A novel strategy for defining haplotypes by selective depletion using restriction enzymes.

TitleA novel strategy for defining haplotypes by selective depletion using restriction enzymes.
Publication TypeJournal Article
Year of Publication2007
AuthorsSmirnova AS, Ferreira-Silva KC, Mine KL, Andrade-Oliveira V, Shulzhenko N, Gerbase-DeLima M, Morgun A
JournalImmunogenetics
Volume59
Issue1
Pagination93-8
Date Published2007 Jan
ISSN0093-7711
KeywordsAlleles, Brazil, DNA Restriction Enzymes, Genetic Testing, Genotype, Haplotypes, Humans, Lymphotoxin-alpha, Polymerase Chain Reaction, Polymorphism, Single Nucleotide
Abstract

Various single nucleotide polymorphisms (SNPs) have been investigated regarding association with gene expression levels or human diseases. Although different SNPs within one gene are frequently analyzed individually, it is highly probable that in the majority of the cases, a precise combination of SNP alleles, i.e., haplotype, determines a functional trait. Methods commonly used for haplotype determination, involving studies in families, cloning, or somatic cell hybrids, are expensive and time-consuming. We herein suggest a novel and simple strategy for haplotype determination, involving selective haplotype depletion with a restriction enzyme, followed by sequencing. We studied 11 LTA gene polymorphisms in 102 Brazilian individuals, and we applied this novel methodology for haplotyping 67 out of 70 LTA heterozygous individuals. We concluded that the method is rapid and efficient, and, as it includes only simple and widespread-used techniques, it could be used in most of the laboratories without further investment in equipments. The wider usage of haplotyping could be important to clarify contradictory results frequently observed among studies that focus on a single SNP.

DOI10.1007/s00251-006-0172-8
Alternate JournalImmunogenetics