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4 results on '"Abdullah, M. Syafiq"'

1. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Mallick, Swapan, Li, Heng, Lipson, Mark, Mathieson, Iain, Gymrek, Melissa, Racimo, Fernando, Zhao, Mengyao, Chennagiri, Niru, Nordenfelt, Susanne, Tandon, Arti, Skoglund, Pontus, Lazaridis, Iosif, Sankararaman, Sriram, Fu, Qiaomei, Rohland, Nadin, Renaud, Gabriel, Erlich, Yaniv, Willems, Thomas, Gallo, Carla, Spence, Jeffrey P, Song, Yun S, Poletti, Giovanni, Balloux, Francois, van Driem, George, de Knijff, Peter, Romero, Irene Gallego, Jha, Aashish R, Behar, Doron M, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Moreno-Estrada, Andres, Posukh, Olga L, Balanovska, Elena, Balanovsky, Oleg, Karachanak-Yankova, Sena, Sahakyan, Hovhannes, Toncheva, Draga, Yepiskoposyan, Levon, Tyler-Smith, Chris, Xue, Yali, Abdullah, M Syafiq, Ruiz-Linares, Andres, Beall, Cynthia M, Di Rienzo, Anna, Jeong, Choongwon, Starikovskaya, Elena B, Metspalu, Ene, Parik, Jüri, Villems, Richard, Henn, Brenna M, Hodoglugil, Ugur, Mahley, Robert, Sajantila, Antti, Stamatoyannopoulos, George, Wee, Joseph TS, Khusainova, Rita, Khusnutdinova, Elza, Litvinov, Sergey, Ayodo, George, Comas, David, Hammer, Michael F, Kivisild, Toomas, Klitz, William, Winkler, Cheryl A, Labuda, Damian, Bamshad, Michael, Jorde, Lynn B, Tishkoff, Sarah A, Watkins, W Scott, Metspalu, Mait, Dryomov, Stanislav, Sukernik, Rem, Singh, Lalji, Thangaraj, Kumarasamy, Pääbo, Svante, Kelso, Janet, Patterson, Nick, and Reich, David

Subjects
Human Genome, Genetics, Animals, Australia, Black People, Datasets as Topic, Genetic Variation, Genetics, Population, Genome, Human, Genomics, History, Ancient, Human Migration, Humans, Mutation Rate, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Phylogeny, Racial Groups, Sequence Analysis, DNA, Species Specificity, Time Factors, General Science & Technology
Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Published
2016

2. Global diversity, population stratification, and selection of human copy-number variation

Author

Sudmant, Peter H, Mallick, Swapan, Nelson, Bradley J, Hormozdiari, Fereydoun, Krumm, Niklas, Huddleston, John, Coe, Bradley P, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn B, Posukh, Olga L, Sahakyan, Hovhannes, Watkins, W Scott, Yepiskoposyan, Levon, Abdullah, M Syafiq, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Wee, Joseph TS, Tyler-Smith, Chris, van Driem, George, Romero, Irene Gallego, Jha, Aashish R, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Henn, Brenna, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena B, Ayodo, George, Beall, Cynthia M, Di Rienzo, Anna, Hammer, Michael F, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah A, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, and Eichler, Evan E

Subjects
Genetics, Human Genome, Animals, Black People, DNA Copy Number Variations, Evolution, Molecular, Gene Duplication, Genome, Human, Hominidae, Humans, Native Hawaiian or Other Pacific Islander, Phylogeny, Polymorphism, Single Nucleotide, Population, Selection, Genetic, Sequence Deletion, General Science & Technology
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Published
2015

3. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Capelli, Cristian, Sankararaman, Sriram, Thangaraj, Kumarasamy, Willems, Thomas, De Knijff, Peter, Hervig, Tor, Ayodo, George, Chennagiri, Niru, Lazaridis, Iosif, Karachanak-Yankova, Sena, Gallo, Carla, Wee, Joseph T. S., Mallick, Swapan, Jorde, Lynn B., Behar, Doron M., Hodoglugil, Ugur, Jha, Aashish R., Skoglund, Pontus, Khusainova, Rita, Jeong, Choongwon, Posukh, Olga L., Beall, Cynthia M., Bravi, Claudio M., Hammer, Michael F., Tishkoff, Sarah A., Balloux, Francois, Singh, Lalji, Van Driem, George, Henn, Brenna M., Winkler, Cheryl, Mahley, Robert, Kivisild, Toomas, Klitz, William, Tyler-Smith, Chris, Racimo, Fernando, Poletti, Giovanni, Parik, Jüri, Lipson, Mark, Toncheva, Draga, Fu, Qiaomei, Dryomov, Stanislav, Tandon, Arti, Nordenfelt, Susanne, Bamshad, Michael, Di Rienzo, Anna, Stamatoyannopoulos, George, Reich, David, Abdullah, M. Syafiq, Khusnutdinova, Elza, Sajantila, Antti, Gymrek, Melissa, Litvinov, Sergey, Yepiskoposyan, Levon, Ruiz-Linares, Andres, Metspalu, Ene, Patterson, Nick, Rohland, Nadin, Villems, Richard, Labuda, Damian, Renaud, Gabriel, Comas, David, Li, Heng, Balanovska, Elena, Metspalu, Mait, Mathieson, Iain, Gallego Romero, Irene, Watkins, W. Scott, Yong, Yun S., Zhao, Mengyao, Sukernik, Rem, Xue, Yali, Pääbo, Svante, Starikovskaya, Elena B., Balanovsky, Oleg, Moreno-Estrada, Andres, Kelso, Janet, Spence, Jeffrey P., Erlich, Yaniv, and Sahakyan, Hovhannes

Subjects
570 Life sciences, biology, 410 Linguistics, 3. Good health

4. Global diversity, population stratification and selection of human copy number variation

Author

Ayodo, George, Beall, Cynthia M., Metspalu, Mait, Henn, Brenna, Hammer, Michael, Bamshad, Michael, Yepiskoposyan, Levon, Posukh, Olga L., Sahakyan, Hovhannes, Nelson, Bradley J., Tyler-Smith, Chris, Khusainova, Rita, Parik, Jüri, Hervig, Tor, Sudmant, Peter H., Jorde, Lynn B., Toncheva, Draga, Hormozdiari, Fereydoun, Eichler, Evan E., Coe, Bradley P., Winkler, Cheryl, Sukernik, Rem, Starikovskaya, Elena B., Abdullah, M. Syafiq, Metspalu, Ene, Baker, Carl, Di Rienzo, Anna, Klitz, William, Mallick, Swapan, Wee, Joseph T.S., Watkins, W. Scott, Khusnutdinova, Elza, Bravi, Claudio M., Comas, David, Karachanak-Yankova, Sena, Huddleston, John, Tishkoff, Sarah A., Van Driem, George, Krumm, Niklas, Reich, David, Patterson, Nick, Ruiz-Linares, Andres, Kivisild, Toomas, Villems, Richard, Jha, Aashish R., Gallego Romero, Irene, Labuda, Damian, Nordenfeldt, Susanne, Dryomov, Stanislav, Sajantila, Antti, and Capelli, Christian

Subjects
410 Linguistics, 3. Good health
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single nucleotide variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

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