucleic acid sequence have about the same length.

### Claim 9 (depends on 4)

The method of claim 4 wherein the mitochondrial target nucleic acid sequence is 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; or 15% longer or shorter than the nuclear target nucleic acid sequence.

### Claim 10 (depends on 4)

The method of claim 4 wherein the mitochondrial and nuclear target nucleic acid sequences have the same length.

### Claim 11 (depends on 4)

The method of claim 4 wherein the mitochondrial and nuclear target nucleic acid sequences have a length of less than 110 base pairs.

### Claim 12 (depends on 4)

The method of claim 4 wherein the mitochondrial and nuclear target nucleic acid sequences have a length of 20; 21; 22; 23; 24; 25; 26; 27; 28; 29; 30; 31; 32; 33; 34; 35; 36; 37; 38; 39; 40; 41; 42; 43; 44; 45; 46; 47; 48; 49; 50; 51; 52; 53; 54; 55; 56; 57; 58; 59; 60; 61; 62; 63; 64; 65; 66; 67; 68; 69; 70; 71; 72; 73; 74; 75; 76; 77; 78; 79; 80; 81; 82; 83; 84; 85; 86; 87; 88; 89; 90; 91; 92; 93; 94; 95; 96; 97; 98; 99; 100; 101; 102; 103; 104; 105; 106; 107; 108; 109; or 110 base pairs.

### Claim 13 (depends on 4)

The method of claim 4, wherein 2 sets of 2 primers are used, and wherein one set of the 2 primers is used for amplifying the nuclear target nucleic acid sequence and one set of the 2 primers is used for amplifying the mitochondrial target nucleic acid sequence.

### Claim 14 (depends on 1)

The method of claim 1 wherein the sample is a body fluid sample selected form the group consisting of blood, ascite, urine, amniotic fluid, feces, saliva and cerebrospinal fluids.

### Claim 15 (depends on 1)

The method of claim 1 wherein the sample is a blood sample.

### Claim 16 (depends on 1)

The method of claim 1 wherein the cancer is selected from the group consisting of breast cancer, hepatocellular cancer, ovarian cancer, and lymphoma.

### Claim 17 (depends on 1)

The method of claim 1, wherein the anticancer treatment is at least one of radiotherapy, chemotherapy, immunotherapy, adjuvant therapy, or surgical resection.