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1. Polygenic profiles define aspects of clinical heterogeneity in attention deficit hyperactivity disorder

Author: LaBianca, Sonja, Brikell, Isabell, Helenius, Dorte, Loughnan, Robert, Mefford, Joel, Palmer, Clare E, Walker, Rebecca, Gådin, Jesper R, Krebs, Morten, Appadurai, Vivek, Vaez, Morteza, Agerbo, Esben, Pedersen, Marianne Giørtz, Børglum, Anders D, Hougaard, David M, Mors, Ole, Nordentoft, Merete, Mortensen, Preben Bo, Kendler, Kenneth S, Jernigan, Terry L, Geschwind, Daniel H, Ingason, Andrés, Dahl, Andrew W, Zaitlen, Noah, Dalsgaard, Søren, Werge, Thomas M, and Schork, Andrew J
Subjects: Biological Sciences, Genetics, Pediatric, Behavioral and Social Science, Autism, Human Genome, Mental Illness, Mental Health, Prevention, Attention Deficit Hyperactivity Disorder (ADHD), Clinical Research, Intellectual and Developmental Disabilities (IDD), Brain Disorders, 2.1 Biological and endogenous factors, 2.3 Psychological, social and economic factors, Mental health, Good Health and Well Being, Humans, Autism Spectrum Disorder, Attention Deficit Disorder with Hyperactivity, Multifactorial Inheritance, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract: Attention deficit hyperactivity disorder (ADHD) is a complex disorder that manifests variability in long-term outcomes and clinical presentations. The genetic contributions to such heterogeneity are not well understood. Here we show several genetic links to clinical heterogeneity in ADHD in a case-only study of 14,084 diagnosed individuals. First, we identify one genome-wide significant locus by comparing cases with ADHD and autism spectrum disorder (ASD) to cases with ADHD but not ASD. Second, we show that cases with ASD and ADHD, substance use disorder and ADHD, or first diagnosed with ADHD in adulthood have unique polygenic score (PGS) profiles that distinguish them from complementary case subgroups and controls. Finally, a PGS for an ASD diagnosis in ADHD cases predicted cognitive performance in an independent developmental cohort. Our approach uncovered evidence of genetic heterogeneity in ADHD, helping us to understand its etiology and providing a model for studies of other disorders.
Published: 2024

2. The selection landscape and genetic legacy of ancient Eurasians

Author: Irving-Pease, Evan K, Refoyo-Martínez, Alba, Barrie, William, Ingason, Andrés, Pearson, Alice, Fischer, Anders, Sjögren, Karl-Göran, Halgren, Alma S, Macleod, Ruairidh, Demeter, Fabrice, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew H, Speidel, Leo, Stern, Aaron J, Scorrano, Gabriele, Ramsøe, Abigail, Schork, Andrew J, Rosengren, Anders, Zhao, Lei, Kristiansen, Kristian, Iversen, Astrid KN, Fugger, Lars, Sudmant, Peter H, Lawson, Daniel J, Durbin, Richard, Korneliussen, Thorfinn, Werge, Thomas, Allentoft, Morten E, Sikora, Martin, Nielsen, Rasmus, Racimo, Fernando, and Willerslev, Eske
Subjects: Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Archaeology, Historical Studies, Anthropology, Good Health and Well Being, Humans, Alzheimer Disease, Affect, Alleles, Agriculture, Europe, General Science & Technology
Abstract: The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
Published: 2024

3. 100 ancient genomes show repeated population turnovers in Neolithic Denmark

Author: Allentoft, Morten E, Sikora, Martin, Fischer, Anders, Sjögren, Karl-Göran, Ingason, Andrés, Macleod, Ruairidh, Rosengren, Anders, Schulz Paulsson, Bettina, Jørkov, Marie Louise Schjellerup, Novosolov, Maria, Stenderup, Jesper, Price, T Douglas, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Sørensen, Lasse, Nielsen, Poul Otto, Rasmussen, Peter, Jensen, Theis Zetner Trolle, Refoyo-Martínez, Alba, Irving-Pease, Evan K, Barrie, William, Pearson, Alice, Sousa da Mota, Bárbara, Demeter, Fabrice, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Johannsen, Niels Nørkjær, Ramsøe, Abigail Daisy, Schork, Andrew Joseph, Ruter, Anthony, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, Brinch Petersen, Erik, Kannegaard, Esben, Hansen, Jesper, Buck Pedersen, Kristoffer, Pedersen, Lisbeth, Klassen, Lutz, Meldgaard, Morten, Johansen, Morten, Uldum, Otto Christian, Lotz, Per, Lysdahl, Per, Bangsgaard, Pernille, Petersen, Peter Vang, Maring, Rikke, Iversen, Rune, Wåhlin, Sidsel, Anker Sørensen, Søren, Andersen, Søren H, Jørgensen, Thomas, Lynnerup, Niels, Lawson, Daniel J, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Kjær, Kurt H, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Kristiansen, Kristian, and Willerslev, Eske
Subjects: Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Archaeology, Historical Studies, Anthropology, Humans, Genomics, Genotype, Denmark, Emigrants and Immigrants, Scandinavians and Nordic People, General Science & Technology
Abstract: Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
Published: 2024

4. Population genomics of post-glacial western Eurasia

Author: Allentoft, Morten E, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V, Cuenca-Solana, David, Lordkipanidze, David O, En’shin, Dmitri, Salazar-García, Domingo C, Price, T Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V, Usmanova, Emma R, Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N, Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, and Silvestrini, Mara
Subjects: Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, Biotechnology, Humans, Genomics, Diploidy, Agriculture, Europe, Metagenomics, General Science & Technology
Abstract: Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Published: 2024

5. Quantifying the relative importance of genetics and environment on the comorbidity between mental and cardiometabolic disorders using 17 million Scandinavians

Author: Meijsen, Joeri, Hu, Kejia, Krebs, Morten D., Athanasiadis, Georgios, Washbrook, Sarah, Zetterberg, Richard, Avelar e Silva, Raquel Nogueira, Shorter, John R., Gådin, Jesper R., Bergstedt, Jacob, Howard, David M., Ye, Weimin, Lu, Yi, Valdimarsdóttir, Unnur A., Ingason, Andrés, Helenius, Dorte, Plana-Ripoll, Oleguer, McGrath, John J., Micali, Nadia, Andreassen, Ole A., Werge, Thomas M., Fang, Fang, and Buil, Alfonso
Published: 2024
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6. Associations of psychiatric disorders with sex chromosome aneuploidies in the Danish iPSYCH2015 dataset: a case-cohort study.

Author: Sánchez, Xabier, Montalbano, Simone, Vaez, Morteza, Krebs, Morten, Byberg-Grauholm, Jonas, Mortensen, Preben, Børglum, Anders, Hougaard, David, Nordentoft, Merete, Geschwind, Daniel, Buil, Alfonso, Schork, Andrew, Raznahan, Armin, Helenius, Dorte, Werge, Thomas, Ingason, Andrés, and Thompson, Wesley
Subjects: Child, Young Adult, Humans, Male, Female, Infant, Newborn, Infant, Child, Preschool, Adolescent, Adult, Aneuploidy, Cohort Studies, Depressive Disorder, Major, Autism Spectrum Disorder, Mental Disorders, Chromosomes, Human, X, Denmark
Abstract: BACKGROUND: Increased prevalence of mental illness has been reported in clinical studies of sex chromosome aneuploidies, but accurate population-based estimates of the prevalence and clinical detection rate of sex chromosome aneuploidies and the associated risks of psychiatric disorders are needed. In this study, we provide such estimates, valid for children and young adults of the contemporary Danish population. METHODS: We used the iPSYCH2015 case-cohort dataset, which is based on a source population of single-born individuals born in Denmark between May 1, 1981, and Dec 31, 2008. The case sample comprises all individuals from the source population with a diagnosis of any index psychiatric disorder (schizophrenia spectrum disorder, bipolar disorder, major depressive disorder, autism spectrum disorder, or ADHD) by the end of follow-up (Dec 31, 2015), registered in the hospital-based Danish Psychiatric Central Research Register. The cohort consists of individuals randomly selected from the source population, and overlaps with the case sample. Biobanked blood samples for individuals in the case and cohort samples underwent genotyping and quality-control filtering, after which we analysed microarray data to detect sex chromosome aneuploidy karyotypes (45,X, 47,XXX, 47,XXY, and 47,XYY). We estimated the population-valid prevalence of these karyotypes from the cohort sample. Weighted Cox proportional hazards models were used to estimate the risks of each index psychiatric disorder associated with each sex chromosome aneuploidy karyotype, by use of date of first hospitalisation with the index disorder in the respective case group and the cohort as outcome. The clinical detection rate was determined by comparing records of clinical diagnoses of genetic conditions from the Danish National Patient Register with sex chromosome aneuploidy karyotype determined by our study. FINDINGS: The assessed sample comprised 119 481 individuals (78 726 in the case sample and 43 326 in the cohort) who had genotyped and quality-control-filtered blood samples, including 64 533 (54%) people of gonadal male sex and 54 948 (46%) of gonadal female sex. Age during follow-up ranged from 0 to 34·7 years (mean 10·9 years [SD 3·5 years]). Information on ethnicity was not available. We identified 387 (0·3%) individuals as carriers of sex chromosome aneuploidies. The overall prevalence of sex chromosome aneuploidies was 1·5 per 1000 individuals. Each sex chromosome aneuploidy karyotype was associated with an increased risk of at least one index psychiatric disorder, with hazard ratios (HRs) of 2·20 (95% CI 1·42-3·39) for 47,XXY; 2·73 (1·25-6·00) for 47,XXX; 3·56 (1·01-12·53) for 45,X; and 4·30 (2·48-7·55) for 47,XYY. All karyotypes were associated with an increased risk of ADHD (HRs ranging from 1·99 [1·24-3·19] to 6·15 [1·63-23·19]), autism spectrum disorder (2·72 [1·72-4·32] to 8·45 [2·49-28·61]), and schizophrenia spectrum disorder (1·80 [1·15-2·80] to 4·60 [1·57-13·51]). Increased risk of major depressive disorder was found for individuals with 47,XXY (1·88 [1·07-3·33]) and 47,XYY (2·65 [1·12-5·90]), and of bipolar disorder for those with 47,XXX (4·32 [1·12-16·62]). The proportion of sex chromosome aneuploidy carriers who had been clinically diagnosed was 93% for 45,X, but lower for 47,XXY (22%), 47,XXX (15%), and 47,XYY (15%). Among carriers, the risk of diagnosis of at least one index psychiatric disorder did not significantly differ between those who had and had not been clinically diagnosed with sex chromosome aneuploidies (p=0·65). INTERPRETATION: Increased risks of psychiatric disorders associated with sex chromosome aneuploidies, combined with low rates of clinical diagnosis of sex chromosome aneuploidies, compromise the adequate provision of necessary health care and counselling to affected individuals and their families, which might be helped by increased application of genetic testing in clinical settings. FUNDING: Lundbeck Foundation and National Institutes of Health.
Published: 2023

