Granted Patent B2

US 12,247,255 · App. 17/484,928 · Granted Mar 11, 2025

Inventors: Gabriela Ecco (Saint-Sulpice, CH); Xiaobin Xing (Saint-Sulpice, CH); Adrian Willig (Saint-Sulpice, CH); Zhenyu Xu (Saint-Sulpice, CH)

Assignee: SOPHIA GENETICS S.A.

C12Q1/6874C12N15/1068C12Q1/6853

Abstract

Claims (23)

1. A probe set comprising:

at least one probe comprising:

a first portion of the probe complementary to a primary nucleotide portion of a target nucleic acid, and

a second portion of the probe complementary to a secondary nucleotide portion of the target nucleic acid,

wherein the probe overlaps a breakpoint between the primary and the secondary nucleotide portion of the target nucleic acid, and

wherein the length of second portion of the probe represents about 9% to about 42% of a total probe length, and

at least one further probe complementary only to the primary nucleotide portion of the target nucleic acid, wherein the further probe does not overlap a breakpoint between the primary and the secondary nucleotide portion of the target nucleic acid.

2. The probe set of claim 1 , wherein the primary nucleotide portion of the target nucleic acid is selected from the group consisting of: a fusion gene, a transcript encoding primary fusion partner, or an exon skipping transcript encoding one exon, and

wherein the second portion of the probe complementary to the secondary nucleotide portion of the target nucleic acid is selected from the group consisting of: a fusion gene, a transcript encoding secondary fusion partner, or an exon skipping transcript encoding secondary exon.

3. The probe set of claim 1 , wherein the length of the second portion of the probe represents a segment of the total length, the segment of the total length selected from the group consisting of: 9%, 17%, 25%, 33% or 42% of a total probe length.

4. The probe set of claim 1 , wherein the primary nucleotide portion of the target nucleic acid is the primary fusion partner that is a kinase molecule, and the secondary nucleotide portion of the target nucleic acid is the secondary fusion partner that is a non-kinase molecule.

5. The probe set of claim 1 , wherein the probe set is included within a kit.

6. The probe set of claim 1 , wherein the probe set is contained within a composition.

7. A probe comprising:

a first portion of the probe complementary to a primary nucleotide portion of a target nucleic acid that is selected from the group consisting of:

a fusion gene or transcript encoding primary fusion partner, or

an exon skipping transcript encoding one exon, and

a second portion of the probe complementary to a secondary nucleotide portion of the target nucleic acid that is selected from the group consisting of:

a fusion gene or transcript encoding a secondary fusion partner, or

an exon skipping transcript encoding secondary exon, and

wherein the probe overlaps a breakpoint between the primary and the secondary nucleotide portion of the target nucleic acid, and

wherein the length of second portion of the probe is 10 to 50 base pair (bp) long and a total probe length is 120 bp.

8. The probe of claim 7 , wherein the length of the second portion of the probe has 10, 20, 30, 40, or 50 bp.

Assignments (1)

Priority Claims (1)

Continuity (1)

References Cited (11)