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1. Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits—The Hispanic/Latino Anthropometry Consortium

Author

Fernández-Rhodes, Lindsay, Graff, Mariaelisa, Buchanan, Victoria L, Justice, Anne E, Highland, Heather M, Guo, Xiuqing, Zhu, Wanying, Chen, Hung-Hsin, Young, Kristin L, Adhikari, Kaustubh, Palmer, Nicholette D, Below, Jennifer E, Bradfield, Jonathan, Pereira, Alexandre C, Glover, LáShauntá, Kim, Daeeun, Lilly, Adam G, Shrestha, Poojan, Thomas, Alvin G, Zhang, Xinruo, Chen, Minhui, Chiang, Charleston WK, Pulit, Sara, Horimoto, Andrea, Krieger, Jose E, Guindo-Martínez, Marta, Preuss, Michael, Schumann, Claudia, Smit, Roelof AJ, Torres-Mejía, Gabriela, Acuña-Alonzo, Victor, Bedoya, Gabriel, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, González-José, Rolando, Poletti, Giovanni, Rothhammer, Francisco, Hakonarson, Hakon, Igo, Robert, Adler, Sharon G, Iyengar, Sudha K, Nicholas, Susanne B, Gogarten, Stephanie M, Isasi, Carmen R, Papnicolaou, George, Stilp, Adrienne M, Qi, Qibin, Kho, Minjung, Smith, Jennifer A, Langefeld, Carl D, Wagenknecht, Lynne, Mckean-Cowdin, Roberta, Gao, Xiaoyi Raymond, Nousome, Darryl, Conti, David V, Feng, Ye, Allison, Matthew A, Arzumanyan, Zorayr, Buchanan, Thomas A, Chen, Yii-Der Ida, Genter, Pauline M, Goodarzi, Mark O, Hai, Yang, Hsueh, Willa, Ipp, Eli, Kandeel, Fouad R, Lam, Kelvin, Li, Xiaohui, Nadler, Jerry L, Raffel, Leslie J, Roll, Kathryn, Sandow, Kevin, Tan, Jingyi, Taylor, Kent D, Xiang, Anny H, Yao, Jie, Audirac-Chalifour, Astride, Peralta Romero, Jose de Jesus, Hartwig, Fernando, Horta, Bernando, Blangero, John, Curran, Joanne E, Duggirala, Ravindranath, Lehman, Donna E, Puppala, Sobha, Fejerman, Laura, John, Esther M, Aguilar-Salinas, Carlos, Burtt, Noël P, Florez, Jose C, García-Ortíz, Humberto, González-Villalpando, Clicerio, Mercader, Josep, Orozco, Lorena, Tusié-Luna, Teresa, Blanco, Estela, Gahagan, Sheila, Cox, Nancy J, and Hanis, Craig

Abstract

[This corrects the article DOI: 10.1016/j.xhgg.2022.100099.].

Published
2023

2. Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits—The Hispanic/Latino Anthropometry Consortium

Author

Fernández-Rhodes, Lindsay, Graff, Mariaelisa, Buchanan, Victoria L, Justice, Anne E, Highland, Heather M, Guo, Xiuqing, Zhu, Wanying, Chen, Hung-Hsin, Young, Kristin L, Adhikari, Kaustubh, Palmer, Nicholette D, Below, Jennifer E, Bradfield, Jonathan, Pereira, Alexandre C, Glover, LáShauntá, Kim, Daeeun, Lilly, Adam G, Shrestha, Poojan, Thomas, Alvin G, Zhang, Xinruo, Chen, Minhui, Chiang, Charleston WK, Pulit, Sara, Horimoto, Andrea, Krieger, Jose E, Guindo-Martínez, Marta, Preuss, Michael, Schumann, Claudia, Smit, Roelof AJ, Torres-Mejía, Gabriela, Acuña-Alonzo, Victor, Bedoya, Gabriel, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, González-José, Rolando, Poletti, Giovanni, Rothhammer, Francisco, Hakonarson, Hakon, Igo, Robert, Adler, Sharon G, Iyengar, Sudha K, Nicholas, Susanne B, Gogarten, Stephanie M, Isasi, Carmen R, Papnicolaou, George, Stilp, Adrienne M, Qi, Qibin, Kho, Minjung, Smith, Jennifer A, Langefeld, Carl D, Wagenknecht, Lynne, Mckean-Cowdin, Roberta, Gao, Xiaoyi Raymond, Nousome, Darryl, Conti, David V, Feng, Ye, Allison, Matthew A, Arzumanyan, Zorayr, Buchanan, Thomas A, Chen, Yii-Der Ida, Genter, Pauline M, Goodarzi, Mark O, Hai, Yang, Hsueh, Willa, Ipp, Eli, Kandeel, Fouad R, Lam, Kelvin, Li, Xiaohui, Nadler, Jerry L, Raffel, Leslie J, Roll, Kathryn, Sandow, Kevin, Tan, Jingyi, Taylor, Kent D, Xiang, Anny H, Yao, Jie, Audirac-Chalifour, Astride, de Jesus Peralta Romero, Jose, Hartwig, Fernando, Horta, Bernando, Blangero, John, Curran, Joanne E, Duggirala, Ravindranath, Lehman, Donna E, Puppala, Sobha, Fejerman, Laura, John, Esther M, Aguilar-Salinas, Carlos, Burtt, Noël P, Florez, Jose C, García-Ortíz, Humberto, González-Villalpando, Clicerio, Mercader, Josep, Orozco, Lorena, Tusié-Luna, Teresa, Blanco, Estela, Gahagan, Sheila, Cox, Nancy J, and Hanis, Craig

Subjects
Biological Sciences, Genetics, Obesity, Human Genome, Hispanic/Latino, anthropometrics, diversity, fine-mapping, obesity, population stratification, trans-ancestral or trans-ethnic
Abstract

Hispanic/Latinos have been underrepresented in genome-wide association studies (GWAS) for anthropometric traits despite their notable anthropometric variability, ancestry proportions, and high burden of growth stunting and overweight/obesity. To address this knowledge gap, we analyzed densely imputed genetic data in a sample of Hispanic/Latino adults to identify and fine-map genetic variants associated with body mass index (BMI), height, and BMI-adjusted waist-to-hip ratio (WHRadjBMI). We conducted a GWAS of 18 studies/consortia as part of the Hispanic/Latino Anthropometry (HISLA) Consortium (stage 1, n = 59,771) and generalized our findings in 9 additional studies (stage 2, n = 10,538). We conducted a trans-ancestral GWAS with summary statistics from HISLA stage 1 and existing consortia of European and African ancestries. In our HISLA stage 1 + 2 analyses, we discovered one BMI locus, as well as two BMI signals and another height signal each within established anthropometric loci. In our trans-ancestral meta-analysis, we discovered three BMI loci, one height locus, and one WHRadjBMI locus. We also identified 3 secondary signals for BMI, 28 for height, and 2 for WHRadjBMI in established loci. We show that 336 known BMI, 1,177 known height, and 143 known WHRadjBMI (combined) SNPs demonstrated suggestive transferability (nominal significance and effect estimate directional consistency) in Hispanic/Latino adults. Of these, 36 BMI, 124 height, and 11 WHRadjBMI SNPs were significant after trait-specific Bonferroni correction. Trans-ancestral meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our findings demonstrate that future studies may also benefit from leveraging diverse ancestries and differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification.

