Single nucleotide polymorphism in HLA-B*15:02 and use thereof
Disclosed herein is a novel single nucleotide polymorphism (SNP) in HLA-B*15:02 that can be used as a biomarker for carbamazepine-induced severe adverse skin reactions in Asians. Also provided herein are methods and reagents for assessing the specific SNP, and applying the SNP in predicting an increased risk of carbamazepine-induced severe adverse skin reactions.
1. A method for detecting the HLA-B*15:02 allele, comprising: obtaining a sample; and determining the presence of rs144012689 minor allele T in the sample.
2. The method of claim 1 , further comprising subjecting the sample to an assay selected from the group consisting of TaqMan® genotyping, SNP array and next generation sequencing.
3. The method of claim 2 , wherein said TaqMan® genotyping comprises subjecting the sample to a polymerase chain reaction in the presence of a Taq DNA polymerase, a pair of primers designated at the HLA-B gene such that an amplicon produced therefrom includes rs144012689, and a non-naturally modified probe that hybridizes with a portion of the amplicon at or near rs1.44012689.
4. The method of claim 3 , wherein said probe comprises one or more sequences selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9 and/or SEQ ID NO: 10.
5. The method of claim 3 , further comprising subjecting the sample to TaqMan® genotyping with three probes having the sequences of SEQ ID NO: 5, SEQ ID NO: 6, and SEQ ID NO: 7.
6. The method of claim 3 , further comprising subjecting the sample to TaqMan® genotyping with three probes having the sequences of SEQ ID NO: 8, SEQ ID NO: 9 and SEQ ID NO: 10.
7. The method of claim 3 , wherein said probe has a reporter dye and a quencher dye attached thereto such that when both attached, the quencher dye quenches a signal from the reporter dye, and when one or both of the reporter dye and the quencher dye is released from the probe, the reporter dye emits the signal.
8. The method of claim 7 , wherein the signal is fluorescence.
9. The method of claim 7 , wherein one or both of the reporter dye and the quencher dye is capable of being released from the probe by Taq DNA polymerase when the probe is hybridized to the amplicon at or near rs144012689.
10. The method of claim 2 , wherein said SNP array comprises a plurality of nucleic acids bound thereto, wherein the plurality of nucleic acids comprise one or more sequences selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9 and/or SEQ ID NO: 10.
11. The method of claim 10 , further comprising hybridizing DNA from the sample to the plurality of nucleic acids.
12. The method of claim 11 , further comprising labelling the DNA from the sample.
13. The method of claim 1 , wherein the sample is from a patient in need of and prior to carbamazepine administration.
14. The method of claim 1 , wherein the sample comprises genomic DNA.