Search

Your search keyword '"Fedorova, Sardana"' showing total 225 results
Start Over Author "Fedorova, Sardana"
225 results on '"Fedorova, Sardana"'

3. A common founder effect of the splice site variant c.-23 + 1G > A in GJB2 gene causing autosomal recessive deafness 1A (DFNB1A) in Eurasia

Author

Solovyev, Aisen V., Kushniarevich, Alena, Bliznetz, Elena, Bady-Khoo, Marita, Lalayants, Maria R., Markova, Tatiana G., Minárik, Gabriel, Kádasi, L’udevít, Metspalu, Ene, Pshennikova, Vera G., Teryutin, Fedor M., Khusnutdinova, Elza K., Poliakov, Alexander, Metspalu, Mait, Posukh, Olga L., Barashkov, Nikolay A., and Fedorova, Sardana A.

Published
2022
Full Text
View/download PDF

4. Genotype–phenotype analysis of hearing function in patients with DFNB1A caused by the c.-23+1G>A splice site variant of the GJB2 gene (Cx26).

Author

Teryutin, Fedor M., Pshennikova, Vera G., Solovyev, Aisen V., Romanov, Georgii P., Fedorova, Sardana A., and Barashkov, Nikolay A.

Subjects
GENETIC variation, DEAFNESS, HEARING disorders, SPEECH, GENOTYPES, RECESSIVE genes
Abstract

The audiological features of hearing loss (HL) in patients with autosomal recessive deafness type 1A (DFNB1A) caused by splice site variants of the GJB2 gene are less studied than those of patients with other variants of this gene. In this study, we present the audiological features of DFNB1A in a large cohort of 134 patients with the homozygous splice site variant c.-23+1G>A and 34 patients with other biallelic GJB2 genotypes (n = 168 patients with DFNB1A). We found that the preservation of hearing thresholds in the speech frequency range (PTA0.5,1.0,2.0,4.0 kHz) in patients with the c.[-23+1G>A];[-23+1G>A] genotype is significantly better than in patients with the "severe" c.[35delG];[35delG] genotype (p = 0.005) and significantly worse than in patients with the "mild" c.[109G>A];[109G>A] genotype (p = 0.041). This finding indicates a "medium" pathological effect of this splice site variant on hearing function. A detailed clinical and audiological analysis showed that in patients with the c.[-23+1G>A];[-23+1G>A] genotype, HL is characterized as congenital or early onset (57.5% onset before 12 months), sensorineural (97.8%), bilateral, symmetrical (82.8%), variable in severity (from mild to profound HL, median hearing threshold in PTA0.5,1.0,2.0,4.0 kHz is 86.73±21.98 dB), with an extremely "flat" audioprofile, and with a tendency toward slow progression (a positive correlation of hearing thresholds with age, r = 0.144, p = 0.041). In addition, we found that the hearing thresholds in PTA0.5,1.0,2.0,4.0 kHz were significantly better preserved in females (82.34 dB) than in males (90.62 dB) (p = 0.001). We can conclude that in patients with DFNB1A caused by the c.-23+1G>A variant, male sex is associated with deteriorating auditory function; in contrast, female sex is a protective factor. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

5. Autosomal recessive cataract (CTRCT18) in the Yakut population isolate of Eastern Siberia: a novel founder variant in the FYCO1 gene

Author

Barashkov, Nikolay A., Konovalov, Fedor A., Borisova, Tuyara V., Teryutin, Fedor M., Solovyev, Aisen V., Pshennikova, Vera G., Sapojnikova, Nadejda V., Vychuzhina, Lyubov S., Romanov, Georgii P., Gotovtsev, Nyurgun N., Morozov, Igor V., Bondar, Alexander A., Platonov, Fedor A., Burtseva, Tatiana E., Khusnutdinova, Elza K., Posukh, Olga L., and Fedorova, Sardana A.

Published
2021
Full Text
View/download PDF

6. Genomic analyses inform on migration events during the peopling of Eurasia

Author

Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Sayres, Melissa A Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Škaro, Vedrana, Mulahasanovic´, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait

Subjects
Human Genome, Biotechnology, Genetics, Generic health relevance, Africa, Animals, Asia, Datasets as Topic, Estonia, Europe, Fossils, Gene Flow, Genetics, Population, Genome, Human, Genomics, Heterozygote, History, Ancient, Human Migration, Humans, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Population Dynamics, Racial Groups, General Science & Technology
Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

