Method of detection of SP-A2 gene variants

• US 7,381,527 B2
• Filed: 11/06/2002
• Issued: 06/03/2008
• Est. Priority Date: 11/06/2002
• Status: Expired due to Fees

• Current Assignee: Council of Scientific & Industrial Research
• Original Assignee: Council of Scientific & Industrial Research
• Inventors: Madan, Taruna, Sarma, Puranam Usha, Saxena, Shweta
• Primary Examiner(s): Chunduru; Suryaprabha
• Application Number:
  US10/289,163
• Publication Number:
  US 20040091868A1
• Time in Patent Office: 2,036 Days
• Field of Search: 435/91.2, 435/6, 536/24.33
• US Class Current: 435/6.16
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The invention provides a method for predicting the susceptibility of an individual to pulmonary tuberculosis, the method comprising amplifying genomic DNA of pulmonary tuberculosis patients and normal control individuals using oligonuecleotide primers, sequencing the amplified PCR product and identifying the sequence variation computationally by comparing it with the already existing sequence of human SP-A2 gene.

Claims

1. A method for predicting the susceptibility of an individual to pulmonary tuberculosis, said method comprising:

a) amplifying genomic DNA of pulmonary tuberculosis patients and normal control individuals using oligonucleotide primers for PCR amplification of the polymorphic site containing A or G base region containing exon-4 of human SP-A2 gene to obtain an amplified product,

b) sequencing the amplified PCR product and identifying the sequence variation computationally by comparing it with the human SP-A2 gene,

c) establishing the association of C and G haplotypes as defined by the nucleotide present at position 1649 and 1660, with pulmonary tuberculosis, based on the haplotype frequency distribution in normal individuals and tuberculosis patients, and

d) predicting the risk or susceptibility to pulmonary tuberculosis based on the haplotype present at the polymorphic sites in the said individual, wherein a haplotype with C at 1649 position and A at 1660 position is at low risk and a haplotype with G at 1649 position and G at 1660 position is at high risk for the disease.

2. A method as claimed in claim 1 wherein the oligonucleotide primers are SEQ ID NOS:

1 and 2 or SEQ ID NOS;

3 and 4.

3. A method of detection of human SP-A2 gene variants comprising:

(a) amplifying genomic DNA of pulmonary tuberculosis patients and normal control individuals using the primers SEQ ID NOS;

1 and 2 or SEQ ID NOS;

3 and 4 for SP-A2 Exon 4;

(b) sequencing the amplified PCR product and identifying the sequence variation computationally by comparing it with the already existing sequence of human SP-A2 gene;

(c) screening normal control individuals and pulmonary tuberculosis patients;

(d) computing the frequency of G/C haplotypes at 1649 position and A/G haplotypes at 1660 position;

(e) establishing the association of G (at 1649 position) and G (at 1660 position) haplotypes with the pulmonary tuberculosis disease based on their frequency distribution in normals and pulmonary tuberculosis patients; and

(g) predicting the risk or susceptibility to pulmonary tuberculosis based on the haplotype present at the polymorphic sites in the individual tested, C (at 1649 position) and A (at 1660 position) haplotypes being at low risk and G (at 1649 position) and G (at 1660 position) haplotypes at high risk to the disease.