scholarly journals Paleo-Eskimo genetic legacy across North America

2017 ◽  
Author(s):  
Pavel Flegontov ◽  
N. Ezgi Altinişik ◽  
Piya Changmai ◽  
Nadin Rohland ◽  
Swapan Mallick ◽  
...  
Keyword(s):  
Native American ◽  
North America ◽  
Allele Frequency ◽  
Genetic Relationship ◽  
Rare Allele ◽  
Comprehensive Model ◽  
Haplotype Sharing ◽  
New Methods ◽  
Genome Wide ◽  
Genome Wide Data

AbstractPaleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Iñupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust'-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.

Admixture In Sickle Cell Disease Defined By Genome Wide Ancestry Informative Markers Varies By Geographic Region In The United States

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 995-995
Author(s):  
Zhengyuan Wang ◽  
Lena Diaw ◽  
Michael Dizon ◽  
Marci Barr ◽  
Meghan Quinn ◽  
...  
Keyword(s):  
Native American ◽  
North America ◽  
Sickle Cell ◽  
Genetic Admixture ◽  
South American ◽  
Genetic Modifiers ◽  
Ancestry Informative Markers ◽  
Genome Wide ◽  
The Us ◽  
Ancestry Proportions

Abstract Genome wide association studies (GWAS) are an important tool for identifying complex human disease loci. A key variable for GWAS is the degree of admixture or recent mixing of previously isolated populations. Undetected admixture can lead to spurious associations, although it may also be used as a strategy for mapping by admixture linkage disequilibrium (MALD). Development of reagents to identify admixture and to perform MALD may help to identify genetic modifiers of sickle cell disease (SCD). We have examined ancestry and genetic admixture in SCD patients living in North America. We first examined ancestry from family histories for 649 adults recruited to the Bethesda Sickle Cell Cohort Study in the eastern US, where 61% of subjects are African American, 22% African, 12% Caribbean or South American and 1.8% of other origins. We hypothesized that the high proportion of subjects from the Africa ancestry group would diminish the expected degree of admixture in the Bethesda cohort compared to other SCD cohorts. To assess admixture at the genetic level, we identified ancestry informative markers (AIMs) from 3,804,602 SNPs genotyped by HapMap Phase III in CEU (European) and YRI (Nigeria) populations. These SNPs were combined with a published admixture mapping panel, yielding a new MALD panel of 2251 AIMs. We assessed the performance of our AIM panel by genotyping 221 HapMap individuals and 489 adults from the Bethesda cohort with an overall completion rate of 98.51% using Illumina iSelect arrays. HapMap samples had 98% concordance with publicly available data. Out of 2251 candidate markers, only 1806 successfully passed all quality controls (289 SNPs could not be genotyped; 82 were not AIMs; 74 had low concordance with HapMap). Using our HapMap genotype data, this admixture panel has a mean δ (difference in allele frequencies between populations) of 0.712 (SD 0.118) with an average inter-marker distance of 1.862 Mb. The utility of this 1806 marker panel for genome wide MALD in SCD was demonstrated with a proof of concept scan to map the known genetic locus underlying SCD in the Bethesda cohort. To compare admixture in the Bethesda cohort to other SCD populations, we defined a subset of AIMs (n=360) that distinguish 6 major geo-ethnic groups from the Human Genome Diversity Panel (n=952 individuals). These results suggest that these 360 markers can distinguish contributions from geo-ethnic ancestry groups besides African and European populations. Using these markers in the Bethesda cohort, principle components analysis (PCA) showed African American or Caribbean/South American subjects had a wider range of admixture compared to Africans or HapMap populations (CEU, YRI and CHB). We then compared admixture proportions in the Bethesda cohort to 2 additional SCD populations, including 469 anonymous samples from a newborn screen SCD cohort in the western US and 439 SCD adults from a clinical trial in North America and Europe (WalkPhasst). Comparison of these SCD cohorts to 3 HapMap populations using PCA showed nearly 50% of the variation is explained by 2 major vectors that distinguish European/African and Asian/Native American ancestry. Finally, we compared admixture proportions across all 3 SCD cohorts using Structure. Here, we observed significant differences in ancestry proportions arising from Africa, Europe and Asia/Americas (P<0.001 by ANOVA). Specifically, African ancestry proportions were 0.640, 0.700, and 0.510 from the Bethesda cohort, WalkPhasst, and western newborns (all pairwise comparisons P<0.01), respectively. Significantly, there were differences between the cohorts from different regions of the US, where the Bethesda cohort had 0.039 Asian/Native American ancestry compared to 0.085 in the western SCD newborns (P<0.001). We conclude that there are significant admixture differences in SCD populations from eastern and western regions of the US. Overall, SCD patients in North America have a variable degree of genetic admixture that could affect interpretation of candidate gene or GWA studies. Furthermore, the degree of admixture adjustment varies for SCD subjects from different geographic regions within the US. Finally, our proof of concept studies suggest SCD may be ideal for MALD whole genome scans to identify genetic modifiers. Disclosures: No relevant conflicts of interest to declare.

