# US 11,028,428 B2 · Peptide nucleic acid probe for multiplex detection of BCR/ABL negative myeloproliferative neoplasm-associated gene mutations

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- Number: US 11,028,428 B2
- Document ID: US11028428B2
- Status: Granted
- Kind: B2
- Application number: 15/775,591
- Filed: 2016-06-03
- Published: 2018-12-13
- Granted: 2021-06-08
- Earliest claimed: 2015-11-11
- Assignees: The Catholic University of Korea Industry-Academic Cooperation Foundation
- Applicants: The Catholic University of Korea Industry-Academic Cooperation Foundation
- Inventors: Yonggoo Kim; Myungshin Kim; Joonhong Park; Minsik Song; Heekyung Park; KyungTak Kim
- Web page: https://patentgrep.com/patent/US11028428B2

## CPC

- C12Q 1/6827: for detection of mutation or polymorphism
- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C12Q 2600/156: Polymorphic or mutational 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 provides a peptide nucleic acid probe including any one or more selected from the group consisting of nucleic acid sequences represented by SEQ ID NOs: 7-10 and nucleic acid sequences complementary to the nucleic acid sequences, and manufactured so as to complementarily bind to a BCR/ABL negative myeloproliferative neoplasm-associated gene, thereby enabling multiplex detection of gene mutations; a composition for multiplex detection of gene mutations comprising the same; a kit; and a method for multiplex detection of BCR/ABL negative myeloproliferative neoplasm-associated gene mutations using the same. Therefore, since multiplex detection of BCR/ABL negative myeloproliferative neoplasm-associated gene mutations can be rapidly and accurately carried out by one detection process, BCR/ABL negative myeloproliferative neoplasm is effectively diagnosed, and thus the present invention can be useful for diagnosis, follow-up, prognosis estimation, and treatment of diseases.

## Claims

### Claim 1

A kit for multiplex detection of a BCR/ABL negative myeloproliferative neoplasm-associated gene mutation, comprising
a set of peptide nucleic acid (PNA) probes, wherein each probe consists of the sequences of
SEQ ID NO: 7 binding to a mutation region of a Janus Tyrosine Kinase 2 (JAK2) gene;
SEQ ID NO: 8 binding to a mutation region of a Mythroproliferative leukemia protein (MPL) gene;
SEQ ID NO: 9 binding to a deletion region of a Calreticulin (CALR) Gene; and
SEQ ID NO: 10 binding to an insertion region of the CALR Gene; respectively, wherein the peptide nucleic acid probe optionally contains a reporter molecule and a quencher molecule at each end of the probe, and
a set of amplification forward and reverse primers comprising the sequences of SEQ ID NOS: 1 to 6, wherein each primer complementarily binds to a BCR/ABL negative myeloproliferative neoplasm-associated gene to specifically amplify a region of a mutation site, and
wherein the BCR/ABL negative myeloproliferative neoplasm-associated gene mutation comprises one or more selected from the group consisting of (i) a substitution of valine at position 617 of the JAK2 gene with phenylalanine (JAK2 V617F), (ii) a substitution of tryptophan at position 515 of the MPL gene with leucine (MPL W515L), (iii) a substitution of tryptophan at position 515 of the MPL gene with lysine (MPL W515K), (iv) a substitution of tryptophan at position 515 of the MPL gene with arginine (MPL W515R), (v) a substitution of tryptophan at position 515 of the MPL gene with alanine (MPL W515A), (vi) a substitution of tryptophan at position 515 of the MPL gene with serine (MPL W515S), (vii) a c.1092_1143del52 base deletion of the CALR gene (L367fs*46) and (viii) a c.1154_1155insTTGTC base insertion of the CALR gene (K385fs*47).

### Claim 2 (depends on 1)

The kit of claim 1, wherein the reporter molecule is any one selected from the group consisting of FAM (6-carboxyfluorescein), Texas red, HEX (2′,4′,5′,7′-tetrachloro-6-carboxy-4,7-dichlorofluorescein), and Cy5.

### Claim 3 (depends on 1)

The kit of claim 1, wherein the quencher molecule is any one selected from the group consisting of TAMRA (6-carboxytetramethyl-rhodamine), BHQ1, BHQ2, and Dabcyl.

### Claim 4

A method for multiplex detection of a BCR/ABL negative myeloproliferative neoplasm-associated gene mutation, the method comprising:
hybridizing a set of amplification forward and reverse primers comprising the sequences of SEQ ID NOS: 1 to 6, wherein each primer complementarily binds to a BCR/ABL negative myeloproliferative neoplasm-associated gene to specifically amplify a region of a mutation site, to a target DNA sample,
amplifying a product obtained from the hybridizing step by PCR,
adding a set of PNA probes to the amplified product, wherein each probe consists of the sequences of:
SEQ ID NO: 7 binding to a mutation region of a Janus Tyrosine Kinase 2 (JAK2) gene;
SEQ ID NO: 8 binding to a mutation region of a Myeloproliferative leukemia protein (MPL) gene;
SEQ ID NO: 9 binding to a deletion region of a Calreticulin (CALR) Gene; and
SEQ ID NO: 10 binding to an insertion region of the CALR Gene; respectively, wherein the peptide nucleic acid probe optionally contains a reporter molecule and a quencher molecule at each end of the probe,
obtaining a melting curve; and
comparing said melting curve with the standard melting temperatures of mutant genes,
wherein the BCR/ABL negative myeloproliferative neoplasm-associated gene mutation comprises one or more selected from the group consisting of (i) a substitution of valine at position 617 of the JAK2 gene with phenylalanine (JAK2 V617F), (ii) a substitution of tryptophan at position 515 of the MPL gene with leucine (MPL W515L), (iii) a substitution of tryptophan at position 515 of the MPL gene with lysine (MPL W515K), (iv) a substitution of tryptophan at position 515 of the MPL gene with arginine (MPL W515R), (v) a substitution of tryptophan at position 515 of the MPL gene with alanine (MPL W515A), (vi) a substitution of tryptophan at position 515 of the MPL gene with serine (MPL W515S), (vii) a c.1092_1143del52 base deletion of the CALR gene (L367fs*46) and (viii) a c.1154_1155insTTGTC base insertion of the CALR gene (K385fs*47).