Mutations associated with cystic fibrosis

• US 8,728,731 B2
• Filed: 03/22/2011
• Issued: 05/20/2014
• Est. Priority Date: 03/22/2010
• Status: Active Grant

• Current Assignee: Laboratory Corporation Of America Holdings
• Original Assignee: Laboratory Corporation Of America Holdings
• Inventors: Rohlfs, Elizabeth, Rosenblum, Lynne, Nagan, Narasimhan, Zhou, Zhaoqing, Heim, Ruth, Sirko-Osadsa, Deborah Alexa
• Primary Examiner(s): HANEY, AMANDA MARIE
• Application Number:
  US13/053,626
• Publication Number:
  US 20110230365A1
• Time in Patent Office: 1,155 Days
• Field of Search: None
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 2800/382 Cystic fibrosis
• CPC Class Codes: G01N 33/6872 Intracellular protein regulatory factors and their receptors, e.g. including ion channels

Abstract

The present invention provides novel mutations identified in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that can be used for a more accurate diagnosis of cystic fibrosis (CF) and CF related disorders. Methods for testing a sample obtained from a subject to determine the presence of one or more mutations in the CFTR gene are provided wherein the presence of one or more mutations indicates that the subject has CF or a CF related disorder, or is a carrier of a CFTR mutation.

Claims

1. A method comprising:

detecting in a sample obtained from a human subject the presence of a 1824delA mutation in a cystic fibrosis transmembrane conductance regulator (CFTR) gene or protein; and

indicating that the subject has cystic fibrosis, or is at risk of developing cystic fibrosis when the subject is homozygous for the 1824delA mutation, or is a carrier of cystic fibrosis when the subject is heterozygous for the 1824delA mutation.

2. The method of claim 1, further comprising detecting one or more of a 269C>

T, 2902G>

T, 3814G>

A, 502G>

C, 1520G>

T, 511-513 dup TTA, 978A>

T, 843G>

C, 829C>

T, 4096-6C>

T, 4375-7delT, 1586G>

C, 875+4G>

T, or 4005+3G>

T mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene or protein.

3. The method of claim 1, further comprising detecting one or more of a 2711T>

C, 3891G>

C, 2524C>

T or 2894G>

A mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene or protein.

4. The method of claim 1, further comprising detecting one or more of a 405+10247C>

T, 405+10255 del C, 1811+1643 G>

T, 1812-13A>

G, 2752-33insA, 3849+12192 G>

A, 724G>

A, 3899C>

T, 3986C>

T, 901G>

A, 392T>

C, 3463T>

C, 1757G>

A, 4025G>

C, 4129G>

T, 663T>

G, 3200T>

C, 4412T>

C, 620A>

C, 1738A>

G, 3370A>

C, 1129C>

T, 2383C>

T, 2761delTCT, 1106A>

G or 622A>

G mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene or protein.

5. The method of claim 1, wherein the 1824delA mutation is detected as part of a CFTR mutation panel.

6. The method of claim 1, wherein the sample comprises nucleic acid.

7. The method of claim 6, wherein the detecting step comprises nucleic acid sequencing.

8. The method of claim 6, wherein the detecting step comprises hybridization.

9. The method of claim 8, wherein the hybridization is performed using one or more oligonucleotide probes specific for SEQ ID NO:

1 under conditions sufficiently stringent to disallow a single nucleotide mismatch.

10. The method of claim 8, wherein the hybridization is performed with a microarray.

11. The method of claim 6, wherein the detecting step comprises restriction enzyme digestion.

12. The method of claim 6, wherein the detecting step comprises PCR amplification.

13. The method of claim 12, wherein the PCR amplification is digital PCR amplification or real-time PCR.

14. The method of claim 6, wherein the detecting step comprises primer extension.

15. The method of claim 14, wherein the primer extension is single-base primer extension.

16. The method of claim 6, wherein the detecting step comprises performing a multiplex allele-specific primer extension (ASPE).

17. The method of claim 1, wherein the sample comprises protein.

18. The method of claim 17, wherein the detecting step comprises amino acid sequencing.

19. The method of claim 17, wherein the detecting step comprises performing an immunoassay using one or more antibodies that specifically recognize one or more epitopes corresponding to the 1824delA mutation.

20. The method of claim 17, wherein the detecting step comprises protease digestion.

21. The method of claim 20, wherein the protease digestion is trypsin digestion.

22. The method of claim 20, wherein the detecting step further comprises performing 2D-gel electrophoresis.

23. The method of claim 1, wherein the detecting step comprises determining the presence of the one or more mutations using mass spectrometry.

24. The method of claim 23, wherein the mass spectrometric format is selected from among Matrix-Assisted Laser Desorption/Ionization, Time-of-Flight (MALDI-TOF), Electrospray (ES), IR-MALDI, Ion Cyclotron Resonance (ICR), Fourier Transform, and combinations thereof.

25. The method of claim 1, wherein the sample is obtained from cells, tissue, whole blood, mouthwash, plasma, serum, urine, stool, saliva, cord blood, chorionic villus sample, chorionic villus sample culture, amniotic fluid, amniotic fluid culture, or transcervical lavage fluid, or a combination thereof.

26. The method of claim 1, wherein the method is used in conjunction with an additional test for CFTR mutations.

27. The method of claim 1 further comprising providing a sample obtained from the subject.

28. The method of claim 1, wherein the presence of the mutation is determined by comparing the identity of the nucleotide and/or amino acid at the 1824delA mutation to a control.

29. The method of claim 1, further comprising detecting one or more of a 2957delT, 4089ins4, 4374+2T>

C, 3064A>

T, or 246C>

G mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene or protein.