Published
2016

7. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

Lazaridis, Iosif, Patterson, Nick, Mittnik, Alissa, Renaud, Gabriel, Mallick, Swapan, Kirsanow, Karola, Sudmant, Peter H., Schraiber, Joshua G., Castellano, Sergi, Lipson, Mark, Berger, Bonnie, Economou, Christos, Bollongino, Ruth, Fu, Qiaomei, Bos, Kirsten I., Nordenfelt, Susanne, Li, Heng, de Filippo, Cesare, Prüfer, Kay, Sawyer, Susanna, Posth, Cosimo, Haak, Wolfgang, Hallgren, Fredrik, Fornander, Elin, Rohland, Nadin, Delsate, Dominique, Francken, Michael, Guinet, Jean-Michel, Wahl, Joachim, Ayodo, George, Babiker, Hamza A., Bailliet, Graciela, Balanovska, Elena, Balanovsky, Oleg, Barrantes, Ramiro, Bedoya, Gabriel, Ben-Ami, Haim, Bene, Judit, Berrada, Fouad, Bravi, Claudio M., Brisighelli, Francesca, Busby, George, Cali, Francesco, Churnosov, Mikhail, Cole, David E. C., Corach, Daniel, Damba, Larissa, van Driem, George, Dryomov, Stanislav, Dugoujon, Jean-Michel, Fedorova, Sardana A., Romero, Irene Gallego, Gubina, Marina, Hammer, Michael, Henn, Brenna, Hervig, Tor, Hodoglugil, Ugur, Jha, Aashish R., Karachanak-Yankova, Sena, Khusainova, Rita, Khusnutdinova, Elza, Kittles, Rick, Kivisild, Toomas, Klitz, William, Kučinskas, Vaidutis, Kushniarevich, Alena, Laredj, Leila, Litvinov, Sergey, Loukidis, Theologos, Mahley, Robert W., Melegh, Béla, Metspalu, Ene, Molina, Julio, Mountain, Joanna, Näkkäläjärvi, Klemetti, Nesheva, Desislava, Nyambo, Thomas, Osipova, Ludmila, Parik, Jüri, Platonov, Fedor, Posukh, Olga, Romano, Valentino, Rothhammer, Francisco, Rudan, Igor, Ruizbakiev, Ruslan, Sahakyan, Hovhannes, Sajantila, Antti, Salas, Antonio, Starikovskaya, Elena B., Tarekegn, Ayele, Toncheva, Draga, Turdikulova, Shahlo, Uktveryte, Ingrida, Utevska, Olga, Vasquez, René, Villena, Mercedes, Voevoda, Mikhail, Winkler, Cheryl, Yepiskoposyan, Levon, Zalloua, Pierre, Zemunik, Tatijana, Cooper, Alan, Capelli, Cristian, Thomas, Mark G., Ruiz-Linares, Andres, Tishkoff, Sarah A., Singh, Lalji, Thangaraj, Kumarasamy, Villems, Richard, Comas, David, Sukernik, Rem, Metspalu, Mait, Meyer, Matthias, Eichler, Evan E., Burger, Joachim, Slatkin, Montgomery, Pääbo, Svante, Kelso, Janet, Reich, David, and Krause, Johannes

Subjects
Quantitative Biology - Populations and Evolution
Abstract

We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

Published
2013
Full Text
View/download PDF

9. Genomic evidence for the Pleistocene and recent population history of Native Americans

Author

Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María C, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian R, Wall, Jeff, Cornejo, Omar E, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn S, Pierre, Tracey, Rasmussen, Morten, Campos, Paula F, de Barros Damgaard, Peter, Allentoft, Morten E, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash S, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew D, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose Luis, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G, Heyer, Evelyne, Zollikofer, Christoph PE, Ponce de León, Marcia S, Smith, Colin I, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T, Arriaza, Bernardo, Standen, Vivien, Luz, Maria F, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I, Posukh, Olga L, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, MJ, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J, Parham, Peter, Kemp, Brian M, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder S, Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R, Goebel, Ted, Johnson, John R, Malhi, Ripan S, Jakobsson, Mattias, Meltzer, David J, Manica, Andrea, Durbin, Richard, Bustamante, Carlos D, Song, Yun S, and Nielsen, Rasmus

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, Minority Health, Human Genome, American Indian or Alaska Native, Americas, Gene Flow, Genomics, History, Ancient, Human Migration, Humans, Indians, North American, Models, Genetic, Siberia, General Science & Technology
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

10. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Author

Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María C, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian R, Wall, Jeff, Cornejo, Omar E, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn S, Pierre, Tracey, Rasmussen, Morten, Campos, Paula F, de Barros Damgaard, Peter, Allentoft, Morten E, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash S, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew D, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose Luis, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G, Heyer, Evelyne, Zollikofer, Christoph PE, Ponce de León, Marcia S, Smith, Colin I, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T, Arriaza, Bernardo, Standen, Vivien, Luz, Maria F, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I, Posukh, Olga L, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, MJ, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J, Parham, Peter, Kemp, Brian M, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder S, Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R, Goebel, Ted, Johnson, John R, Malhi, Ripan S, Jakobsson, Mattias, Meltzer, David J, Manica, Andrea, Durbin, Richard, Bustamante, Carlos D, Song, Yun S, and Nielsen, Rasmus

Subjects
Humans, Genomics, Models, Genetic, History, Ancient, Indians, North American, Americas, Siberia, Gene Flow, Human Migration, Human Genome, Genetics, General Science & Technology
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

11. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin, Monika, Saag, Lauri, Vicente, Mário, Sayres, Melissa A Wilson, Järve, Mari, Talas, Ulvi Gerst, Rootsi, Siiri, Ilumäe, Anne-Mai, Mägi, Reedik, Mitt, Mario, Pagani, Luca, Puurand, Tarmo, Faltyskova, Zuzana, Clemente, Florian, Cardona, Alexia, Metspalu, Ene, Sahakyan, Hovhannes, Yunusbayev, Bayazit, Hudjashov, Georgi, DeGiorgio, Michael, Loogväli, Eva-Liis, Eichstaedt, Christina, Eelmets, Mikk, Chaubey, Gyaneshwer, Tambets, Kristiina, Litvinov, Sergei, Mormina, Maru, Xue, Yali, Ayub, Qasim, Zoraqi, Grigor, Korneliussen, Thorfinn Sand, Akhatova, Farida, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Ricaut, François-Xavier, Kusuma, Pradiptajati, Razafindrazaka, Harilanto, Pierron, Denis, Cox, Murray P, Sultana, Gazi Nurun Nahar, Willerslev, Rane, Muller, Craig, Westaway, Michael, Lambert, David, Skaro, Vedrana, Kovačevic´, Lejla, Turdikulova, Shahlo, Dalimova, Dilbar, Khusainova, Rita, Trofimova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Lichman, Daria V, Isakova, Jainagul, Pocheshkhova, Elvira, Sabitov, Zhaxylyk, Barashkov, Nikolay A, Nymadawa, Pagbajabyn, Mihailov, Evelin, Seng, Joseph Wee Tien, Evseeva, Irina, Migliano, Andrea Bamberg, Abdullah, Syafiq, Andriadze, George, Primorac, Dragan, Atramentova, Lubov, Utevska, Olga, Yepiskoposyan, Levon, Marjanovic´, Damir, Kushniarevich, Alena, Behar, Doron M, Gilissen, Christian, Vissers, Lisenka, Veltman, Joris A, Balanovska, Elena, Derenko, Miroslava, Malyarchuk, Boris, Metspalu, Andres, Fedorova, Sardana, Eriksson, Anders, Manica, Andrea, Mendez, Fernando L, Karafet, Tatiana M, Veeramah, Krishna R, Bradman, Neil, Hammer, Michael F, Osipova, Ludmila P, Balanovsky, Oleg, Khusnutdinova, Elza K, Johnsen, Knut, Remm, Maido, Thomas, Mark G, Tyler-Smith, Chris, Underhill, Peter A, Willerslev, Eske, Nielsen, Rasmus, Metspalu, Mait, Villems, Richard, and Kivisild, Toomas

