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

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

Author Smirnova, Anna S. Google Scholar
Ferreira-Silva, Katia C. Google Scholar
Mine, Karina L. Google Scholar
Andrade-Oliveira, Vinicius Google Scholar
Shulzhenko, Natalia Google Scholar
Gerbase-DeLima, Maria Google Scholar
Morgun, Andrey Google Scholar
Institution Universidade Federal de São Paulo (UNIFESP)
NIAID
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.
Keywords haplotype
polymorphism
restriction enzyme
selective depletion
lymphotoxin alpha
LTA
Language English
Date 2007-01-01
Published in Immunogenetics. New York: Springer, v. 59, n. 1, p. 93-98, 2007.
ISSN 0093-7711 (Sherpa/Romeo, impact factor)
Publisher Springer
Extent 93-98
Origin http://dx.doi.org/10.1007/s00251-006-0172-8
Access rights Closed access
Type Article
Web of Science ID WOS:000243001100010
URI http://repositorio.unifesp.br/handle/11600/29366

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