Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium

2009 ◽  
Vol 33 (3) ◽  
pp. 266-274 ◽  
Author(s):  
Anders Albrechtsen ◽  
Thorfinn Sand Korneliussen ◽  
Ida Moltke ◽  
Thomas van Overseem Hansen ◽  
Finn Cilius Nielsen ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genome Wide ◽  
Genome Wide Data

scholarly journals Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions

2015 ◽  
Author(s):  
Ying Zhou ◽  
Kai Yuan ◽  
Yaoliang Yu ◽  
Xumin Ni ◽  
Pengtao Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Exponential Functions ◽  
Dynamic Changes ◽  
Multiple Wave ◽  
Flow Parameters ◽  
Genome Wide ◽  
Complex Population ◽  
Genome Wide Data ◽  
Admixed Population ◽  
Source Populations

Admixture-introduced linkage disequilibrium (LD) has recently been introduced into the inference of the histories of complex admixtures. However, the influence of ancestral source populations on the LD pattern in admixed populations is not properly taken into consideration by currently available methods, which affects the estimation of several gene flow parameters from empirical data. We first illustrated the dynamic changes of LD in admixed populations and mathematically formulated the LD under a generalized admixture model with finite population size. We next developed a new method, MALDmef, by fitting LD with multiple exponential functions for inferring and dating multiple-wave admixtures. MALDmef takes into account the effects of source populations which substantially affect modeling LD in admixed population, which renders it capable of efficiently detecting and dating multiple-wave admixture events. The performance of MALDmef was evaluated by simulation and it was shown to be more accurate than MALDER, a state-of-the-art method that was recently developed for similar purposes, under various admixture models. We further applied MALDmef to analyzing genome-wide data from the Human Genome Diversity Project (HGDP) and the HapMap Project. Interestingly, we were able to identify more than one admixture events in several populations, which have yet to be reported. For example, two major admixture events were identified in the Xinjiang Uyghur, occurring around 27???30 generations ago and 182???195 generations ago, respectively. In an African population (MKK), three recent major admixtures occurring 13???16, 50???67, and 107???139 generations ago were detected. Our method is a considerable improvement over other current methods and further facilitates the inference of the histories of complex population admixtures.

scholarly journals Exploiting Linkage Disequilibrium for Ultrahigh-Dimensional Genome-Wide Data with an Integrated Statistical Approach

Genetics ◽  
2015 ◽  
Vol 202 (2) ◽  
pp. 411-426 ◽  
Author(s):  
Michelle Carlsen ◽  
Guifang Fu ◽  
Shaun Bushman ◽  
Christopher Corcoran
Keyword(s):  
Linkage Disequilibrium ◽  
Statistical Approach ◽  
Genome Wide ◽  
Genome Wide Data

scholarly journals Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types

2021 ◽  
Vol 7 (3) ◽  
pp. eabd9036
Author(s):  
Sara Saez-Atienzar ◽  
Sara Bandres-Ciga ◽  
Rebekah G. Langston ◽  
Jonggeol J. Kim ◽  
Shing Wan Choi ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Polygenic Risk Score ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Data Driven Approach ◽  
Single Nucleus ◽  
Lateral Sclerosis

Despite the considerable progress in unraveling the genetic causes of amyotrophic lateral sclerosis (ALS), we do not fully understand the molecular mechanisms underlying the disease. We analyzed genome-wide data involving 78,500 individuals using a polygenic risk score approach to identify the biological pathways and cell types involved in ALS. This data-driven approach identified multiple aspects of the biology underlying the disease that resolved into broader themes, namely, neuron projection morphogenesis, membrane trafficking, and signal transduction mediated by ribonucleotides. We also found that genomic risk in ALS maps consistently to GABAergic interneurons and oligodendrocytes, as confirmed in human single-nucleus RNA-seq data. Using two-sample Mendelian randomization, we nominated six differentially expressed genes (ATG16L2, ACSL5, MAP1LC3A, MAPKAPK3, PLXNB2, and SCFD1) within the significant pathways as relevant to ALS. We conclude that the disparate genetic etiologies of this fatal neurological disease converge on a smaller number of final common pathways and cell types.

scholarly journals Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

2021 ◽  
Vol 7 (13) ◽  
pp. eabe4414
Author(s):  
Guido Alberto Gnecchi-Ruscone ◽  
Elmira Khussainova ◽  
Nurzhibek Kahbatkyzy ◽  
Lyazzat Musralina ◽  
Maria A. Spyrou ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Gene Pools ◽  
Social Rules ◽  
Eurasian Steppe ◽  
Central Asian ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

scholarly journals Genome diversity in Ukraine

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Taras K Oleksyk ◽  
Walter W Wolfsberger ◽  
Alexandra M Weber ◽  
Khrystyna Shchubelka ◽  
Olga T Oleksyk ◽  
...  
Keyword(s):  
Sequence Data ◽  
Copy Number Variations ◽  
Genomic Variation ◽  
High Coverage ◽  
Genome Data ◽  
New Information ◽  
Genome Wide ◽  
Public Data ◽  
Genome Wide Data ◽  
Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

scholarly journals Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Nature ◽  
2021 ◽  
Vol 592 (7853) ◽  
pp. 253-257 ◽  
Author(s):  
Mateja Hajdinjak ◽  
Fabrizio Mafessoni ◽  
Laurits Skov ◽  
Benjamin Vernot ◽  
Alexander Hübner ◽  
...  
Keyword(s):  
Family History ◽  
East Asia ◽  
Late Pleistocene ◽  
Modern Human ◽  
Human Migration ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Genome Wide ◽  
Genome Wide Data

AbstractModern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

Genome-wide linkage disequilibrium in two Japanese beef cattle breeds

2006 ◽  
Vol 37 (2) ◽  
pp. 139-144 ◽  
Author(s):  
M. Odani ◽  
A. Narita ◽  
T. Watanabe ◽  
K. Yokouchi ◽  
Y. Sugimoto ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Beef Cattle ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Beef Cattle Breeds ◽  
Genome Wide Linkage Disequilibrium

scholarly journals Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack)

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 235 ◽  
Author(s):  
Katharina V Alheit ◽  
Hans Maurer ◽  
Jochen C Reif ◽  
Matthew R Tucker ◽  
Volker Hahn ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
X Triticosecale ◽  
Genome Wide ◽  
Spring Triticale ◽  
Triticosecale Wittmack ◽  
X Triticosecale Wittmack
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