7. Genetic liability estimated from large-scale family data improves genetic prediction, risk score profiling, and gene mapping for major depression

Author: Dybdahl Krebs, Morten, Georgii Hellberg, Kajsa-Lotta, Lundberg, Mischa, Appadurai, Vivek, Ohlsson, Henrik, Pedersen, Emil, Steinbach, Jette, Matthews, Jamie, Border, Richard, LaBianca, Sonja, Calle, Xabier, Meijsen, Joeri J., Ingason, Andrés, Buil, Alfonso, Vilhjálmsson, Bjarni J., Flint, Jonathan, Bacanu, Silviu-Alin, Cai, Na, Dahl, Andy, Zaitlen, Noah, Werge, Thomas, Kendler, Kenneth S., and Schork, Andrew J.
Published: 2024
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8. Metabolic signature of the pathogenic 22q11.2 deletion identifies carriers and provides insight into systemic dysregulation

Author: Courraud, Julie, Russo, Francesco, Themudo, Gonçalo Espregueira, Laursen, Susan Svane, Ingason, Andrés, Hougaard, David M., Cohen, Arieh S., Werge, Thomas, and Ernst, Madeleine
Published: 2023
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9. Multi-PGS enhances polygenic prediction by combining 937 polygenic scores

Author: Albiñana, Clara, Zhu, Zhihong, Schork, Andrew J., Ingason, Andrés, Aschard, Hugues, Brikell, Isabell, Bulik, Cynthia M., Petersen, Liselotte V., Agerbo, Esben, Grove, Jakob, Nordentoft, Merete, Hougaard, David M., Werge, Thomas, Børglum, Anders D., Mortensen, Preben Bo, McGrath, John J., Neale, Benjamin M., Privé, Florian, and Vilhjálmsson, Bjarni J.
Published: 2023
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10. Accuracy of haplotype estimation and whole genome imputation affects complex trait analyses in complex biobanks

Author: Appadurai, Vivek, Bybjerg-Grauholm, Jonas, Krebs, Morten Dybdahl, Rosengren, Anders, Buil, Alfonso, Ingason, Andrés, Mors, Ole, Børglum, Anders D., Hougaard, David M., Nordentoft, Merete, Mortensen, Preben B., Delaneau, Olivier, Werge, Thomas, and Schork, Andrew J.
Published: 2023
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11. DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals

Author: Banasik, Karina, Møller, Peter L., Techlo, Tanya R., Holm, Peter C., Walters, G. Bragi, Ingason, Andrés, Rosengren, Anders, Rohde, Palle D., Kogelman, Lisette J. A., Westergaard, David, Siggaard, Troels, Chmura, Piotr J., Chalmer, Mona A., Magnússon, Ólafur Þ., Þórisson, Guðmundur Á., Stefánsson, Hreinn, Guðbjartsson, Daníel F., Stefánsson, Kári, Olesen, Jes, Winther, Simon, Bøttcher, Morten, Brunak, Søren, Werge, Thomas, Nyegaard, Mette, and Hansen, Thomas F.
Published: 2023
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12. A comprehensive map of genetic relationships among diagnostic categories based on 48.6 million relative pairs from the Danish genealogy

Author: Athanasiadis, Georgios, Meijsen, Joeri J, Helenius, Dorte, Schork, Andrew J, Ingason, Andrés, Thompson, Wesley K, Geschwind, Daniel H, Werge, Thomas, and Buil, Alfonso
Subjects: Genetics, Good Health and Well Being, Denmark, Genetic Diseases, Inborn, Genetic Predisposition to Disease, Health Services Research, Humans, Mental Disorders, heritability, genetic correlation, human disease, register data
Abstract: For more than half a century, Denmark has maintained population-wide demographic, health care, and socioeconomic registers that provide detailed information on the interaction between all residents and the extensive national social services system. We leverage this resource to reconstruct the genealogy of the entire nation based on all individuals legally residing in Denmark since 1968. We cross-reference 6,691,426 individuals with nationwide health care registers to estimate heritability and genetic correlations of 10 broad diagnostic categories involving all major organs and systems. Heritability estimates for mental disorders were consistently the highest across demographic cohorts (average h2 = 0.406, 95% CI = [0.403, 0.408]), whereas estimates for cancers were the lowest (average h2 = 0.130, 95% CI = [0.125, 0.134]). The average genetic correlation of each of the 10 diagnostic categories with the other nine was highest for gastrointestinal conditions (average rg = 0.567, 95% CI = [0.566, 0.567]) and lowest for urogenital conditions (average rg = 0.386, 95% CI = [0.385, 0.388]). Mental, pulmonary, gastrointestinal, and neurological conditions had similar genetic correlation profiles.
Published: 2022

13. Shared genetic basis between genetic generalized epilepsy and background electroencephalographic oscillations

Author: Stevelink, Remi, Luykx, Jurjen J, Lin, Bochao D, Leu, Costin, Lal, Dennis, Smith, Alexander W, Schijven, Dick, Carpay, Johannes A, Rademaker, Koen, Baldez, Roiza A Rodrigues, Devinsky, Orrin, Braun, Kees PJ, Jansen, Floor E, Smit, Dirk JA, Koeleman, Bobby PC, Abou‐Khalil, Bassel, Auce, Pauls, Avbersek, Andreja, Bahlo, Melanie, Balding, David J, Bast, Thomas, Baum, Larry, Becker, Albert J, Becker, Felicitas, Berghuis, Bianca, Berkovic, Samuel F, Boysen, Katja E, Bradfield, Jonathan P, Brody, Lawrence C, Buono, Russell J, Campbell, Ellen, Cascino, Gregory D, Catarino, Claudia B, Cavalleri, Gianpiero L, Cherny, Stacey S, Chinthapalli, Krishna, Coffey, Alison J, Compston, Alastair, Coppola, Antonietta, Cossette, Patrick, Craig, John J, de Haan, Gerrit‐Jan, De Jonghe, Peter, de Kovel, Carolien GF, Delanty, Norman, Depondt, Chantal, Dlugos, Dennis J, Doherty, Colin P, Elger, Christian E, Eriksson, Johan G, Ferraro, Thomas N, Feucht, Martha, Francis, Ben, Franke, Andre, French, Jacqueline A, Freytag, Saskia, Gaus, Verena, Geller, Eric B, Gieger, Christian, Glauser, Tracy, Glynn, Simon, Goldstein, David B, Gui, Hongsheng, Guo, Youling, Haas, Kevin F, Hakonarson, Hakon, Hallmann, Kerstin, Haut, Sheryl, Heinzen, Erin L, Helbig, Ingo, Hengsbach, Christian, Hjalgrim, Helle, Iacomino, Michele, Ingason, Andrés, Jamnadas‐Khoda, Jennifer, Johnson, Michael R, Kälviäinen, Reetta, Kantanen, Anne‐Mari, Kasperavičiūte, Dalia, Trenite, Dorothee Kasteleijn‐Nolst, Kirsch, Heidi E, Knowlton, Robert C, Krause, Roland, Krenn, Martin, Kunz, Wolfram S, Kuzniecky, Ruben, Kwan, Patrick, Lau, Yu‐Lung, Lehesjoki, Anna‐Elina, Lerche, Holger, Lieb, Wolfgang, Lindhout, Dick, Lo, Warren D, Lopes‐Cendes, Iscia, Lowenstein, Daniel H, Malovini, Alberto, Marson, Anthony G, Mayer, Thomas, McCormack, Mark, and Mills, James L
Subjects: Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Genetics, Brain Disorders, Clinical Research, Human Genome, Neurodegenerative, Epilepsy, 2.1 Biological and endogenous factors, Aetiology, Neurological, Adult, Algorithms, Beta Rhythm, Cohort Studies, Databases, Factual, Electroencephalography, Epilepsy, Generalized, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Mendelian Randomization Analysis, Risk Assessment, Theta Rhythm, beta power, EEG, generalized epilepsy, GGE, oscillations, PRS, International League Against Epilepsy Consortium on Complex Epilepsies, Epi25 Collaborative, Neurology & Neurosurgery, Clinical sciences
Abstract: ObjectiveParoxysmal epileptiform abnormalities on electroencephalography (EEG) are the hallmark of epilepsies, but it is uncertain to what extent epilepsy and background EEG oscillations share neurobiological underpinnings. Here, we aimed to assess the genetic correlation between epilepsy and background EEG oscillations.MethodsConfounding factors, including the heterogeneous etiology of epilepsies and medication effects, hamper studies on background brain activity in people with epilepsy. To overcome this limitation, we compared genetic data from a genome-wide association study (GWAS) on epilepsy (n = 12 803 people with epilepsy and 24 218 controls) with that from a GWAS on background EEG (n = 8425 subjects without epilepsy), in which background EEG oscillation power was quantified in four different frequency bands: alpha, beta, delta, and theta. We replicated our findings in an independent epilepsy replication dataset (n = 4851 people with epilepsy and 20 428 controls). To assess the genetic overlap between these phenotypes, we performed genetic correlation analyses using linkage disequilibrium score regression, polygenic risk scores, and Mendelian randomization analyses.ResultsOur analyses show strong genetic correlations of genetic generalized epilepsy (GGE) with background EEG oscillations, primarily in the beta frequency band. Furthermore, we show that subjects with higher beta and theta polygenic risk scores have a significantly higher risk of having generalized epilepsy. Mendelian randomization analyses suggest a causal effect of GGE genetic liability on beta oscillations.SignificanceOur results point to shared biological mechanisms underlying background EEG oscillations and the susceptibility for GGE, opening avenues to investigate the clinical utility of background EEG oscillations in the diagnostic workup of epilepsy.
Published: 2021

