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Results: 33
Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes.
Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate...
Advances in Genomic Discovery and Implications for Personalized Prevention and Medicine
Bram Peter Prins, Liis Leitsalu, Katri Pärna, Krista Fischer, Andres Metspalu, Toomas Haller, Harold Snieder
Apr 30, 2021
The current paradigm of personalized medicine envisages the use of genomic data to provide predictive information on the health course of an individual with the aim of prevention and individualized care. However, substantial...
Advances in Genomic Discovery and Implications for Personalized Prevention and Medicine
Bram Peter Prins, Liis Leitsalu, Katri Pärna, Krista Fischer, Andres Metspalu, Toomas Haller, Harold Snieder
Jun 04, 2021
The current paradigm of personalized medicine envisages the use of genomic data to provide predictive information on the health course of an individual with the aim of prevention and individualized care. However, substantial...
The Genetic Origin of Daunians and the Pan-Mediterranean Southern Italian Iron Age Context.
Serena Aneli, Tina Saupe, Francesco Montinaro, Anu Solnik, Ludovica Molinaro, Cinzia Scaggion, Nicola Carrara, Alessandro Raveane, Toomas Kivisild, Mait Metspalu, Christiana L Scheib, Luca Pagani
Feb 17, 2022
The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at...
An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim.
Meriam Guellil, Marcel Keller, Jenna M Dittmar, Sarah A Inskip, Craig Cessford, Anu Solnik, Toomas Kivisild, Mait Metspalu, John E Robb, Christiana L Scheib
Feb 03, 2022
BACKGROUND: The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the...
An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim.
Meriam Guellil, Marcel Keller, Jenna M Dittmar, Sarah A Inskip, Craig Cessford, Anu Solnik, Toomas Kivisild, Mait Metspalu, John E Robb, Christiana L Scheib
Mar 06, 2022
BACKGROUND: The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the...
Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa.
Erwan Pennarun, Toomas Kivisild, Ene Metspalu, Mait Metspalu, Tuuli Reisberg, Jean-Paul Moisan, Doron M Behar, Sacha C Jones, Richard Villems
Jun 17, 2021
BACKGROUND: A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar...
The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.
Chandana Basu Mallick, Florin Mircea Iliescu, Märt Möls, Sarah Hill, Rakesh Tamang, Gyaneshwer Chaubey, Rie Goto, Simon YW Ho, Irene Gallego Romero, Federica Crivellaro, Georgi Hudjashov, Niraj Rai, Mait Metspalu, CG Nicholas Mascie-Taylor, Ramasamy Pitchappan, Lalji Singh, Marta Mirazon-Lahr, Kumarasamy Thangaraj, Richard Villems, Toomas Kivisild
Sep 08, 2018
Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous...
Evidence of Early-Stage Selection on EPAS1 and GPR126 Genes in Andean High Altitude Populations.
Christina A Eichstaedt, Luca Pagani, Tiago Antao, Charlotte E Inchley, Alexia Cardona, Alexander Mörseburg, Florian J Clemente, Timothy J Sluckin, Ene Metspalu, Mario Mitt, Reedik Mägi, Georgi Hudjashov, Mait Metspalu, Maru Mormina, Guy S Jacobs, Toomas Kivisild
Mar 21, 2018
The aim of this study is to identify genetic variants that harbour signatures of recent positive selection and may facilitate physiological adaptations to hypobaric hypoxia. To achieve this, we conducted whole genome sequencing...
Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.
Gyaneshwer Chaubey, Monika Karmin, Ene Metspalu, Mait Metspalu, Deepa Selvi-Rani, Vijay Kumar Singh, Jüri Parik, Anu Solnik, B Prathap Naidu, Ajay Kumar, Niharika Adarsh, Chandana Basu Mallick, Bhargav Trivedi, Swami Prakash, Ramesh Reddy, Parul Shukla, Sanjana Bhagat, Swati Verma, Samiksha Vasnik, Imran Khan, Anshu Barwa, Dipti Sahoo, Archana Sharma, Mamoon Rashid, Vishal Chandra, Alla G Reddy, Antonio Torroni, Robert A Foley, Kumarasamy Thangaraj, Lalji Singh, Toomas Kivisild, Richard Villems
Jun 14, 2011
"Like sugar in milk"
Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi, Kurush Dalal, Shagufta Khaliq, Syed Qasim Mehdi, Lalji Singh, Mait Metspalu, Toomas Kivisild, Chris Tyler-Smith, Richard Villems, Kumarasamy Thangaraj
Nov 21, 2018
BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using...
A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.
