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.
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Acknowledgment
This study was partially supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; Grant 2001/0520-2). We thank the staff of the Immunogenetics Division and the Chorus and Guitar Orchestra of UNIFESP for the kind agreement to participate in our study as volunteers. A.S. Smirnova and K.L. Mine are recipients of FAPESP fellowships. K.C. Ferreira-Silva and V. Andrade-Oliveira are undergraduate students, recipients of Conselho Nacional de Desenvolvimento Científico e Tecnológico fellowships. We thank William Pinheiro-Asam for the technical assistance.
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Maria Gerbase-DeLima and Andrey Morgun are co-senior authors.
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Smirnova, A.S., Ferreira-Silva, K.C., Mine, K.L. et al. A novel strategy for defining haplotypes by selective depletion using restriction enzymes. Immunogenetics 59, 93–98 (2007). https://doi.org/10.1007/s00251-006-0172-8
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DOI: https://doi.org/10.1007/s00251-006-0172-8