< B>4.2. Detection of DNA polymorphism and its Use

p. 40 in Bioethics and the Impact of Human Genome Research in the 21st Century

Author: Takeshi Hayashi (Genome Information Centre, Kyushu University)

Editors: Norio Fujiki, Masakatu Sudo, and Darryl R. J. Macer
Eubios Ethics Institute

Copyright 2001, Eubios Ethics Institute All commercial rights reserved. This publication may be reproduced for limited educational or academic use, however please enquire with the author.
Genome sequence is different among individuals, and the nucleotide divergence are said to be found once per every kb or less. Some of the nucleotide differences are determinants of hereditary characteristics of individuals, such as skin colour, susceptibility to diseases or characters, although most of them are neutral, and does not influence our everyday lives. Nucleotide changes, or mutations, which are causatively related to various monogenic hereditary diseases have been identified utilizing limited information of human genome, and diagnosis or therapy of the diseases have been significantly benefited from such knowledge. Genetic studies of more common traits such as susceptibility to infectious disease or hypertension have been difficult to tackle, because such traits are under the control of more than two genes (i.e., polygenic), and conventional genetic analysis does not have the power to solve the problem. Recently, however, nucleotide sequencing of the whole human genome are approaching to completion owing to the effort in human genome project, and together with the development of techniques to analyze many loci and many samples, common traits became the target of genetic study!

Genome-widely distributed polymorphic markers are required to pin-point genes responsible for polygenic traits by genetic analysis. The most common polymorhphisms in the human genome is single nucleotide polymorphisms (SNPs). A large scale detection of SNPS (i.e., detection of many SNPs) became relatively easy owing to recent developments of various high throughput analysis techniques. However, SNPS are informative (useful in genetic study) only if they are highly heterozygous. Thus, collection of SNPS with high heterozygosity as markers in the genetic study is a prerequisite. We introduce here, a new technique named PLACE-SSCP, in which PCR products from genomic DNA are fluorescently labeled and separated by a DNA sequencer under non<denaturing conditions. SNP alleles are efficiently detected as separated peaks in the electrophoresis at a high specificity. We also show that by pooling DNA samples and analyzing by PLACE-SSCP, SNP alleles are quantitatively detected, and allele frequencies are very precisely estimated. Using this pooling strategy, we found widely different SNP allele frequencies among populations of different ethnicity.

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