CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR GENE MUTATIONS

• US 20110008790A1
• Filed: 07/30/2010
• Published: 01/13/2011
• Est. Priority Date: 12/22/2006
• Status: Active Grant

• Current Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated)
• Original Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated)
• Inventors: Buller, Arlene, Peng, Mei, McGinniss, Matthew J., Fenwick, Raymond, Huang, Donghui, Quan, Franklin, Sun, Weimin
• Granted Patent: US 8,124,345 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 2333/705 Assays involving receptors, cell surface antigens or cell surface determinants
• CPC Class Codes: G01N 2800/382 Cystic fibrosis
• CPC Class Codes: G01N 2800/50 Determining the risk of developing a disease
• CPC Class Codes: G01N 33/6872 Intracellular protein regulatory factors and their receptors, e.g. including ion channels
• CPC Class Codes: G01N 33/6893 related to diseases not provided for elsewhere
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention provides novel mutations of the CFTR gene related to cystic fibrosis or to conditions associated with cystic fibrosis. Also provided are probes for detecting the mutant sequences. Methods of identifying if an individual has a genotype containing one or more mutations in the CFTR gene are further provided.

Claims

1. A method of determining whether a human is predisposed to cystic fibrosis, comprising determining whether the human is homozygous for the 2777insTG mutation in the cystic fibrosis transmembrane regulatory (CFTR) gene in a nucleic acid sample obtained from the human and identifying the human as having a predisposition to cystic fibrosis when the human is homozygous.

2. The method of claim 1, comprising further determining the presence or absence of a second CFTR gene mutation selected from the group consisting of 3443A>

T, 2443delA, 3123-3125delGTT, 4177delG, 630delG, 2068G>

T, 1342−

2A>

G, 297−

1G>

A 3500−

2A>

T, 4375−

2A>

G, 3172-3174delTAC, 2902G>

C, 4115T>

C, 4185G>

C, 520C>

G, 842A>

C, 4528G>

T, 448A>

G, 574A>

T, 3704T>

C, 1248+5T>

C, 296+12T>

G, 3849+3G>

A, 497A>

G, −

141C>

A, 2875G>

C, 2689A>

G, 3039A>

G, 405G>

C, 886G>

A, 4445G>

A, −

228G>

C, −

295C>

T, −

379delC, and −

540A>

G.

3. The method of claim 1, wherein said 2777insTG mutation is assessed using genomic DNA.

4. The method of claim 1, wherein the presence of said 2777insTG mutation is determined by nucleic acid sequencing.

5. The method of claim 1, wherein the presence of said 2777insTG mutation is determined by allele specific amplification.

6. The method of claim 1, wherein the presence of said 2777insTG mutation is determined by primer extension.

7. The method of claim 1, wherein the presence of said 2777insTG mutation is determined by oligonucleotide ligation.

8. The method of claim 1, wherein the presence of said 2777insTG mutation is determined by hybridization with a detectably labeled probe.

9. The method of claim 1, wherein the presence of said 2777insTG mutation is determined by detecting the mutation in the encoded CFTR protein using an antibody with binding specificity for the mutated CFTR protein.

10. A method of identifying a human with an increased likelihood of having an offspring predisposed to cystic fibrosis, comprising determining the presence of the 2777insTG mutation of the cystic fibrosis transmembrane regulatory (CFTR) gene in a nucleic acid sample obtained from the human and identifying the human as having an increased likelihood of having an offspring predisposed to cystic fibrosis when the 2777insTG mutation is present in at least one allele.

11. The method of claim 10, comprising further determining the presence or absence of a second CFTR gene mutation selected from the group consisting of 3443A>

T, 2443delA, 3123-3125delGTT, 4177delG, 630delG, 2068G>

T, 1342−

2A>

G, 297−

1G>

A 3500−

2A>

T, 4375−

2A>

G, 3172-3174delTAC, 2902G>

C, 4115T>

C, 4185G>

C, 520C>

G, 842A>

C, 4528G>

T, 448A>

G, 574A>

T, 3704T>

C, 1248+5T>

C, 296+12T>

G, 3849+3G>

A, 497A>

G, −

141C>

A, 2875G>

C, 2689A>

G, 3039A>

G, 405G>

C, 886G>

A, 4445G>

A, −

228G>

C, −

295C>

T, −

379delC, and −

540A>

G.

12. The method of claim 10, wherein said 2777insTG mutation is assessed using genomic DNA.

13. The method of claim 10, wherein the presence of said 2433delA mutation is determined by nucleic acid sequencing.

14. The method of claim 10, wherein the presence of said 2777insTG mutation is determined by allele specific amplification.

15. The method of claim 10, wherein the presence of said 2777insTG mutation is determined by primer extension.

16. The method of claim 10, wherein the presence of said 2777insTG mutation is determined by oligonucleotide ligation.

17. The method of claim 10, wherein the presence of said 2777insTG mutation is determined by hybridization with a detectably labeled probe.

18. The method of claim 10, wherein the presence of said 2777insTG mutation is determined by detecting the mutation in the encoded CFTR protein using an antibody with binding specificity for the mutated CFTR protein.

19. A method of determining the cystic fibrosis status of a human, comprising:

(a) determining the presence or absence of the 2777insTG mutation in both alleles of the cystic fibrosis transmembrane regulatory (CFTR) gene of the human in a nucleic acid sample obtained from the human, and

(b) identifying the human

(i) as having cystic fibrosis or being predisposed to cystic fibrosis when the human is homozygous for the 2777insTG mutation in the CFTR gene, or

(ii) as being cystic fibrosis carrier when the human is heterozygous for the 2777insTG mutation in the CFTR gene, or

(iii) as having no predisposition or carrier status caused by the 2777insTG mutations when the 2777insTG mutation is absent from both alleles of the CFTR gene.

20. The method of claim 19, comprising further determining the presence or absence of a second CFTR gene mutation selected from the group consisting of 3443A>

T, 2443delA, 3123-3125delGTT, 4177delG, 630delG, 2068G>

T, 1342−

2A>

G, 297−

1G>

A 3500−

2A>

T, 4375−

2A>

G, 3172-3174delTAC, 2902G>

C, 4115T>

C, 4185G>

C, 520C>

G, 842A>

C, 4528G>

T, 448A>

G, 574A>

T, 3704T>

C, 1248+5T>

C, 296+12T>

G, 3849+3G>

A, 497A>

G, −

141C>

A, 2875G>

C, 2689A>

G, 3039A>

G, 405G>

C, 886G>

A, 4445G>

A, −

228G>

C, −

295C>

T, −

379delC, and −

540A>

G.

21. The method of claim 19, wherein said 2777insTG mutation is assessed using genomic DNA or cDNA.

22. The method of claim 19, wherein the presence of said 2777insTG mutation is determined by allele specific amplification.

23. The method of claim 19, wherein the presence of said 2777insTG mutation is determined by primer extension.

24. The method of claim 19, wherein the presence of said 2777insTG mutation is determined by oligonucleotide ligation.

25. The method of claim 19, wherein the presence of said 2777insTG mutation is determined by hybridization with a detectably labeled probe containing the mutant sequence.

26. The method of claim 19, wherein the presence of said 2777insTG mutation is determined by detecting the mutation in the encoded CFTR protein using an antibody with binding specificity for the mutated CFTR protein.