scholarly journals A COMPRESSED SENSING BASED APPROACH FOR SUBTYPING OF LEUKEMIA FROM GENE EXPRESSION DATA

2011 ◽  
Vol 09 (05) ◽  
pp. 631-645 ◽  
Author(s):  
WENLONG TANG ◽  
HONGBAO CAO ◽  
JUNBO DUAN ◽  
YU-PING WANG
Keyword(s):  
Gene Expression ◽  
Compressed Sensing ◽  
Gene Expression Analysis ◽  
Expression Data ◽  
Data Set ◽  
New Methods ◽  
Genome Wide ◽  
Different Types ◽  
Genome Wide Data ◽  
Improved Accuracy

With the development of genomic techniques, the demand for new methods that can handle high-throughput genome-wide data effectively is becoming stronger than ever before. Compressed sensing (CS) is an emerging approach in statistics and signal processing. With the CS theory, a signal can be uniquely reconstructed or approximated from its sparse representations, which can therefore better distinguish different types of signals. However, the application of CS approach to genome-wide data analysis has been rarely investigated. We propose a novel CS-based approach for genomic data classification and test its performance in the subtyping of leukemia through gene expression analysis. The detection of subtypes of cancers such as leukemia according to different genetic markups is significant, which holds promise for the individualization of therapies and improvement of treatments. In our work, four statistical features were employed to select significant genes for the classification. With our selected genes out of 7,129 ones, the proposed CS method achieved a classification accuracy of 97.4% when evaluated with the cross validation and 94.3% when evaluated with another independent data set. The robustness of the method to noise was also tested, giving good performance. Therefore, this work demonstrates that the CS method can effectively detect subtypes of leukemia, implying improved accuracy of diagnosis of leukemia.

scholarly journals The impact of recent events on human genetic diversity

2012 ◽  
Vol 367 (1590) ◽  
pp. 793-799 ◽  
Author(s):  
Mark A. Jobling
Keyword(s):  
Genetic Diversity ◽  
Historical Record ◽  
Social Selection ◽  
New Methods ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Male Specific ◽  
Demographic Impact ◽  
The Impact ◽  
And Linguistics

The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.

scholarly journals Genomic insights into the early peopling of the Caribbean

Science ◽  
2020 ◽  
pp. eaba8697 ◽  
Author(s):  
Kathrin Nägele ◽  
Cosimo Posth ◽  
Miren Iraeta Orbegozo ◽  
Yadira Chinique de Armas ◽  
Silvia Teresita Hernández Godoy ◽  
...  
Keyword(s):  
North America ◽  
South America ◽  
Genetic Differences ◽  
Genome Wide ◽  
Western Caribbean ◽  
Genome Wide Data ◽  
The Caribbean

The Caribbean was one of the last regions of the Americas to be settled by humans, but how, when, and from where they reached the islands remains unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200-400 cal. BP and find evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detect genetic differences between the early settlers and the newcomers from South America with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.

scholarly journals Reconstructing Austronesian population history in Island Southeast Asia

2014 ◽  
Author(s):  
Mark Lipson ◽  
Po-Ru Loh ◽  
Nick Patterson ◽  
Priya Moorjani ◽  
Ying-Chin Ko ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Population History ◽  
Austronesian Languages ◽  
Ancestral Gene ◽  
Mainland Population ◽  
Island Southeast Asia ◽  
New Methods ◽  
Asian Populations ◽  
Genome Wide ◽  
Genome Wide Data

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the "Austronesian expansion," which began 4-5 thousand years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, focusing primarily on Island Southeast Asia, we analyze genome-wide data from 56 populations using new methods for tracing ancestral gene flow. We show that all sampled Austronesian groups harbor ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.

scholarly journals A performance assessment of relatedness inference methods using genome-wide data from thousands of relatives

2017 ◽  
Author(s):  
Monica D. Ramstetter ◽  
Thomas D. Dyer ◽  
Donna M. Lehman ◽  
Joanne E. Curran ◽  
Ravindranath Duggirala ◽  
...  
Keyword(s):  
State Of The Art ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Real Data ◽  
New Methods ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Inference Methods ◽  
Multiple Samples ◽  
Combining Information

AbstractInferring relatedness from genomic data is an essential component of genetic association studies, population genetics, forensics, and genealogy. While numerous methods exist for inferring relatedness, thorough evaluation of these approaches in real data has been lacking. Here, we report an assessment of 12 state-of-the-art pairwise relatedness inference methods using a dataset with 2,485 individuals contained in several large pedigrees that span up to six generations. We find that all methods have high accuracy (~92% – 99%) when detecting first and second degree relationships, but their accuracy dwindles to less than 43% for seventh degree relationships. However, most IBD segment-based methods inferred seventh degree relatives correct to within one relatedness degree for more than 76% of relative pairs. Overall, the most accurate methods are ERSA and approaches that compute total IBD sharing using the output from GERMLINE and Refined IBD to infer relatedness. Combining information from the most accurate methods provides little accuracy improvement, indicating that novel approaches—such as new methods that leverage relatedness signals from multiple samples—are needed to achieve a sizeable jump in performance.