14. Publisher Correction: Population genomics of post-glacial western Eurasia

Author: Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C., Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, de Barros Damgaard, Peter, Vang Petersen, Peter, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Published: 2024
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15. Population genomics of the Viking world

Author: Margaryan, Ashot, Lawson, Daniel J, Sikora, Martin, Racimo, Fernando, Rasmussen, Simon, Moltke, Ida, Cassidy, Lara M, Jørsboe, Emil, Ingason, Andrés, Pedersen, Mikkel W, Korneliussen, Thorfinn, Wilhelmson, Helene, Buś, Magdalena M, de Barros Damgaard, Peter, Martiniano, Rui, Renaud, Gabriel, Bhérer, Claude, Moreno-Mayar, J Víctor, Fotakis, Anna K, Allen, Marie, Allmäe, Raili, Molak, Martyna, Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, Alexandra, Fox, Allison, Albrechtsen, Anders, Schütz, Berit, Skar, Birgitte, Arcini, Caroline, Falys, Ceri, Jonson, Charlotte Hedenstierna, Błaszczyk, Dariusz, Pezhemsky, Denis, Turner-Walker, Gordon, Gestsdóttir, Hildur, Lundstrøm, Inge, Gustin, Ingrid, Mainland, Ingrid, Potekhina, Inna, Muntoni, Italo M, Cheng, Jade, Stenderup, Jesper, Ma, Jilong, Gibson, Julie, Peets, Jüri, Gustafsson, Jörgen, Iversen, Katrine H, Simpson, Linzi, Strand, Lisa, Loe, Louise, Sikora, Maeve, Florek, Marek, Vretemark, Maria, Redknap, Mark, Bajka, Monika, Pushkina, Tamara, Søvsø, Morten, Grigoreva, Natalia, Christensen, Tom, Kastholm, Ole, Uldum, Otto, Favia, Pasquale, Holck, Per, Sten, Sabine, Arge, Símun V, Ellingvåg, Sturla, Moiseyev, Vayacheslav, Bogdanowicz, Wiesław, Magnusson, Yvonne, Orlando, Ludovic, Pentz, Peter, Jessen, Mads Dengsø, Pedersen, Anne, Collard, Mark, Bradley, Daniel G, Jørkov, Marie Louise, Arneborg, Jette, Lynnerup, Niels, Price, Neil, Gilbert, M Thomas P, Allentoft, Morten E, Bill, Jan, Sindbæk, Søren M, Hedeager, Lotte, Kristiansen, Kristian, Nielsen, Rasmus, Werge, Thomas, and Willerslev, Eske
Subjects: Biological Sciences, Genetics, History, Heritage and Archaeology, Archaeology, Historical Studies, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Alleles, Datasets as Topic, England, Evolution, Molecular, Gene Flow, Genetics, Population, Genome, Human, Genomics, Greenland, History, Medieval, Human Migration, Humans, Immunity, Ireland, Lactase, Male, Scandinavian and Nordic Countries, Selection, Genetic, Spatio-Temporal Analysis, Young Adult, General Science & Technology
Abstract: The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
Published: 2020

16. Human Disease Variation in the Light of Population Genomics.

Author: Prohaska, Ana, Racimo, Fernando, Schork, Andrew J, Sikora, Martin, Stern, Aaron J, Ilardo, Melissa, Allentoft, Morten Erik, Folkersen, Lasse, Buil, Alfonso, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn, Geschwind, Daniel, Ingason, Andrés, Werge, Thomas, Nielsen, Rasmus, and Willerslev, Eske
Subjects: Humans, Genetic Diseases, Inborn, Genetics, Population, Genomics, Adaptation, Physiological, Evolution, Molecular, Phylogeny, Gene Frequency, Genetic Drift, Alleles, Models, Genetic, Genetic Variation, Metagenomics, Human Genome, Genetics, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract: Identifying the causes of similarities and differences in genetic disease prevalence among humans is central to understanding disease etiology. While present-day humans are not strongly differentiated, vast amounts of genomic data now make it possible to study subtle patterns of genetic variation. This allows us to trace our genomic history thousands of years into the past and its implications for the distribution of disease-associated variants today. Genomic analyses have shown that demographic processes shaped the distribution and frequency of disease-associated variants over time. Furthermore, local adaptation to new environmental conditions-including pathogens-has generated strong patterns of differentiation at particular loci. Researchers are also beginning to uncover the genetic architecture of complex diseases, affected by many variants of small effect. The field of population genomics thus holds great potential for providing further insights into the evolution of human disease.
Published: 2019

17. Steppe Ancestry in western Eurasia and the spread of the Germanic Languages

Author: McColl, Hugh, primary, Kroonen, Guus, additional, Moreno-Mayar, J. Víctor, additional, Valeur Seersholm, Frederik, additional, Scorrano, Gabriele, additional, Pinotti, Thomaz, additional, Vimala, Tharsika, additional, Sindbæk, Søren M., additional, Ethelberg, Per, additional, Fyfe, Ralph, additional, Gaillard, Marie-José, additional, Larsen, Hanne M. Ellegård, additional, Mortensen, Morten Fischer, additional, Demeter, Fabrice, additional, Jørkov, Marie Louise S., additional, Bergerbrant, Sophie, additional, Damgaard, Peter de Barros, additional, Allentoft, Morten E., additional, Vinner, Lasse, additional, Gaunitz, Charleen, additional, Ramsøe, Abigail, additional, Altinkaya, Isin, additional, Amund Henriksen, Rasmus, additional, Irving-Pease, Evan K., additional, Sabatini, Serena, additional, Fischer, Anders, additional, Barrie, William, additional, Ingason, Andrés, additional, Rosengren, Anders, additional, Vaughn, Andrew, additional, Cao, Jialu, additional, Staring, Jacqueline, additional, Stenderup, Jesper, additional, Yediay, Fulya Eylem, additional, Ahlström, Torbjörn, additional, Albris, Sofie Laurine, additional, Atabiev, Biyaslan, additional, Bangsgaard, Pernille, additional, Belcastro, Maria Giovanna, additional, Card, Nick, additional, Charlier, Philippe, additional, Chernykh, Elizaveta, additional, Christiansen, Torben Trier, additional, Coppa, Alfredo, additional, De Coster, Maura, additional, Denham, Sean Dexter, additional, Desenne, Sophie, additional, Downes, Jane, additional, Frei, Karin Margarita, additional, Gábor, Olivér, additional, Gårdsvoll, Johan Zakarias, additional, Glørstad, Zanette Tsigaridas, additional, Hansen, Jesper, additional, Heeren, Stijn, additional, Henriksen, Merete, additional, Heyd, Volker, additional, Høj, Mette, additional, Holst, Mads Kähler, additional, Jankauskas, Rimantas, additional, Janson, Henrik, additional, Jessen, Mads Dengsø, additional, Johannsen, Jens Winther, additional, Johansen, Torkel, additional, Kastholm, Ole Thirup, additional, Kern, Anton, additional, Khaskhanov, Ruslan, additional, Kjær, Katrine, additional, Kolosov, Vladimir, additional, Kootker, Lisette M., additional, Larsen, Anne Christine, additional, Lejars, Thierry, additional, Løvschal, Mette, additional, Lynnerup, Niels, additional, Magnusson, Yvonne, additional, Mannermaa, Kristiina, additional, Masyakin, Vyacheslav, additional, Melheim, Anne Lene, additional, Merkyte, Inga, additional, Moiseyev, Vyacheslav, additional, Møller, Stig Bergmann, additional, Molnár, Erika, additional, Mortensen, Nadja, additional, Murphy, Eileen, additional, Nielsen, Bjarne Henning, additional, Pany-Kucera, Doris, additional, Paulsson, Bettina Schulz, additional, Ponce de León, Marcia S, additional, Reiersen, Håkon, additional, Reinhard, Walter, additional, Sajantila, Antti, additional, Skar, Birgitte, additional, Slavchev, Vladimir, additional, Smrčka, Václav, additional, Sørensen, Lasse, additional, Tiefengraber, Georg, additional, Uldum, Otto Christian, additional, Vega, Jorge, additional, Vitali, Daniele, additional, Voloshinov, Alexey, additional, Wåhlin, Sidsel, additional, Wendling, Holger, additional, Wessman, Anna, additional, Wilhelmson, Helene, additional, Wiltschke, Karin, additional, Zilhao, João, additional, Zollikofer, Christoph PE, additional, Sand Korneliussen, Thorfinn, additional, Chaume, Bruno, additional, Demoule, Jean-Paul, additional, Werge, Thomas, additional, Olsen, Line, additional, Nielsen, Rasmus, additional, Hedeager, Lotte, additional, Kristiansen, Kristian, additional, Sikora, Martin, additional, and Willerslev, Eske, additional
Published: 2024
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18. Publisher Correction: Population genomics of post-glacial western Eurasia (Nature, (2024), 625, 7994, (301-311), 10.1038/s41586-023-06865-0)

Author: Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila, Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina, Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson,Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delanea, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila, Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina, Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson,Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delanea, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: In the version of this article initially published, there were errors in the second affiliations for Levon Yepiskoposyan (Russian-Armenian University, Yerevan, Armenia) and Sergey Vasilyev (Center for Egyptological Studies, Russian Academy of Sciences, Moscow, Russian Federation), and in the first affiliation for Ruben Badalyan (Institute of Archaeology and Ethnography, National Academy of Sciences, Yerevan, Armenia); the affiliations are amended in the HTML and PDF versions of the article.
Published: 2024

19. Population genomics of post-glacial western Eurasia

Author: Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C., Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, de Barros Damgaard, Peter, Vang Petersen, Peter, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C., Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, de Barros Damgaard, Peter, Vang Petersen, Peter, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Published: 2024

