Browsing by Author "Santpere, G."

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    Great ape genetic diversity and population history
    (Nature Publishing Group, 2013) Prado-Martinez, J.; Eichler, E. E.; Marques-Bonet, T.; Sudmant, P. H.; Kidd, J. M.; Li, H.; Kelley, J. L.; Lorente-Galdos, B.; Veeramah, K. R.; Woerner, A. E.; O’Connor, T. D.; Santpere, G.; Cagan, A.; Theunert, C.; Casals, F.; Laayouni, H.; Munch, K.; Hobolth, A.; Halager, A. E.; Malig, M.; Hernandez-Rodriguez, J.; Hernando-Herraez, I.; Prüfer, K.; Pybus, M.; Johnstone, L.; Lachmann, M.; Alkan C.; Twig, D.; Petit, N.; Baker, C.; Hormozdiari, F.; Fernandez-Callejo, M.; Dabad, M.; Wilson, M. L.; Stevison, L.; Camprubí, C.; Carvalho, T.; RuizHerrera, A.; Vives, L.; Mele, M.; Abello, T.; Kondova, I.; Bontrop, R. E.; Pusey, A.; Lankester, F.; Kiyang, J. A.; Bergl, R. A.; Lonsdorf, E.; Myers, S.; Ventura, M.; Gagneux, P.; Comas, D.; Siegismund, H.; Blanc, J.; Agueda-Calpena, L.; Gut, M.; Fulton, L.; Tishkoff, S. A.; Mullikin, J. C.; Wilson, R. K.; Gut, I. G.; Gonder, M K.; Ryder, O. A.; Hahn, B. H.; Navarro, A.; Akey, J. M.; Bertranpetit, J.; Reich, D.; Mailund, T.; Schierup, M. H.; Hvilsom, C.; Andrés, A. M.; Wall, J. D.; Bustamante, C. D.; Hammer, M. F.
    Most great ape genetic variation remains uncharacterized(1,2); however, its study is critical for understanding population history(3-6), recombination(7), selection(8) and susceptibility to disease(9,10). Here we sequence to high coverage a total of 79 wild-and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
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    Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex
    (Elsevier, 2020-04) Werling, D. M.; Pochareddy, S.; Choi, J.; An, J.-Y.; Sheppard, B.; Peng, M.; Li, Z.; Dastmalchi, C.; Santpere, G.; Sousa, A. M. M.; Tebbenkamp, A. T. N.; Kaur, N.; Gulden, F. O.; Breen, M. S.; Liang, L.; Gilson, M. C.; Zhao, X.; Dong, S.; Klei, L.; Çiçek, A. Ercüment; Buxbaum, J. D.; Adle-Biassette, H.; Thomas, J.-L.; Aldinger, K. A.; O’Day, D. R.; Glass, I. A.; Zaitlen, N. A.; Talkowski, M. E.; Roeder, K.; State, M. W.; Devlin, B.; Sanders, S. J.; Sestan, N.
    Gene expression levels vary across developmental stage, cell type, and region in the brain. Genomic variants also contribute to the variation in expression, and some neuropsychiatric disorder loci may exert their effects through this mechanism. To investigate these relationships, we present BrainVar, a unique resource of paired whole-genome and bulk tissue RNA sequencing from the dorsolateral prefrontal cortex of 176 individuals across prenatal and postnatal development. Here we identify common variants that alter gene expression (expression quantitative trait loci [eQTLs]) constantly across development or predominantly during prenatal or postnatal stages. Both “constant” and “temporal-predominant” eQTLs are enriched for loci associated with neuropsychiatric traits and disorders and colocalize with specific variants. Expression levels of more than 12,000 genes rise or fall in a concerted late-fetal transition, with the transitional genes enriched for cell-type-specific genes and neuropsychiatric risk loci, underscoring the importance of cataloging developmental trajectories in understanding cortical physiology and pathology.