Human genetic clustering refers to patterns of relative genetic similarity among human individuals and populations, as well as the wide range of scientific and statistical methods used to study this aspect of human genetic variation.
Clustering studies are thought to be valuable for characterizing the general structure of genetic variation among human populations, to contribute to the study of ancestral origins, evolutionary history, and precision medicine. Since the mapping of the human genome, and with the availability of increasingly powerful analytic tools, cluster analyses have revealed a range of ancestral and migratory trends among human populations and individuals.[1] Human genetic clusters tend to be organized by geographic ancestry, with divisions between clusters aligning largely with geographic barriers such as oceans or mountain ranges.[2][3] Clustering studies have been applied to global populations,[4] as well as to population subsets like post-colonial North America.[5][6] Notably, the practice of defining clusters among modern human populations is largely arbitrary and variable due to the continuous nature of human genotypes; although individual genetic markers can be used to produce smaller groups, there are no models that produce completely distinct subgroups when larger numbers of genetic markers are used.[2][7][8]
Many studies of human genetic clustering have been implicated in discussions of race, ethnicity, and scientific racism, as some have controversially suggested that genetically derived clusters may be understood as proof of genetically determined races.[9][10] Although cluster analyses invariably organize humans (or groups of humans) into subgroups, debate is ongoing on how to interpret these genetic clusters with respect to race and its social and phenotypic features. And, because there is such a small fraction of genetic variation between human genotypes overall, genetic clustering approaches are highly dependent on the sampled data, genetic markers, and statistical methods applied to their construction.
A wide range of methods have been developed to assess the structure of human populations with the use of genetic data. Early studies of within and between-group genetic variation used physical phenotypes and blood groups, with modern genetic studies using genetic markers such as Alu sequences, short tandem repeat polymorphisms, and single nucleotide polymorphisms (SNPs), among others.[11] Models for genetic clustering also vary by algorithms and programs used to process the data. Most sophisticated methods for determining clusters can be categorized as model-based clustering methods (such as the algorithm STRUCTURE[12]) or multidimensional summaries (typically through principal component analysis).[1][13] By processing a large number of SNPs (or other genetic marker data) in different ways, both approaches to genetic clustering tend to converge on similar patterns by identifying similarities among SNPs and/or haplotype tracts to reveal ancestral genetic similarities.[13]
Common model-based clustering algorithms include STRUCTURE, ADMIXTURE, and HAPMIX. These algorithms operate by finding the best fit for genetic data among an arbitrary or mathematically derived number of clusters, such that differences within clusters are minimized and differences between clusters are maximized. This clustering method is also referred to as "admixture inference," as individual genomes (or individuals within populations) can be characterized by the proportions of alleles linked to each cluster.[1] In other words, algorithms like STRUCTURE generate results that assume the existence of discrete ancestral populations, operationalized through unique genetic markers, which have combined over time to form the admixed populations of the modern day.
