Cystic fibrosis transmembrane conductance regulator gene mutations

• US 9,422,606 B2
• Filed: 10/21/2010
• Issued: 08/23/2016
• 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:
  US12/909,141
• Publication Number:
  US 20110082050A1
• Time in Patent Office: 2,133 Days
• Field of Search: None
• US Class Current: 1/1
• 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 of detecting the presence of a gIVS6a+415_IVS10+2987Dup26817bp mutation in the cystic fibrosis transmembrane regulatory (CFTR) gene in a human individual comprising:

(a) amplifying a nucleic acid molecule comprising the sequence of SEQ ID NO;

2 from a nucleic acid sample obtained from the human individual using;

(i) a forward primer that comprises 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; and

(b) detecting the amplified nucleic acid molecule, if present, thereby detecting the gIVS6a+415_IVS10+2987Dup26817bp mutation, wherein detecting the amplified nucleic acid comprising the sequence of SEQ ID NO;

2 indicates the presence of the gIVS6a+415_IVS10+2987Dup26817bp mutation.

2. The method of claim 1, wherein the nucleic acid sample is genomic DNA or cDNA.

3. The method of claim 1, wherein the method comprises sequencing the amplified nucleic acid molecule.

4. The method of claim 1, wherein the amplified nucleic acid molecule is detected using a detectably labeled probe.

5. 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+2987Dup26817bp mutation in at least one allele of the CFTR gene in a nucleic acid sample obtained from the human individual, wherein detection comprises;

(i) amplifying a nucleic acid molecule comprising the sequence of SEQ ID NO;

2 from the nucleic acid sample using;

(1) a forward primer that comprises 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; and

(ii) detecting the amplified nucleic acid molecule, if present, thereby detecting the gIVS6a+415_IVS10+2987Dup26817bp mutation at least one allele of the CFTR gene; and

(b) identifying the human individual as having an increased likelihood of having an offspring predisposed to cystic fibrosis when the gIVS6a+415_IVS10+2987Dup26817bp 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.

6. The method of claim 5, wherein the nucleic acid sample is genomic DNA or cDNA.

7. The method of claim 5, wherein the amplified nucleic acid molecule is detected using a detectably labeled probe.

8. The method of claim 5, wherein the method comprises sequencing the amplified nucleic acid molecule.

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

(a) detecting the presence of a gIVS6a+415_IVS10+2987Dup26817bp mutation in one or both alleles of the CFTR gene in a nucleic acid sample obtained from the human individual, wherein detection comprises;

(i) amplifying a nucleic acid molecule comprising the sequence of SEQ ID NO;

2 from the nucleic acid sample;

(1) a forward primer that comprises 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; and

(ii) detecting the amplified nucleic acid molecule, if present, thereby detecting the gIVS6a+415_IVS10+2987Dup26817bp mutation in the CFTR gene; and

(b) identifying the human individual as;

(i) having cystic fibrosis or being predisposed to cystic fibrosis when the gIVS6a+415_IVS10+2987Dup26817bp 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+2987Dup26817bp mutation in the CFTR gene is detected in at least one allele of the CFTR gene of the human individual in step (a).

10. The method of claim 9, wherein the nucleic acid sample is genomic DNA or cDNA.

11. The method of claim 9, wherein the forward primer or the reverse primer is labeled with a detectable moiety.

12. The method of claim 9, wherein said amplifying step further comprises multiplex ligation-dependent probe amplification or multiplex amplifiable probe hybridization.

13. The method of claim 9, wherein the amplified nucleic acid molecule is detected using a detectably labeled probe.

14. The method of claim 9, wherein the method comprises sequencing the amplified nucleic acid molecule.