Published
2022

3. Modelamiento molecular y análisis estructural de la variante I684S en la enzima TYK2 y su relación con la propensión a la psoriasis/Molecular modeling and structural analysis of variant I684S in the TYK2 enzyme and its relation with the susceptibility to psoriasis

Author

Alvarez, Yesid, Soto-Ospina, Alejandro, Villegas-Lanau, Andrés, Araque, Pedronel, Naranjo, Carlos Andrés, Uribe, Esteban, Jiménez, Sol, Vásquez, Elsa, de Jesús Bedoya, Gabriel, and Velásquez, Margarita

Published
2023
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4. Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates.

Author

Sul, Jae Hoon, Service, Susan K, Huang, Alden Y, Ramensky, Vasily, Hwang, Sun-Goo, Teshiba, Terri M, Park, YoungJun, Ori, Anil PS, Zhang, Zhongyang, Mullins, Niamh, Olde Loohuis, Loes M, Fears, Scott C, Araya, Carmen, Araya, Xinia, Spesny, Mitzi, Bejarano, Julio, Ramirez, Margarita, Castrillón, Gabriel, Gomez-Makhinson, Juliana, Lopez, Maria C, Montoya, Gabriel, Montoya, Claudia P, Aldana, Ileana, Escobar, Javier I, Ospina-Duque, Jorge, Kremeyer, Barbara, Bedoya, Gabriel, Ruiz-Linares, Andres, Cantor, Rita M, Molina, Julio, Coppola, Giovanni, Ophoff, Roel A, Macaya, Gabriel, Lopez-Jaramillo, Carlos, Reus, Victor, Bearden, Carrie E, Sabatti, Chiara, and Freimer, Nelson B

Subjects
Clinical Sciences, Public Health and Health Services, Psychology
Abstract

Current evidence from case/control studies indicates that genetic risk for psychiatric disorders derives primarily from numerous common variants, each with a small phenotypic impact. The literature describing apparent segregation of bipolar disorder (BP) in numerous multigenerational pedigrees suggests that, in such families, large-effect inherited variants might play a greater role. To identify roles of rare and common variants on BP, we conducted genetic analyses in 26 Colombia and Costa Rica pedigrees ascertained for bipolar disorder 1 (BP1), the most severe and heritable form of BP. In these pedigrees, we performed microarray SNP genotyping of 838 individuals and high-coverage whole-genome sequencing of 449 individuals. We compared polygenic risk scores (PRS), estimated using the latest BP1 genome-wide association study (GWAS) summary statistics, between BP1 individuals and related controls. We also evaluated whether BP1 individuals had a higher burden of rare deleterious single-nucleotide variants (SNVs) and rare copy number variants (CNVs) in a set of genes related to BP1. We found that compared with unaffected relatives, BP1 individuals had higher PRS estimated from BP1 GWAS statistics (P = 0.001 ~ 0.007) and displayed modest increase in burdens of rare deleterious SNVs (P = 0.047) and rare CNVs (P = 0.002 ~ 0.033) in genes related to BP1. We did not observe rare variants segregating in the pedigrees. These results suggest that small-to-moderate effect rare and common variants are more likely to contribute to BP1 risk in these extended pedigrees than a few large-effect rare variants.

Published
2020

5. Understanding the Hidden Complexity of Latin American Population Isolates.

Author

Mooney, Jazlyn A, Huber, Christian D, Service, Susan, Sul, Jae Hoon, Marsden, Clare D, Zhang, Zhongyang, Sabatti, Chiara, Ruiz-Linares, Andrés, Bedoya, Gabriel, Costa Rica/Colombia Consortium for Genetic Investigation of Bipolar Endophenotypes, Freimer, Nelson, and Lohmueller, Kirk E

Subjects
Costa Rica/Colombia Consortium for Genetic Investigation of Bipolar Endophenotypes, Humans, Pedigree, Genetics, Population, Genomics, Consanguinity, Homozygote, Genome, Human, Costa Rica, Colombia, Female, Male, Whole Genome Sequencing, White People, deleterious mutations, identity by descent, linkage disequilibrium, pedigree, population genetics, population isolate, Genetics, Human Genome, Whites, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Most population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16th century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole-genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 36×. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals is significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we find that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests that there is no single genetic signature of a population isolate.

Published
2018

6. Sodium-calcium exchanger-3 regulates pain “wind-up”: From human psychophysics to spinal mechanisms

Author

Trendafilova, Teodora, Adhikari, Kaustubh, Schmid, Annina B., Patel, Ryan, Polgár, Erika, Chisholm, Kim I., Middleton, Steven J., Boyle, Kieran, Dickie, Allen C., Semizoglou, Evangelia, Perez-Sanchez, Jimena, Bell, Andrew M., Ramirez-Aristeguieta, Luis Miguel, Khoury, Samar, Ivanov, Aleksandar, Wildner, Hendrik, Ferris, Eleanor, Chacón-Duque, Juan-Camilo, Sokolow, Sophie, Saad Boghdady, Mohamed A., Herchuelz, André, Faux, Pierre, Poletti, Giovanni, Gallo, Carla, Rothhammer, Francisco, Bedoya, Gabriel, Zeilhofer, Hanns Ulrich, Diatchenko, Luda, McMahon, Stephen B., Todd, Andrew J., Dickenson, Anthony H., Ruiz-Linares, Andres, and Bennett, David L.

