2017년 1월 4일 수요일

International HapMap plan

International HapMap plan

The international HapMap plan (International HapMap Project) was organized with the goal of building ハプロタイプマップ of the human genome. When this ハプロタイプマップ becomes the thing which accumulated a common pattern of the genetic variation of the Homo sapiens, I am expected.

HapMap becomes the important source of information for the researcher who is going to find genetic variation and a disease and a drug reply, relations of the environmental parameter. The information provided by this project is shown gratis by a researcher of the whole world.

HapMap project is collaborative investigation of the companies of the research organization of the academic system and a nonprofit medical system research organization and each state (Canada, China, Japan, Nigeria, the U.K., the United States). The official start of the project was assumed a plan for 3 years at a meeting of 10/27-29 of 2002 from there. This project is comprised of three phases. All data provided in 1 for a phase were released on October 27, 2005, and an analysis result of the data set was announced in October, 2007 about 2 for a phase. Data set was shown in the spring of 2009 about 3 for a phase.

Table of contents

Background

Unlike a disease of the rare Mendel heredity, it is thought that plural genetic combinations and environment factors participate in the difference in common disease (diabetes, cancer, heart trouble, cerebral infarction, depression, bronchial asthma) and personal drug reply. I decode the genome sequence of the people who do not suffer, and the principle top should compare the difference with the people suffering from a disease to find a hereditary factor to be related to these diseases. However, it is unfeasible at present because this really entails a vast cost for complete decoding of the genome sequence. For this problem, the HapMap project suggests the method that a shortcut can say.

Approximately 99.5% are common to the base sequence of DNA at the unrelated two people interval, but there is a point varying in a base when I compare it on a genome at the same position. Such a point is called SNP (Single nucleotide polymorphism), and by seat rank including such a variation and genetic one of them are called allyl [vagueness evasion required]. I focus it only on common SNP (Common SNP) by the HapMap project and am based whether frequency of allyl exists for a common aim more than 1% in a group.

Each individual has the sex chromosomes of the man by each two chromosomes as an exception in the Homo sapiens. The combination of allyl at the point with one individual is called ジェノタイプ (genotypical). It is called ジェノタイピング I read the DNA base sequence of the point with a certain individual, and to decide a genotype. I performed ジェノタイピング for millions of known SNP about 269 people by the HapMap project and announced the result.

It is related to allyl of the SNP located in the neighborhood on one chromosome. For example, I can often predict allyl of the SNP of the around when allyl information of one SNP of a certain person was provided among two SNP. This is the thing that each SNP happened as point mutation in a process of the evolution, but this is because it reaches it with the older mutation around the point when the variation reaches the descendant. On the other hand, there is not much such a connection when there is long distance between SNP. When a generation changes this; by recombination between two chromosomes of allyl is because line up, and a fellow can be mixed (ハプロタイプ collapses by recombination). I call a thing on the same side of such a consecutive allyl on one chromosome ハプロタイプ.

Target sample

Generally, ハプロタイプ is shared between groups, but a difference considerably varies when it becomes the frequency. It was for four groups by the HapMap project. It is 30 trios (30 sets of parents and children) of the person from ヨルバ of Ibadan, Nigeria, unrelated individual 45 of Utah North European and derived from 30 trios that West Europe is of it origin, individual 44 whom there is not of the relationship of Japanese Tokyo, Han race of Chinese Beijing. It was useful, but other groups were parallel about the usefulness when I included it, and, as for the information of ハプロタイプ obtained from these groups, examination was pushed forward in studying other groups.

The sample of 11 common ancestral groups was accumulated in III for a phase. The breakdowns are as follows.

  • ASW (African ancestry in Southwest USA)
  • CEU (Utah residents with Northern and Western European ancestry from the CEPH collection)
  • CHD (Chinese in Metropolitan Denver, Colorado)
  • GIH (Gujarati Indians in Houston, Texas)
  • LWK (Luhya in Webuye, Kenya)
  • MEX (Mexican ancestry in Los Angeles, California)
  • MKK (Maasai in Kinyawa, Kenya)
  • TSI (Tuscans in Italy)
  • YRI (Yoruba in Ibadan, Nigeria)

Strategic

ジェノタイピング did common SNPs every 5,000base in 1 for a phase. This is more than 1000000 SNPs in total. ジェノタイピング dispersed in the center of 10 bases and was performed, and five kinds of analytical techniques were used. The quality evaluation of ジェノタイピング was carried out between a redundant sample interval and associated samples, and a quality check was performed regularly between the bases that had a set of the common SNPs.

Thomas J. of the McGill University of Montreal, Canada The team of HudsonMontreal and others analyzed chromosome 2 and 4p. Beijing, Shanghai, China, the team of Huanming Yang and others based in Hong Kong analyzed chromosome 3 and 8p, 21p. The team of Yusuke Nakamura and others of Tokyo University analyzed 5, 11, 14, 15, 16, 17, chromosome 19. David R. of British Sanger Institute The Bentley and others analyzed 1, 6, 10, 13, the 20th chromosome. The United States is 4 bases;, as for Mark Chee and the Arnold Oliphant and others of yl Mina Corporation of San Diego, chromosome 8q, 9, 18q, 22, X, David Altshuler and others of Broad Institute of Cambridge are Richard A. of Baylor College of Medicine of Houston with chromosome 4q, 7q, 18p, Y mitochondria As for the Gibbs and others, chromosome 12, the Pui-Yan Kwok and others of the Univ. of California of San Francisco analyzed chromosome 7p.

At first approximately 1 million SNPs was considered to be a target, but there was too little SNPs by the domain of the chromosome, and typing of the additional SNPs was necessary for much SNPs various analysis to make a map to use it because there was too little frequency. Therefore, you would add millions of SNPs in the consortium and had to assign a large amount of budget for the large-scale re-sequencing work. (PhaseII) which it is added 2,800,000 in September, 2003 by this project whereas SNPs registered with dbSNP at the time of a project start was 2,800,000, and exceeds 10 million in total in August, 2006. 25-35% of things were Common SNPs of MAF≥0.05 among 9,000,000-10,000,000 SNPs at the time of this PhaseII. [1] Judging from only around 10% of SNPs having had seasonal polymorphism, the available SNPs largely increased for various analysis (genome wide correlative analysis, linkage disequilibrium, recombination, natural selection) among a little less than 3 million SNPs at the time of the start of the project.

Documents

Footnote

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