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in category genetics

4,349 results found. For more information, click each entry to expand.

41: Genome-wide association studies of brain structure and function in the UK Biobank
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Posted to bioRxiv 21 Aug 2017

Genome-wide association studies of brain structure and function in the UK Biobank
6,125 downloads genetics

Lloyd T. Elliott, Kevin Sharp, Fidel Alfaro-Almagro, Sinan Shi, Karla L Miller, Gwenaëlle Douaud, Jonathan Marchini, Stephen M. Smith

The genetic basis of brain structure and function is largely unknown. We carried out genome-wide association studies of 3,144 distinct functional and structural brain imaging derived phenotypes in UK Biobank (discovery dataset 8,428 subjects). We show that many of these phenotypes are heritable. We identify 148 clusters of SNP-imaging associations with lead SNPs that replicate at p<0.05, when we would expect 21 to replicate by chance. Notable significant and interpretable associations include: iron transport and storage genes, related to changes in T2* in subcortical regions; extracellular matrix and the epidermal growth factor genes, associated with white matter micro-structure and lesion volume; genes regulating mid-line axon guidance development associated with pontine crossing tract organisation; and overall 17 genes involved in development, pathway signalling and plasticity. Our results provide new insight into the genetic architecture of the brain with relevance to complex neurological and psychiatric disorders, as well as brain development and aging. The full set of results is available on the interactive Oxford Brain Imaging Genetics (BIG) web browser.

42: Meta-analysis of genome-wide association studies for height and body mass index in ~700,000 individuals of European ancestry
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Posted to bioRxiv 02 Mar 2018

Meta-analysis of genome-wide association studies for height and body mass index in ~700,000 individuals of European ancestry
6,053 downloads genetics

Loic Yengo, Julia Sidorenko, Kathryn E. Kemper, Zhili Zheng, Andrew R. Wood, Sian Ellard, Timothy M Frayling, Joel Hirschhorn, Jian Yang, Peter M. Visscher, the GIANT Consortium

Genome-wide association studies (GWAS) stand as powerful experimental designs for identifying DNA variants associated with complex traits and diseases. In the past decade, both the number of such studies and their sample sizes have increased dramatically. Recent GWAS of height and body mass index (BMI) in ~250,000 European participants have led to the discovery of ~700 and ~100 nearly independent SNPs associated with these traits, respectively. Here we combine summary statistics from those two studies with GWAS of height and BMI performed in ~450,000 UK Biobank participants of European ancestry. Overall, our combined GWAS meta-analysis reaches N~700,000 individuals and substantially increases the number of GWAS signals associated with these traits. We identified 3,290 and 716 near-independent SNPs associated with height and BMI, respectively (at a revised genome-wide significance threshold of p<10-8), including 1,185 height-associated SNPs and 554 BMI-associated SNPs located within loci not previously identified by these two GWAS. The genome-wide significant SNPs explain ~24.6% of the variance of height and ~5% of the variance of BMI in an independent sample from the Health and Retirement Study (HRS). Correlations between polygenic scores based upon these SNPs with actual height and BMI in HRS participants were 0.44 and 0.20, respectively. From analyses of integrating GWAS and eQTL data by Summary-data based Mendelian Randomization (SMR), we identified an enrichment of eQTLs amongst lead height and BMI signals, prioritisting 684 and 134 genes, respectively. Our study demonstrates that, as previously predicted, increasing GWAS sample sizes continues to deliver, by discovery of new loci, increasing prediction accuracy and providing additional data to achieve deeper insight into complex trait biology. All summary statistics are made available for follow up studies.

43: LIMIX: genetic analysis of multiple traits
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Posted to bioRxiv 21 May 2014

LIMIX: genetic analysis of multiple traits
5,909 downloads genetics

Christoph Lippert, Franceso Paolo Casale, Barbara Rakitsch, Oliver Stegle

Multi-trait mixed models have emerged as a promising approach for joint analyses of multiple traits. In principle, the mixed model framework is remarkably general. However, current methods implement only a very specific range of tasks to optimize the necessary computations. Here, we present a multi-trait modeling framework that is versatile and fast: LIMIX enables to flexibly adapt mixed models for a broad range of applications with different observed and hidden covariates, and variable study designs. To highlight the novel modeling aspects of LIMIX we performed three vastly different genetic studies: joint GWAS of correlated blood lipid phenotypes, joint analysis of the expression levels of the multiple transcript-isoforms of a gene, and pathway-based modeling of molecular traits across environments. In these applications we show that LIMIX increases GWAS power and phenotype prediction accuracy, in particular when integrating stepwise multi-locus regression into multi-trait models, and when analyzing large numbers of traits. An open source implementation of LIMIX is freely available at: https://github.com/PMBio/limix.