Published
2022
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7. Clotting factor genes are associated with preeclampsia in high-altitude pregnant women in the Peruvian Andes

Author

Nieves-Colón, Maria A., Badillo Rivera, Keyla M., Sandoval, Karla, Villanueva Dávalos, Vanessa, Enriquez Lencinas, Luis E., Mendoza-Revilla, Javier, Adhikari, Kaustubh, González-Buenfil, Ram, Chen, Jessica W., Zhang, Elisa T., Sockell, Alexandra, Ortiz-Tello, Patricia, Hurtado, Gloria Malena, Condori Salas, Ramiro, Cebrecos, Ricardo, Manzaneda Choque, José C., Manzaneda Choque, Franz P., Yábar Pilco, Germán P., Rawls, Erin, Eng, Celeste, Huntsman, Scott, Burchard, Esteban, Ruiz-Linares, Andrés, González-José, Rolando, Bedoya, Gabriel, Rothhammer, Francisco, Bortolini, Maria Cátira, Poletti, Giovanni, Gallo, Carla, Bustamante, Carlos D., Baker, Julie C., Gignoux, Christopher R., Wojcik, Genevieve L., and Moreno-Estrada, Andrés

Published
2022
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9. 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
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10. The impact of socioeconomic and phenotypic traits on self-perception of ethnicity in Latin America

Author

Paschetta, Carolina, de Azevedo, Soledad, Ramallo, Virginia, Cintas, Celia, Pérez, Orlando, Navarro, Pablo, Bandieri, Lucas, Sánchez, Mirsha Quinto, Adhikari, Kaustubh, Bortolini, M. Catira, Ferrara, Giovanni Poletti, Gallo, Carla, Bedoya, Gabriel, Rothhammer, Francisco, Alonzo, Victor Acuña, Ruiz-Linares, Andrés, and González-José, Rolando

Published
2021
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11. Reconstructing Native American Migrations from Whole-genome and Whole-exome Data

Author

Gravel, Simon, Zakharia, Fouad, Moreno-Estrada, Andres, Byrnes, Jake K, Muzzio, Marina, Rodriguez-Flores, Juan L., Kenny, Eimear E., Gignoux, Christopher R., Maples, Brian K., Guiblet, Wilfried, Dutil, Julie, Via, Marc, Sandoval, Karla, Bedoya, Gabriel, Oleksyk, Taras K, Ruiz-Linares, Andres, Burchard, Esteban G, Martinez-Cruzado, Juan Carlos, Bustamante, Carlos D., and Project, The 1000 Genomes

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics, 92D25
Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Ta\'ino people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent and ancestry tract length, we show that post-contact populations differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe., Comment: 30 pages, inludes supplement. v2 contains clarifications, extra analyses, and a change in the language classification scheme used

Published
2013

13. Origin of the PSEN1 E280A mutation causing early‐onset Alzheimer's disease

Author

Lalli, Matthew A, Cox, Hannah C, Arcila, Mary L, Cadavid, Liliana, Moreno, Sonia, Garcia, Gloria, Madrigal, Lucia, Reiman, Eric M, Arcos‐Burgos, Mauricio, Bedoya, Gabriel, Brunkow, Mary E, Glusman, Gustavo, Roach, Jared C, Hood, Leroy, Kosik, Kenneth S, and Lopera, Francisco

Subjects
Acquired Cognitive Impairment, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease, Genetics, Dementia, Brain Disorders, Aging, Neurodegenerative, Neurosciences, Age of Onset, Alzheimer Disease, Colombia, Founder Effect, Genetic Predisposition to Disease, Haplotypes, Humans, Inheritance Patterns, Mutation, Presenilin-1, Whites, Alzheimer's disease, PSEN1, population genetics, whole-genome sequencing, White People, Alzheimer’s disease, Clinical Sciences, Geriatrics
Abstract

BackgroundA mutation in presenilin 1 (E280A) causes early-onset Alzheimer's disease. Understanding the origin of this mutation will inform medical genetics.MethodsWe sequenced the genomes of 102 individuals from Antioquia, Colombia. We applied identity-by-descent analysis to identify regions of common ancestry. We estimated the age of the E280A mutation and the local ancestry of the haplotype harboring this mutation.ResultsAll affected individuals share a minimal haplotype of 1.8 Mb containing E280A. We estimate a time to most recent common ancestor of E280A of 10 (95% credible interval, 7.2-12.6) generations. We date the de novo mutation event to 15 (95% credible interval, 11-25) generations ago. We infer a western European geographic origin of the shared haplotype.ConclusionsThe age and geographic origin of E280A are consistent with a single founder dating from the time of the Spanish Conquistadors who began colonizing Colombia during the early 16th century.

Published
2014

14. CNV analysis in Tourette syndrome implicates large genomic rearrangements in COL8A1 and NRXN1.

Author

Nag, Abhishek, Bochukova, Elena, Kremeyer, Barbara, Campbell, Desmond, Muller, Heike, Valencia-Duarte, Ana, Cardona, Julio, Rivas, Isabel, Mesa, Sandra, Cuartas, Mauricio, Garcia, Jharley, Bedoya, Gabriel, Cornejo, William, Herrera, Luis, Romero, Roxana, Fournier, Eduardo, McGrath, Lauren, Yu, Dongmei, Cook, Ed, Wang, Kai, Scharf, Jeremiah, Pauls, David, Plagnol, Vincent, Ruiz-Linares, Andrés, Farooqi, I, Reus, Victor, Mathews, Carol, Lowe, Thomas, and Freimer, Nelson

Subjects
Adolescent, Calcium-Binding Proteins, Cell Adhesion Molecules, Neuronal, Child, Collagen Type IX, DNA Copy Number Variations, Female, Genetic Predisposition to Disease, Genotype, Humans, Male, Nerve Tissue Proteins, Neural Cell Adhesion Molecules, Polymorphism, Single Nucleotide, Tourette Syndrome
Abstract

Tourette syndrome (TS) is a neuropsychiatric disorder with a strong genetic component. However, the genetic architecture of TS remains uncertain. Copy number variation (CNV) has been shown to contribute to the genetic make-up of several neurodevelopmental conditions, including schizophrenia and autism. Here we describe CNV calls using SNP chip genotype data from an initial sample of 210 TS cases and 285 controls ascertained in two Latin American populations. After extensive quality control, we found that cases (N = 179) have a significant excess (P = 0.006) of large CNV (>500 kb) calls compared to controls (N = 234). Amongst 24 large CNVs seen only in the cases, we observed four duplications of the COL8A1 gene region. We also found two cases with ∼400 kb deletions involving NRXN1, a gene previously implicated in neurodevelopmental disorders, including TS. Follow-up using multiplex ligation-dependent probe amplification (and including 53 more TS cases) validated the CNV calls and identified additional patients with rearrangements in COL8A1 and NRXN1, but none in controls. Examination of available parents indicates that two out of three NRXN1 deletions detected in the TS cases are de-novo mutations. Our results are consistent with the proposal that rare CNVs play a role in TS aetiology and suggest a possible role for rearrangements in the COL8A1 and NRXN1 gene regions.

Published
2013

15. 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

16. Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci

Author

Li, Yi, primary, Xiong, Ziyi, additional, Zhang, Manfei, additional, Hysi, Pirro G., additional, Qian, Yu, additional, Adhikari, Kaustubh, additional, Weng, Jun, additional, Wu, Sijie, additional, Du, Siyuan, additional, Gonzalez-Jose, Rolando, additional, Schuler-Faccini, Lavinia, additional, Bortolini, Maria-Catira, additional, Acuna-Alonzo, Victor, additional, Canizales-Quinteros, Samuel, additional, Gallo, Carla, additional, Poletti, Giovanni, additional, Bedoya, Gabriel, additional, Rothhammer, Francisco, additional, Wang, Jiucun, additional, Tan, Jingze, additional, Yuan, Ziyu, additional, Jin, Li, additional, Uitterlinden, André G., additional, Ghanbari, Mohsen, additional, Ikram, M. Arfan, additional, Nijsten, Tamar, additional, Zhu, Xiangyu, additional, Lei, Zhen, additional, Jia, Peilin, additional, Ruiz-Linares, Andres, additional, Spector, Timothy D., additional, Wang, Sijia, additional, Kayser, Manfred, additional, and Liu, Fan, additional

Published
2023
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17. Geographic patterns of genome admixture in Latin American Mestizos.

