Granted Patent B2

US 12,497,664 · App. 18/332,648 · Granted Dec 16, 2025

Inventors: Bram De Craene (Mechelen, BE); Klaas Decanniere (Mechelen, BE); Jan Van De Velde (Mechelen, BE); Geert Maertens (Mechelen, BE)

Assignee: BIOCARTIS NV

C12Q1/6886C12Q2600/156

Abstract

Claims (30)

1 . A kit for analyzing microsatellite instability (MSI) status of a colorectal, endometrial, ovarian or gastric cancer sample, the kit comprising fluorophore-labeled molecular beacon probes that are designed to specifically hybridize to target nucleic acid regions as mapped to GRCh38/hg38 human reference genome, wherein the target nucleic acid regions comprise:

(i) human DIDO1 gene starting at position chr20:62,905,340 and encompassing a DIDO1 homopolymeric repeat region, the homopolymeric repeat region comprising 11 consecutive adenines in the reference genome;

(ii) human MRE11 gene starting at position chr11:94,479,765, and encompassing a MRE11 homopolymeric repeat region, the homopolymeric repeat region comprising 11 consecutive adenines in the reference genome;

(iii) human SULF2 gene starting at position chr20:47,657,577 and encompassing a SULF2 homopolymeric repeat region, the homopolymeric repeat region comprising 10 consecutive adenines in the reference genome; and

(iv) human ACVR2A gene starting at position chr2:147,926,117 and encompassing an ACVR2A homopolymeric repeat region, the homopolymeric repeat region comprising 8 consecutive adenines in the reference genome,

wherein each fluorophore-labeled molecular beacon probe comprises a different number of consecutive adenines than the target nucleic acid region for which it is designed.

2 . The kit of claim 1 , wherein the target nucleic acid regions further comprise:

(v) human SEC31A gene starting at position chr4:82,864,412 and encompassing a SEC31A homopolymeric repeat region, the homopolymeric repeat region comprising 9 consecutive thymines in the reference genome;

(vi) human BTBD7 gene starting at position chr14:93,241,685 and encompassing a BTBD7 homopolymeric repeat region, the homopolymeric repeat region comprising 10 consecutive adenines in the reference genome; and

(vii) human RYR3 gene starting at position chr15:33,865,341 and encompassing a RYR3 homopolymeric repeat region, the homopolymeric repeat region comprising 10 consecutive adenines in the reference genome.

3 . The kit of claim 2 , wherein the fluorophore-labeled molecular beacon probes comprise SEQ ID NOs: 17, 20, and 21.

4 . The kit of claim 2 , further comprising a positive control sample that comprises nucleic acid comprising one or more of the target nucleic acid regions of claim 2 .

5 . The kit of claim 4 , wherein at least one of the target nucleic acid regions of the positive control sample comprises an indel.

6 . The kit of claim 5 , wherein the positive control sample is derived from cell line HTC116cl.110268743.

7 . The kit of claim 1 , wherein the fluorophore-labeled molecular beacon probes comprise SEQ ID NOs: 15, 16, 18 and 19.

8 . The kit of claim 1 , further comprising a cartridge.

9 . The kit according to claim 8 , wherein the fluorophore-labeled molecular beacon probes are provided inside of the cartridge.

10 . An automated system comprising the kit of claim 1 .

11 . The automated system of claim 10 , wherein the system is adapted to perform PCR.

12 . A biomarker panel for analyzing microsatellite instability (MSI) status in a biological sample, the panel comprising components for detecting each of the following target nucleic acid regions as mapped to GRCh38/hg38 human reference genome, wherein the target nucleic acid regions comprise:

(i) human DIDO1 gene starting at position chr20:62,905,340 and encompassing a DIDO1 homopolymeric repeat region, the homopolymeric repeat region comprising 11 consecutive adenines in the reference genome;

(ii) human MRE11 gene starting at position chr11:94,479,765, and encompassing a MRE11 homopolymeric repeat region, the homopolymeric repeat region comprising 11 consecutive adenines in the reference genome;

(iii) human SULF2 gene starting at position chr20:47,657,577 and encompassing a SULF2 homopolymeric repeat region, the homopolymeric repeat region comprising 10 consecutive adenines in the reference genome; and

(iv) human ACVR2A gene starting at position chr2:147,926,117 and encompassing an ACVR2A homopolymeric repeat region, the homopolymeric repeat region comprising 8 consecutive adenines in the reference genome,

wherein the components are fluorophore-labeled molecular beacon probes, and

wherein each fluorophore-labeled molecular beacon probe comprises a different number of consecutive adenines than the target nucleic acid region for which it is designed.

13 . The panel of claim 12 , wherein the target nucleic acid regions further comprise:

(v) human SEC31A gene starting at position chr4:82,864,412 and encompassing a SEC31A homopolymeric repeat region, the homopolymeric repeat region comprising 9 consecutive thymines in the reference genome;

(vi) human BTBD7 gene starting at position chr14:93,241,685 and encompassing a BTBD7 homopolymeric repeat region, the homopolymeric repeat region comprising 10 consecutive adenines in the reference genome; and

(vii) human RYR3 gene starting at position chr15:33,865,341 and encompassing a RYR3 homopolymeric repeat region, the homopolymeric repeat region comprising 10 consecutive adenines in the reference genome.

Assignments (2)

Priority Claims (2)

Continuity (2)

References Cited (29)