System and method for high resolution analysis of nucleic acids to detect sequence variations
Provided herein are methods for assaying a biological sample for microorganisms having drug resistant and/or drug sensitive phenotypes, wherein the methods are capable of detecting resistant and sensitive phenotypes associated with known and/or unknown mutations. In some aspects, methods are provided for detecting drug resistant Myobacterium tuberculosis (MTb), including multi-drug resistant MTb, wherein drug resistance is associated with one or more novel mutations. Also provided are systems, kits, and compositions related to such methods.
1. A method for determining if a patient is amenable to treatment with a drug, comprising:
obtaining a biological sample from a patient, the sample containing Mycobacterium tuberculosis (MTb);
amplifying a segment of MTb DNA consisting of SEQ ID NO:142, the segment including at least one polymorphism associated with sensitivity of the MTb to an antibiotic drug; and
assaying the amplified DNA segment for sequence variations relative to the corresponding sequence of SEQ ID NO:142, wherein a variation in the amplified DNA segment indicates sensitivity of MTb to the antibiotic drug.
2. The method of claim 1 , wherein two or more variations in the amplified DNA segment indicates sensitivity of MTb to the antibiotic drug.
3. The method of claim 1 , wherein the MTb DNA of SEQ ID NO:142 is amplified by PCR using the corresponding primers of SEQ ID NOS:11 and 12.
4. The method of claim 1 , wherein a variation in the amplified DNA segment indicates sensitivity of MTb to rifampicin.