Subjects
Biological Sciences, Genetics, Human Genome, Base Sequence, Chromosomes, Human, Y, DNA, Mitochondrial, Evolution, Molecular, Genetic Variation, Genetics, Population, Haplotypes, Humans, Male, Models, Genetic, Phylogeny, Racial Groups, Sequence Analysis, DNA, Medical and Health Sciences, Bioinformatics
Abstract

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

12. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Author

Raghavan, Maanasa, Skoglund, Pontus, Graf, Kelly E, Metspalu, Mait, Albrechtsen, Anders, Moltke, Ida, Rasmussen, Simon, Stafford Jr, Thomas W, Orlando, Ludovic, Metspalu, Ene, Karmin, Monika, Tambets, Kristiina, Rootsi, Siiri, Mägi, Reedik, Campos, Paula F, Balanovska, Elena, Balanovsky, Oleg, Khusnutdinova, Elza, Litvinov, Sergey, Osipova, Ludmila P, Fedorova, Sardana A, Voevoda, Mikhail I, DeGiorgio, Michael, Sicheritz-Ponten, Thomas, Brunak, Søren, Demeshchenko, Svetlana, Kivisild, Toomas, Villems, Richard, Nielsen, Rasmus, Jakobsson, Mattias, and Willerslev, Eske

Subjects
Biological Sciences, Genetics, Human Society, Human Genome, American Indian or Alaska Native, Animals, Asia, Asian People, Chromosomes, Human, Y, DNA, Mitochondrial, Emigration and Immigration, Gene Flow, Genome, Human, Genome, Mitochondrial, Haplotypes, Humans, Indians, North American, Male, Phylogeny, Phylogeography, Siberia, Skeleton, White People, General Science & Technology
Abstract

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

Published
2014

13. A Systematic Review and Meta-Analysis of Free Triiodothyronine (FT3) Levels in Humans Depending on Seasonal Air Temperature Changes: Is the Variation in FT3 Levels Related to Nonshivering Thermogenesis?

Author

Nikanorova, Alena A., primary, Barashkov, Nikolay A., additional, Pshennikova, Vera G., additional, Teryutin, Fedor M., additional, Nakhodkin, Sergey S., additional, Solovyev, Aisen V., additional, Romanov, Georgii P., additional, Burtseva, Tatiana E., additional, and Fedorova, Sardana A., additional

Published
2023
Full Text
View/download PDF

14. Reconstructing Native American population history

Author

Reich, David, Patterson, Nick, Campbell, Desmond, Tandon, Arti, Mazieres, Stéphane, Ray, Nicolas, Parra, Maria V, Rojas, Winston, Duque, Constanza, Mesa, Natalia, García, Luis F, Triana, Omar, Blair, Silvia, Maestre, Amanda, Dib, Juan C, Bravi, Claudio M, Bailliet, Graciela, Corach, Daniel, Hünemeier, Tábita, Bortolini, Maria Cátira, Salzano, Francisco M, Petzl-Erler, María Luiza, Acuña-Alonzo, Victor, Aguilar-Salinas, Carlos, Canizales-Quinteros, Samuel, Tusié-Luna, Teresa, Riba, Laura, Rodríguez-Cruz, Maricela, Lopez-Alarcón, Mardia, Coral-Vazquez, Ramón, Canto-Cetina, Thelma, Silva-Zolezzi, Irma, Fernandez-Lopez, Juan Carlos, Contreras, Alejandra V, Jimenez-Sanchez, Gerardo, Gómez-Vázquez, Maria José, Molina, Julio, Carracedo, Ángel, Salas, Antonio, Gallo, Carla, Poletti, Giovanni, Witonsky, David B, Alkorta-Aranburu, Gorka, Sukernik, Rem I, Osipova, Ludmila, Fedorova, Sardana A, Vasquez, René, Villena, Mercedes, Moreau, Claudia, Barrantes, Ramiro, Pauls, David, Excoffier, Laurent, Bedoya, Gabriel, Rothhammer, Francisco, Dugoujon, Jean-Michel, Larrouy, Georges, Klitz, William, Labuda, Damian, Kidd, Judith, Kidd, Kenneth, Di Rienzo, Anna, Freimer, Nelson B, Price, Alkes L, and Ruiz-Linares, Andrés

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, American Indian or Alaska Native, Americas, Asia, Cluster Analysis, Emigration and Immigration, Gene Flow, Genetics, Population, History, Ancient, Humans, Indians, North American, Models, Genetic, Phylogeny, Polymorphism, Single Nucleotide, Siberia, General Science & Technology
Abstract

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Published
2012

15. Study of the natural and cultural space of the Sakha ethnos

Author

Fedorova Sardana and Konopleva Nina

Subjects
Social Sciences
Abstract

The article is devoted to the problem of preserving interethnic tolerance and cultural heritage of the Republic of Sakha (Yakutia), which is relevant for modern theory and history of culture. The authors analyze theoretical and methodological approaches to the essence of the concepts: ethnos, ethnicity, cultural space, natural and cultural heritage. They demonstrate the peculiarities of the linguistic and cultural heritage of Yakutia, its possibilities in positioning the region and promoting the culture of Yakut people.

Published
2022
Full Text
View/download PDF

16. The genetic legacy of legendary and historical Siberian chieftains

Author

Zvénigorosky, Vincent, Duchesne, Sylvie, Romanova, Liubomira, Gérard, Patrice, Petit, Christiane, Petit, Michel, Alexeev, Anatoly, Melnichuk, Olga, Gonzalez, Angéla, Fausser, Jean-Luc, Solovyev, Aisen, Romanov, Georgii, Barashkov, Nikolay, Fedorova, Sardana, Ludes, Bertrand, Crubézy, Eric, and Keyser, Christine

Published
2020
Full Text
View/download PDF

17. The genetics of kinship in remote human groups

Author

Zvénigorosky, Vincent, Crubézy, Eric, Gibert, Morgane, Thèves, Catherine, Hollard, Clémence, Gonzalez, Angéla, Fedorova, Sardana A., Alexeev, Anatoly N., Bravina, Rozalia I., Ludes, Bertrand, and Keyser, Christine

Published
2016
Full Text
View/download PDF

21. The GJB2 (Cx26) Gene Variants in Patients with Hearing Impairment in the Baikal Lake Region (Russia).

Author

Pshennikova, Vera G., Teryutin, Fedor M., Cherdonova, Alexandra M., Borisova, Tuyara V., Solovyev, Aisen V., Romanov, Georgii P., Morozov, Igor V., Bondar, Alexander A., Posukh, Olga L., Fedorova, Sardana A., and Barashkov, Nikolay A.

Subjects
GENETIC variation, HEARING disorders, RECESSIVE genes, KOREANS, HAPLOTYPES, LAKES
Abstract

The GJB2 (Cx26) gene pathogenic variants are associated with autosomal recessive deafness type 1A (DFNB1A, OMIM #220290). Direct sequencing of the GJB2 gene among 165 hearing-impaired individuals living in the Baikal Lake region of Russia identified 14 allelic variants: pathogenic/likely pathogenic—nine variants, benign—three variants, unclassified—one variant, and one novel variant. The contribution of the GJB2 gene variants to the etiology of hearing impairment (HI) in the total sample of patients was 15.8% (26 out of 165) and significantly differed in patients of different ethnicity (5.1% in Buryat patients and 28.9% in Russian patients). In patients with DFNB1A (n = 26), HIs were congenital/early onset (92.3%), symmetric (88.5%), sensorineural (100.0%), and variable in severity (moderate—11.6%, severe—26.9% or profound—61.5%). The reconstruction of the SNP haplotypes with three frequent GJB2 pathogenic variants (c.-23+1G>A, c.35delG or c.235delC), in comparison with previously published data, supports a major role of the founder effect in the expansion of the c.-23+1G>A and c.35delG variants around the world. Comparative analysis of the haplotypes with c.235delC revealed one major haplotype G A C T (97.5%) in Eastern Asians (Chinese, Japanese and Korean patients) and two haplotypes, G A C T (71.4%) and G A C C (28.6%), in Northern Asians (Altaians, Buryats and Mongols). The variable structure of the c.235delC-haplotypes in Northern Asians requires more studies to expand our knowledge about the origin of this pathogenic variant. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

22. Agent-Based Modeling of Autosomal Recessive Deafness 1A (DFNB1A) Prevalence with Regard to Intensity of Selection Pressure in Isolated Human Population

Author

Romanov, Georgii P., primary, Smirnova, Anna A., additional, Zamyatin, Vladimir I., additional, Mukhin, Aleksey M., additional, Kazantsev, Fedor V., additional, Pshennikova, Vera G., additional, Teryutin, Fedor M., additional, Solovyev, Aisen V., additional, Fedorova, Sardana A., additional, Posukh, Olga L., additional, Lashin, Sergey A., additional, and Barashkov, Nikolay A., additional

Published
2022
Full Text
View/download PDF

23. A common founder effect of the splice site variant c.-23 + 1G > A in GJB2 gene causing autosomal recessive deafness 1A (DFNB1A) in Eurasia

Author

Solovyev, Aisen V., primary, Kushniarevich, Alena, additional, Bliznetz, Elena, additional, Bady-Khoo, Marita, additional, Lalayants, Maria R., additional, Markova, Tatiana G., additional, Minárik, Gabriel, additional, Kádasi, L’udevít, additional, Metspalu, Ene, additional, Pshennikova, Vera G., additional, Teryutin, Fedor M., additional, Khusnutdinova, Elza K., additional, Poliakov, Alexander, additional, Metspalu, Mait, additional, Posukh, Olga L., additional, Barashkov, Nikolay A., additional, and Fedorova, Sardana A., additional

Published
2021
Full Text
View/download PDF

24. The Russian Old-Settlers in the Arctic Coast of Eastern Siberia: Family Name Diversity in the Context of Their Origin

Author

Solovyev, Aisen V., primary, Borisova, Tuyara V., additional, Cherdonova, Aleksandra M., additional, Romanov, Georgii P., additional, Teryutin, Fedor M., additional, Pshennikova, Vera G., additional, Gotovtsev, Nyurgun N., additional, Vasileva, Olga V., additional, Nikitina, Sargylana E., additional, Barashkov, Nikolay A., additional, Alekseev, Anatoly N., additional, and Fedorova, Sardana A., additional

Published
2021
Full Text
View/download PDF

25. Agent-based modeling of DFNB1A prevalence with regard to intensity of selection pressure in isolated human population: will cochlear implantation increase the cases of hereditary deafness?