20. 100 ancient genomes show repeated population turnovers in Neolithic Denmark

Author: Allentoft, Morten E., Sikora, Martin, Fischer, Anders, Sjögren, Karl Göran, Ingason, Andrés, Macleod, Ruairidh, Rosengren, Anders, Schulz Paulsson, Bettina, Jørkov, Marie Louise Schjellerup, Novosolov, Maria, Stenderup, Jesper, Price, T. Douglas, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Sørensen, Lasse, Nielsen, Poul Otto, Rasmussen, Peter, Jensen, Theis Zetner Trolle, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Barrie, William, Pearson, Alice, Sousa da Mota, Bárbara, Demeter, Fabrice, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Johannsen, Niels Nørkjær, Ramsøe, Abigail Daisy, Schork, Andrew Joseph, Ruter, Anthony, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, Brinch Petersen, Erik, Kannegaard, Esben, Hansen, Jesper, Buck Pedersen, Kristoffer, Pedersen, Lisbeth, Klassen, Lutz, Meldgaard, Morten, Johansen, Morten, Uldum, Otto Christian, Lotz, Per, Lysdahl, Per, Bangsgaard, Pernille, Petersen, Peter Vang, Maring, Rikke, Iversen, Rune, Wåhlin, Sidsel, Anker Sørensen, Søren, Andersen, Søren H., Jørgensen, Thomas, Lynnerup, Niels, Lawson, Daniel J., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Kjær, Kurt H., Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten E., Sikora, Martin, Fischer, Anders, Sjögren, Karl Göran, Ingason, Andrés, Macleod, Ruairidh, Rosengren, Anders, Schulz Paulsson, Bettina, Jørkov, Marie Louise Schjellerup, Novosolov, Maria, Stenderup, Jesper, Price, T. Douglas, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Sørensen, Lasse, Nielsen, Poul Otto, Rasmussen, Peter, Jensen, Theis Zetner Trolle, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Barrie, William, Pearson, Alice, Sousa da Mota, Bárbara, Demeter, Fabrice, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Johannsen, Niels Nørkjær, Ramsøe, Abigail Daisy, Schork, Andrew Joseph, Ruter, Anthony, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, Brinch Petersen, Erik, Kannegaard, Esben, Hansen, Jesper, Buck Pedersen, Kristoffer, Pedersen, Lisbeth, Klassen, Lutz, Meldgaard, Morten, Johansen, Morten, Uldum, Otto Christian, Lotz, Per, Lysdahl, Per, Bangsgaard, Pernille, Petersen, Peter Vang, Maring, Rikke, Iversen, Rune, Wåhlin, Sidsel, Anker Sørensen, Søren, Andersen, Søren H., Jørgensen, Thomas, Lynnerup, Niels, Lawson, Daniel J., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Kjær, Kurt H., Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Kristiansen, Kristian, and Willerslev, Eske
Abstract: Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1–4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5–7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
Published: 2024

21. Population genomics of post-glacial western Eurasia

Author: Lundbeck Foundation, Novo Nordisk Foundation, Wellcome Trust, Carlsberg Foundation, Danish National Research Foundation, University of Copenhagen, Ferring Pharmaceuticals, Swedish Foundation for Humanities and Social Sciences, Villum Fonden, Independent Research Fund Denmark, Hanne and Torkel Weis-Fogh Fund, Wellcome, Swiss National Science Foundation, European Research Council, Aarhus University Research Foundation, Ministry of Education and Science (Kazakhstan), Ministerio de Economía y Competitividad (España), Ministero dell'Istruzione, dell'Università e della Ricerca, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat Valenciana, Nomis Foundation, European Commission, Ministry of Science and Higher Education of the Russian Federation, Ministry of Education, Science, Culture and Sports of the Republic of Armenia, National Institute of General Medical Sciences (US), Sikora, Martin [0000-0003-2818-8319], Lalueza-Fox, Carles [0000-0002-1730-5914], Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Mota, Bárbara Sousa da, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise S., Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Trolle Jensen, Theis Zetner, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana María, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martínez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar García, Domingo Carlos, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Barros Damgaard, Peter de, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Lundbeck Foundation, Novo Nordisk Foundation, Wellcome Trust, Carlsberg Foundation, Danish National Research Foundation, University of Copenhagen, Ferring Pharmaceuticals, Swedish Foundation for Humanities and Social Sciences, Villum Fonden, Independent Research Fund Denmark, Hanne and Torkel Weis-Fogh Fund, Wellcome, Swiss National Science Foundation, European Research Council, Aarhus University Research Foundation, Ministry of Education and Science (Kazakhstan), Ministerio de Economía y Competitividad (España), Ministero dell'Istruzione, dell'Università e della Ricerca, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat Valenciana, Nomis Foundation, European Commission, Ministry of Science and Higher Education of the Russian Federation, Ministry of Education, Science, Culture and Sports of the Republic of Armenia, National Institute of General Medical Sciences (US), Sikora, Martin [0000-0003-2818-8319], Lalueza-Fox, Carles [0000-0002-1730-5914], Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Mota, Bárbara Sousa da, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise S., Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Trolle Jensen, Theis Zetner, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana María, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martínez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar García, Domingo Carlos, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Barros Damgaard, Peter de, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: Western Eurasia witnessed several large-scale human migrations during the Holocene1,2,3,4,5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Published: 2024

22. Population genomics of post-glacial western Eurasia

Author: Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila, Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina, Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson,Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delanea, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila, Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina, Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson,Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delanea, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods— from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Published: 2024

23. Vittrup Man–The life-history of a genetic foreigner in Neolithic Denmark

Author: Fischer, Anders, Sjögren, Karl-Göran, Jensen, Theis Zetner Trolle, Jørkov, Marie Louise, Lysdahl, Per, Vimala, Tharsika, Refoyo-martínez, Alba, Scorrano, Gabriele, Price, T. Douglas, Gröcke, Darren R., Gotfredsen, Anne Birgitte, Sørensen, Lasse, Alexandersen, Verner, Wåhlin, Sidsel, Stenderup, Jesper, Bennike, Ole, Ingason, Andrés, Iversen, Rune, Sikora, Martin, Racimo, Fernando, Willerslev, Eske, Allentoft, Morten E., Kristiansen, Kristian, Fischer, Anders, Sjögren, Karl-Göran, Jensen, Theis Zetner Trolle, Jørkov, Marie Louise, Lysdahl, Per, Vimala, Tharsika, Refoyo-martínez, Alba, Scorrano, Gabriele, Price, T. Douglas, Gröcke, Darren R., Gotfredsen, Anne Birgitte, Sørensen, Lasse, Alexandersen, Verner, Wåhlin, Sidsel, Stenderup, Jesper, Bennike, Ole, Ingason, Andrés, Iversen, Rune, Sikora, Martin, Racimo, Fernando, Willerslev, Eske, Allentoft, Morten E., and Kristiansen, Kristian
Abstract: The lethally maltreated body of Vittrup Man was deposited in a Danish bog, probably as part of a ritualised sacrifice. It happened between c. 3300 and 3100 cal years BC, i.e., during the period of the local farming-based Funnel Beaker Culture. In terms of skull morphological features, he differs from the majority of the contemporaneous farmers found in Denmark, and associates with hunter-gatherers, who inhabited Scandinavia during the previous millennia. His skeletal remains were selected for transdisciplinary analysis to reveal his life-history in terms of a population historical perspective. We report the combined results of an integrated set of genetic, isotopic, physical anthropological and archaeological analytical approaches. Strontium signature suggests a foreign birthplace that could be in Norway or Sweden. In addition, enamel oxygen isotope values indicate that as a child he lived in a colder climate, i.e., to the north of the regions inhabited by farmers. Genomic data in fact demonstrates that he is closely related to Mesolithic humans known from Norway and Sweden. Moreover, dietary stable isotope analyses on enamel and bone collagen demonstrate a fisher-hunter way of life in his childhood and a diet typical of farmers later on. Such a variable life-history is also reflected by proteomic analysis of hardened organic deposits on his teeth, indicating the consumption of forager food (seal, whale and marine fish) as well as farmer food (sheep/goat). From a dietary isotopic transect of one of his teeth it is shown that his transfer between societies of foragers and farmers took place near to the end of his teenage years.
Published: 2024

24. Vittrup Man–The life-history of a genetic foreigner in Neolithic Denmark

Author: Fischer, Anders, primary, Sjögren, Karl-Göran, additional, Jensen, Theis Zetner Trolle, additional, Jørkov, Marie Louise, additional, Lysdahl, Per, additional, Vimala, Tharsika, additional, Refoyo-Martínez, Alba, additional, Scorrano, Gabriele, additional, Price, T. Douglas, additional, Gröcke, Darren R., additional, Gotfredsen, Anne Birgitte, additional, Sørensen, Lasse, additional, Alexandersen, Verner, additional, Wåhlin, Sidsel, additional, Stenderup, Jesper, additional, Bennike, Ole, additional, Ingason, Andrés, additional, Iversen, Rune, additional, Sikora, Martin, additional, Racimo, Fernando, additional, Willerslev, Eske, additional, Allentoft, Morten E., additional, and Kristiansen, Kristian, additional
Published: 2024
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25. New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis

Author: Lee, S Hong, Byrne, Enda M, Hultman, Christina M, Kähler, Anna, Vinkhuyzen, Anna AE, Ripke, Stephan, Andreassen, Ole A, Frisell, Thomas, Gusev, Alexander, Hu, Xinli, Karlsson, Robert, Mantzioris, Vasilis X, McGrath, John J, Mehta, Divya, Stahl, Eli A, Zhao, Qiongyi, Kendler, Kenneth S, Sullivan, Patrick F, Price, Alkes L, O’Donovan, Michael, Okada, Yukinori, Mowry, Bryan J, Raychaudhuri, Soumya, Wray, Naomi R, Byerley, William, Cahn, Wiepke, Cantor, Rita M, Cichon, Sven, Cormican, Paul, Curtis, David, Djurovic, Srdjan, Escott-Price, Valentina, Gejman, Pablo V, Georgieva, Lyudmila, Giegling, Ina, Hansen, Thomas F, Ingason, Andrés, Kim, Yunjung, Konte, Bettina, Lee, Phil H, McIntosh, Andrew, McQuillin, Andrew, Morris, Derek W, Nöthen, Markus M, O’Dushlaine, Colm, Olincy, Ann, Olsen, Line, Pato, Carlos N, Pato, Michele T, Pickard, Benjamin S, Posthuma, Danielle, Rasmussen, Henrik B, Rietschel, Marcella, Rujescu, Dan, Schulze, Thomas G, Silverman, Jeremy M, Thirumalai, Srinivasa, Werge, Thomas, Agartz, Ingrid, Amin, Farooq, Azevedo, Maria H, Bass, Nicholas, Black, Donald W, Blackwood, Douglas HR, Bruggeman, Richard, Buccola, Nancy G, Choudhury, Khalid, Cloninger, Robert C, Corvin, Aiden, Craddock, Nicholas, Daly, Mark J, Datta, Susmita, Donohoe, Gary J, Duan, Jubao, Dudbridge, Frank, Fanous, Ayman, Freedman, Robert, Freimer, Nelson B, Friedl, Marion, Gill, Michael, Gurling, Hugh, De Haan, Lieuwe, Hamshere, Marian L, Hartmann, Annette M, Holmans, Peter A, Kahn, René S, Keller, Matthew C, Kenny, Elaine, Kirov, George K, Krabbendam, Lydia, Krasucki, Robert, Lawrence, Jacob, Lencz, Todd, Levinson, Douglas F, Lieberman, Jeffrey A, Lin, Dan-Yu, Linszen, Don H, Magnusson, Patrik KE, Maier, Wolfgang, and Malhotra, Anil K
Subjects: Epidemiology, Health Sciences, Human Genome, Mental Health, Brain Disorders, Autoimmune Disease, Schizophrenia, Clinical Research, Arthritis, Serious Mental Illness, Genetics, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Mental health, Adolescent, Adult, Arthritis, Rheumatoid, Cohort Studies, Cross-Sectional Studies, Female, Gene-Environment Interaction, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Young Adult, Schizophrenia Working Group of the Psychiatric Genomics Consortium and Rheumatoid Arthritis Consortium International, Schizophrenia Working Group of the Psychiatric Genomics Consortium Authors, Schizophrenia Working Group of the Psychiatric Genomics Consortium Collaborators, Rheumatoid Arthritis Consortium International Authors, Rheumatoid Arthritis Consortium International Collaborators, Statistics, Public Health and Health Services, Public health
Abstract: BackgroundA long-standing epidemiological puzzle is the reduced rate of rheumatoid arthritis (RA) in those with schizophrenia (SZ) and vice versa. Traditional epidemiological approaches to determine if this negative association is underpinned by genetic factors would test for reduced rates of one disorder in relatives of the other, but sufficiently powered data sets are difficult to achieve. The genomics era presents an alternative paradigm for investigating the genetic relationship between two uncommon disorders.MethodsWe use genome-wide common single nucleotide polymorphism (SNP) data from independently collected SZ and RA case-control cohorts to estimate the SNP correlation between the disorders. We test a genotype X environment (GxE) hypothesis for SZ with environment defined as winter- vs summer-born.ResultsWe estimate a small but significant negative SNP-genetic correlation between SZ and RA (-0.046, s.e. 0.026, P = 0.036). The negative correlation was stronger for the SNP set attributed to coding or regulatory regions (-0.174, s.e. 0.071, P = 0.0075). Our analyses led us to hypothesize a gene-environment interaction for SZ in the form of immune challenge. We used month of birth as a proxy for environmental immune challenge and estimated the genetic correlation between winter-born and non-winter born SZ to be significantly less than 1 for coding/regulatory region SNPs (0.56, s.e. 0.14, P = 0.00090).ConclusionsOur results are consistent with epidemiological observations of a negative relationship between SZ and RA reflecting, at least in part, genetic factors. Results of the month of birth analysis are consistent with pleiotropic effects of genetic variants dependent on environmental context.
Published: 2015

26. DanMAC5:a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals

Author: Banasik, Karina, Møller, Peter L., Techlo, Tanya R., Holm, Peter C., Walters, G. Bragi, Ingason, Andrés, Rosengren, Anders, Rohde, Palle D., Kogelman, Lisette J.A., Westergaard, David, Siggaard, Troels, Chmura, Piotr J., Chalmer, Mona A., Magnússon, Ólafur, Þórisson, Guðmundur, Stefánsson, Hreinn, Guðbjartsson, Daníel F., Stefánsson, Kári, Olesen, Jes, Winther, Simon, Bøttcher, Morten, Brunak, Søren, Werge, Thomas, Nyegaard, Mette, Hansen, Thomas F., Banasik, Karina, Møller, Peter L., Techlo, Tanya R., Holm, Peter C., Walters, G. Bragi, Ingason, Andrés, Rosengren, Anders, Rohde, Palle D., Kogelman, Lisette J.A., Westergaard, David, Siggaard, Troels, Chmura, Piotr J., Chalmer, Mona A., Magnússon, Ólafur, Þórisson, Guðmundur, Stefánsson, Hreinn, Guðbjartsson, Daníel F., Stefánsson, Kári, Olesen, Jes, Winther, Simon, Bøttcher, Morten, Brunak, Søren, Werge, Thomas, Nyegaard, Mette, and Hansen, Thomas F.
Abstract: Objectives Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8,671 (5,418 females) individuals from the Danish population. The data resource is based on WGS data from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders. To enable the sharing of information on sequence variation in Danish individuals, we created summarized statistics on allele counts from anonymized data and made them available through the European Genome-phenome Archive (EGA, https:// ident ifiers. org/ ega. datas et: EGAD0 00010 09756) and in a dedicated browser, DanMAC5 (available at www. danma c5. dk). The summary level data and the DanMAC5 browser provide insight into the allelic spectrum of sequence variants segregating in the Danish population, which is important in variant interpretation. Data description Three WGS datasets with an average coverage of 30x were processed independently using the same quality control pipeline. Subsequently, we summarized, filtered, and merged allele counts to create a high-quality summary level dataset of sequence variants., Objectives: Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8,671 (5,418 females) individuals from the Danish population. The data resource is based on WGS data from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders. To enable the sharing of information on sequence variation in Danish individuals, we created summarized statistics on allele counts from anonymized data and made them available through the European Genome-phenome Archive (EGA, https://identifiers.org/ega.dataset:EGAD00001009756) and in a dedicated browser, DanMAC5 (available at www.danmac5.dk). The summary level data and the DanMAC5 browser provide insight into the allelic spectrum of sequence variants segregating in the Danish population, which is important in variant interpretation. Data description: Three WGS datasets with an average coverage of 30x were processed independently using the same quality control pipeline. Subsequently, we summarized, filtered, and merged allele counts to create a high-quality summary level dataset of sequence variants.
Published: 2023

27. Associations of psychiatric disorders with sex chromosome aneuploidies in the Danish iPSYCH2015 dataset:a case-cohort study

Author: Sánchez, Xabier Calle, Montalbano, Simone, Vaez, Morteza, Krebs, Morten Dybdahl, Byberg-Grauholm, Jonas, Mortensen, Preben B., Børglum, Anders D., Hougaard, David M., Nordentoft, Merete, Geschwind, Daniel H., Buil, Alfonso, Schork, Andrew J., Thompson, Wesley K., Raznahan, Armin, Helenius, Dorte, Werge, Thomas, Ingason, Andrés, Sánchez, Xabier Calle, Montalbano, Simone, Vaez, Morteza, Krebs, Morten Dybdahl, Byberg-Grauholm, Jonas, Mortensen, Preben B., Børglum, Anders D., Hougaard, David M., Nordentoft, Merete, Geschwind, Daniel H., Buil, Alfonso, Schork, Andrew J., Thompson, Wesley K., Raznahan, Armin, Helenius, Dorte, Werge, Thomas, and Ingason, Andrés
Abstract: Background: Increased prevalence of mental illness has been reported in clinical studies of sex chromosome aneuploidies, but accurate population-based estimates of the prevalence and clinical detection rate of sex chromosome aneuploidies and the associated risks of psychiatric disorders are needed. In this study, we provide such estimates, valid for children and young adults of the contemporary Danish population. Methods: We used the iPSYCH2015 case-cohort dataset, which is based on a source population of single-born individuals born in Denmark between May 1, 1981, and Dec 31, 2008. The case sample comprises all individuals from the source population with a diagnosis of any index psychiatric disorder (schizophrenia spectrum disorder, bipolar disorder, major depressive disorder, autism spectrum disorder, or ADHD) by the end of follow-up (Dec 31, 2015), registered in the hospital-based Danish Psychiatric Central Research Register. The cohort consists of individuals randomly selected from the source population, and overlaps with the case sample. Biobanked blood samples for individuals in the case and cohort samples underwent genotyping and quality-control filtering, after which we analysed microarray data to detect sex chromosome aneuploidy karyotypes (45,X, 47,XXX, 47,XXY, and 47,XYY). We estimated the population-valid prevalence of these karyotypes from the cohort sample. Weighted Cox proportional hazards models were used to estimate the risks of each index psychiatric disorder associated with each sex chromosome aneuploidy karyotype, by use of date of first hospitalisation with the index disorder in the respective case group and the cohort as outcome. The clinical detection rate was determined by comparing records of clinical diagnoses of genetic conditions from the Danish National Patient Register with sex chromosome aneuploidy karyotype determined by our study. Findings: The assessed sample comprised 119 481 individuals (78 726 in the case sample and 43 326 in
Published: 2023

28. Author Correction: Population genomics of the Viking world

Author: Margaryan, Ashot, Lawson, Daniel J., Sikora, Martin, Racimo, Fernando, Rasmussen, Simon, Moltke, Ida, Cassidy, Lara M., Jørsboe, Emil, Ingason, Andrés, Pedersen, Mikkel W., Korneliussen, Thorfinn, Wilhelmson, Helene, Buś, Magdalena M., de Barros Damgaard, Peter, Martiniano, Rui, Renaud, Gabriel, Bhérer, Claude, Moreno-Mayar, J. Víctor, Fotakis, Anna K., Allen, Marie, Allmäe, Raili, Molak, Martyna, Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, Alexandra, Fox, Allison, Albrechtsen, Anders, Schütz, Berit, Skar, Birgitte, Arcini, Caroline, Falys, Ceri, Jonson, Charlotte Hedenstierna, Błaszczyk, Dariusz, Pezhemsky, Denis, Turner-Walker, Gordon, Gestsdóttir, Hildur, Lundstrøm, Inge, Gustin, Ingrid, Mainland, Ingrid, Potekhina, Inna, Muntoni, Italo M., Cheng, Jade, Stenderup, Jesper, Ma, Jilong, Gibson, Julie, Peets, Jüri, Gustafsson, Jörgen, Iversen, Katrine H., Simpson, Linzi, Strand, Lisa, Loe, Louise, Sikora, Maeve, Florek, Marek, Vretemark, Maria, Redknap, Mark, Bajka, Monika, Pushkina, Tamara, Søvsø, Morten, Grigoreva, Natalia, Christensen, Tom, Kastholm, Ole, Uldum, Otto, Favia, Pasquale, Holck, Per, Sten, Sabine, Arge, Símun V., Ellingvåg, Sturla, Moiseyev, Vayacheslav, Bogdanowicz, Wiesław, Magnusson, Yvonne, Orlando, Ludovic, Pentz, Peter, Jessen, Mads Dengsø, Pedersen, Anne, Collard, Mark, Bradley, Daniel G., Jørkov, Marie Louise, Arneborg, Jette, Lynnerup, Niels, Price, Neil, Gilbert, M. Thomas P., Allentoft, Morten E., Bill, Jan, Sindbæk, Søren M., Hedeager, Lotte, Kristiansen, Kristian, Nielsen, Rasmus, Werge, Thomas, and Willerslev, Eske
Published: 2021
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29. Linkage and whole genome sequencing identify a locus on 6q25–26 for formal thought disorder and implicate MEF2A regulation