44: Current clinical use of polygenic scores will risk exacerbating health disparities
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Posted to bioRxiv 11 Oct 2018

Current clinical use of polygenic scores will risk exacerbating health disparities
5,885 downloads genetics

Alicia R. Martin, M Kanai, Yoichiro Kamatani, Yukinori Okada, Benjamin M Neale, Mark J. Daly

Polygenic risk scores (PRS) are poised to improve biomedical outcomes via precision medicine. However, the major ethical and scientific challenge surrounding clinical implementation is that they are many-fold more accurate in European ancestry individuals than others. This disparity is an inescapable consequence of Eurocentric genome-wide association study biases. This highlights that--unlike clinical biomarkers and prescription drugs, which may individually work better in some populations but do not ubiquitously perform far better in European populations--clinical uses of PRS today would systematically afford greater improvement to European descent populations. Early diversifying efforts show promise in levelling this vast imbalance, even when non-European sample sizes are considerably smaller than the largest studies to date. To realize the full and equitable potential of PRS, we must prioritize greater diversity in genetic studies and public dissemination of summary statistics to ensure that health disparities are not increased for those already most underserved.

45: Tracing the genetic origin of Europe's first farmers reveals insights into their social organization
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Posted to bioRxiv 03 Sep 2014

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization
5,881 downloads genetics

Kurt W. Alt

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis has not been revealed yet. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (7th/6th millennium BC) from the Carpathian Basin and south-eastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early farming south-eastern European and Carpathian Basin cultures on Central European populations of the 6th-4th millennium BC. Our comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through south-eastern Europe and the Carpathian Basin into Central Europe. Our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting patrilineal descent system and patrilocal residential rules among the early farmers.

46: The GTEx Consortium atlas of genetic regulatory effects across human tissues
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Posted to bioRxiv 03 Oct 2019

The GTEx Consortium atlas of genetic regulatory effects across human tissues
5,867 downloads genetics

François Aguet, Alvaro Barbeira, Rodrigo Bonazzola, Andrew Brown, Stephane E. Castel, Brian Jo, Silva Kasela, Sarah Kim-Hellmuth, Yanyu Liang, Meritxell Oliva, Princy E Parsana, Elise Flynn, Laure Fresard, Eric R Gaamzon, Andrew R Hamel, Yuan He, Farhad Hormozdiari, Pejman Mohammadi, Manuel Muñoz-Aguirre, YoSon Park, Ashis Saha, Ayellet V Segrć, Benjamin J. Strober, Xiaoquan Wen, Valentin Wucher, Sayantan Das, Diego Garrido-Martín, Nicole R. Gay, Robert E Handsaker, Paul J. Hoffman, Seva Kashin, Alan Kwong, Xiao Li, Daniel MacArthur, John M Rouhana, Matthew Stephens, Ellen Todres, Ana Viñuela, Gao Wang, Yuxin Zou, The GTEx Consortium, Christopher D Brown, Nancy Cox, Emmanouil Dermitzakis, Barbara E Engelhardt, Gad Getz, Roderic Guigo, Stephen B. Montgomery, Barbara E. Stranger, Hae K. Im, Alexis Battle, Kristin Ardlie, Tuuli Lappalainen

The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues, and to link these regulatory mechanisms to trait and disease associations. Here, we present analyses of the v8 data, based on 17,382 RNA-sequencing samples from 54 tissues of 948 post-mortem donors. We comprehensively characterize genetic associations for gene expression and splicing in cis and trans, showing that regulatory associations are found for almost all genes, and describe the underlying molecular mechanisms and their contribution to allelic heterogeneity and pleiotropy of complex traits. Leveraging the large diversity of tissues, we provide insights into the tissue-specificity of genetic effects, and show that cell type composition is a key factor in understanding gene regulatory mechanisms in human tissues.

47: A comprehensive map of genetic variation in the world's largest ethnic group - Han Chinese
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Posted to bioRxiv 13 Jul 2017

A comprehensive map of genetic variation in the world's largest ethnic group - Han Chinese
5,628 downloads genetics

Karyn Meltz Steinberg, Serghei Mangul, Christopher R. Robles, Warren W. Kretzschmar, Na Cai, Kenneth S. Kendler, Sriram Sankararam, Jonathan Flint

As are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from our study come from 19 out of 22 provinces across China, allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identify previously unrecognized population structure along the East-West axis of China and report unique signals of admixture across geographical space, such as European influences among the Northwestern provinces of China. Finally, we identified a number of highly differentiated loci, indicative of local adaptation in the Han Chinese. In particular, we detected extreme differentiation among the Han Chinese at MTHFR, ADH7, and FADS loci, suggesting that these loci may not be specifically selected in Tibetan and Inuit populations as previously suggested. On the other hand, we find that Neandertal ancestry does not vary significantly across the provinces, consistent with admixture prior to the dispersal of modern Han Chinese. Furthermore, contrary to a previous report, Neandertal ancestry does not explain a significant amount of heritability in depression. Our findings provide the largest genetic data set so far made available for Han Chinese and provide insights into the history and population structure of the world's largest ethnic group.

48: Iron Age and Anglo-Saxon genomes from East England reveal British migration history
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Posted to bioRxiv 17 Jul 2015

Iron Age and Anglo-Saxon genomes from East England reveal British migration history
5,585 downloads genetics

Stephan Schiffels, Wolfgang Haak, Pirita Paajanen, Bastien Llamas, Elizabeth Popescu, Louise Lou, Rachel Clarke, Alice Lyons, Richard Mortimer, Duncan Sayer, Chris Tyler-Smith, Alan Cooper, Richard Durbin

British population history has been shaped by a series of immigrations and internal movements, including the early Anglo-Saxon migrations following the breakdown of the Roman administration after 410CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences generated from ten ancient individuals found in archaeological excavations close to Cambridge in the East of England, ranging from 2,300 until 1,200 years before present (Iron Age to Anglo-Saxon period). We use present-day genetic data to characterize the relationship of these ancient individuals to contemporary British and other European populations. By analyzing the distribution of shared rare variants across ancient and modern individuals, we find that today’s British are more similar to the Iron Age individuals than to most of the Anglo-Saxon individuals, and estimate that the contemporary East English population derives 30% of its ancestry from Anglo-Saxon migrations, with a lower fraction in Wales and Scotland. We gain further insight with a new method, rarecoal, which fits a demographic model to the distribution of shared rare variants across a large number of samples, enabling fine scale analysis of subtle genetic differences and yielding explicit estimates of population sizes and split times. Using rarecoal we find that the ancestors of the Anglo-Saxon samples are closest to modern Danish and Dutch populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

49: The Multiple Sclerosis Genomic Map: Role of peripheral immune cells and resident microglia in susceptibility
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Posted to bioRxiv 13 Jul 2017

The Multiple Sclerosis Genomic Map: Role of peripheral immune cells and resident microglia in susceptibility
5,453 downloads genetics