Author

Romanov, Georgii P., primary, Smirnova, Anna A., additional, Zamyatin, Vladimir I., additional, Mukhin, Aleksey M., additional, Kazantsev, Fedor V., additional, Pshennikova, Vera G., additional, Teryutin, Fedor M., additional, Solovyev, Aisen V., additional, Fedorova, Sardana A., additional, Posukh, Olga L., additional, Lashin, Sergey A., additional, and Barashkov, Nikolay A., additional

Published
2021
Full Text
View/download PDF

26. A Common Founder Effect of the Splice Site Variant c.-23+1G>A in GJB2 Gene Causing Autosomal Recessive Deafness 1A (DFNB1A) in Eurasia

Author

Solovyev, Aisen V, primary, Kushniarevich, Alena, additional, Bliznetz, Elena, additional, Bady-Khoo, Marita, additional, Lalayants, Maria R, additional, Markova, Tatiana G, additional, Minárik, Gabriel, additional, Kádasi, L'udevít, additional, Metspalu, Ene, additional, Pshennikova, Vera G, additional, Teryutin, Fedor M, additional, Alekseev, Anatoly N, additional, Khusnutdinova, Elza K, additional, Poliakov, Alexander, additional, Мetspalu, Mait, additional, Posukh, Olga L, additional, Barashkov, Nikolay A, additional, and Fedorova, Sardana A, additional

Published
2021
Full Text
View/download PDF

27. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

Lazaridis, Iosif, Patterson, Nick, Mittnik, Alissa, Renaud, Gabriel, Mallick, Swapan, Kirsanow, Karola, Sudmant, Peter H., Schraiber, Joshua G., Castellano, Sergi, Lipson, Mark, Berger, Bonnie, Economou, Christos, Bollongino, Ruth, Fu, Qiaomei, Bos, Kirsten I., Nordenfelt, Susanne, Li, Heng, de Filippo, Cesare, Prüfer, Kay, Sawyer, Susanna, Posth, Cosimo, Haak, Wolfgang, Hallgren, Fredrik, Fornander, Elin, Rohland, Nadin, Delsate, Dominique, Francken, Michael, Guinet, Jean-Michel, Wahl, Joachim, Ayodo, George, Babiker, Hamza A., Bailliet, Graciela, Balanovska, Elena, Balanovsky, Oleg, Barrantes, Ramiro, Bedoya, Gabriel, Ben-Ami, Haim, Bene, Judit, Berrada, Fouad, Bravi, Claudio M., Brisighelli, Francesca, Busby, George B. J., Cali, Francesco, Churnosov, Mikhail, Cole, David E. C., Corach, Daniel, Damba, Larissa, van Driem, George, Dryomov, Stanislav, Dugoujon, Jean-Michel, Fedorova, Sardana A., Gallego Romero, Irene, Gubina, Marina, Hammer, Michael, Henn, Brenna M., Hervig, Tor, Hodoglugil, Ugur, Jha, Aashish R., Karachanak-Yankova, Sena, Khusainova, Rita, Khusnutdinova, Elza, Kittles, Rick, Kivisild, Toomas, Klitz, William, Kučinskas, Vaidutis, Kushniarevich, Alena, Laredj, Leila, Litvinov, Sergey, Loukidis, Theologos, Mahley, Robert W., Melegh, Béla, Metspalu, Ene, Molina, Julio, Mountain, Joanna, Näkkäläjärvi, Klemetti, Nesheva, Desislava, Nyambo, Thomas, Osipova, Ludmila, Parik, Jüri, Platonov, Fedor, Posukh, Olga, Romano, Valentino, Rothhammer, Francisco, Rudan, Igor, Ruizbakiev, Ruslan, Sahakyan, Hovhannes, Sajantila, Antti, Salas, Antonio, Starikovskaya, Elena B., Tarekegn, Ayele, Toncheva, Draga, Turdikulova, Shahlo, Uktveryte, Ingrida, Utevska, Olga, Vasquez, René, Villena, Mercedes, Voevoda, Mikhail, Winkler, Cheryl A., Yepiskoposyan, Levon, Zalloua, Pierre, Zemunik, Tatijana, Cooper, Alan, Capelli, Cristian, Thomas, Mark G., Ruiz-Linares, Andres, Tishkoff, Sarah A., Singh, Lalji, Thangaraj, Kumarasamy, Villems, Richard, Comas, David, Sukernik, Rem, Metspalu, Mait, Meyer, Matthias, Eichler, Evan E., Burger, Joachim, Slatkin, Montgomery, Pääbo, Svante, Kelso, Janet, Reich, David, and Krause, Johannes

Published
2014
Full Text
View/download PDF

28. The Role of Nonshivering Thermogenesis Genes on Leptin Levels Regulation in Residents of the Coldest Region of Siberia

Author

Nikanorova, Alena A., primary, Barashkov, Nikolay A., additional, Pshennikova, Vera G., additional, Nakhodkin, Sergey S., additional, Gotovtsev, Nyurgun N., additional, Romanov, Georgii P., additional, Solovyev, Aisen V., additional, Kuzmina, Sargylana S., additional, Sazonov, Nikolay N., additional, and Fedorova, Sardana A., additional

Published
2021
Full Text
View/download PDF

30. The attitude of young people in the city of Yakutsk to DNA-testing

Author

Kononova, Sardana, primary, Vinokurova, Dekabrina, additional, Barashkov, Nikolay A, additional, Semenova, Ariadna, additional, Sofronova, Sargylana, additional, Oksana, Sidorova, additional, Tatiana, Davydova, additional, Struchkov, Valentin, additional, Burtseva, Tatiana, additional, Romanova, Anna, additional, and Fedorova, Sardana, additional