Author

Wang, Sijia, Ray, Nicolas, Rojas, Winston, Parra, Maria V, Bedoya, Gabriel, Gallo, Carla, Poletti, Giovanni, Mazzotti, Guido, Hill, Kim, Hurtado, Ana M, Camrena, Beatriz, Nicolini, Humberto, Klitz, William, Barrantes, Ramiro, Molina, Julio A, Freimer, Nelson B, Bortolini, Maria Cátira, Salzano, Francisco M, Petzl-Erler, Maria L, Tsuneto, Luiza T, Dipierri, José E, Alfaro, Emma L, Bailliet, Graciela, Bianchi, Nestor O, Llop, Elena, Rothhammer, Francisco, Excoffier, Laurent, and Ruiz-Linares, Andrés

Subjects
Chromosomes, Human, X, Humans, Genetics, Population, Microsatellite Repeats, Heterozygote, Genome, Human, African Continental Ancestry Group, American Native Continental Ancestry Group, European Continental Ancestry Group, Latin America, Female, Male, Genetic Variation, Chromosomes, Human, X, Genetics, Population, Genome, Developmental Biology
Abstract

The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.

Published
2008

18. Native American ancestry significantly contributes to neuromyelitis optica susceptibility in the admixed Mexican population

Author

Romero-Hidalgo, Sandra, Flores-Rivera, José, Rivas-Alonso, Verónica, Barquera, Rodrigo, Villarreal-Molina, María Teresa, Antuna-Puente, Bárbara, Macias-Kauffer, Luis Rodrigo, Villalobos-Comparán, Marisela, Ortiz-Maldonado, Jair, Yu, Neng, Lebedeva, Tatiana V., Alosco, Sharon M., García-Rodríguez, Juan Daniel, González-Torres, Carolina, Rosas-Madrigal, Sandra, Ordoñez, Graciela, Guerrero-Camacho, Jorge Luis, Treviño-Frenk, Irene, Escamilla-Tilch, Monica, García-Lechuga, Maricela, Tovar-Méndez, Víctor Hugo, Pacheco-Ubaldo, Hanna, Acuña-Alonzo, Victor, Bortolini, Maria-Cátira, Gallo, Carla, Bedoya, Gabriel, Rothhammer, Francisco, González-Jose, Rolando, Ruiz-Linares, Andrés, Canizales-Quinteros, Samuel, Yunis, Edmond, Granados, Julio, and Corona, Teresa

Published
2020
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19. A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia

Author

Adhikari, Kaustubh, Mendoza-Revilla, Javier, Sohail, Anood, Fuentes-Guajardo, Macarena, Lampert, Jodie, Chacón-Duque, Juan Camilo, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Acuña-Alonzo, Victor, Jaramillo, Claudia, Arias, William, Lozano, Rodrigo Barquera, Everardo, Paola, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Silva de Cerqueira, Caio C., Hunemeier, Tábita, Ramallo, Virginia, Schuler-Faccini, Lavinia, Salzano, Francisco M., Gonzalez-José, Rolando, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Tobin, Desmond J., Fumagalli, Matteo, Balding, David, and Ruiz-Linares, Andrés

Published
2019
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21. Genome-wide association studies identify DNA variants influencing eyebrow thickness variation in Europeans and across continental populations

Author

Peng, Fuduan, primary, Xiong, Ziyi, additional, Zhu, Gu, additional, Hysi, Pirro G., additional, Eller, Ryan J., additional, Wu, Sijie, additional, Adhikari, Kaustubh, additional, Chen, Yan, additional, Li, Yi, additional, Gonzalez-José, Rolando, additional, Schüler-Faccini, Lavinia, additional, Bortolini, Maria-Cátira, additional, Acuña-Alonzo, Victor, additional, Canizales-Quinteros, Samuel, additional, Gallo, Carla, additional, Poletti, Giovanni, additional, Bedoya, Gabriel, additional, Rothhammer, Francisco, additional, Uitterlinden, André G., additional, Ikram, M. Arfan, additional, Nijsten, Tamar, additional, Ruiz-Linares, Andrés, additional, Wang, Sijia, additional, Walsh, Susan, additional, Spector, Timothy D., additional, Martin, Nicholas G., additional, Kayser, Manfred, additional, and Liu, Fan, additional

Published
2023
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22. Erratum: Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium.

Author

Fernández-Rhodes, Lindsay, Fernández-Rhodes, Lindsay, Graff, Mariaelisa, Buchanan, Victoria L, Justice, Anne E, Highland, Heather M, Guo, Xiuqing, Zhu, Wanying, Chen, Hung-Hsin, Young, Kristin L, Adhikari, Kaustubh, Palmer, Nicholette D, Below, Jennifer E, Bradfield, Jonathan, Pereira, Alexandre C, Glover, LáShauntá, Kim, Daeeun, Lilly, Adam G, Shrestha, Poojan, Thomas, Alvin G, Zhang, Xinruo, Chen, Minhui, Chiang, Charleston WK, Pulit, Sara, Horimoto, Andrea, Krieger, Jose E, Guindo-Martínez, Marta, Preuss, Michael, Schumann, Claudia, Smit, Roelof AJ, Torres-Mejía, Gabriela, Acuña-Alonzo, Victor, Bedoya, Gabriel, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, González-José, Rolando, Poletti, Giovanni, Rothhammer, Francisco, Hakonarson, Hakon, Igo, Robert, Adler, Sharon G, Iyengar, Sudha K, Nicholas, Susanne B, Gogarten, Stephanie M, Isasi, Carmen R, Papnicolaou, George, Stilp, Adrienne M, Qi, Qibin, Kho, Minjung, Smith, Jennifer A, Langefeld, Carl D, Wagenknecht, Lynne, Mckean-Cowdin, Roberta, Gao, Xiaoyi Raymond, Nousome, Darryl, Conti, David V, Feng, Ye, Allison, Matthew A, Arzumanyan, Zorayr, Buchanan, Thomas A, Chen, Yii-Der Ida, Genter, Pauline M, Goodarzi, Mark O, Hai, Yang, Hsueh, Willa, Ipp, Eli, Kandeel, Fouad R, Lam, Kelvin, Li, Xiaohui, Nadler, Jerry L, Raffel, Leslie J, Roll, Kathryn, Sandow, Kevin, Tan, Jingyi, Taylor, Kent D, Xiang, Anny H, Yao, Jie, Audirac-Chalifour, Astride, Peralta Romero, Jose de Jesus, Hartwig, Fernando, Horta, Bernando, Blangero, John, Curran, Joanne E, Duggirala, Ravindranath, Lehman, Donna E, Puppala, Sobha, Fejerman, Laura, John, Esther M, Aguilar-Salinas, Carlos, Burtt, Noël P, Florez, Jose C, García-Ortíz, Humberto, González-Villalpando, Clicerio, Mercader, Josep, Orozco, Lorena, Tusié-Luna, Teresa, Blanco, Estela, Gahagan, Sheila, Cox, Nancy J, Hanis, Craig, Fernández-Rhodes, Lindsay, Fernández-Rhodes, Lindsay, Graff, Mariaelisa, Buchanan, Victoria L, Justice, Anne E, Highland, Heather M, Guo, Xiuqing, Zhu, Wanying, Chen, Hung-Hsin, Young, Kristin L, Adhikari, Kaustubh, Palmer, Nicholette D, Below, Jennifer E, Bradfield, Jonathan, Pereira, Alexandre C, Glover, LáShauntá, Kim, Daeeun, Lilly, Adam G, Shrestha, Poojan, Thomas, Alvin G, Zhang, Xinruo, Chen, Minhui, Chiang, Charleston WK, Pulit, Sara, Horimoto, Andrea, Krieger, Jose E, Guindo-Martínez, Marta, Preuss, Michael, Schumann, Claudia, Smit, Roelof AJ, Torres-Mejía, Gabriela, Acuña-Alonzo, Victor, Bedoya, Gabriel, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, González-José, Rolando, Poletti, Giovanni, Rothhammer, Francisco, Hakonarson, Hakon, Igo, Robert, Adler, Sharon G, Iyengar, Sudha K, Nicholas, Susanne B, Gogarten, Stephanie M, Isasi, Carmen R, Papnicolaou, George, Stilp, Adrienne M, Qi, Qibin, Kho, Minjung, Smith, Jennifer A, Langefeld, Carl D, Wagenknecht, Lynne, Mckean-Cowdin, Roberta, Gao, Xiaoyi Raymond, Nousome, Darryl, Conti, David V, Feng, Ye, Allison, Matthew A, Arzumanyan, Zorayr, Buchanan, Thomas A, Chen, Yii-Der Ida, Genter, Pauline M, Goodarzi, Mark O, Hai, Yang, Hsueh, Willa, Ipp, Eli, Kandeel, Fouad R, Lam, Kelvin, Li, Xiaohui, Nadler, Jerry L, Raffel, Leslie J, Roll, Kathryn, Sandow, Kevin, Tan, Jingyi, Taylor, Kent D, Xiang, Anny H, Yao, Jie, Audirac-Chalifour, Astride, Peralta Romero, Jose de Jesus, Hartwig, Fernando, Horta, Bernando, Blangero, John, Curran, Joanne E, Duggirala, Ravindranath, Lehman, Donna E, Puppala, Sobha, Fejerman, Laura, John, Esther M, Aguilar-Salinas, Carlos, Burtt, Noël P, Florez, Jose C, García-Ortíz, Humberto, González-Villalpando, Clicerio, Mercader, Josep, Orozco, Lorena, Tusié-Luna, Teresa, Blanco, Estela, Gahagan, Sheila, Cox, Nancy J, and Hanis, Craig

Abstract

[This corrects the article DOI: 10.1016/j.xhgg.2022.100099.].

Published
2023

23. Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci

Author

Li, Yi, Xiong, Ziyi, Zhang, Manfei, Hysi, Pirro G., Qian, Yu, Adhikari, Kaustubh, Weng, Jun, Wu, Sijie, Du, Siyuan, Gonzalez-Jose, Rolando, Schuler-Faccini, Lavinia, Bortolini, Maria Catira, Acuna-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Wang, Jiucun, Tan, Jingze, Yuan, Ziyu, Jin, Li, Uitterlinden, André G., Ghanbari, Mohsen, Ikram, M. Arfan, Nijsten, Tamar, Zhu, Xiangyu, Lei, Zhen, Jia, Peilin, Ruiz-Linares, Andres, Spector, Timothy D., Wang, Sijia, Kayser, Manfred, Liu, Fan, Li, Yi, Xiong, Ziyi, Zhang, Manfei, Hysi, Pirro G., Qian, Yu, Adhikari, Kaustubh, Weng, Jun, Wu, Sijie, Du, Siyuan, Gonzalez-Jose, Rolando, Schuler-Faccini, Lavinia, Bortolini, Maria Catira, Acuna-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Wang, Jiucun, Tan, Jingze, Yuan, Ziyu, Jin, Li, Uitterlinden, André G., Ghanbari, Mohsen, Ikram, M. Arfan, Nijsten, Tamar, Zhu, Xiangyu, Lei, Zhen, Jia, Peilin, Ruiz-Linares, Andres, Spector, Timothy D., Wang, Sijia, Kayser, Manfred, and Liu, Fan

Abstract

Human ear morphology, a complex anatomical structure represented by a multidimensional set of correlated and heritable phenotypes, has a poorly understood genetic architecture. In this study, we quantitatively assessed 136 ear morphology traits using deep learning analysis of digital face images in 14,921 individuals from five different cohorts in Europe, Asia, and Latin America. Through GWAS meta-analysis and C-GWASs, a recently introduced method to effectively combine GWASs of many traits, we identified 16 genetic loci involved in various ear phenotypes, eight of which have not been previously associated with human ear features. Our findings suggest that ear morphology shares genetic determinants with other surface ectoderm-derived traits such as facial variation, mono eyebrow, and male pattern baldness. Our results enhance the genetic understanding of human ear morphology and shed light on the shared genetic contributors of different surface ectoderm-derived phenotypes. Additionally, gene editing experiments in mice have demonstrated that knocking out the newly ear-associated gene (Intu) and a previously ear-associated gene (Tbx15) causes deviating mouse ear morphology.

