Haplotype tagging single nucleotide polymorphisms and use of same to predict childhood lymphoblastic leukemia
The present invention is directed to novel haplotype tagging single nucleotide polymorphisms (SNPs) in specific regions outside the HFE gene that serve as a reliable biomarker for a decreased risk for childhood lymphoblastic leukemia (ALL) in a child. There is provided herein methods and reagents for assessing the haplotype tagging SNPs selected from the group consisting of rs807212, rs198853, rs9467664, rs2213284, rs2230655 and rs12346. The method useful in applying these SNPs in predicting a decreased risk of childhood lymphoblastic leukemia (ALL) is also disclosed.
1. A method for determining whether a human male child has a reduced risk of childhood acute lymphoblastic leukemia (ALL), comprising the steps of:
(a) obtaining a biological sample from a human male child;
(b) isolating nucleic acid from said biological sample;
(c) performing a polymerase chain reaction-restriction fragment length polymorphism assay (PCR-RFLP) in the isolated nucleic acid obtained in (b), said PCR-RFLP comprises the steps of:
(i) performing a PCR on said isolated nucleic acid to produce an amplicon containing haplotype tagging SNP rs807212; and
(ii) digesting said amplicon with a restriction endonuclease to produce a plurality of fragments, wherein said restriction endonuclease is MspI;
(d) determining heterozygosity for thymine (T) allele at said haplotype tagging SNP rs807212 in said amplicon based on the presence of said plurality of fragments; and
(e) determining that said human male child has a reduced risk of childhood ALL based on said determined heterozygosity.
2. The method of claim 1 , wherein said biological sample is cord blood or peripheral blood.
3. The method of claim 1 , wherein said isolating step is performed using phenol-chloroform.
4. The method of claim 1 , wherein said nucleic acid is genomic DNA.