Where model-based clustering characterizes populations using proportions of presupposed ancestral clusters, multidimensional summary statistics characterize populations on a continuous spectrum. The most common multidimensional statistical method used for genetic clustering is principal component analysis (PCA), which plots individuals by two or more axes (their "principal components") that represent aggregations of genetic markers that account for the highest variance. Clusters can then be identified by visually assessing the distribution of data; with larger samples of human genotypes, data tends to cluster in distinct groups as well as admixed positions between groups.[1][13]
There are caveats and limitations to genetic clustering methods of any type, given the degree of admixture and relative similarity within the human population. All genetic cluster findings are biased by the sampling process used to gather data, and by the quality and quantity of that data. For example, many clustering studies use data derived from populations that are geographically distinct and far apart from one another, which may present an illusion of discrete clusters where, in reality, populations are much more blended with one another when intermediary groups are included.[1] Sample size also plays an important moderating role on cluster findings, as different sample size inputs can influence cluster assignment, and more subtle relationships between genotypes may only emerge with larger sample sizes.[1][8] In particular, the use of STRUCTURE has been widely criticized as being potentially misleading through requiring data to be sorted into a predetermined number of clusters which may or may not reflect the actual population's distribution.[8][14] The creators of STRUCTURE originally described the algorithm as an "exploratory" method to be interpreted with caution and not as a test with statistically significant power.[12][15]
Modern applications of genetic clustering methods to global-scale genetic data were first marked by studies associated with the Human Genome Diversity Project (HGDP) data.[1] These early HGDP studies, such as those by Rosenberg et al. (2002),[4][16] contributed to theories of the serial founder effect and early human migration out of Africa, and clustering methods have been notably applied to describe admixed continental populations.[5][6][17] Genetic clustering and HGDP studies have also contributed to methods for, and criticisms of, the genetic ancestry consumer testing industry.[18]
A number of landmark genetic cluster studies have been conducted on global human populations since 2002, including the following:
Clusters of individuals are often geographically structured. For example, when clustering a population of East Asians and Europeans, each group will likely form its own respective cluster based on similar allele frequencies. In this way, clusters can have a correlation with traditional concepts of race and self-identified ancestry; in some cases, such as medical questionnaires, the latter variables can be used as a proxy for genetic ancestry where genetic data is unavailable.[9][4] However, genetic variation is distributed in a complex, continuous, and overlapping manner, so this correlation is imperfect and the use of racial categories in medicine can introduce additional hazards.[9]
Some scholars[who?] have challenged the idea that race can be inferred by genetic clusters, drawing distinctions between arbitrarily assigned genetic clusters, ancestry, and race. One recurring caution against thinking of human populations in terms of clusters is the notion that genotypic variation and traits are distributed evenly between populations, along gradual clines rather than along discrete population boundaries; so although genetic similarities are usually organized geographically, their underlying populations have never been completely separated from one another. Due to migration, gene flow, and baseline homogeneity, features between groups are extensively overlapping and intermixed.[2][9] Moreover, genetic clusters do not typically match socially defined racial groups; many commonly understood races may not be sorted into the same genetic cluster, and many genetic clusters are made up of individuals who would have distinct racial identities.[7] In general, clusters may most simply be understood as products of the methods used to sample and analyze genetic data; not without meaning for understanding ancestry and genetic characteristics, but inadequate to fully explaining the concept of race, which is more often described in terms of social and cultural forces.
In the related context of personalized medicine, race is currently listed as a risk factor for a wide range of medical conditions with genetic and non-genetic causes. Questions have emerged regarding whether or not genetic clusters support the idea of race as a valid construct to apply to medical research and treatment of disease, because there are many diseases that correspond with specific genetic markers and/or with specific populations, as seen with Tay-Sachs disease or sickle cell disease.[3][25] Researchers are careful to emphasize that ancestryrevealed in part through cluster analysesplays an important role in understanding risk of disease. But racial or ethnic identity does not perfectly align with genetic ancestry, and so race and ethnicity do not reveal enough information to make a medical diagnosis.[25] Race as a variable in medicine is more likely to reflect social factors, where ancestry information is more likely to be meaningful when considering genetic ancestry.[2][25]