Published
2023

25. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

Author

Chacón-Duque, Juan-Camilo, Adhikari, Kaustubh, Fuentes-Guajardo, Macarena, Mendoza-Revilla, Javier, Acuña-Alonzo, Victor, Barquera, Rodrigo, Quinto-Sánchez, Mirsha, Gómez-Valdés, Jorge, Everardo Martínez, Paola, Villamil-Ramírez, Hugo, Hünemeier, Tábita, Ramallo, Virginia, Silva de Cerqueira, Caio C., Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Villena, Mercedes, Vásquez, René, Llop, Elena, Sandoval, José R., Salazar-Granara, Alberto A., Parolin, Maria-Laura, Sandoval, Karla, Peñaloza-Espinosa, Rosenda I., Rangel-Villalobos, Hector, Winkler, Cheryl A., Klitz, William, Bravi, Claudio, Molina, Julio, Corach, Daniel, Barrantes, Ramiro, Gomes, Verónica, Resende, Carlos, Gusmão, Leonor, Amorim, Antonio, Xue, Yali, Dugoujon, Jean-Michel, Moral, Pedro, González-José, Rolando, Schuler-Faccini, Lavinia, Salzano, Francisco M., Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Poletti, Giovanni, Gallo, Carla, Bedoya, Gabriel, Rothhammer, Francisco, Balding, David, Hellenthal, Garrett, and Ruiz-Linares, Andrés

Published
2018
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26. GWAs Identify DNA Variants Influencing Eyebrow Thickness Variation in Europeans and Across Continental Populations

Author

Peng, Fuduan, Xiong, Ziyi, Zhu, Gu, Hysi, Pirro G., Eller, Ryan J., Wu, Sijie, Adhikari, Kaustubh, Chen, Yan, Li, Yi, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Uitterlinden, André G., Ikram, M. Arfan, Nijsten, Tamar, Ruiz-Linares, Andrés, Wang, Sijia, Walsh, Susan, Spector, Timothy D., Martin, Nicholas G., Kayser, Manfred, and Liu, Fan

Published
2023
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27. Proyecto puesta en marcha bajo contrato de colaboración Joint Venture

Author

Rivera-Lozano, Miller, dir., Paz-Ortega, Wilson Andrés, dir., Roa, Lina Naydu, Sánchez-Bedoya, Gabriel, Rivera-Lozano, Miller, dir., Paz-Ortega, Wilson Andrés, dir., Roa, Lina Naydu, and Sánchez-Bedoya, Gabriel

Abstract

En el terminal de carga aéreo de Bogotá se ha identificado la necesidad de suplir a través de un punto comercial el servicio de impresiones, fotocopias, venta de productos no perecederos y herramientas de ferretería, por lo que este trabajo muestra qué tan viable es la puesta en marcha de un proyecto de inversión bajo modelo Joint Venture brindando información financiera mediante la proyección de estados financieros, y algunos resultados importantes como margen operacional, punto de equilibrio, margen de contribución por unidad y tasa interna de retorno.

Published
2022

28. Disentangling Signatures of Selection Before and After European Colonization in Latin Americans

Author

Mendoza-Revilla, Javier, Chacón-Duque, J. Camilo, Fuentes-Guajardo, Macarena, Ormond, Louise, Wang, Ke, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Acuña-Alonzo, Victor, Jaramillo, Claudia, Arias, William, Barquera, Rodrigo, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, de Cerqueira, Caio C. Silva, Rivera, Keyla M. Badillo, Nieves-Colón, Maria A., Gignoux, Christopher R., Wojcik, Genevieve L., Moreno-Estrada, Andrés, Hünemeier, Tábita, Ramallo, Virginia, Schuler-Faccini, Lavinia, Gonzalez-José, Rolando, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Balding, David, Fumagalli, Matteo, Adhikari, Kaustubh, Ruiz-Linares, Andrés, Hellenthal, Garrett, Mendoza-Revilla, Javier, Chacón-Duque, J. Camilo, Fuentes-Guajardo, Macarena, Ormond, Louise, Wang, Ke, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Acuña-Alonzo, Victor, Jaramillo, Claudia, Arias, William, Barquera, Rodrigo, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, de Cerqueira, Caio C. Silva, Rivera, Keyla M. Badillo, Nieves-Colón, Maria A., Gignoux, Christopher R., Wojcik, Genevieve L., Moreno-Estrada, Andrés, Hünemeier, Tábita, Ramallo, Virginia, Schuler-Faccini, Lavinia, Gonzalez-José, Rolando, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Balding, David, Fumagalli, Matteo, Adhikari, Kaustubh, Ruiz-Linares, Andrés, and Hellenthal, Garrett

Abstract

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

Published
2022
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29. Proyecto puesta en marcha bajo contrato de colaboración Joint Venture

Author

Rivera-Lozano, Miller, Paz-Ortega, Wilson Andrés, Roa, Lina Naydu, Sánchez-Bedoya, Gabriel, Rivera-Lozano, Miller, Paz-Ortega, Wilson Andrés, Roa, Lina Naydu, and Sánchez-Bedoya, Gabriel

Abstract

En el terminal de carga aéreo de Bogotá se ha identificado la necesidad de suplir a través de un punto comercial el servicio de impresiones, fotocopias, venta de productos no perecederos y herramientas de ferretería, por lo que este trabajo muestra qué tan viable es la puesta en marcha de un proyecto de inversión bajo modelo Joint Venture brindando información financiera mediante la proyección de estados financieros, y algunos resultados importantes como margen operacional, punto de equilibrio, margen de contribución por unidad y tasa interna de retorno.

Published
2022

32. Disentangling Signatures of Selection Before and After European Colonization in Latin Americans

Author

Mendoza-Revilla, Javier, primary, Chacón-Duque, J. Camilo, additional, Fuentes-Guajardo, Macarena, additional, Ormond, Louise, additional, Wang, Ke, additional, Hurtado, Malena, additional, Villegas, Valeria, additional, Granja, Vanessa, additional, Acuña-Alonzo, Victor, additional, Jaramillo, Claudia, additional, Arias, William, additional, Barquera, Rodrigo, additional, Gómez-Valdés, Jorge, additional, Villamil-Ramírez, Hugo, additional, Silva de Cerqueira, Caio C., additional, Badillo Rivera, Keyla M., additional, Nieves-Colón, Maria A., additional, Gignoux, Christopher R., additional, Wojcik, Genevieve L., additional, Moreno-Estrada, Andrés, additional, Hünemeier, Tábita, additional, Ramallo, Virginia, additional, Schuler-Faccini, Lavinia, additional, Gonzalez-José, Rolando, additional, Bortolini, Maria-Cátira, additional, Canizales-Quinteros, Samuel, additional, Gallo, Carla, additional, Poletti, Giovanni, additional, Bedoya, Gabriel, additional, Rothhammer, Francisco, additional, Balding, David, additional, Fumagalli, Matteo, additional, Adhikari, Kaustubh, additional, Ruiz-Linares, Andrés, additional, and Hellenthal, Garrett, additional

Published
2022
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33. Proyecto puesta en marcha bajo contrato de colaboración Joint Venture

Author

Roa, Lina Naydu, Sánchez-Bedoya, Gabriel, Rivera-Lozano, Miller, and Paz-Ortega, Wilson Andrés

Subjects
OPERARIOS, OPAIN, MARGEN DE CONTRIBUCIÓN, FUNCIONARIOS, ZUNCHADO, MARGEN DE SEGURIDAD, EMBALAJE, MARGEN OPERACIONAL, JOINT VENTURE
Abstract