Author: Thygesen, Johan Hilge, Zambach, Sine Katharina, Ingason, Andrés, Lundin, Pär, Hansen, Thomas, Bertalan, Marcelo, Rosengren, Anders, Bjerre, Ditte, Ferrero-Miliani, Laura, Rasmussen, Henrik Berg, Parnas, Josef, and Werge, Thomas
Published: 2015
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30. Two rare deletions upstream of the NRXN1 gene (2p16.3) affecting the non-coding mRNA AK127244 segregate with diverse psychopathological phenotypes in a family

Author: Duong, Linh T.T., Hoeffding, Louise K., Petersen, Kirsten B., Knudsen, Charlotte D., Thygesen, Johan H., Klitten, Laura L., Tommerup, Niels, Ingason, Andrés, and Werge, Thomas
Published: 2015
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31. Accurate and Effective Detection of Recurrent Copy Number Variants in Large SNP Genotype Datasets

Author: Montalbano, Simone, primary, Sánchez, Xabier Calle, additional, Vaez, Morteza, additional, Helenius, Dorte, additional, Werge, Thomas, additional, and Ingason, Andrés, additional
Published: 2022
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32. The Selection Landscape and Genetic Legacy of Ancient Eurasians

Author: Irving-Pease, Evan K., primary, Refoyo-Martínez, Alba, additional, Ingason, Andrés, additional, Pearson, Alice, additional, Fischer, Anders, additional, Barrie, William, additional, Sjögren, Karl-Göran, additional, Halgren, Alma S., additional, Macleod, Ruairidh, additional, Demeter, Fabrice, additional, Henriksen, Rasmus A., additional, Vimala, Tharsika, additional, McColl, Hugh, additional, Vaughn, Andrew, additional, Stern, Aaron J., additional, Speidel, Leo, additional, Scorrano, Gabriele, additional, Ramsøe, Abigail, additional, Schork, Andrew J., additional, Rosengren, Anders, additional, Zhao, Lei, additional, Kristiansen, Kristian, additional, Sudmant, Peter H., additional, Lawson, Daniel J., additional, Durbin, Richard, additional, Korneliussen, Thorfinn, additional, Werge, Thomas, additional, Allentoft, Morten E., additional, Sikora, Martin, additional, Nielsen, Rasmus, additional, Racimo, Fernando, additional, and Willerslev, Eske, additional
Published: 2022
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33. Multi-PGS enhances polygenic prediction: weighting 937 polygenic scores

Author: Albiñana, Clara, primary, Zhu, Zhihong, additional, Schork, Andrew J., additional, Ingason, Andrés, additional, Aschard, Hugues, additional, Brikell, Isabell, additional, Bulik, Cynthia M., additional, Petersen, Liselotte V., additional, Agerbo, Esben, additional, Grove, Jakob, additional, Nordentoft, Merete, additional, Hougaard, David M., additional, Werge, Thomas, additional, Børglum, Anders D., additional, Mortensen, Preben Bo, additional, McGrath, John J., additional, Neale, Benjamin M., additional, Privé, Florian, additional, and Vilhjálmsson, Bjarni J., additional
Published: 2022
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34. Genetic variation in CFH predicts phenytoin-induced maculopapular exanthema in European-descent patients

Author: McCormack, Mark, Gui, Hongsheng, Ingason, Andrés, Speed, Doug, Wright, Galen E.B., Zhang, Eunice J., Secolin, Rodrigo, Yasuda, Clarissa, Kwok, Maxwell, Wolking, Stefan, Becker, Felicitas, Rau, Sarah, Avbersek, Andreja, Heggeli, Kristin, Leu, Costin, Depondt, Chantal, Sills, Graeme J., Marson, Anthony G., Auce, Pauls, Brodie, Martin J., Francis, Ben, Johnson, Michael R., Koeleman, Bobby P.C., Striano, Pasquale, Coppola, Antonietta, Zara, Federico, Kunz, Wolfram S., Sander, Josemir W., Lerche, Holger, Klein, Karl Martin, Weckhuysen, Sarah, Krenn, Martin, Gudmundsson, Lárus J., Stefánsson, Kári, Krause, Roland, Shear, Neil, Ross, Colin J.D., Delanty, Norman, Pirmohamed, Munir, Carleton, Bruce C., Cendes, Fernando, Lopes-Cendes, Iscia, Liao, Wei-ping, OʼBrien, Terence J., Sisodiya, Sanjay M., Cherny, Stacey, Kwan, Patrick, Baum, Larry, and Cavalleri, Gianpiero L.
Published: 2018
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35. Infection Polygenic Factors Account for a Small Proportion of the Relationship Between Infections and Mental Disorders

Author: Shorter, John R., primary, Meijsen, Joeri, additional, Nudel, Ron, additional, Krebs, Morten, additional, Gådin, Jesper, additional, Mikkelsen, Dorte H., additional, Nogueira Avelar e Silva, Raquel, additional, Benros, Michael E., additional, Thompson, Wesley K., additional, Ingason, Andrés, additional, and Werge, Thomas, additional
Published: 2022
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36. Accurate and Effective Detection of Recurrent Copy Number Variants in Large SNP Genotype Datasets

Author: Montalbano, Simone, Sánchez, Xabier Calle, Vaez, Morteza, Helenius, Dorte, Werge, Thomas, Ingason, Andrés, Montalbano, Simone, Sánchez, Xabier Calle, Vaez, Morteza, Helenius, Dorte, Werge, Thomas, and Ingason, Andrés
Abstract: Structural variations, including recurrent Copy Number Variants (CNVs) at specific genomic loci, have been found to be associated with increased risk of several diseases and syndromes. CNV carrier status can be determined in large collections of samples using SNP arrays and, more recently, sequencing data. Although there is some consensus among researchers about the essential steps required in such analysis (i.e., CNV calling, filtering of putative carriers, and visual validation using intensity data plots of the genomic region), standard methodologies and processes to control the quality and consistency of the results are lacking. Here, we present a comprehensive and user-friendly protocol that we have refined from our extensive research experience in the field. We cover every aspect of the analysis, from input data curation to final results. For each step, we highlight which parameters affect the analysis the most and how different settings may lead to different results. We provide a pipeline to run the complete analysis with effective (but customizable) pre-sets. We present software that we developed to better handle and filter putative CNV carriers and perform visual inspection to validate selected candidates. Finally, we describe methods to evaluate the critical sections and actions to counterbalance potential problems. The current implementation is focused on Illumina SNP array data. All the presented software is freely available and provided in a ready-to-use docker container.
Published: 2022

37. The Selection Landscape and Genetic Legacy of Ancient Eurasians

Author: Irving-Pease, Evan, Refoyo Martínez, Alba, Ingason, Andrés, Pearson, Alice, Fischer, Anders, Barrie, William, Sjögren, Karl-Göran, Halgren, Alma S., Macleod, Ruairidh, Demeter, Fabrice, Henriksen, Rasmus Henrik Amund, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew, Stern, Aaron J., Speidel, Leo, Scorrano, Gabriele, Ramsøe, Abigail, Schork, Andrew J., Rosengren, Anders, Zhao, Lei, Kristiansen, Kristian, Sudmant, Peter H., Lawson, Daniel J., Durbin, Richard, Korneliussen, Thorfinn, Werge, Thomas, Allentoft, Morten E., Sikora, Martin, Nielsen, Rasmus, Racimo, Fernando, Willerslev, Eske, Irving-Pease, Evan, Refoyo Martínez, Alba, Ingason, Andrés, Pearson, Alice, Fischer, Anders, Barrie, William, Sjögren, Karl-Göran, Halgren, Alma S., Macleod, Ruairidh, Demeter, Fabrice, Henriksen, Rasmus Henrik Amund, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew, Stern, Aaron J., Speidel, Leo, Scorrano, Gabriele, Ramsøe, Abigail, Schork, Andrew J., Rosengren, Anders, Zhao, Lei, Kristiansen, Kristian, Sudmant, Peter H., Lawson, Daniel J., Durbin, Richard, Korneliussen, Thorfinn, Werge, Thomas, Allentoft, Morten E., Sikora, Martin, Nielsen, Rasmus, Racimo, Fernando, and Willerslev, Eske
Abstract: The Eurasian Holocene (beginning c. 12 thousand years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using an imputed dataset of >1600 complete ancient genome sequences, and new computational methods for locating selection in time and space, we reconstructed the selection landscape of the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, possibly associated with the dietary shift occurring in this period. We show that the selection on loci such as the FADS cluster, associated with fatty acid metabolism, and the lactase persistence locus, began earlier than previously thought. A substantial amount of selection is also found in the HLA region and other loci associated with immunity, possibly due to the increased exposure to pathogens during the Neolithic, which may explain the current high prevalence of auto-immune disease, such as psoriasis, due to genetic trade-offs. By using ancient populations to infer local ancestry tracks in hundreds of thousands of samples from the UK Biobank, we find strong genetic differentiation among ancient Europeans in loci associated with anthropometric traits and susceptibility to several diseases that contribute to present-day disease burden. These were previously thought to be caused by local selection, but in fact can be attributed to differential genetic contributions from various source populations that are ancestral to present-day Europeans. Thus, alleles associated with increased height seem to have increased in frequency following the Yamnaya migration into northwestern Europe around 5,000 years ago. Alleles associated with increased risk of some mood-related phenotypes are overrepresented in the farmer ancestry component entering Europe from Anatolia around 11,000 years ago, while western hunter-gathere
Published: 2022