Florian J Clemente, Alexia Cardona, Charlotte E Inchley, Benjamin M Peter, Guy Jacobs, Luca Pagani, Daniel J Lawson, Tiago Antão, Mário Vicente, Mario Mitt, Michael DeGiorgio, Zuzana Faltyskova, Yali Xue, Qasim Ayub, Michal Szpak, Reedik Mägi, Anders Eriksson, Andrea Manica, Maanasa Raghavan, Morten Rasmussen, Simon Rasmussen, Eske Willerslev, Antonio Vidal-Puig, Chris Tyler-Smith, Richard Villems, Rasmus Nielsen, Mait Metspalu, Boris Malyarchuk, Miroslava Derenko, Toomas Kivisild
Nov 12, 2014
The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.
Lehti Saag, Margot Laneman, Liivi Varul, Martin Malve, Heiki Valk, Maria A Razzak, Ivan G Shirobokov, Valeri I Khartanovich, Elena R Mikhaylova, Alena Kushniarevich, Christiana Lyn Scheib, Anu Solnik, Tuuli Reisberg, Jüri Parik, Lauri Saag, Ene Metspalu, Siiri Rootsi, Francesco Montinaro, Maido Remm, Reedik Mägi, Eugenia D'Atanasio, Enrico Ryunosuke Crema, David Díez-Del-Molino, Mark G Thomas, Aivar Kriiska, Toomas Kivisild, Richard Villems, Valter Lang, Mait Metspalu, Kristiina Tambets
May 03, 2019
In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist...
Rare variant analyses across multiethnic cohorts identify novel genes for refractive error.
Anthony M Musolf, Annechien EG Haarman, Robert N Luben, Jue-Sheng Ong, Karina Patasova, Rolando Hernandez Trapero, Joseph Marsh, Ishika Jain, Riya Jain, Paul Zhiping Wang, Deyana D Lewis, Milly S Tedja, Adriana I Iglesias, Hengtong Li, Cameron S Cowan, Consortium for Refractive Error and Myopia (CREAM), Ginevra Biino, Alison P Klein, Priya Duggal, David A Mackey, Caroline Hayward, Toomas Haller, Andres Metspalu, Juho Wedenoja, Olavi Pärssinen, Ching-Yu Cheng, Seang-Mei Saw, Dwight Stambolian, Pirro G Hysi, Anthony P Khawaja, Veronique Vitart, Christopher J Hammond, Cornelia M van Duijn, Virginie JM Verhoeven, Caroline CW Klaver, Joan E Bailey-Wilson
Feb 09, 2023
Refractive error, measured here as mean spherical equivalent (SER), is a complex eye condition caused by both genetic and environmental factors. Individuals with strong positive or negative values of SER require spectacles or...
Ancient human parallel lineages within North America contributed to a coastal expansion.
CL Scheib, Hongjie Li, Tariq Desai, Vivian Link, Christopher Kendall, Genevieve Dewar, Peter William Griffith, Alexander Mörseburg, John R Johnson, Amiee Potter, Susan L Kerr, Phillip Endicott, John Lindo, Marc Haber, Yali Xue, Chris Tyler-Smith, Manjinder S Sandhu, Joseph G Lorenz, Tori D Randall, Zuzana Faltyskova, Luca Pagani, Petr Danecek, Tamsin C O'Connell, Patricia Martz, Alan S Boraas, Brian F Byrd, Alan Leventhal, Rosemary Cambra, Ronald Williamson, Louis Lesage, Brian Holguin, Ernestine Ygnacio-De Soto, JohnTommy Rosas, Mait Metspalu, Jay T Stock, Andrea Manica, Aylwyn Scally, Daniel Wegmann, Ripan S Malhi, Toomas Kivisild
Oct 16, 2018
Little is known regarding the first people to enter the Americas and their genetic legacy. Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population...
The blood metabolome of incident kidney cancer
Florence Guida, Vanessa Y Tan, Laura J Corbin, Karl Smith-Byrne, Karine Alcala, Claudia Langenberg, Isobel D Stewart, Adam S Butterworth, Praveen Surendran, David Achaintre, Jerzy Adamski, Pilar Amiano Exezarreta, Manuela M Bergmann, Caroline J Bull, Christina C Dahm, Audrey Gicquiau, Graham G Giles, Marc J Gunter, Toomas Haller, Arnulf Langhammer, Tricia L Larose, Börje Ljungberg, Andres Metspalu, Roger L Milne, David C Muller, Therese H Nøst, Elin Pettersen Sørgjerd, Cornelia Prehn, Elio Riboli, Sabina Rinaldi, Joseph A Rothwell, Augustin Scalbert, Julie A Schmidt, Gianluca Severi, Sabina Sieri, Roel Vermeulen, Emma E Vincent, Melanie Waldenberger, Nicholas J Timpson, Mattias Johansson
Oct 18, 2021
BACKGROUND: Excess bodyweight and related metabolic perturbations have been implicated in kidney cancer aetiology, but the specific molecular mechanisms underlying these relationships are poorly understood. In this study, we...
Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes.
Maria A Spyrou, Marcel Keller, Rezeda I Tukhbatova, Christiana L Scheib, Elizabeth A Nelson, Aida Andrades Valtueña, Gunnar U Neumann, Don Walker, Amelie Alterauge, Niamh Carty, Craig Cessford, Hermann Fetz, Michaël Gourvennec, Robert Hartle, Michael Henderson, Kristin von Heyking, Sarah A Inskip, Sacha Kacki, Felix M Key, Elizabeth L Knox, Christian Later, Prishita Maheshwari-Aplin, Joris Peters, John E Robb, Jürgen Schreiber, Toomas Kivisild, Dominique Castex, Sandra Lösch, Michaela Harbeck, Alexander Herbig, Kirsten I Bos, Johannes Krause
Oct 28, 2019
The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period...
The blood metabolome of incident kidney cancer
Florence Guida, Vanessa Y. Tan, Laura J. Corbin, Karl Smith-Byrne, Karine Alcala, Claudia Langenberg, Isobel D. Stewart, Adam S. Butterworth, Praveen Surendran, David Achaintre, Jerzy Adamski, Pilar Amiano, Manuela M. Bergmann, Caroline J. Bull, Christina C. Dahm, Audrey Gicquiau, Graham G. Giles, Marc J. Gunter, Toomas Haller, Arnulf Langhammer, Tricia L. Larose, Börje Ljungberg, Andres Metspalu, Roger L. Milne, David C. Muller, Therese H. Nøst, Elin Pettersen Sørgjerd, Cornelia Prehn, Elio Riboli, Sabina Rinaldi, Joseph A. Rothwell, Augustin Scalbert, Julie A. Schmidt, Gianluca Severi, Sabina Sieri, Roel Vermeulen, Emma E. Vincent, Melanie Waldenberger, Nicholas J. Timpson, Mattias Johansson
Oct 07, 2021
Background: Excess bodyweight and related metabolic perturbations have been implicated in kidney cancer aetiology, but the specific molecular mechanisms underlying these relationships are poorly understood. In this study, we...
Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes
Maria A. Spyrou, Marcel Keller, Rezeda I. Tukhbatova, Christiana L. Scheib, Elizabeth A. Nelson, Aida Andrades Valtueña, Gunnar U. Neumann, Don Walker, Amelie Alterauge, Niamh Carty, Craig Cessford, Hermann Fetz, Michaël Gourvennec, Robert Hartle, Michael Henderson, Kristin von Heyking, Sarah A. Inskip, Sacha Kacki, Felix M. Key, Elizabeth L. Knox, Christian Later, Prishita Maheshwari-Aplin, Joris Peters, John E. Robb, Jürgen Schreiber, Toomas Kivisild, Dominique Castex, Sandra Lösch, Michaela Harbeck, Alexander Herbig, Kirsten I. Bos, Johannes Krause
Oct 01, 2020
Abstract: The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this...
The blood metabolome of incident kidney cancer
Florence Guida, Vanessa Y Tan, Laura J Corbin, Karl Smith-Byrne, Karine Alcala, Claudia Langenberg, Isobel D Stewart, Adam S Butterworth, Praveen Surendran, David Achaintre, Jerzy Adamski, Pilar Amiano, Manuela M Bergmann, Caroline J Bull, Christina C Dahm, Audrey Gicquiau, Graham G Giles, Marc J Gunter, Toomas Haller, Arnulf Langhammer, Tricia L Larose, Börje Ljungberg, Andres Metspalu, Roger L Milne, David C Muller, Therese H Nøst, Elin Pettersen Sørgjerd, Cornelia Prehn, Elio Riboli, Sabina Rinaldi, Joseph A Rothwell, Augustin Scalbert, Julie A Schmidt, Gianluca Severi, Sabina Sieri, Roel Vermeulen, Emma E Vincent, Melanie Waldenberger, Nicholas J Timpson, Mattias Johansson
Oct 21, 2021
Background
Excess bodyweight and related metabolic perturbations have been implicated in kidney cancer aetiology, but the specific molecular mechanisms underlying these relationships are poorly understood. In this study...
Published by: PLoS Medicine
Rare variant analyses across multiethnic cohorts identify novel genes for refractive error.