Published
2021
Full Text
View/download PDF

32. Origin and diffusion of mtDNA haplogroup X

Author

Reidla, Maere, Kivisild, Toomas, Metspalu, Ene, Kaldma, Katrin, Tambets, Kristiina, Tolk, Helle-Viivi, Parik, Juri, Loogvali, Eva-Liis, Derenko, Miroslava, Malyarchuk, Boris, Bermisheva, Marina, Zhadonov, Sergey, Pennarun, Erwan, Gubina, Marina, Golubenko, Maria, Damba, Larisa, Fedorova, Sardana, Gusar, Vladislava, Grechanina, Elena, Mikerezi, Ilia, Moisan, Jean-Paul, Chaventre, Andre, Khusnutdinova, Elsa, Osipova, Ludmila, Stepanov, Vadim, Voevoda, Mikhail, Achilli, Alessandro, Rengo, Chiara, Rickards, Olga, De Stefano, Gian Franco, Papiha, Surinder, Beckman, Lars, Janicijevic, Branka, Rudan, Pavao, Anagnou, Nicholas, Michalodimitrakis, Emmanuel, Koziel, Slawomir, Usanga, Esien, Geberhiwot, Tarekegn, Herrnstadt, Corinna, Howell, Neil, Torroni, Antonio, and Villems, Richard

Subjects
DNA -- Research, Biological sciences
Published
2003

33. A new approach to estimating the prevalence of hereditary hearing loss: An analysis of the distribution of sign language users based on census data in Russia

Author

Romanov, Georgii P., primary, Pshennikova, Vera G., additional, Lashin, Sergey A., additional, Solovyev, Aisen V., additional, Teryutin, Fedor M., additional, Cherdonova, Aleksandra M., additional, Borisova, Tuyara V., additional, Sazonov, Nikolay N., additional, Khusnutdinova, Elza K., additional, Posukh, Olga L., additional, Fedorova, Sardana A., additional, and Barashkov, Nikolay A., additional

Published
2020
Full Text
View/download PDF

34. The Role of Leptin Levels in Adaptation to Cold Climates

Author

Nikanorova, Alena A., primary, Barashkov, Nikolay A., additional, Nakhodkin, Sergey S., additional, Pshennikova, Vera G., additional, Solovyev, Aisen V., additional, Romanov, Georgii P., additional, Kuzmina, Sargylana S., additional, Sazonov, Nikolay N., additional, Burtseva, Tatyana E., additional, Odland, Jon Øyvind, additional, and Fedorova, Sardana A., additional

Published
2020
Full Text
View/download PDF

36. Ancient human genome sequence of an extinct Palaeo-Eskimo

Author

Rasmussen, Morten, Li, Yingrui, Lindgreen, Stinus, Pedersen, Jakob Skou, Albrechtsen, Anders, Moltke, Ida, Metspalu, Mait, Metspalu, Ene, Kivisild, Toomas, Gupta, Ramneek, Bertalan, Marcelo, Nielsen, Kasper, Gilbert, Thomas M. P., Wang, Yong, Raghavan, Maanasa, Campos, Paula F., Kamp, Hanne Munkholm, Wilson, Andrew S., Gledhill, Andrew, Tridico, Silvana, Bunce, Michael, Lorenzen, Eline D., Binladen, Jonas, Guo, Xiaosen, Zhao, Jing, Zhang, Xiuqing, Zhang, Hao, Li, Zhuo, Chen, Minfeng, Orlando, Ludovic, Kristiansen, Karsten, Bak, Mads, Tommerup, Niels, Bendixen, Christian, Pierre, Tracey L., Grønnow, Bjarne, Meldgaard, Morten, Andreasen, Claus, Fedorova, Sardana A., Osipova, Ludmila P., Higham, Thomas F. G., Ramsey, Christopher Bronk, Hansen, Thomas v. O., Nielsen, Finn C., Crawford, Michael H., Brunak, Søren, Sicheritz-Pontén, Thomas, Villems, Richard, Nielsen, Rasmus, Krogh, Anders, Wang, Jun, and Willerslev, Eske

Published
2010
Full Text
View/download PDF

38. Comparison of PredictiveIn SilicoTools on Missense Variants inGJB2,GJB6, andGJB3Genes Associated with Autosomal Recessive Deafness 1A (DFNB1A)

Author

Pshennikova, Vera G., primary, Barashkov, Nikolay A., additional, Romanov, Georgii P., additional, Teryutin, Fedor M., additional, Solov’ev, Aisen V., additional, Gotovtsev, Nyurgun N., additional, Nikanorova, Alena A., additional, Nakhodkin, Sergey S., additional, Sazonov, Nikolay N., additional, Morozov, Igor V., additional, Bondar, Alexander A., additional, Dzhemileva, Lilya U., additional, Khusnutdinova, Elza K., additional, Posukh, Olga L., additional, and Fedorova, Sardana A., additional

Published
2019
Full Text
View/download PDF

41. A serological survey of echinococcosis, toxocariasis and trichinellosis among rural inhabitants of Central Yakutia

Author

Nakhodkin, Sergey S., primary, Pshennikova, Vera G., additional, Dyachkovskaya, Paraskovia S., additional, Barashkov, Nikolay A., additional, Nikanorova, Alena A., additional, Teryutin, Fedor M., additional, Melnichuk, Olga A., additional, Crubézy, Eric, additional, Fedorova, Sardana A., additional, and Magnaval, Jean-François, additional

Published
2019
Full Text
View/download PDF

42. A rare case of Waardenburg syndrome with unilateral hearing loss caused by nonsense variant c.772C>T (p.Arg259*) in the MITF gene in Yakut patient from the Eastern Siberia (Sakha Republic, Russia)