Trabajo de Síntesis Aplicada En el terminal de carga aéreo de Bogotá se ha identificado la necesidad de suplir a través de un punto comercial el servicio de impresiones, fotocopias, venta de productos no perecederos y herramientas de ferretería, por lo que este trabajo muestra qué tan viable es la puesta en marcha de un proyecto de inversión bajo modelo Joint Venture brindando información financiera mediante la proyección de estados financieros, y algunos resultados importantes como margen operacional, punto de equilibrio, margen de contribución por unidad y tasa interna de retorno. Especialización Especialista en Análisis y Administración Financiera RESUMEN 1. Introducción 2. Planteamiento del problema 3. Pregunta de investigación 4. Justificación 5. Objetivo general 6. Objetivos específicos 7. Marco conceptual / variables técnicas 8. Estructura estratégica 9. Marco legal 10. Marco metodológico y presentación de resultados 11. Estudio financiero Recomendaciones Conclusiones

Published
2022

37. Inbreeding, Native American ancestry and child mortality: linking human selection and paediatric medicine

Author

Koenigstein, Fabienne, primary, Boekstegers, Felix, additional, Wilson, James F, additional, Fuentes-Guajardo, Macarena, additional, Gonzalez-Jose, Rolando, additional, Bedoya, Gabriel, additional, Bortolini, Maria Cátira, additional, Acuña-Alonzo, Victor, additional, Gallo, Carla, additional, Ruiz Linares, Andres, additional, Rothhammer, Francisco, additional, and Lorenzo Bermejo, Justo, additional

Published
2021
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38. NNT mediates redox-dependent pigmentation via a UVB- and MITF-independent mechanism

Author

Allouche, Jennifer, primary, Rachmin, Inbal, additional, Adhikari, Kaustubh, additional, Pardo, Luba M., additional, Lee, Ju Hee, additional, McConnell, Alicia M., additional, Kato, Shinichiro, additional, Fan, Shaohua, additional, Kawakami, Akinori, additional, Suita, Yusuke, additional, Wakamatsu, Kazumasa, additional, Igras, Vivien, additional, Zhang, Jianming, additional, Navarro, Paula P., additional, Lugo, Camila Makhlouta, additional, Noonan, Haley R., additional, Christie, Kathleen A., additional, Itin, Kaspar, additional, Mujahid, Nisma, additional, Lo, Jennifer A., additional, Won, Chong Hyun, additional, Evans, Conor L., additional, Weng, Qing Yu, additional, Wang, Hequn, additional, Osseiran, Sam, additional, Lovas, Alyssa, additional, Németh, István, additional, Cozzio, Antonio, additional, Navarini, Alexander A., additional, Hsiao, Jennifer J., additional, Nguyen, Nhu, additional, Kemény, Lajos V., additional, Iliopoulos, Othon, additional, Berking, Carola, additional, Ruzicka, Thomas, additional, Gonzalez-José, Rolando, additional, Bortolini, Maria-Cátira, additional, Canizales-Quinteros, Samuel, additional, Acuna-Alonso, Victor, additional, Gallo, Carla, additional, Poletti, Giovanni, additional, Bedoya, Gabriel, additional, Rothhammer, Francisco, additional, Ito, Shosuke, additional, Schiaffino, Maria Vittoria, additional, Chao, Luke H., additional, Kleinstiver, Benjamin P., additional, Tishkoff, Sarah, additional, Zon, Leonard I., additional, Nijsten, Tamar, additional, Ruiz-Linares, Andrés, additional, Fisher, David E., additional, and Roider, Elisabeth, additional

Published
2021
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39. A global reference for human genetic variation

Author

Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming

Published
2015
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41. Frequency of Aspirin Resistance in Ischemic Stroke Patients and Healthy Controls from Colombia

Author

Roman-Gonzalez, Alejandro, primary, Naranjo, Carlos Andrés, additional, Cardona-Maya, Walter D., additional, Vallejo, Dionis, additional, Garcia, Francisco, additional, Franco, Cesar, additional, Alvarez, Leonor, additional, Tobón, Luis Ignacio, additional, López, Marta Ibeth, additional, Rua, Carolina, additional, Bedoya, Gabriel, additional, Cadavid, Ángela, additional, and Torres, José Domingo, additional

Published
2021
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42. NNT mediates redox-dependent pigmentation via a UVB- and MITF-independent mechanism

Author

Allouche, Jennifer, Rachmin, Inbal, Adhikari, Kaustubh, Pardo, Luba M., Lee, Ju Hee, McConnell, Alicia M., Kato, Shinichiro, Fan, Shaohua, Kawakami, Akinori, Suita, Yusuke, Wakamatsu, Kazumasa, Igras, Vivien, Zhang, Jianming, Navarro, Paula P., Lugo, Camila Makhlouta, Noonan, Haley R., Christie, Kathleen A., Itin, Kaspar, Mujahid, Nisma, Lo, Jennifer A., Won, Chong Hyun, Evans, Conor L., Weng, Qing Yu, Wang, Hequn, Osseiran, Sam, Lovas, Alyssa, Németh, István, Cozzio, Antonio, Navarini, Alexander A., Hsiao, Jennifer J., Nguyen, Nhu, Kemény, Lajos V., Iliopoulos, Othon, Berking, Carola, Ruzicka, Thomas, Gonzalez-José, Rolando, Bortolini, Maria Cátira, Canizales-Quinteros, Samuel, Acuna-Alonso, Victor, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Ito, Shosuke, Schiaffino, Maria Vittoria, Chao, Luke H., Kleinstiver, Benjamin P., Tishkoff, Sarah, Zon, Leonard I., Nijsten, Tamar, Ruiz-Linares, Andrés, Fisher, David E., Roider, Elisabeth, Allouche, Jennifer, Rachmin, Inbal, Adhikari, Kaustubh, Pardo, Luba M., Lee, Ju Hee, McConnell, Alicia M., Kato, Shinichiro, Fan, Shaohua, Kawakami, Akinori, Suita, Yusuke, Wakamatsu, Kazumasa, Igras, Vivien, Zhang, Jianming, Navarro, Paula P., Lugo, Camila Makhlouta, Noonan, Haley R., Christie, Kathleen A., Itin, Kaspar, Mujahid, Nisma, Lo, Jennifer A., Won, Chong Hyun, Evans, Conor L., Weng, Qing Yu, Wang, Hequn, Osseiran, Sam, Lovas, Alyssa, Németh, István, Cozzio, Antonio, Navarini, Alexander A., Hsiao, Jennifer J., Nguyen, Nhu, Kemény, Lajos V., Iliopoulos, Othon, Berking, Carola, Ruzicka, Thomas, Gonzalez-José, Rolando, Bortolini, Maria Cátira, Canizales-Quinteros, Samuel, Acuna-Alonso, Victor, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Ito, Shosuke, Schiaffino, Maria Vittoria, Chao, Luke H., Kleinstiver, Benjamin P., Tishkoff, Sarah, Zon, Leonard I., Nijsten, Tamar, Ruiz-Linares, Andrés, Fisher, David E., and Roider, Elisabeth

