The Experts below are selected from a list of 25506 Experts worldwide ranked by ideXlab platform
Yun Sung Cho - One of the best experts on this subject based on the ideXlab platform.
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an ethnically relevant consensus korean reference Genome is a step towards personal reference Genomes
Nature Communications, 2016Co-Authors: Yun Sung Cho, Hwajung Kim, Hakmin Kim, Sungwoong Jho, Jehoon Jun, Yongjoo Lee, Kyun Shik Chae, Chang Geun KimAbstract:Human Genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference Genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous Genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of Human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population Genome projects, the leveraging of ethnicity-specific Genome assemblies as well as the Human reference Genome will accelerate mapping all Human Genome Diversity. The utility of a universal reference sequence for Human Genome comparisons is dependent on the ethnic origins of the individuals being sequenced. Here the authors report a Korean reference Genome and consensus variome, and show that an ethnically-relevant reference can improve variant detection.
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ethnically relevant consensus korean reference Genome towards personal reference Genomes
bioRxiv, 2016Co-Authors: Yun Sung Cho, Hwajung Kim, Sungwoong Jho, Jehoon Jun, Yongjoo Lee, Kyun Shik Chae, Chang Geun Kim, Sangsoo Kim, Anders Eriksson, Jeremy S EdwardsAbstract:Human Genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal Genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established Human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population Genome projects, the leveraging of ethnicity-specific Genome assemblies as well as the Human reference Genome will accelerate mapping all Human Genome Diversity.
L L Cavallisforza - One of the best experts on this subject based on the ideXlab platform.
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the role of geography in Human adaptation
PLOS Genetics, 2009Co-Authors: Graham Coop, L L Cavallisforza, Joseph K Pickrell, Richard M Myers, Joh Novembre, Sridha Kudaravalli, Devi Abshe, Marcus W Feldma, Jonatha K PritchardAbstract:Various observations argue for a role of adaptation in recent Human evolution, including results from Genome-wide studies and analyses of selection signals at candidate genes. Here, we use Genome-wide SNP data from the HapMap and CEPH-Human Genome Diversity Panel samples to study the geographic distributions of putatively selected alleles at a range of geographic scales. We find that the average allele frequency divergence is highly predictive of the most extreme FST values across the whole Genome. On a broad scale, the geographic distribution of putatively selected alleles almost invariably conforms to population clusters identified using randomly chosen genetic markers. Given this structure, there are surprisingly few fixed or nearly fixed differences between Human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.
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worldwide Human relationships inferred from Genome wide patterns of variation
Science, 2008Co-Authors: Devin Absher, L L Cavallisforza, Amanda M Casto, Marcus W Feldman, Howard M Cann, Hua Tang, Audrey Southwick, Sohini Ramachandran, Gregory S Barsh, Richard M MyersAbstract:Human genetic Diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of Human genetic variation.
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the Human Genome Diversity project past present and future
Nature Reviews Genetics, 2005Co-Authors: L L CavallisforzaAbstract:The Human Genome Project, in accomplishing its goal of sequencing one Human Genome, heralded a new era of research, a component of which is the systematic study of Human genetic variation. Despite delays, the Human Genome Diversity Project has started to make progress in understanding the patterns of this variation and its causes, and also promises to provide important information for biomedical studies.
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the chinese Human Genome Diversity project
Proceedings of the National Academy of Sciences of the United States of America, 1998Co-Authors: L L CavallisforzaAbstract:The Chinese population comprises one-fifth of the Human species. The Chinese government officially recognizes 56 ethnic groups, one of which is the Han majority (1 billion and 100 million people), and the other 55 are ethnic minorities (totaling about 100 million). The latter are spread over most of China, but especially in the south. Close to half of the minorities are found in one of the 28 provinces of China, Yunnan. The distinction is primarily linguistic but corresponds closely to other cultural differences. The paper by Chu et al . published in this issue of the Proceedings (1) explores the genetic stratification of about half of the official ethnic subdivisions by means of microsatellites, a class of genetic markers recently discovered that has proved very useful for several purposes. The paper represents the collective effort of several institutes participating in the Chinese Human Genome Diversity Project (CHGDP). The broader Human Genome Diversity Project (HGDP) was generated in 1991 by the international Human Genome Organization (HUGO) and is regionally organized (see http://www.stanford.edu/group/morrinst/HGDP/html). The CHGDP has started collecting cell lines from the official ethnic groups and testing their DNAs. The 56 official ethnic groups do not exhaust current Chinese Diversity, as there are more than 100 languages spoken in China, but they include the most important ones. Microsatellites are repeats of short DNA segments, practically less than five nucleotides long. They have a high mutation rate and therefore a large number of alleles, which makes them perhaps three times more informative on average than the most common type of genetic polymorphisms, single nucleotide substitutions, which are mostly biallelic. They are used very widely in genetic linkage studies and have begun to be used in evolutionary analyses (e.g., refs. 2–4). Thirty microsatellites were tested by Chu et al. (1) for reconstructing …
Chang Geun Kim - One of the best experts on this subject based on the ideXlab platform.
