Cystic fibrosis transmembrane conductance regulator gene mutations

• US 9,863,000 B2
• Filed: 07/28/2016
• Issued: 01/09/2018
• Est. Priority Date: 08/18/2005
• Status: Active Grant

• Current Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated)
• Original Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated)
• Inventors: Hantash, Feras
• Primary Examiner(s): HANEY, AMANDA MARIE
• Application Number:
  US15/222,218
• Publication Number:
  US 20170022566A1
• Time in Patent Office: 530 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

The present invention provides novel mutations of the CFTR gene related to cystic fibrosis or to conditions associated with cystic fibrosis. The mutations include duplication of exons including duplication of exons 6b through 10. Methods of identifying if an individual contains the exons 6b through 10 duplication are provided as well as nucleic acid fragments that contain the junction site of the duplicated segment. The detection of additional mutations in the CFTR gene are also provided.

Claims

1. A method for detecting the presence of a gIVS6a+415_IVS10+2987Dup26817 bp mutation in the cystic fibrosis transmembrane regulatory (CFTR) gene in a human individual comprising:

(a) contacting a nucleic acid sample comprising a CFTR nucleic acid with a detectably labeled nucleic acid probe that hybridizes to a mutant CFTR nucleic acid comprising the gIVS6a+415_IVS10+2987Dup26817 bp mutation, if present, but not to a wild-type CFTR nucleic acid, wherein the detectably labeled nucleic acid probe comprises SEQ ID NO;

2; and

(b) detecting the gIVS6a+415_IVS10+2987Dup26817 bp mutation when a hybrid is formed between the detectably labeled nucleic acid probe and the mutant CFTR nucleic acid.

2. The method of claim 1, wherein the method comprises nucleic acid amplification.

3. The method of claim 2, wherein nucleic acid amplification comprises allele specific amplification or real-time polymerase chain reaction (RT-PCR).

4. The method of claim 2, wherein nucleic acid amplification comprises amplification with:

(i) a forward primer comprising the sequence of SEQ ID NO;

89 and a reverse primer that hybridizes to intron 6b or exon 6b of the CFTR gene;

or

(ii) a forward primer that hybridizes to intron 9 or exon 10 of the CFTR gene- and a reverse primer that comprises the sequence of SEQ ID NO;

90.

5. The method of claim 1, wherein the nucleic acid is genomic DNA, cDNA or an amplification product.

6. The method of claim 1, wherein the method further comprises sequencing the CFTR nucleic acid.

7. The method of claim 1, wherein the detectably labeled nucleic acid probe comprises SEQ ID NO:

3 or SEQ ID NO;

4.

8. A method of identifying a human individual with an increased likelihood of having an offspring predisposed to cystic fibrosis, comprising:

(a) detecting the presence of a gIVS6a+415_IVS10+2987Dup26817 bp mutation in at least one allele of the CFTR gene in a sample comprising a CFTR nucleic acid from the human individual, wherein detection comprises;

(i) contacting the nucleic acid sample with a detectably labeled nucleic acid probe that hybridizes to a mutant CFTR nucleic acid comprising the gIVS6a+415_IVS10+2987Dup26817 bp mutation, if present, but not to a wild-type CFTR nucleic acid, wherein the detectably labeled nucleic acid probe comprises SEQ ID NO;

2; and

(b) detecting the gIVS6a+415_IVS10+2987Dup26817 bp mutation when a hybrid is formed between the detectably labeled nucleic acid probe and the mutant CFTR nucleic acid; and

(b) identifying the human individual as having an increased likelihood of having an offspring predisposed to cystic fibrosis when the gIVS6a+415_IVS10+2987Dup26817 bp mutation is detected in at least one allele of the CFTR gene in step (a) in comparison to a human individual that has a wild-type CFTR gene.

9. The method of claim 8, wherein the method comprises nucleic acid amplification.

10. The method of claim 9, wherein nucleic acid amplification comprises allele specific amplification or real-time polymerase chain reaction (RT-PCR).

11. The method of claim 9, wherein nucleic acid amplification comprises amplification with:

(1) a forward primer comprising the sequence of SEQ ID NO;

89 and a reverse primer that hybridizes to intron 6b or exon 6b of the CFTR gene;

or

(2) a forward primer that hybridizes to intron 9 or exon 10 of the CFTR gene- and a reverse primer that comprises the sequence of SEQ ID NO;

90.

12. The method of claim 8, wherein the nucleic acid is genomic DNA, cDNA or an amplification product.

13. The method of claim 8, wherein the method further comprises sequencing the CFTR nucleic acid.

14. The method of claim 8, wherein the detectably labeled nucleic acid probe comprises SEQ ID NO:

3 or SEQ ID NO;

4.

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

(a) detecting the presence of a gIVS6a+415_IVS10+2987Dup26817 bp mutation in one or both alleles of the CFTR gene in a nucleic acid sample obtained from the human individual, wherein detection comprises;

(i) contacting the nucleic acid sample with a detectably labeled nucleic acid probe that hybridizes to a mutant CFTR nucleic acid comprising the gIVS6a+415_IVS10+2987Dup26817 bp mutation, if present, but not to a wild-type CFTR nucleic acid, wherein the detectably labeled nucleic acid probe comprises SEQ ID NO;

2; and

(ii) detecting the gIVS6a+415_IVS10+2987Dup26817 bp mutation when a hybrid is formed between the detectably labeled nucleic acid probe and the mutant CFTR nucleic acid; and

(b) identifying the human individual as;

(i) having cystic fibrosis or being predisposed to cystic fibrosis when the gIVS6a+415_IVS10+2987Dup26817 bp mutation in the CFTR gene is detected in both alleles of the CFTR gene of the human individual in step (a);

or

(ii) being a cystic fibrosis carrier when the gIVS6a+415_IVS10+2987Dup26817 bp mutation in the CFTR gene is detected in at least one allele of the CFTR gene of the human individual in step (a).

16. The method of claim 15, wherein the method comprises nucleic acid amplification.

17. The method of claim 16, wherein nucleic acid amplification comprises allele specific amplification or real-time polymerase chain reaction (RT-PCR).

18. The method of claim 16, wherein nucleic acid amplification comprises amplification with:

(1) a forward primer comprising the sequence of SEQ ID NO;

89 and a reverse primer that hybridizes to intron 6b or exon 6b of the CFTR gene;

or

(2) a forward primer that hybridizes to intron 9 or exon 10 of the CFTR gene- and a reverse primer that comprises the sequence of SEQ ID NO;

90.

19. The method of claim 15, wherein the nucleic acid is genomic DNA, cDNA or an amplification product.

20. The method of claim 15, wherein the method further comprises sequencing the CFTR nucleic acid.