Originally posted here:
Human genetic clustering - Wikipedia
- SCARY GHOST ENCOUNTER! (The Hidden) - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Human Genetics and Genomics: The Science for the 21st Century - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- DNA Research - 07-09-2012 - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Replying to Equestions on Junk DNA - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- 2013 Rosalind Franklin Young Investigator Awards Announced [Last Updated On: September 8th, 2012] [Originally Added On: September 8th, 2012]
- Jackson Lab CEO Leads From Heart [Last Updated On: September 28th, 2012] [Originally Added On: September 28th, 2012]
- Love of science lifts Hobe Sound teen to genetics conference in Germany [Last Updated On: September 30th, 2012] [Originally Added On: September 30th, 2012]
- Nobel Laureates and Experts Gather to Discuss Genetics and Society [Last Updated On: September 30th, 2012] [Originally Added On: September 30th, 2012]
- Seattle Genetics and Millennium Complete Enrollment in Phase III AETHERA Trial of ADCETRIS® for Post-Transplant ... [Last Updated On: September 30th, 2012] [Originally Added On: September 30th, 2012]
- GENETICS Journal Highlights for October 2012 [Last Updated On: October 2nd, 2012] [Originally Added On: October 2nd, 2012]
- Myriad Genetics Sponsors Cancer Awareness Initiatives in Support of National Hereditary Breast and Ovarian Cancer Week [Last Updated On: October 3rd, 2012] [Originally Added On: October 3rd, 2012]
- Study Says Genetics Of Intelligence Remains A Riddle, For Now [Last Updated On: October 3rd, 2012] [Originally Added On: October 3rd, 2012]
- ORF Genetics to Offer endotoxin- and Animal-free FGFb and mLIF for Stem Cell Research [Last Updated On: October 4th, 2012] [Originally Added On: October 4th, 2012]
- Research and Markets: Human Genes and Genomes. Science, Health, Society Provides Students and Professionals Alike With ... [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Mosquito genetics may offer clues to control malaria, researchers say [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Delphi Genetics Grants Merck License for the Use of the StabyExpress™ System [Last Updated On: October 8th, 2012] [Originally Added On: October 8th, 2012]
- This Week in PNAS [Last Updated On: October 10th, 2012] [Originally Added On: October 10th, 2012]
- Outsmarting breast cancer [Last Updated On: October 10th, 2012] [Originally Added On: October 10th, 2012]
- Economics and genetics meet in uneasy union [Last Updated On: October 10th, 2012] [Originally Added On: October 10th, 2012]
- Nurture trumps nature in study of oral bacteria in human twins, study finds [Last Updated On: October 12th, 2012] [Originally Added On: October 12th, 2012]
- Nurture trumps nature in study of oral bacteria in human twins, says CU study [Last Updated On: October 12th, 2012] [Originally Added On: October 12th, 2012]
- Claim That Links Economic Success and Genetic Diversity Draws Criticism [Last Updated On: October 12th, 2012] [Originally Added On: October 12th, 2012]
- Master-builder of the Human Genetics Unit [Last Updated On: October 15th, 2012] [Originally Added On: October 15th, 2012]
- Genetics Society of America announces 2013 award recipients [Last Updated On: October 15th, 2012] [Originally Added On: October 15th, 2012]
- Myriad Genetics to Announce First Fiscal Quarter 2013 Results on Monday, November 5, 2012 [Last Updated On: October 15th, 2012] [Originally Added On: October 15th, 2012]
- Petes Wins Lifetime Achievement Award in Genetics [Last Updated On: October 16th, 2012] [Originally Added On: October 16th, 2012]
- 23andMe Names Christine Castro, Neil Rothstein and Jonathan Ward to Leadership Positions [Last Updated On: October 16th, 2012] [Originally Added On: October 16th, 2012]
- Privately owned genetic databases may hinder diagnosis and bar the way to the arrival of personalized medicine [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- Neil Risch - Wiki Article - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- GHOST DANCE (The Hidden) - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- SCARY GAME - "The Hidden" With Mr.Mitch361, Charlie, and ChildDolphin - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- International Academy of Cardiology: Neil Bowles, Ph.D.: GENETIC CAUSES OF CONGENITAL HEART DEFECTS - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- The Best Of: "The Hidden" - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- MEAT SHIELD (The Hidden) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- The 10000 Year Explosion: How Civilization Accelerated Human Evolution - , Henry Harpending - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Humans, chimpanzees and monkeys share DNA but not gene regulatory mechanisms [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- Surprising findings from NHLBI Exome Sequencing Project reported [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- New method helps link genomic variation to protein production [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- Ariosa