38. Population Genomics of Stone Age Eurasia

Author: Allentoft, Morten, Sikora, Martin, Alba, Refoyo-Martínez, Evan K. Irving-Pease, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Novosolov, Maria, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus H.A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Hede, Mikkel Ulfeldt, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Theis Zetner Trolle Jensen, Johannsen, Niels Nørkjær, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Daisy Ramsøe, Abigail, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Tortosa, Joan Emili Aura, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila, Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina, Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Turin, Ruslan, Vasilyiev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merz, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten, Sikora, Martin, Alba, Refoyo-Martínez, Evan K. Irving-Pease, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Novosolov, Maria, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus H.A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Hede, Mikkel Ulfeldt, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Theis Zetner Trolle Jensen, Johannsen, Niels Nørkjær, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Daisy Ramsøe, Abigail, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Tortosa, Joan Emili Aura, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila, Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina, Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Turin, Ruslan, Vasilyiev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merz, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: Several major migrations and population turnover events during the later Stone Age (after c. 11,000 cal. BP) are believed to have shaped the contemporary population genetic diversity in Eurasia. While the genetic impacts of these migrations have been investigated on regional scales, a detailed understanding of their spatiotemporal dynamics both within and between major geographic regions across Northern Eurasia remains largely elusive. Here, we present the largest shotgun-sequenced genomic dataset from the Stone Age to date, representing 317 primarily Mesolithic and Neolithic individuals from across Eurasia, with associated radiocarbon dates, stable isotope data, and pollen records. Using recent advances, we imputed >1,600 ancient genomes to obtain accurate diploid genotypes, enabling previously unachievable fine-grained population structure inferences. We show that 1) Eurasian Mesolitic hunter-gatherers were more genetically diverse than previously known, and deeply divergent between the west and the east; 2) Hitherto genetically undescribed huntergatherers from the Middle Don region contributed significant ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the transition from Mesolithic hunter-gatherers to Neolithic farmers was highly distinct, east and west of a “Great Divide” boundary zone extending from the Black Sea to the Baltic, with large-scale shifts in genetic ancestry to the west. This include an almost complete replacement of hunter-gatherers in Denmark, but no substantial shifts during the same period further to the east; 4) Within-group relatedness changes substantially during the Neolithic transition in the west, where clusters of Neolithic farmer-associated individuals show overall reduced relatedness, while genetic relatedness remains high until ~4,000 BP in the east, consistent with a much longer persistence of smaller localised hunter-gatherer groups; 5) A fastpaced second major genetic transformation beginning around 5,0
Published: 2022

39. Infection Polygenic Factors Account for a Small Proportion of the Relationship Between Infections and Mental Disorders

Author: Shorter, John R., Meijsen, Joeri, Nudel, Ron, Krebs, Morten, Gådin, Jesper, Mikkelsen, Dorte H., Nogueira Avelar e Silva, Raquel, Benros, Michael E., Thompson, Wesley K., Ingason, Andrés, Werge, Thomas, Shorter, John R., Meijsen, Joeri, Nudel, Ron, Krebs, Morten, Gådin, Jesper, Mikkelsen, Dorte H., Nogueira Avelar e Silva, Raquel, Benros, Michael E., Thompson, Wesley K., Ingason, Andrés, and Werge, Thomas
Abstract: Background: Several recent studies have suggested a role for infections in the development of mental disorders; however, the genetic contribution to this association is understudied. Methods: We use the iPSYCH case-cohort genotyped sample (n = 65,534) and Danish health care registry data to study the genetic association between infections and mental disorders. To test the hypothesis that these associations are due to genetic pleiotropy, we estimated the genetic correlation between infection and mental disorders. Polygenic risk scores (PRSs) were used to assess whether genetic pleiotropy of infections and mental disorders was mediated by actual infection diagnoses. Results: We observed that schizophrenia, attention-deficit/hyperactivity disorder, major depressive disorder, bipolar disorder, and posttraumatic stress disorder (rg ranging between 0.18 and 0.83), but not autism spectrum disorder and anorexia nervosa, were significantly genetically correlated with infection diagnoses. PRSs for infections were associated with modest increase in risk of attention-deficit/hyperactivity disorder, major depressive disorder, and schizophrenia in the iPSYCH case-cohort (hazard ratios = 1.04 to 1.10) but was not associated with risk of anorexia, autism, or bipolar disorder. Using mediation analysis, we show that infection diagnoses account for only a small proportion (6%–14%) of the risk for mental disorders conferred by infection PRSs. Conclusions: Infections and mental disorders share a modest genetic architecture. Infection PRSs can predict risk of certain mental disorders; however, this effect is moderate. Finally, recorded infections partially explain the relationship between infection PRSs and mental disorders.
Published: 2022

40. Population Genomics of Stone Age Eurasia

Author: Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Mota, Barbara, Paulsson, Bettina Schulz, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Novosolov, Maria, Sørensen, Lasse, Nielsen, Poul-Otto, Henriksen, Rasmus H. A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Hede, Mikkel Ulfeldt, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Trolle Jensen, Theis Zetner, Johannsen, Niels Nørkjær, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Tortosa, Joan Emili Aura, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yeppiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per Åke, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyiev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merz, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Mota, Barbara, Paulsson, Bettina Schulz, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Novosolov, Maria, Sørensen, Lasse, Nielsen, Poul-Otto, Henriksen, Rasmus H. A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Hede, Mikkel Ulfeldt, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Trolle Jensen, Theis Zetner, Johannsen, Niels Nørkjær, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Tortosa, Joan Emili Aura, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yeppiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per Åke, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyiev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merz, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this “Great Divide”, including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, e
Published: 2022

41. Comparing Copy Number Variations in a Danish Case Cohort of Individuals with Psychiatric Disorders

Author: Calle Sánchez, Xabier, Helenius, Dorte, Bybjerg-Grauholm, Jonas, Pedersen, Carsten, Hougaard, David M., Børglum, Anders D., Nordentoft, Merete, Mors, Ole, Mortensen, Preben B., Geschwind, Daniel H., Montalbano, Simone, Raznahan, Armin, Thompson, Wesley K., Ingason, Andrés, Werge, Thomas, Calle Sánchez, Xabier, Helenius, Dorte, Bybjerg-Grauholm, Jonas, Pedersen, Carsten, Hougaard, David M., Børglum, Anders D., Nordentoft, Merete, Mors, Ole, Mortensen, Preben B., Geschwind, Daniel H., Montalbano, Simone, Raznahan, Armin, Thompson, Wesley K., Ingason, Andrés, and Werge, Thomas
Abstract: Importance: Although the association between several recurrent genomic copy number variants (CNVs) and mental disorders has been studied for more than a decade, unbiased, population-based estimates of the prevalence, disease risks and trajectories, fertility, and mortality to contrast chromosomal abnormalities and advance precision health care are lacking. Objective: To generate unbiased, population-based estimates of prevalence, disease risks and trajectories, fertility, and mortality of CNVs implicated in neuropsychiatric disorders. Design, Setting, and Participants: In a population-based case-cohort study, using the Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) 2012 database, individuals born between May 1, 1981, and December 31, 2005, and followed up until December 31, 2012, were analyzed. All individuals (n = 57377) with attention-deficit/hyperactivity disorder (ADHD), major depressive disorder (MDD), schizophrenia (SCZ), autism spectrum disorder (ASD), or bipolar disorder (BPD) were included, as well as 30000 individuals randomly drawn from the database. Data analysis was conducted from July 1, 2017, to September 7, 2021. Exposures: Copy number variants at 6 genomic loci (1q21.1, 15q11.2, 15q13.3, 16p11.2, 17p12, and 17q12). Main Outcomes and Measures: Population-unbiased hazard ratio (HR) and survival estimates of CNV associations with the 5 ascertained psychiatric disorders, epilepsy, intellectual disability, selected somatic disorders, fertility, and mortality. Results: Participants' age ranged from 1 to 32 years (mean, 12.0 [IQR, 6.9] years) during follow-up, and 38 662 were male (52.3%). Copy number variants broadly associated with an increased risk of autism spectrum disorder and ADHD, whereas risk estimates of SCZ for most CNVs were lower than previously reported. Comparison with previous studies suggests that the lower risk estimates are associated with a higher CNV prevalence in the general population than in control
Published: 2022

