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1. Uncovering Signals of Positive Selection in Peruvian Populations from Three Ecological Regions

Author

Caro-Consuegra, Rocio, Nieves-Colón, Maria A, Rawls, Erin, Rubin-de-Celis, Verónica, Lizárraga, Beatriz, Vidaurre, Tatiana, Sandoval, Karla, Fejerman, Laura, Stone, Anne C, Moreno-Estrada, Andrés, and Bosch, Elena

Subjects
Genetics, Adaptation, Physiological, Altitude, Ecosystem, Humans, Hypoxia, Peru, Polymorphism, Single Nucleotide, Selection, Genetic, Tolloid-Like Metalloproteinases, Peruvian populations, high-altitude adaptation, human adaptation, Biochemistry and Cell Biology, Evolutionary Biology
Abstract

Peru hosts extremely diverse ecosystems which can be broadly classified into the following three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might have differentially adapted to their contrasting environmental pressures. Previous studies have described several candidate genes underlying adaptation to hypobaric hypoxia among Andean highlanders. However, the adaptive genetic diversity of coastal and rainforest populations has been less studied. Here, we gathered genome-wide single-nucleotide polymorphism-array data from 286 Peruvians living across the three ecoregions and analyzed signals of recent positive selection through population differentiation and haplotype-based selection scans. Among highland populations, we identify candidate genes related to cardiovascular function (TLL1, DUSP27, TBX5, PLXNA4, SGCD), to the Hypoxia-Inducible Factor pathway (TGFA, APIP), to skin pigmentation (MITF), as well as to glucose (GLIS3) and glycogen metabolism (PPP1R3C, GANC). In contrast, most signatures of adaptation in coastal and rainforest populations comprise candidate genes related to the immune system (including SIGLEC8, TRIM21, CD44, and ICAM1 in the coast; CBLB and PRDM1 in the rainforest; and BRD2, HLA-DOA, HLA-DPA1 regions in both), possibly as a result of strong pathogen-driven selection. This study identifies candidate genes related to human adaptation to the diverse environments of South America.

Published
2022

2. Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components

Author

Verdugo, Ricardo A, Di Genova, Alex, Herrera, Luisa, Moraga, Mauricio, Acuña, Mónica, Berríos, Soledad, Llop, Elena, Valenzuela, Carlos Y, Bustamante, M Leonor, Digman, Dayhana, Symon, Adriana, Asenjo, Soledad, López, Pamela, Blanco, Alejandro, Suazo, José, Barozet, Emmanuelle, Caba, Fresia, Villalón, Marcelo, Alvarado, Sergio, Cáceres, Dante, Salgado, Katherine, Portales, Pilar, Moreno-Estrada, Andrés, Gignoux, Christopher R, Sandoval, Karla, Bustamante, Carlos D, Eng, Celeste, Huntsman, Scott, Burchard, Esteban G, Loira, Nicolás, Maass, Alejandro, and Cifuentes, Lucía

Subjects
Chile, Ethnicity, Female, Gene Frequency, Genetic Markers, Genetics, Population, Genotype, Genotyping Techniques, Humans, Indians, South American, Male, Phylogeography, Polymorphism, Single Nucleotide, Population Groups, Saliva, Admixture, Ancestry, Aymara, Mapuche, SNPs panel, Biological Sciences, Biochemistry & Molecular Biology
Abstract

BackgroundCurrent South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south.ResultsA panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country's average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors.ConclusionsWe have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.

Published
2020

3. Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes.

Author

Ávila-Arcos, María C, McManus, Kimberly F, Sandoval, Karla, Rodríguez-Rodríguez, Juan Esteban, Villa-Islas, Viridiana, Martin, Alicia R, Luisi, Pierre, Peñaloza-Espinosa, Rosenda I, Eng, Celeste, Huntsman, Scott, Burchard, Esteban G, Gignoux, Christopher R, Bustamante, Carlos D, and Moreno-Estrada, Andrés

Subjects
Native Americans, adaptive evolution, demographic inference, exome sequencing, Biochemistry and Cell Biology, Evolutionary Biology, Genetics
Abstract

Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico's Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.

Published
2020

4. Genetic analyses of diverse populations improves discovery for complex traits.

Author

Wojcik, Genevieve L, Graff, Mariaelisa, Nishimura, Katherine K, Tao, Ran, Haessler, Jeffrey, Gignoux, Christopher R, Highland, Heather M, Patel, Yesha M, Sorokin, Elena P, Avery, Christy L, Belbin, Gillian M, Bien, Stephanie A, Cheng, Iona, Cullina, Sinead, Hodonsky, Chani J, Hu, Yao, Huckins, Laura M, Jeff, Janina, Justice, Anne E, Kocarnik, Jonathan M, Lim, Unhee, Lin, Bridget M, Lu, Yingchang, Nelson, Sarah C, Park, Sung-Shim L, Poisner, Hannah, Preuss, Michael H, Richard, Melissa A, Schurmann, Claudia, Setiawan, Veronica W, Sockell, Alexandra, Vahi, Karan, Verbanck, Marie, