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장호영,한영주,정상진,박종,이성훈,김태형,김철홍,김상수,Fahd Al-Mulla,윤찬현,유향숙,The HUGO Pan-Asian SNP Consortium 한국유전체학회 2011 Genomics & informatics Vol.9 No.4
In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method,from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.
Planning the Human Variome Project: The Spain report
Kaput, Jim,Cotton, Richard G.H.,Hardman, Lauren,Watson, Michael,Al Aqeel, Aida I.,Al-Aama, Jumana Y.,Al-Mulla, Fahd,Alonso, Santos,Aretz, Stefan,Auerbach, Arleen D.,Bapat, Bharati,Bernstein, Inge T.,B Wiley Subscription Services, Inc., A Wiley Company 2009 Human mutation Vol.30 No.4
<P>The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008. Hum Mutat 30, 496–510, 2009. © 2009 Wiley-Liss, Inc.</P>
Ghang, Ho-Young,Han, Young-Joo,Jeong, Sang-Jin,Bhak, Jong,Lee, Sung-Hoon,Kim, Tae-Hyung,Kim, Chul-Hong,Kim, Sang-Soo,Al-Mulla, Fahd,Youn, Chan-Hyun,Yoo, Hyang-Sook,The HUGO Pan-Asian SNP Consortium, T Korea Genome Organization 2011 Genomics & informatics Vol.9 No.4
In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method, from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.