42. Population genomics of postglacial western eurasia

Author: Allentoft, Morten E., primary, Sikora, Martin, additional, Refoyo-Martínez, Alba, additional, Irving-Pease, Evan K., additional, Fischer, Anders, additional, Barrie, William, additional, Ingason, Andrés, additional, Stenderup, Jesper, additional, Sjögren, Karl-Göran, additional, Pearson, Alice, additional, Sousa da Mota, Bárbara, additional, Paulsson, Bettina Schulz, additional, Halgren, Alma, additional, Macleod, Ruairidh, additional, Schjellerup Jørkov, Marie Louise, additional, Demeter, Fabrice, additional, Sørensen, Lasse, additional, Nielsen, Poul Otto, additional, Henriksen, Rasmus A., additional, Vimala, Tharsika, additional, McColl, Hugh, additional, Margaryan, Ashot, additional, Ilardo, Melissa, additional, Vaughn, Andrew, additional, Mortensen, Morten Fischer, additional, Nielsen, Anne Birgitte, additional, Hede, Mikkel Ulfeldt, additional, Johannsen, Niels Nørkjær, additional, Rasmussen, Peter, additional, Vinner, Lasse, additional, Renaud, Gabriel, additional, Stern, Aaron, additional, Trolle Jensen, Theis Zetner, additional, Scorrano, Gabriele, additional, Schroeder, Hannes, additional, Lysdahl, Per, additional, Ramsøe, Abigail Daisy, additional, Skorobogatov, Andrei, additional, Schork, Andrew Joseph, additional, Rosengren, Anders, additional, Ruter, Anthony, additional, Outram, Alan, additional, Timoshenko, Aleksey A., additional, Buzhilova, Alexandra, additional, Coppa, Alfredo, additional, Zubova, Alisa, additional, Silva, Ana Maria, additional, Hansen, Anders J., additional, Gromov, Andrey, additional, Logvin, Andrey, additional, Gotfredsen, Anne Birgitte, additional, Nielsen, Bjarne Henning, additional, González-Rabanal, Borja, additional, Lalueza-Fox, Carles, additional, McKenzie, Catriona J., additional, Gaunitz, Charleen, additional, Blasco, Concepción, additional, Liesau, Corina, additional, Martinez-Labarga, Cristina, additional, Pozdnyakov, Dmitri V., additional, Cuenca-Solana, David, additional, Lordkipanidze, David O., additional, En’shin, Dmitri, additional, Salazar-García, Domingo C., additional, Price, T. Douglas, additional, Borić, Dušan, additional, Kostyleva, Elena, additional, Veselovskaya, Elizaveta V., additional, Usmanova, Emma R., additional, Cappellini, Enrico, additional, Petersen, Erik Brinch, additional, Kannegaard, Esben, additional, Radina, Francesca, additional, Yediay, Fulya Eylem, additional, Duday, Henri, additional, Gutiérrez-Zugasti, Igor, additional, Merts, Ilya, additional, Potekhina, Inna, additional, Shevnina, Irina, additional, Altinkaya, Isin, additional, Guilaine, Jean, additional, Hansen, Jesper, additional, Aura Tortosa, Joan Emili, additional, Zilhão, João, additional, Vega, Jorge, additional, Pedersen, Kristoffer Buck, additional, Tunia, Krzysztof, additional, Zhao, Lei, additional, Mylnikova, Liudmila N., additional, Larsson, Lars, additional, Metz, Laure, additional, Yepiskoposyan, Levon, additional, Pedersen, Lisbeth, additional, Sarti, Lucia, additional, Orlando, Ludovic, additional, Slimak, Ludovic, additional, Klassen, Lutz, additional, Blank, Malou, additional, González-Morales, Manuel, additional, Silvestrini, Mara, additional, Vretemark, Maria, additional, Nesterova, Marina S., additional, Rykun, Marina, additional, Rolfo, Mario Federico, additional, Szmyt, Marzena, additional, Przybyła, Marcin, additional, Calattini, Mauro, additional, Sablin, Mikhail, additional, Dobisíková, Miluše, additional, Meldgaard, Morten, additional, Johansen, Morten, additional, Berezina, Natalia, additional, Card, Nick, additional, Saveliev, Nikolai A., additional, Poshekhonova, Olga, additional, Rickards, Olga, additional, Lozovskaya, Olga V., additional, Gábor, Olivér, additional, Uldum, Otto Christian, additional, Aurino, Paola, additional, Kosintsev, Pavel, additional, Courtaud, Patrice, additional, Ríos, Patricia, additional, Mortensen, Peder, additional, Lotz, Per, additional, Persson, Per, additional, Bangsgaard, Pernille, additional, Barros Damgaard, Peter de, additional, Petersen, Peter Vang, additional, Martinez, Pilar Prieto, additional, Włodarczak, Piotr, additional, Smolyaninov, Roman V., additional, Maring, Rikke, additional, Menduiña, Roberto, additional, Badalyan, Ruben, additional, Iversen, Rune, additional, Turin, Ruslan, additional, Vasilyev, Sergey, additional, Wåhlin, Sidsel, additional, Borutskaya, Svetlana, additional, Skochina, Svetlana, additional, Sørensen, Søren Anker, additional, Andersen, Søren H., additional, Jørgensen, Thomas, additional, Serikov, Yuri B., additional, Molodin, Vyacheslav I., additional, Smrcka, Vaclav, additional, Merz, Victor, additional, Appadurai, Vivek, additional, Moiseyev, Vyacheslav, additional, Magnusson, Yvonne, additional, Kjær, Kurt H., additional, Lynnerup, Niels, additional, Lawson, Daniel J., additional, Sudmant, Peter H., additional, Rasmussen, Simon, additional, Korneliussen, Thorfinn, additional, Durbin, Richard, additional, Nielsen, Rasmus, additional, Delaneau, Olivier, additional, Werge, Thomas, additional, Racimo, Fernando, additional, Kristiansen, Kristian, additional, and Willerslev, Eske, additional
Published: 2022
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43. A comprehensive map of genetic relationships among diagnostic categories based on 48.6 million relative pairs from the Danish genealogy

Author: Geschwind, Daniel, Werge, Thomas, Buil, Alfonso, Athanasiadis, Georgios, Meijsen, Joeri, Helenius, Dorte, Schork, Andrew, Ingason, Andrés, and Thompson, Wesley
Subjects: Inborn, Genetic Diseases, Denmark, Mental Disorders, register data, Humans, Genetic Predisposition to Disease, human disease, Health Services Research, heritability, genetic correlation
Abstract: For more than half a century, Denmark has maintained population-wide demographic, health care, and socioeconomic registers that provide detailed information on the interaction between all residents and the extensive national social services system. We leverage this resource to reconstruct the genealogy of the entire nation based on all individuals legally residing in Denmark since 1968. We cross-reference 6,691,426 individuals with nationwide health care registers to estimate heritability and genetic correlations of 10 broad diagnostic categories involving all major organs and systems. Heritability estimates for mental disorders were consistently the highest across demographic cohorts (average h 2 = 0.406, 95% CI = [0.403, 0.408]), whereas estimates for cancers were the lowest (average h 2 = 0.130, 95% CI = [0.125, 0.134]). The average genetic correlation of each of the 10 diagnostic categories with the other nine was highest for gastrointestinal conditions (average rg = 0.567, 95% CI = [0.566, 0.567]) and lowest for urogenital conditions (average rg = 0.386, 95% CI = [0.385, 0.388]). Mental, pulmonary, gastrointestinal, and neurological conditions had similar genetic correlation profiles.
Published: 2022

44. Reproductive fitness and genetic risk of psychiatric disorders in the general population

Author: Mullins, Niamh, Ingason, Andrés, Porter, Heather, Euesden, Jack, Gillett, Alexandra, Ólafsson, Sigurgeir, Gudbjartsson, Daniel F., Lewis, Cathryn M., Sigurdsson, Engilbert, Saemundsen, Evald, Gudmundsson, Ólafur Ó, Frigge, Michael L., Kong, Augustine, Helgason, Agnar, Walters, G. Bragi, Gustafsson, Omar, Stefansson, Hreinn, and Stefansson, Kari
Published: 2017
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45. Comparing Copy Number Variations in a Danish Case Cohort of Individuals With Psychiatric Disorders

Author: Calle Sánchez, Xabier, primary, Helenius, Dorte, additional, Bybjerg-Grauholm, Jonas, additional, Pedersen, Carsten, additional, Hougaard, David M., additional, Børglum, Anders D., additional, Nordentoft, Merete, additional, Mors, Ole, additional, Mortensen, Preben B., additional, Geschwind, Daniel H., additional, Montalbano, Simone, additional, Raznahan, Armin, additional, Thompson, Wesley K., additional, Ingason, Andrés, additional, and Werge, Thomas, additional
Published: 2022
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46. Sex Chromosome Aneuploidies are Underdiagnosed and Associated with Increased Risk of Mental Disorders

Author: Calle Sanchez, Xabier, primary, Montalbano, Simone, additional, Vaez, Morteza, additional, Krebs, Morten Dybdahl, additional, Bygbjerg-Grauholm, Jonas, additional, Mortensen, Preben B., additional, Børglum, Anders D., additional, Hougaard, David M., additional, Nordentoft, Merete, additional, Geschwind, Daniel H., additional, Buil, Alfonso, additional, Schork, Andrew J., additional, Thompson, Wesley K., additional, Raznahan, Armin, additional, Helenius, Dorte, additional, Werge, Thomas, additional, and Ingason, Andrés, additional
Published: 2022
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47. Polygenic profiles define aspects of clinical heterogeneity in ADHD

Author: LaBianca, Sonja, primary, Brikell, Isabell, additional, Helenius, Dorte, additional, Loughnan, Robert, additional, Mefford, Joel, additional, Palmer, Clare E., additional, Walker, Rebecca, additional, Gådin, Jesper R., additional, Krebs, Morten, additional, Appadurai, Vivek, additional, Vaez, Morteza, additional, Agerbo, Esben, additional, Gørtz Pedersen, Marianne, additional, Børglum, Anders D., additional, Hougaard, David M., additional, Mors, Ole, additional, Nordentoft, Merete, additional, Mortensen, Preben Bo, additional, Kendler, Kenneth S., additional, Jernigan, Terry L., additional, Geschwind, Daniel H., additional, Ingason, Andrés, additional, Dahl, Andrew W., additional, Zaitlen, Noah, additional, Dalsgaard, Søren, additional, Werge, Thomas M., additional, and Schork, Andrew J., additional
Published: 2021
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48. T56. NEONATAL BLOOD TRANSCRIPTOMICS REVEAL EXPRESSION SIGNATURES OF ADHD RISK

Author: Yakimov, Victor, Ingason, Andres, Hansen, Christine, Bækvad-Hansen, Marie, Bo Mortensen, Preben, Nordentoft, Merete, Mors, Ole, Børglum, Anders, Hougaard, David M., Feenstra, Bjarke, Werge, Thomas, Buil, Alfonso, and Bybjerg-Grauholm, Jonas
Published: 2023
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49. ENHANCING POLYGENIC PREDICTION WITH AN AGNOSTIC MULTI-PGS METHOD THAT LEVERAGES HUNDREDS OF POLYGENIC SCORES

Author: Albiñana, Clara, Zhu, Zhihong, Schork, Andrew, Ingason, Andres, Aschard, Hugues, Brikell, Isabell, Petersen, Liselotte, Agerbo, Esben, Grove, Jakob, Børglum, Anders, Bo Mortensen, Preben, McGrath, John, Neale, Benjamin, Privé, Florian, and Vilhjalmsson, Bjarni
Published: 2023
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50. Sequence analysis of 17 NRXN1 deletions

Author: Hoeffding, Louise Kristine Enggaard, Hansen, Thomas, Ingason, Andrés, Doung, Linh, Thygesen, Johan H., Møller, Rikke S., Tommerup, Niels, Kirov, George, Rujescu, Dan, Larsen, Lars A., and Werge, Thomas
Published: 2014
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