Granted Patent B2

US 12,410,478 · App. 17/383,093 · Granted Sep 9, 2025

Inventors: Kirsten Timms (Salt Lake City, UT); Brian Allen (Salt Lake City, UT); Anne-Renee Hartman (Salt Lake City, UT)

Assignee: Myriad Genetics, Inc.

C12Q1/6886A61K31/138C12P19/34G01N33/57415G01N33/57449G16B20/00G16B20/10G16B20/20C12Q2600/156C12Q2600/16G16B30/00G16B30/10

Abstract

Claims (68)

1. A method comprising:

a) extracting genomic DNA from a sample comprising germline cells of a patient;

b) forming a mixture by hybridizing nucleic acid probes that hybridize to the genomic DNA, wherein the genomic DNA comprises a plurality of nucleic acid molecules, wherein said plurality of nucleic acid molecules comprise the coding regions of a plurality of test genes and wherein said plurality of test genes comprise target genes: APC gene, ATM gene, BARD 1 gene, BMPRIA gene, Breast Cancer 1 (BRCA1) gene, Breast Cancer 2 (BRCA2) gene, BRIP1 gene, CDH1 gene, CDK4 gene, CDKN2A gene, CHEK2 gene, EPCAM gene, MLH1 gene, MSH2 gene, MSH6 gene, MUTYH gene, NBN1 gene, PALB2 gene, PMS2 gene, phosphatase and tensin homolog (PTEN) gene, RADSIC gene, RADS1D gene, SMAD4 gene, STK11 gene, and TP53 gene;

c) performing one or more amplification reactions for amplifying said plurality of nucleic acid molecules in the DNA mixture in the presence of one or more primer pairs, wherein each of the primer pairs generates amplification products comprising a portion of each of the target genes;

d) sequencing said amplification products; and

e) comparing the sequences of the amplification products with one or more reference sequences of each of the target genes using an alignment software, thereby determining whether the patient has germline mutations in the target genes based on the presence of at least one insertion or deletion greater than 1,000 nucleotides in the sequences of the amplification products from the plurality of test genes.

2. The method of claim 1 , wherein the one or more reference sequences comprise the sequence of each of the target genes in the following table:

Entrez

Gene

Symbol

SEQ ID NO

APC

 1

ATM

 20

BARD1

 21

BMPR1A

 60

BRCA1

 97

BRCA2

128

BRIP1

158

CDH1

182

CDK4

201

CDKN2A

212

CHEK2

223

EPCAM

244

MLH1

289

MSH2

355

MSH6

374

MUTYH

387

NBN

411

PALB2

430

PMS2

450

PTEN

475

RAD51C

516

RAD51D

521

SMAD4

546

STK11

561

TP53

576.

3. The method of claim 1 , wherein at least one of the amplification products comprises at least a portion of an exon sequence and an intron sequence comprising at least 10 base pairs in length flanking at least one end of said exon sequence.

4. The method of claim 1 further comprising determining if the patient has at least one second level risk factors comprising personal risk factors and family risk factors.

5. The method of claim 4 , wherein the personal risk factors comprise that the patient has a history of multiple primary cancers, a positive triple negative breast cancer, a history of ovarian cancer, a history of smoking, a positive tissue biopsy for a cancer, a positive vaginal pap smear for a cancer, a history of male breast cancer, an enlarged prostate, colon polyps, and an age of the patient if a cancer is diagnosed, an age of menopause of the patient, and an age of menarche of the patient.

6. The method of claim 4 , wherein the family risk factors comprise that the patient has Ashkenazi Jewish ancestry, a relative with early onset cancer, a relative with multiple primary cancers, a relative with male breast cancer, a relative with ovarian cancer, and a relative with triple negative breast cancer.

7. The method of claim 1 , wherein the target genes comprise at least 25% of the plurality of test genes.

8. The method of claim 1 , wherein the target genes comprise at least 50% of the plurality of test genes.

9. The method of claim 1 , wherein the sample is a human sample.

Assignments (4)

Continuity (5)

References Cited (122)