International Multiple Sclerosis Genetics Consortium, NA Patsopoulos, SE Baranzini, A Santaniello, P Shoostari, C Cotsapas, G Wong, AH Beecham, T James, J Replogle, I Vlachos, C McCabe, T Pers, A Brandes, C White, B Keenan, M Cimpean, P Winn, IP Panteliadis, A Robbins, TFM Andlauer, O Zarzycki, B Dubois, A Goris, H Bach Sondergaard, F Sellebjerg, P Soelberg Sorensen, H Ullum, L Wegner Thoerner, J Saarela, I Cournu Rebeix, V Damotte, B Fontaine, L Guillot Noel, M Lathrop, S Vukusik, A Berthele, V Biberacher, D Buck, C Gasperi, C Graetz, V Grummel, B Hemmer, M Hoshi, B Knier, T Korn, CM Lill, F Luessi, M Mühlau, F Zipp, E Dardiotis, C Agliardi, A Amoroso, N Barizzone, MD Benedetti, L Bernardinelli, P Cavalla, F Clarelli, G Comi, D Cusi, F Esposito, L Ferrè, D Galimberti, C Guaschino, MA Leone, V Martinelli, L Moiola, M Salvetti, M Sorosina, D Vecchio, A Zauli, S Santoro, M Zuccalà, J Mescheriakova, C van Duijn, SD Bos, EG Celius, A Spurkland, M Comabella, X Montalban, L Alfredsson, I Bomfim, D Gomez-Cabrero, J Hillert, M Jagodic, M Lindén, F Piehl, I Jelčić, R Martin, M Sospedra, A Baker, M Ban, C Hawkins, P Hysi, S Kalra, F Karpe, J Khadake, G Lachance, P Molyneux, M Neville, J Thorpe, E Bradshaw, SJ Caillier, P Calabresi, BAC Cree, A Cross, M Davis, PWI de Bakker, S Delgado, M Dembele, K Edwards, K Fitzgerald, IY Frohlich, PA Gourraud, JL Haines, H Hakonarson, D Kimbrough, N Isobe, I Konidari, E Lathi, MH Lee, T Li, D An, A Zimmer, A Lo, L Madireddy, CP Manrique, M Mitrovic, M Olah, E Patrick, Margaret Pericak-Vance, L Piccio, C Schaefer, H Weiner, K Lage, A Compston, D Hafler, HF Harbo, SL Hauser, G Stewart, S D’Alfonso, G Hadjigeorgiou, B Taylor, LF Barcellos, D Booth, R Hintzen, I Kockum, F Martinelli-Boneschi, JL McCauley, JR Oksenberg, A Oturai, S Sawcer, AJ Ivinson, T Olsson, P.L. De Jager, Murray Barclay, Laurent Peyrin-Biroulet, Mathias Chamaillard, Jean-Frederick Colombe, Mario Cottone, Anthony Croft, Renata D’Incà, Jonas Halfvarson, Katherine Hanigan, Paul Henderson, Jean-Pierre Hugot, Amir Karban, Nicholas A Kennedy, Mohammed Azam Khan, Marc Lémann, Arie Levine, Dunecan Massey, Monica Milla, Grant W. Montgomery, Sok Meng Evelyn Ng, Ioannis Oikonomou, Harald Peeters, Deborah D. Proctor, Jean-Francois Rahier, Rebecca Roberts, Paul Rutgeerts, Frank Seibold, Laura Stronati, Kirstin M. Taylor, Leif Törkvist, Kullak Ublick, Johan Van Limbergen, Andre Van Gossum, Morten H. Vatn, Hu Zhang, Wei Zhang, Australia and New Zealand IBDGC, Belgium Genetic Consortium, Initiative on Crohn and Colitis, NIDDK IBDGC, United Kingdom IBDGC, Wellcome Trust Case Control Consortium

We assembled and analyzed genetic data of 47,351 multiple sclerosis (MS) subjects and 68,284 control subjects and establish a reference map of the genetic architecture of MS that includes 200 autosomal susceptibility variants outside the major histocompatibility complex (MHC), one chromosome X variant, and 32 independent associations within the extended MHC. We used an ensemble of methods to prioritize up to 551 potentially associated MS susceptibility genes, that implicate multiple innate and adaptive pathways distributed across the cellular components of the immune system. Using expression profiles from purified human microglia, we do find enrichment for MS genes in these brain-resident immune cells. Thus, while MS is most likely initially triggered by perturbation of peripheral immune responses the functional responses of microglia and other brain cells are also altered and may have a role in targeting an autoimmune process to the central nervous system.

50: Genome-wide Variants of Eurasian Facial Shape Differentiation and a prospective model of DNA based Face Prediction
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Posted to bioRxiv 10 Jul 2016

Genome-wide Variants of Eurasian Facial Shape Differentiation and a prospective model of DNA based Face Prediction
5,260 downloads genetics

Lu Qiao, Yajun Yang, Pengcheng Fu, Sile Hu, Hang Zhou, Shouneng Peng, Jingze Tan, Yan Lu, Haiyi Lou, Dongsheng Lu, Sijie Wu, Jing Guo, Li Jin, Yaqun Guan, Sijia Wang, Shuhua Xu, Kun Tang

It is a long standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Europeans and Han Chinese look different. Facial traits were analyzed based on high-dense 3D facial images; numerous biometric spaces were examined for divergent facial features between European and Han Chinese, ranging from inter-landmark distances to dense shape geometrics. Genome-wide association analyses were conducted on a discovery panel of Uyghurs. Six significant loci were identified four of which, rs1868752, rs118078182, rs60159418 at or near UBASH3B, COL23A1, PCDH7 and rs17868256 were replicated in independent cohorts of Uyghurs or Southern Han Chinese. A prospective model was also developed to predict 3D faces based on top GWAS signals, and tested in hypothetic forensic scenarios.