Anthony M Musolf, Annechien EG Haarman, Robert N Luben, Jue-Sheng Ong, Karina Patasova, Rolando Hernandez Trapero, Joseph Marsh, Ishika Jain, Riya Jain, Paul Zhiping Wang, Deyana D Lewis, Milly S Tedja, Adriana I Iglesias, Hengtong Li, Cameron S Cowan, Consortium for Refractive Error and Myopia (CREAM), Ginevra Biino, Alison P Klein, Priya Duggal, David A Mackey, Caroline Hayward, Toomas Haller, Andres Metspalu, Juho Wedenoja, Olavi Pärssinen, Ching-Yu Cheng, Seang-Mei Saw, Dwight Stambolian, Pirro G Hysi, Anthony P Khawaja, Veronique Vitart, Christopher J Hammond, Cornelia M van Duijn, Virginie JM Verhoeven, Caroline CW Klaver, Joan E Bailey-Wilson
Jan 04, 2023
The genetic prehistory of the New World Arctic.
Maanasa Raghavan, Michael DeGiorgio, Anders Albrechtsen, Ida Moltke, Pontus Skoglund, Thorfinn S Korneliussen, Bjarne Grønnow, Martin Appelt, Hans Christian Gulløv, T Max Friesen, William Fitzhugh, Helena Malmström, Simon Rasmussen, Jesper Olsen, Linea Melchior, Benjamin T Fuller, Simon M Fahrni, Thomas Stafford, Vaughan Grimes, MA Priscilla Renouf, Jerome Cybulski, Niels Lynnerup, Marta Mirazon Lahr, Kate Britton, Rick Knecht, Jette Arneborg, Mait Metspalu, Omar E Cornejo, Anna-Sapfo Malaspinas, Yong Wang, Morten Rasmussen, Vibha Raghavan, Thomas vO Hansen, Elza Khusnutdinova, Tracey Pierre, Kirill Dneprovsky, Claus Andreasen, Hans Lange, M Geoffrey Hayes, Joan Coltrain, Victor A Spitsyn, Anders Götherström, Ludovic Orlando, Toomas Kivisild, Richard Villems, Michael H Crawford, Finn C Nielsen, Jørgen Dissing, Jan Heinemeier, Morten Meldgaard, Carlos Bustamante, Dennis H O'Rourke, Mattias Jakobsson, M Thomas P Gilbert, Rasmus Nielsen, Eske Willerslev
Dec 17, 2014
Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error.
Milly S Tedja, Robert Wojciechowski, Pirro G Hysi, Nicholas Eriksson, Nicholas A Furlotte, Virginie JM Verhoeven, Adriana I Iglesias, Magda A Meester-Smoor, Stuart W Tompson, Qiao Fan, Anthony P Khawaja, Ching-Yu Cheng, René Höhn, Kenji Yamashiro, Adam Wenocur, Clare Grazal, Toomas Haller, Andres Metspalu, Juho Wedenoja, Jost B Jonas, Ya Xing Wang, Jing Xie, Paul Mitchell, Paul J Foster, Barbara EK Klein, Ronald Klein, Andrew D Paterson, S Mohsen Hosseini, Rupal L Shah, Cathy Williams, Yik Ying Teo, Yih Chung Tham, Preeti Gupta, Wanting Zhao, Yuan Shi, Woei-Yuh Saw, E-Shyong Tai, Xue Ling Sim, Jennifer E Huffman, Ozren Polašek, Caroline Hayward, Goran Bencic, Igor Rudan, James F Wilson, CREAM Consortium, 23andMe Research Team, UK Biobank Eye and Vision Consortium, Peter K Joshi, Akitaka Tsujikawa, Fumihiko Matsuda, Kristina N Whisenhunt, Tanja Zeller, Peter J van der Spek, Roxanna Haak, Hanne Meijers-Heijboer, Elisabeth M van Leeuwen, Sudha K Iyengar, Jonathan H Lass, Albert Hofman, Fernando Rivadeneira, André G Uitterlinden, Johannes R Vingerling, Terho Lehtimäki, Olli T Raitakari, Ginevra Biino, Maria Pina Concas, Tae-Hwi Schwantes-An, Robert P Igo, Gabriel Cuellar-Partida, Nicholas G Martin, Jamie E Craig, Puya Gharahkhani, Katie M Williams, Abhishek Nag, Jugnoo S Rahi, Phillippa M Cumberland, Cécile Delcourt, Céline Bellenguez, Janina S Ried, Arthur A Bergen, Thomas Meitinger, Christian Gieger, Tien Yin Wong, Alex W Hewitt, David A Mackey, Claire L Simpson, Norbert Pfeiffer, Olavi Pärssinen, Paul N Baird, Veronique Vitart, Najaf Amin, Cornelia M van Duijn, Joan E Bailey-Wilson, Terri L Young, Seang-Mei Saw, Dwight Stambolian, Stuart MacGregor, Jeremy A Guggenheim, Joyce Y Tung, Christopher J Hammond, Caroline CW Klaver
Jul 29, 2019
Refractive errors, including myopia, are the most frequent eye disorders worldwide and an increasingly common cause of blindness. This genome-wide association meta-analysis in 160,420 participants and replication in 95,505...
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