Diagnostics to Present Clinical Data on the Harmony™ Prenatal Test at American Society of Human Genetics Annual ... [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- ALEX JONES Talks To DAVID ICKE: Human Genetics, Election FRAUD [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- David Icke Exposes ROYAL PAEDOPHILES - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- Alex Jones - David Icke: Human Genetics, The Religion Of Death - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- David Icke - Infowars Election Coverage 2012 - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- David Icke: Human Genetics, The Religion of Death - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- Evening with the UC Davis Genome Center - Oct 6, 2012 - David Segal - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- The Hidden - (Blood For The Blood God, I Must Feed) - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- GHOST ISSUES (The Hidden) - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- The Hidden - (Fart Grenades And Friendly Fire) - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- GHOST ISLAND (The Hidden) - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- Growth Hormone - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- Social Anthropology And Human Origins - Alan Barnard - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- Protein Structural Biology In Biomedical Research. Advances In Molecular And Cell Biology, Volume 22 - Video [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]
- Exome sequencing: Potential diagnostic assay for unexplained intellectual disability [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Unexplained intellectual disability explained by state-of-the-art genetic analysis [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- DNA variants explain over 10 percent of inherited genetic risk for heart disease [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Novel type 2 diabetes genetic study involves 5 major ancestry groups [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Significant relationship between mortality and telomere length discovered [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Alex Jones on David Icke 2001 - The Turd - Video [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- David Icke Human Genetics [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- BLINDNESS (The Hidden) - Video [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Human Genetics, The Religion of Death : David Icke - Video [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Alex Jones Show - David Icke: Human Genetics, Paedophile Gov., The Religion of Death - Video [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Human Genetics - Video [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- DAVID ICKE: Human Genetics, The Religion of Death (11/6/2012) - Video [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Human Genetics: The Basics - Ricki Lewis - Video [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- The Hidden - (Meat Shields Everywhere, Face Of Protection) - Video [Last Updated On: November 9th, 2012] [Originally Added On: November 9th, 2012]
- Leading Genomic Services Company and Its Partners Raise More Than $150,000 in Support of Pediatric Genetics Research [Last Updated On: November 11th, 2012] [Originally Added On: November 11th, 2012]
- Verinata Health Announces New Findings At The American Society Of Human Genetics [Last Updated On: November 11th, 2012] [Originally Added On: November 11th, 2012]
- DAVID ICKE: Human Genetics, The Religion of Death! ALEX JONES [INFOWARS Nightly News] - Video [Last Updated On: November 11th, 2012] [Originally Added On: November 11th, 2012]
- ALEX-JONES-Talks-To-DAVID-ICKE--Human-Genetics,-Election-FRAUD-n-The-Religion-Of-DEATH - Video [Last Updated On: November 11th, 2012] [Originally Added On: November 11th, 2012]
- Illumina Bioninformatics Overview at ASHG 2012 - Video [Last Updated On: November 11th, 2012] [Originally Added On: November 11th, 2012]
- The Hidden - Fun With No Silence [Last Updated On: November 11th, 2012] [Originally Added On: November 11th, 2012]
- David Icke - Human Genetics, The Religion of Death [11/06/2012] - Video [Last Updated On: November 11th, 2012] [Originally Added On: November 11th, 2012]
- Genetics Center takes part in global meet [Last Updated On: November 12th, 2012] [Originally Added On: November 12th, 2012]
- Half Life 2 Mods: The Hidden | Part 4 | TO WIN, OR NOT TO WIN! - Video [Last Updated On: November 12th, 2012] [Originally Added On: November 12th, 2012]
- US-X - Video [Last Updated On: November 12th, 2012] [Originally Added On: November 12th, 2012]
- Personalized Medicine From Genomics and Bioinformatics Highlighted at UCSF Genetics Symposium [Last Updated On: November 14th, 2012] [Originally Added On: November 14th, 2012]
- News in Brief: Highlights from the American Society of Human Genetics annual meeting [Last Updated On: November 14th, 2012] [Originally Added On: November 14th, 2012]
- Star Visitors - Dr. Richard Boylan - Coast to Coast AM Classic - Video [Last Updated On: November 14th, 2012] [Originally Added On: November 14th, 2012]
- Protein Structural Biology In Biomedical Research, Part A - C. Woodward - Video [Last Updated On: November 14th, 2012] [Originally Added On: November 14th, 2012]