scholarly journals Cross-Population Genetic Variation of Loci Identified by Genome-Wide Association Studies conducted in British participants of European-descent from the UK Biobank

2020 ◽  
Author(s):  
Antonella De Lillo ◽  
Salvatore D'antona ◽  
Maria Fuciarelli ◽  
Renato Polimanti
Keyword(s):  
Allele Frequency ◽  
Regulatory Elements ◽  
Genome Wide Association Studies ◽  
Monocyte Count ◽  
Uk Biobank ◽  
European Descent ◽  
Standing Height ◽  
Genome Wide ◽  
Significant Difference ◽  
Genome Wide Data

To provide novel insight regarding the inter-population diversity of loci associated with complex traits, we integrated genome-wide data from UK Biobank (UKB) and 1,000 Genomes Project (1KG) data representative of the genetic diversity among worldwide populations. We investigated genome-wide data of 4,359 traits from 361,194 UKB participants of European descent. Using 1KG data, we explored the allele frequency differences and linkage disequilibrium (LD) structure of UKB genome-wide significant (GWS) loci across worldwide populations. Functional annotation data were used to identify regulatory elements and evaluate the tagging properties of GWS variants. No significant difference was observed in allele frequency between UKB and 1KG GBR (British in England and Scotland). Considering other population groups, we identified genome-wide significant alleles with frequencies different from what expected by chance: UKB vs. 1KG Europeans without GBR (rs74945666; allele=T [0.908 vs. 0.03], standing height pGWAS=1.48x10-17), UKB vs. 1KG African (rs556562; allele=A [0.942 vs. 0.083], platelet count pGWAS=4.84x10-15), UKB vs. 1KG Admixed Americans (rs1812378; allele=T [0.931 vs. 0.089], standing height pGWAS=4.23x10-12), UKB vs. 1KG East Asian (rs55881864; allele=T [0.911 vs. 0.001], monocyte count pGWAS=7.29x10-13), and UKB vs. South Asian (rs74945666; allele=T [0.908 vs. 0.061], standing height pGWAS=1.48x10-17). LD-structure analysis and computational prediction showed differences in how these alleles tag functional elements across human populations. In conclusion, the human diversity of certain GWS loci appear to be affected by local adaptation while in other cases the associations may be biased by residual population stratification.

scholarly journals Reconstructed lost Native American populations from Eastern Brazil are shaped by differential Jê/Tupi ancestry

2019 ◽  
Author(s):  
Alex Mas-Sandoval ◽  
Lara R Arauna ◽  
Mateus H Gouveia ◽  
Mauricio L Barreto ◽  
Bernardo L Horta ◽  
...  
Keyword(s):  
Native American ◽  
North East ◽  
Genetic Components ◽  
Genome Wide ◽  
Eastern Brazil ◽  
Show Evidence ◽  
Genome Wide Data ◽  
Sub Saharan ◽  
Brazilian Populations ◽  
American Genetic

Abstract After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African and the Native American. The study of the Native American genetic history is challenged by the availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies and the low proportions of the Native American component in the admixed Brazilian populations (in average 7%). We analysed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North East), Bambui (South East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui and 197 in Pelotas). We compared the reconstructed populations with non-admixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê- speaking ancestry related groups. We also show evidence of a decrease of the diversity of non-admixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.

North America

2018 ◽  
Author(s):  
Gregory Shushan
Keyword(s):  
Native American ◽  
North America ◽  
Reciprocal Relationship ◽  
Native American Religions ◽  
Widespread Acceptance ◽  
Revitalization Movements ◽  
Per Se ◽  
High Level ◽  
Near Death Experiences ◽  
Afterlife Beliefs

Dozens of Native American near-death experiences (NDEs) from the late sixteenth to early twentieth centuries are presented, ranging from across the continent. Many were accompanied by indigenous claims that they were the source for local afterlife beliefs. There were also many afterlife-related myths, and shamanic practices with NDE-like afterlife themes. In addition, numerous religious/cultural revitalization movements were claimed to have been grounded in the NDEs of their founders, and were conceptually related to the phenomenon. Near-death experiences could thus be an empowering force on a socio-cultural-political level in response to the threat of European dominance. There was a widespread acceptance and valorization of NDEs and related phenomena, and a high level of interest in the afterlife per se. Native American religions often showed a clear reciprocal relationship between shamanism, afterlife beliefs, and NDEs.

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