51: Inferring human population size and separation history from multiple genome sequences
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Posted to bioRxiv 21 May 2014

Inferring human population size and separation history from multiple genome sequences
5,094 downloads genetics

Stephan Schiffels, Richard Durbin

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.

52: Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences
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Posted to bioRxiv 26 May 2017

Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences
5,061 downloads genetics

Marc Haber, Claude Doumet-Serhal, Christiana Scheib, Yali Xue, Petr Danecek, Massimo Mezzavilla, Sonia Youhanna, Rui Martiniano, Javier Prado-Martinez, Michal Szpak, Elizabeth Matisoo-Smith, Holger Schutkowski, Richard Mikulski, Pierre Zalloua, Toomas Kivisild, Chris Tyler-Smith

The Canaanites inhabited the Levant region during the Bronze Age and established a culture which became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole-genomes from ~3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalogue modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with massive population movements in the mid-Holocene triggered by aridification ~4,200 years ago. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations such as the Persians and Macedonians.

53: Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline
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Posted to bioRxiv 04 Jul 2018

Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline
4,959 downloads genetics

Hannah A. Grunwald, Valentino M. Gantz, Gunnar Poplawski, Xiang-ru S. Xu, Ethan Bier, Kimberly L. Cooper

A gene drive biases the transmission of a particular allele of a gene such that it is inherited at a greater frequency than by random assortment. Recently, a highly efficient gene drive was developed in insects, which leverages the sequence-targeted DNA cleavage activity of CRISPR/Cas9 and endogenous homology directed repair mechanisms to convert heterozygous genotypes to homozygosity. If implemented in laboratory rodents, this powerful system would enable the rapid assembly of genotypes that involve multiple genes (e.g., to model multigenic human diseases). Such complex genetic models are currently precluded by time, cost, and a requirement for a large number of animals to obtain a few individuals of the desired genotype. However, the efficiency of a CRISPR/Cas9 gene drive system in mammals has not yet been determined. Here, we utilize an active genetic 'CopyCat' element embedded in the mouse Tyrosinase gene to detect genotype conversions after Cas9 activity in the embryo and in the germline. Although Cas9 efficiently induces double strand DNA breaks in the early embryo and is therefore highly mutagenic, these breaks are not resolved by homology directed repair. However, when Cas9 expression is limited to the developing female germline, resulting double strand breaks are resolved by homology directed repair that copies the CopyCat allele from the donor to the receiver chromosome and leads to its super-Mendelian inheritance. These results demonstrate that the CRISPR/Cas9 gene drive mechanism can be implemented to simplify complex genetic crosses in laboratory mice and also contribute valuable data to the ongoing debate about applications to combat invasive rodent populations in island communities.

54: A Tale of Two Hypotheses: Genetics and the Ethnogenesis of Ashkenazi Jewry
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Posted to bioRxiv 12 Dec 2013

A Tale of Two Hypotheses: Genetics and the Ethnogenesis of Ashkenazi Jewry
4,944 downloads genetics

M.A. Aram Yardumian

The debate over the ethnogenesis of Ashkenazi Jewry is longstanding, and has been hampered by a lack of Jewish historiographical work between the Biblical and the early Modern eras. Most historians, as well as geneticists, situate them as the descendants of Israelite tribes whose presence in Europe is owed to deportations during the Roman conquest of Palestine, as well as migration from Babylonia, and eventual settlement along the Rhine. By contrast, a few historians and other writers, most famously Arthur Koestler, have looked to migrations following the decline of the little-understood Medieval Jewish kingdom of Khazaria as the main source for Ashkenazi Jewry. A recent study of genetic variation in southeastern European populations (Elhaik 2012) also proposed a Khazarian origin for Ashkenazi Jews, eliciting considerable criticism from other scholars investigating Jewish ancestry who favor a Near Eastern origin of Ashkenazi populations. This paper re-examines the genetic data and analytical approaches used in these studies of Jewish ancestry, and situates them in the context of historical, linguistic, and archaeological evidence from the Caucasus, Europe and the Near East. Based on this reanalysis, it appears not only that the Khazar Hypothesis per se is without serious merit, but also the veracity of the ‘Rhineland Hypothesis’ may also be questionable.

55: Genetic meta-analysis identifies 9 novel loci and functional pathways for Alzheimers disease risk
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Posted to bioRxiv 20 Feb 2018

Genetic meta-analysis identifies 9 novel loci and functional pathways for Alzheimers disease risk
4,933 downloads genetics

Iris E Jansen, Jeanne E Savage, Kyoko Watanabe, Julien Bryois, Dylan M. Williams, Stacy Steinberg, Julia Sealock, Ida K. Karlsson, Sara Hägg, Lavinia Athanasiu, Nicola Voyle, Petroula Proitsi, Aree Witoelar, Sven Stringer, Dag Aarsland, Ina S Almdahl, Fred Andersen, Sverre Bergh, Francesco Bettella, Sigurbjorn Bjornsson, Anne Brækhus, Geir Bråthen, Christiaan de Leeuw, Rahul S. Desikan, Srdjan Djurovic, Logan Dumitrescu, Tormod Fladby, Timothy Homan, Palmi V Jonsson, Steven J Kiddle, K Arvid Rongve, Ingvild Saltvedt, Sigrid B. Sando, Geir Selbæk, Nathan Skenne, Jon Snaedal, Eystein Stordal, Ingun D. Ulstein, Yunpeng Wang, Linda R White, Jens Hjerling Leffler, Patrick F Sullivan, Wiesje M. van der Flier, Richard Dobson, Lea K. Davis, Hreinn Stefansson, Kari Stefansson, Nancy L Pedersen, Stephan Ripke, Ole A. Andreassen, Danielle Posthuma

Late onset Alzheimer's disease (AD) is the most common form of dementia with more than 35 million people affected worldwide, and no curative treatment available. AD is highly heritable and recent genome-wide meta-analyses have identified over 20 genomic loci associated with AD, yet only explaining a small proportion of the genetic variance indicating that undiscovered loci exist. Here, we performed the largest genome-wide association study of clinically diagnosed AD and AD-by-proxy (71,880 AD cases, 383,378 controls). AD-by-proxy status is based on parental AD diagnosis, and showed strong genetic correlation with AD (rg=0.81). Genetic meta-analysis identified 29 risk loci, of which 9 are novel, and implicating 215 potential causative genes. Independent replication further supports these novel loci in AD. Associated genes are strongly expressed in immune-related tissues and cell types (spleen, liver and microglia). Furthermore, gene-set analyses indicate the genetic contribution of biological mechanisms involved in lipid-related processes and degradation of amyloid precursor proteins. We show strong genetic correlations with multiple health-related outcomes, and Mendelian randomisation results suggest a protective effect of cognitive ability on AD risk. These results are a step forward in identifying more of the genetic factors that contribute to AD risk and add novel insights into the neurobiology of AD to guide new drug development.

56: Genome-wide Analysis of Insomnia (N=1,331,010) Identifies Novel Loci and Functional Pathways
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Posted to bioRxiv 30 Jan 2018

Genome-wide Analysis of Insomnia (N=1,331,010) Identifies Novel Loci and Functional Pathways
4,840 downloads genetics

Philip R Jansen, Kyoko Watanabe, Sven Stringer, Nathan Skene, Julien Bryois, Anke R Hammerschlag, Christiaan A de Leeuw, Jeroen Benjamins, Ana B Muñoz-Manchado, Mats Nagel, Jeanne E Savage, Henning Tiemeier, Tonya White, The 23andMe Research Team, Joyce Y Tung, David A. Hinds, Vladimir Vacic, Patrick F Sullivan, Sophie van der Sluis, Tinca J.C. Polderman, August B Smit, Jens Hjerling-Leffler, Eus J.W. Van Someren, Danielle Posthuma

Insomnia is the second-most prevalent mental disorder, with no sufficient treatment available. Despite a substantial role of genetic factors, only a handful of genes have been implicated and insight into the associated neurobiological pathways remains limited. Here, we use an unprecedented large genetic association sample (N=1,331,010) to allow detection of a substantial number of genetic variants and gain insight into biological functions, cell types and tissues involved in insomnia. We identify 202 genome-wide significant loci implicating 956 genes through positional, eQTL and chromatin interaction mapping. We show involvement of the axonal part of neurons, of specific cortical and subcortical tissues, and of two specific cell-types in insomnia: striatal medium spiny neurons and hypothalamic neurons. These cell-types have been implicated previously in the regulation of reward processing, sleep and arousal in animal studies, but have never been genetically linked to insomnia in humans. We found weak genetic correlations with other sleep-related traits, but strong genetic correlations with psychiatric and metabolic traits. Mendelian randomization identified causal effects of insomnia on specific psychiatric and metabolic traits. Our findings reveal key brain areas and cells implicated in the neurobiology of insomnia and its related disorders, and provide novel targets for treatment.