Author

Barashkov, Nikolay A., primary, Romanov, Georgii P., additional, Borisova, Uigulaana P., additional, Solovyev, Aisen V., additional, Pshennikova, Vera G., additional, Teryutin, Fedor M., additional, Bondar, Alexander A., additional, Morozov, Igor V., additional, Khusnutdinova, Elza K., additional, Posukh, Olga L., additional, Burtseva, Tatiana E., additional, Odland, Jon Øyvind, additional, and Fedorova, Sardana A., additional

Published
2019
Full Text
View/download PDF

43. A novel pathogenic variant c.975G>A (p.Trp325*) in the POU3F4 gene in Yakut family (Eastern Siberia, Russia) with the X-linked deafness-2 (DFNX2)

Author

Barashkov, Nikolay A., primary, Klarov, Leonid A., additional, Teryutin, Fedor M., additional, Solovyev, Aisen V., additional, Pshennikova, Vera G., additional, Konnikova, Edilia E., additional, Romanov, Georgii P., additional, Tobokhov, Alexander V., additional, Morozov, Igor V., additional, Bondar, Alexander A., additional, Posukh, Olga L., additional, Dzhemileva, Lilya U., additional, Tomsky, Mikhail I., additional, Khusnutdinova, Elza K., additional, and Fedorova, Sardana A., additional

Published
2018
Full Text
View/download PDF

44. Comparison of Predictive Tools on Missense Variants in , , and Genes Associated with Autosomal Recessive Deafness 1A (DFNB1A).

Author

Pshennikova, Vera G., Barashkov, Nikolay A., Romanov, Georgii P., Teryutin, Fedor M., Solov'ev, Aisen V., Gotovtsev, Nyurgun N., Nikanorova, Alena A., Nakhodkin, Sergey S., Sazonov, Nikolay N., Morozov, Igor V., Bondar, Alexander A., Dzhemileva, Lilya U., Khusnutdinova, Elza K., Posukh, Olga L., and Fedorova, Sardana A.

Subjects
DEAFNESS, MICROBIAL virulence, AMINO acids, CONNEXIN genetics, CONTROL groups, RECEIVER operating characteristic curves
Abstract

In silico predictive software allows assessing the effect of amino acid substitutions on the structure or function of a protein without conducting functional studies. The accuracy of in silico pathogenicity prediction tools has not been previously assessed for variants associated with autosomal recessive deafness 1A (DFNB1A). Here, we identify in silico tools with the most accurate clinical significance predictions for missense variants of the GJB2 (Cx26), GJB6 (Cx30), and GJB3 (Cx31) connexin genes associated with DFNB1A. To evaluate accuracy of selected in silico tools (SIFT, FATHMM, MutationAssessor, PolyPhen-2, CONDEL, MutationTaster, MutPred, Align GVGD, and PROVEAN), we tested nine missense variants with previously confirmed clinical significance in a large cohort of deaf patients and control groups from the Sakha Republic (Eastern Siberia, Russia): Сх26: p.Val27Ile, p.Met34Thr, p.Val37Ile, p.Leu90Pro, p.Glu114Gly, p.Thr123Asn, and p.Val153Ile; Cx30: p.Glu101Lys; Cx31: p.Ala194Thr. We compared the performance of the in silico tools (accuracy, sensitivity, and specificity) by using the missense variants in GJB2 (Cx26), GJB6 (Cx30), and GJB3 (Cx31) genes associated with DFNB1A. The correlation coefficient (r) and coefficient of the area under the Receiver Operating Characteristic (ROC) curve as alternative quality indicators of the tested programs were used. The resulting ROC curves demonstrated that the largest coefficient of the area under the curve was provided by three programs: SIFT (AUC = 0.833, p = 0.046), PROVEAN (AUC = 0.833, p = 0.046), and MutationAssessor (AUC = 0.833, p = 0.002). The most accurate predictions were given by two tested programs: SIFT and PROVEAN (Ac = 89%, Se = 67%, Sp = 100%, r = 0.75, AUC = 0.833). The results of this study may be applicable for analysis of novel missense variants of the GJB2 (Cx26), GJB6 (Cx30), and GJB3 (Cx31) connexin genes. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
View/download PDF

45. Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

Author

Ilumäe, Anne-Mai, primary, Reidla, Maere, additional, Chukhryaeva, Marina, additional, Järve, Mari, additional, Post, Helen, additional, Karmin, Monika, additional, Saag, Lauri, additional, Agdzhoyan, Anastasiya, additional, Kushniarevich, Alena, additional, Litvinov, Sergey, additional, Ekomasova, Natalya, additional, Tambets, Kristiina, additional, Metspalu, Ene, additional, Khusainova, Rita, additional, Yunusbayev, Bayazit, additional, Khusnutdinova, Elza K., additional, Osipova, Ludmila P., additional, Fedorova, Sardana, additional, Utevska, Olga, additional, Koshel, Sergey, additional, Balanovska, Elena, additional, Behar, Doron M., additional, Balanovsky, Oleg, additional, Kivisild, Toomas, additional, Underhill, Peter A., additional, Villems, Richard, additional, and Rootsi, Siiri, additional

Published
2016
Full Text
View/download PDF

46. Spectrum and Frequency of the GJB2 Gene Pathogenic Variants in a Large Cohort of Patients with Hearing Impairment Living in a Subarctic Region of Russia (the Sakha Republic)

Author

Barashkov, Nikolay A., primary, Pshennikova, Vera G., additional, Posukh, Olga L., additional, Teryutin, Fedor M., additional, Solovyev, Aisen V., additional, Klarov, Leonid A., additional, Romanov, Georgii P., additional, Gotovtsev, Nyurgun N., additional, Kozhevnikov, Andrey A., additional, Kirillina, Elena V., additional, Sidorova, Oksana G., additional, Vasilyevа, Lena M., additional, Fedotova, Elvira E., additional, Morozov, Igor V., additional, Bondar, Alexander A., additional, Solovyevа, Natalya A., additional, Kononova, Sardana K., additional, Rafailov, Adyum M., additional, Sazonov, Nikolay N., additional, Alekseev, Anatoliy N., additional, Tomsky, Mikhail I., additional, Dzhemileva, Lilya U., additional, Khusnutdinova, Elza K., additional, and Fedorova, Sardana A., additional