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an ethnically relevant consensus korean reference Genome is a step towards personal reference Genomes
Nature Communications, 2016Co-Authors: Yun Sung Cho, Hwajung Kim, Hakmin Kim, Sungwoong Jho, Jehoon Jun, Yongjoo Lee, Kyun Shik Chae, Chang Geun KimAbstract:Human Genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference Genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous Genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of Human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population Genome projects, the leveraging of ethnicity-specific Genome assemblies as well as the Human reference Genome will accelerate mapping all Human Genome Diversity. The utility of a universal reference sequence for Human Genome comparisons is dependent on the ethnic origins of the individuals being sequenced. Here the authors report a Korean reference Genome and consensus variome, and show that an ethnically-relevant reference can improve variant detection.
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ethnically relevant consensus korean reference Genome towards personal reference Genomes
bioRxiv, 2016Co-Authors: Yun Sung Cho, Hwajung Kim, Sungwoong Jho, Jehoon Jun, Yongjoo Lee, Kyun Shik Chae, Chang Geun Kim, Sangsoo Kim, Anders Eriksson, Jeremy S EdwardsAbstract:Human Genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal Genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established Human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population Genome projects, the leveraging of ethnicity-specific Genome assemblies as well as the Human reference Genome will accelerate mapping all Human Genome Diversity.
Jehoon Jun - One of the best experts on this subject based on the ideXlab platform.
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an ethnically relevant consensus korean reference Genome is a step towards personal reference Genomes
Nature Communications, 2016Co-Authors: Yun Sung Cho, Hwajung Kim, Hakmin Kim, Sungwoong Jho, Jehoon Jun, Yongjoo Lee, Kyun Shik Chae, Chang Geun KimAbstract:Human Genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference Genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous Genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of Human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population Genome projects, the leveraging of ethnicity-specific Genome assemblies as well as the Human reference Genome will accelerate mapping all Human Genome Diversity. The utility of a universal reference sequence for Human Genome comparisons is dependent on the ethnic origins of the individuals being sequenced. Here the authors report a Korean reference Genome and consensus variome, and show that an ethnically-relevant reference can improve variant detection.
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ethnically relevant consensus korean reference Genome towards personal reference Genomes
bioRxiv, 2016Co-Authors: Yun Sung Cho, Hwajung Kim, Sungwoong Jho, Jehoon Jun, Yongjoo Lee, Kyun Shik Chae, Chang Geun Kim, Sangsoo Kim, Anders Eriksson, Jeremy S EdwardsAbstract:Human Genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal Genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established Human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population Genome projects, the leveraging of ethnicity-specific Genome assemblies as well as the Human reference Genome will accelerate mapping all Human Genome Diversity.
Noah A Rosenberg - One of the best experts on this subject based on the ideXlab platform.
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population differentiation and migration coalescence times in a two sex island model for autosomal and x linked loci
Theoretical Population Biology, 2008Co-Authors: Sohini Ramachandran, Marcus W Feldman, Noah A Rosenberg, John WakeleyAbstract:Evolutionists have debated whether population-genetic parameters, such as effective population size and migration rate, differ between males and females. In Humans, most analyses of this problem have focused on the Y chromosome and the mitochondrial Genome, while the X chromosome has largely been omitted from the discussion. Past studies have compared F(ST) values for the Y chromosome and mitochondrion under a model with migration rates that differ between the sexes but with equal male and female population sizes. In this study we investigate rates of coalescence for X-linked and autosomal lineages in an island model with different population sizes and migration rates for males and females, obtaining the mean time to coalescence for pairs of lineages from the same deme and for pairs of lineages from different demes. We apply our results to microsatellite data from the Human Genome Diversity Panel, and we examine the male and female migration rates implied by observed F(ST) values.
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standardized subsets of the hgdp ceph Human Genome Diversity cell line panel accounting for atypical and duplicated samples and pairs of close relatives
Annals of Human Genetics, 2006Co-Authors: Noah A RosenbergAbstract:The HGDP-CEPH Human Genome Diversity Cell Line Panel is a widely-used resource for studies of Human genetic variation. Here, pairs of close relatives that have been included in the panel are identified. Together with information on atypical and duplicated samples, the inferred relative pairs suggest standardized subsets of the panel for use in future population-genetic studies.