57: GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence
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Posted to bioRxiv 06 Sep 2017

GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence
4,819 downloads genetics

Jeanne E Savage, Philip R Jansen, Sven Stringer, Kyoko Watanabe, Julien Bryois, Christiaan A de Leeuw, Mats Nagel, Swapnil Awasthi, Peter B. Bar, Jonathan R. I. Coleman, Katrina L. Grasby, Anke R Hammerschlag, Jakob Kaminski, Robert Karlsson, Eva Krapohl, Max Lam, Marianne Nygaard, Chandra A. Reynolds, Joey W. Trampush, Hannah Young, Delilah Zabaneh, Sara Hägg, Narelle K. Hansell, Ida K. Karlsson, Sten Linnarsson, Grant W. Montgomery, Ana B Muñoz-Manchado, Erin B. Quinlan, Gunter Schumann, Nathan Skene, Bradley T. Webb, Tonya White, Dan E. Arking, Deborah K. Attix, Dimitrios Avramopoulos, Robert M. Bilder, Panos Bitsios, Katherine E. Burdick, Tyrone D. Cannon, Ornit Chiba-Falek, Andrea Christoforou, Elizabeth T. Cirulli, Eliza Congdon, Aiden Corvin, Gail Davies, I.J. Deary, Pamela DeRosse, Dwight Dickinson, Srdjan Djurovic, Gary Donohoe, Emily Drabant Conley, Johan G. Eriksson, Thomas Espeseth, Nelson A. Freimer, Stella Giakoumaki, Ina Giegling, Michael Gill, David C. Glahn, Ahmad R Hariri, Alex Hatzimanolis, Matthew C. Keller, Emma Knowles, Bettina Konte, Jari Lahti, Stephanie Le Hellard, Todd Lencz, David C Liewald, Edythe London, A.J. Lundervold, Anil K. Malhotra, Ingrid Melle, Derek Morris, Anna C. Need, William Ollier, Aarno Palotie, Antony Payton, Neil Pendleton, Russell A. Poldrack, Katri Räikkönen, Ivar Reinvang, Panos Roussos, Dan Rujescu, Fred W. Sabb, Matthew A. Scult, Olav B Smeland, Nikolaos Smyrnis, John M. Starr, Vidar M. Steen, Nikos C. Stefanis, Richard E Straub, Kjetil Sundet, Aristotle N. Voineskos, Daniel R Weinberger, Elisabeth Widen, Jin Yu, Goncalo Abecasis, Ole A. Andreassen, Gerome Breen, Lene Christiansen, Birgit Debrabant, Danielle M. Dick, Andreas Heinz, Jens Hjerling Leffler, M. Arfan Ikram, Kenneth S Kendler, Nicholas G. Martin, Sarah E Medland, Nancy L Pedersen, Robert Plomin, Tinca J.C. Polderman, Stephan Ripke, Sophie van der Sluis, Patrick F Sullivan, Henning Tiemeier, Scott I. Vrieze, Margaret J Wright, Danielle Posthuma

Intelligence is highly heritable and a major determinant of human health and well-being. Recent genome-wide meta-analyses have identified 24 genomic loci linked to intelligence, but much about its genetic underpinnings remains to be discovered. Here, we present the largest genetic association study of intelligence to date (N=279,930), identifying 206 genomic loci (191 novel) and implicating 1,041 genes (963 novel) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. We find enrichment of genetic effects in conserved and coding regions and identify 89 nonsynonymous exonic variants. Associated genes are strongly expressed in the brain and specifically in striatal medium spiny neurons and cortical and hippocampal pyramidal neurons. Gene-set analyses implicate pathways related to neurogenesis, neuron differentiation and synaptic structure. We confirm previous strong genetic correlations with several neuropsychiatric disorders, and Mendelian Randomization results suggest protective effects of intelligence for Alzheimer's dementia and ADHD, and bidirectional causation with strong pleiotropy for schizophrenia. These results are a major step forward in understanding the neurobiology of intelligence as well as genetically associated neuropsychiatric traits.

58: Variable prediction accuracy of polygenic scores within an ancestry group
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Posted to bioRxiv 07 May 2019

Variable prediction accuracy of polygenic scores within an ancestry group
4,748 downloads genetics

Hakhamanesh Mostafavi, Arbel Harpak, Dalton Conley, Jonathan K. Pritchard, Molly Przeworski

Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group, the prediction accuracy of polygenic scores depends on characteristics such as the age or sex composition of the individuals in which the GWAS and the prediction were conducted, and on the GWAS study design. Our findings highlight both the complexities of interpreting polygenic scores and underappreciated obstacles to their broad use.