Abstract

Ultraviolet (UV) light and incompletely understood genetic and epigenetic variations determine skin color. Here we describe an UV- and microphthalmia-associated transcription factor (MITF)-independent mechanism of skin pigmentation. Targeting the mitochondrial redox-regulating enzyme nicotinamide nucleotide transhydrogenase (NNT) resulted in cellular redox changes that affect tyrosinase degradation. These changes regulate melanosome maturation and, consequently, eumelanin levels and pigmentation. Topical application of small-molecule inhibitors yielded skin darkening in human skin, and mice with decreased NNT function displayed increased pigmentation. Additionally, genetic modification of NNT in zebrafish alters melanocytic pigmentation. Analysis of four diverse human cohorts revealed significant associations of skin color, tanning, and sun protection use with various single-nucleotide polymorphisms within NNT. NNT levels were independent of UVB irradiation and redox modulation. Individuals with postinflammatory hyperpigmentation or lentigines displayed decreased skin NNT levels, suggesting an NNT-driven, redox-dependent pigmentation mechanism that can be targeted with NNT-modifying topical drugs for medical and cosmetic purposes.

Published
2021

46. 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
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49. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation

Author

Bonfante, Betty, primary, Faux, Pierre, additional, Navarro, Nicolas, additional, Mendoza-Revilla, Javier, additional, Dubied, Morgane, additional, Montillot, Charlotte, additional, Wentworth, Emma, additional, Poloni, Lauriane, additional, Varón-González, Ceferino, additional, Jones, Philip, additional, Xiong, Ziyi, additional, Fuentes-Guajardo, Macarena, additional, Palmal, Sagnik, additional, Chacón-Duque, Juan Camilo, additional, Hurtado, Malena, additional, Villegas, Valeria, additional, Granja, Vanessa, additional, Jaramillo, Claudia, additional, Arias, William, additional, Barquera, Rodrigo, additional, Everardo-Martínez, Paola, additional, Sánchez-Quinto, Mirsha, additional, Gómez-Valdés, Jorge, additional, Villamil-Ramírez, Hugo, additional, Silva de Cerqueira, Caio C., additional, Hünemeier, Tábita, additional, Ramallo, Virginia, additional, Liu, Fan, additional, Weinberg, Seth M., additional, Shaffer, John R., additional, Stergiakouli, Evie, additional, Howe, Laurence J., additional, Hysi, Pirro G., additional, Spector, Timothy D., additional, Gonzalez-José, Rolando, additional, Schüler-Faccini, Lavinia, additional, Bortolini, Maria-Cátira, additional, Acuña-Alonzo, Victor, additional, Canizales-Quinteros, Samuel, additional, Gallo, Carla, additional, Poletti, Giovanni, additional, Bedoya, Gabriel, additional, Rothhammer, Francisco, additional, Thauvin-Robinet, Christel, additional, Faivre, Laurence, additional, Costedoat, Caroline, additional, Balding, David, additional, Cox, Timothy, additional, Kayser, Manfred, additional, Duplomb, Laurence, additional, Yalcin, Binnaz, additional, Cotney, Justin, additional, Adhikari, Kaustubh, additional, and Ruiz-Linares, Andrés, additional

Published
2021
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50. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

Author

Bouakaze, Caroline, Delehelle, Franklin, Saenz-Oyhéréguy, Nancy, Moreira, Andreia, Schiavinato, Stéphanie, Croze, Myriam, Delon, Solène, Fortes-Lima, Cesar, Gibert, Morgane, Bujan, Louis, Huyghe, Eric, Bellis, Gil, Calderon, Rosario, Hernández, Candela Lucia, Avendaño-Tamayo, Efren, Bedoya, Gabriel, Salas, Antonio, Mazières, Stéphane, Charioni, Jacques, Migot-Nabias, Florence, Ruiz-Linares, Andres, Dugoujon, Jean-Michel, Thèves, Catherine, Mollereau-Manaute, Catherine, Noûs, Camille, Poulet, Nicolas, King, Turi, D'Amato, Maria Eugenia, Balaresque, Patricia, D’Amato, Maria Eugenia, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Etablissement Français du Sang Provence-Alpes Côte-d'Azur et Corse (EFS), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Groupe d'Activité de Médecine de la Reproduction [CHU Toulouse] (CECOS Toulouse), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Département d'Urologie-Andrologie et Transplantation Rénale [CHU Toulouse], Pôle Urologie - Néphrologie - Dialyse - Transplantations - Brûlés - Chirurgie plastique - Explorations fonctionnelles et physiologiques [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Institut national d'études démographiques (INED), Departamento de Zoologia y Antropologia Fisica, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Archaeogenetics Laboratory, Mère et enfant en milieu tropical : pathogènes, système de santé et transition épidémiologique (MERIT - UMR_D 216), Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Laboratoire Cogitamus, Office national de l'eau et des milieux aquatiques (ONEMA), Ministère de l'écologie, du développement durable et de l'énergie, Department of Oncology, Real Expression Artificial Life (IRIT-REVA), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), UMR 6578 : Adaptabilité Biologique et Culturelle (UAABC), Groupe de recherche en fertilité humaine ( GRFH), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Service d'Urologie - Transplantation Rénale - Andrologie, CHU Toulouse [Toulouse]-Hôpital de Rangueil, CHU Toulouse [Toulouse], Universidad Complutense de Madrid [Madrid] (UCM), Mère et enfant face aux infections tropicales (MERIT - UMR_D 216), Hydrobiologie - antenne de Montpellier (UR HYAX), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Department of Genetics [Leicester], University of Leicester, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Éco-Anthropologie (EAE), CECOS Midi-Pyrénées, centre de sterilité masculine et équipe d'accueil Fertilité Humaine, Hôpital Paule de Viguier, and CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]

Subjects
0301 basic medicine, Forensic Genetics, Male, Mutation rate, [SDV]Life Sciences [q-bio], Bayesian probability, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Machine learning, computer.software_genre, Polymorphism, Single Nucleotide, Haplogroup, Pathology and Forensic Medicine, 03 medical and health sciences, 0302 clinical medicine, Mutation Rate, (Hg prediction), Genetics, Humans, Y-STR, 030216 legal & forensic medicine, Genetik, ComputingMilieux_MISCELLANEOUS, Mathematics, Chromosomes, Human, Y, Artificial neural network, business.industry, Statistical parameter, DNA Fingerprinting, Random forest, Assignation accuracy and haplogroup prediction (Hg prediction), Support vector machine, 030104 developmental biology, Haplotypes, Assignation accuracy and haplogroup prediction, Incremental mutation rates, Artificial intelligence, business, computer, Multiplex Polymerase Chain Reaction, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Microsatellite Repeats
Abstract

International audience; We developed a new mutationally well-balanced 32 Y-STR multiplex ( CombYplex) together with a machine learning (ML) program PredYMa Le to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, Pred YMa Le was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99–100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.

Published
2020

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