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 non-naturally modified probe comprising a sequence selected from SEQ NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9 and/or SEQ ID NO: 10, wherein said probe has a detectable label attached thereto.
2. A double-stranded nucleic acid molecule comprising the non-naturally modified probe of claim 1 and a target sequence complementary and annealed to the probe, wherein said probe has a detectable label attached thereto.
3. A solid phase having a plurality of nucleic acids bound thereto, wherein the plurality of nucleic acids comprise one or more of the non-naturally modified probe of claim 1 .
4. A solid phase having a plurality of nucleic acids bound thereto and a target sequence annealed to the nucleic acid, wherein the plurality of nucleic acids comprise one or more of the non-naturally modified probe of claim 1 .
5. A kit for detecting the HLA-B*15:02 allele in a sample, comprising one or more of the non-naturally modified probes of claim 1 .
6. The kit of claim 5 , comprising three probes having the sequences of SEQ NO: 5, SEQ ID NO: 6, and SEQ ID NO: 7, respectively.
7. The kit of claim 5 , comprising three probes having the sequences of SEQ ID NO: 8, SEQ ID NO: 9 and SEQ ID NO: 10, respectively.
8. The kit of claim 5 , wherein the probe is labeled by a fluorescent dye at the 5′ terminus and a quencher at the 3′ terminus.
9. The kit of claim 5 , further comprising:
a pair of primers designated at the HLA-B gene such that an amplicon produced therefrom includes rs144012689;
dNTPs; and
Taq DNA polymerase.
10. A method of treating a patient in need of carbamazepine, comprising:
obtaining a sample from the patient,
determining the presence or absence of rs144012689 minor allele T in the sample using one or more of the non-naturally modified probes of claim 1 , and
in the absence of rs144012689 minor allele T, administering carbamazepine to the patient.
11. The method of claim 10 , further comprising subjecting the sample to an assay selected from the group consisting of TaqMan® genotyping, SNP array and next generation sequencing.
12. The method of claim 11 , wherein said TagMan® genotyping comprises subjecting the sample to a polymerase chain reaction in the presence of a TaqDNA 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 rs144012689.
13. The method of claim 12 , 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.
14. The method of claim 12 , further comprising subjecting the sample to TaqMan® genotyping with three probes having the sequences of SEQ ID NO: 8, SEQ NO: 9 and SEQ ID NO: 10.
15. The method of claim 12 , 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.
16. The method of claim 15 , wherein the signal is fluorescence.
17. The method of claim 15 , 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.
18. The method of claim 11 , 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.
19. The method of claim 18 , further comprising hybridizing DNA from the sample to the plurality of nucleic acids.
20. The method of claim 19 , further comprising labelling the DNA from the sample.
21. The method of claim 10 , wherein the sample comprises genomic DNA.