59: Genetics of 38 blood and urine biomarkers in the UK Biobank
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Posted to bioRxiv 05 Jun 2019

Genetics of 38 blood and urine biomarkers in the UK Biobank
4,655 downloads genetics

Nicholas A. Sinnott-Armstrong, Yosuke Tanigawa, David Amar, Nina Mars, Matthew Aguirre, Guhan Venkataraman, Michael Wainberg, Hanna M Ollila, James P. Pirruccello, Junyang Qian, Anna Shcherbina, FinnGen, Fatima Rodriguez, Themistocles Assimes, Vineeta Agarwala, Robert Tibshirani, Trevor Hastie, Samuli Ripatti, Jonathan K. Pritchard, Mark J. Daly, Manuel A. Rivas

Clinical laboratory tests are a critical component of the continuum of care and provide a means for rapid diagnosis and monitoring of chronic disease. In this study, we systematically evaluated the genetic basis of 38 blood and urine laboratory tests measured in 358,072 participants in the UK Biobank and identified 1,857 independent loci associated with at least one laboratory test, including 488 large-effect protein truncating, missense, and copy-number variants. We tested these loci for enrichment in specific single cell types in kidney, liver, and pancreas relevant to disease aetiology. We then causally linked the biomarkers to medically relevant phenotypes through genetic correlation and Mendelian randomization. Finally, we developed polygenic risk scores (PRS) for each biomarker and built multi-PRS models using all 38 PRSs simultaneously. We found substantially improved prediction of incidence in FinnGen (n=135,500) with the multi-PRS relative to single-disease PRSs for renal failure, myocardial infarction, liver fat percentage, and alcoholic cirrhosis. Together, our results show the genetic basis of these biomarkers, which tissues contribute to the biomarker function, the causal influences of the biomarkers, and how we can use this to predict disease.

60: Large-scale whole-genome sequencing of three diverse Asian populations in Singapore
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Posted to bioRxiv 11 Aug 2018

Large-scale whole-genome sequencing of three diverse Asian populations in Singapore
4,576 downloads genetics

Degang Wu, Jinzhuang Dou, Xiaoran Chai, Claire Bellis, Andreas Wilm, Chih Chuan Shih, Wendy Wei Jia Soon, Nicolas Bertin, Chiea Chuen Khor, Michael DeGiorgio, Sonia Maria Davila Dominguez, Patrick Tan, Asim Shabbir, Angela Moh, Eng-King Tan, Jia Nee Foo, Tan Tock Seng Hospital Healthy Control Workgroup, Roger S. Foo, Carolyn S.P. Lam, A. Mark Richards, Ching-Yu Cheng, Tin Aung, Tien Yin Wong, Jianjun Liu, Chaolong Wang, on behalf of the SG10K Consortium

Asian populations are currently underrepresented in human genetics research. Here we present whole-genome sequencing data of 4,810 Singaporeans from three diverse ethnic groups: 2,780 Chinese, 903 Malays, and 1,127 Indians. Despite a medium depth of 13.7X, we achieved essentially perfect (>99.8%) sensitivity and accuracy for detecting common variants and good sensitivity (>89%) for detecting extremely rare variants with <0.1% allele frequency. We found 89.2 million single-nucleotide polymorphisms (SNPs) and 9.1 million small insertions and deletions (INDELs), more than half of which have not been cataloged in dbSNP. In particular, we found 126 common deleterious mutations (MAF>0.01) that were absent in the existing public databases, highlighting the importance of local population reference for genetic diagnosis. We describe fine-scale genetic structure of Singapore populations and their relationship to worldwide populations from the 1000 Genomes Project. In addition to revealing noticeable amounts of admixture among three Singapore populations and a Malay-related novel ancestry component that has not been captured by the 1000 Genomes Project, our analysis also identified some fine-scale features of genetic structure consistent with two waves of prehistoric migration from south China to Southeast Asia. Finally, we demonstrate that our data can substantially improve genotype imputation not only for Singapore populations, but also for populations across Asia and Oceania. These results highlight the genetic diversity in Singapore and the potential impacts of our data as a resource to empower human genetics discovery in a broad geographic region.

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