Published
2016
Full Text
View/download PDF

47. A Serological Survey About Zoonoses in the Verkhoyansk Area, Northeastern Siberia (Sakha Republic, Russian Federation)

Author

Magnaval, Jean-François, primary, Leparc-Goffart, Isabelle, additional, Gibert, Morgane, additional, Gurieva, Alla, additional, Outreville, Jonathan, additional, Dyachkovskaya, Praskovia, additional, Fabre, Richard, additional, Fedorova, Sardana, additional, Nikolaeva, Dariya, additional, Dubois, Damien, additional, Melnitchuk, Olga, additional, Daviaud-Fabre, Pascale, additional, Marty, Marie, additional, Alekseev, Anatoly, additional, and Crubezy, Eric, additional

Published
2016
Full Text
View/download PDF

48. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Author

Moreno-Mayar, J, Moreno-Mayar, J, Korneliussen, Thorfinn, Pierre, Tracey, Rasmussen, Morten, Campos, Paula, de Barros Damgaard, Peter, Allentoft, Morten, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren, Heyer, Evelyne, Zollikofer, Christoph, Ponce de León, Marcia, Smith, Colin, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin, Arriaza, Bernardo, Standen, Vivien, Luz, Maria, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail, Posukh, Olga, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, M, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul, Parham, Peter, Kemp, Brian, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder, Crawford, Michael, Villems, Richard, Smith, David, Waters, Michael, Goebel, Ted, Johnson, John, Malhi, Ripan, Jakobsson, Mattias, Meltzer, David, Manica, Andrea, Durbin, Richard, Bustamante, Carlos, Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian, Willerslev, Eske, Wall, Jeff, Nielsen, Rasmus, Song, Yun, Moreno-Mayar, J, Moreno-Mayar, J, Korneliussen, Thorfinn, Pierre, Tracey, Rasmussen, Morten, Campos, Paula, de Barros Damgaard, Peter, Allentoft, Morten, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren, Heyer, Evelyne, Zollikofer, Christoph, Ponce de León, Marcia, Smith, Colin, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin, Arriaza, Bernardo, Standen, Vivien, Luz, Maria, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail, Posukh, Olga, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, M, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul, Parham, Peter, Kemp, Brian, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder, Crawford, Michael, Villems, Richard, Smith, David, Waters, Michael, Goebel, Ted, Johnson, John, Malhi, Ripan, Jakobsson, Mattias, Meltzer, David, Manica, Andrea, Durbin, Richard, Bustamante, Carlos, Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian, Willerslev, Eske, Wall, Jeff, Nielsen, Rasmus, and Song, Yun

Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative Paleoamerican relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

49. A serological survey of echinococcosis, toxocariasis and trichinellosis among rural inhabitants of Central Yakutia.

Author

Nakhodkin, Sergey S., Pshennikova, Vera G., Dyachkovskaya, Paraskovia S., Barashkov, Nikolay A., Nikanorova, Alena A., Teryutin, Fedor M., Melnichuk, Olga A., Crubézy, Eric, Fedorova, Sardana A., and Magnaval, Jean-François

Subjects
EPIDEMIOLOGY, TOXOCARIASIS, ECHINOCOCCOSIS, TRICHINOSIS, FOOD habits, ENZYME-linked immunosorbent assay
Abstract

In 2018, a seroepidemiological survey was carried out in 3 ulus, or districts (Churapchinsky, Megino-Kangalassky and Ust-Aldansky) in Central Yakutia (Sakha Republic, Russian Federation) about 3 helminth zoonoses, namely, echinococcosis (alveolar or cystic), toxocariasis and trichinellosis. Ninety rural volunteers agreed to answer a questionnaire that inquired about demographic and environmental parameters along with food habits. Then they were asked to provide a venous blood sample. Serological investigations were carried out by enzyme-linked immunosorbent assay. Four subjects tested positive for echinococcosis, 1 for toxocariasis and 2 for trichinellosis. No demographic or environmental or dietary possible risk factor was found to be associated with these positive results. In conclusion, only echinococcosis and trichinellosis appeared to be in Yakutia as health threats among the 3 investigated zoonoses. [ABSTRACT FROM AUTHOR]

Published
2018
Full Text
View/download PDF

50. The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia

Author

Yunusbayev, Bayazit, primary, Metspalu, Mait, additional, Metspalu, Ene, additional, Valeev, Albert, additional, Litvinov, Sergei, additional, Valiev, Ruslan, additional, Akhmetova, Vita, additional, Balanovska, Elena, additional, Balanovsky, Oleg, additional, Turdikulova, Shahlo, additional, Dalimova, Dilbar, additional, Nymadawa, Pagbajabyn, additional, Bahmanimehr, Ardeshir, additional, Sahakyan, Hovhannes, additional, Tambets, Kristiina, additional, Fedorova, Sardana, additional, Barashkov, Nikolay, additional, Khidiyatova, Irina, additional, Mihailov, Evelin, additional, Khusainova, Rita, additional, Damba, Larisa, additional, Derenko, Miroslava, additional, Malyarchuk, Boris, additional, Osipova, Ludmila, additional, Voevoda, Mikhail, additional, Yepiskoposyan, Levon, additional, Kivisild, Toomas, additional, Khusnutdinova, Elza, additional, and Villems, Richard, additional

Published
2015
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results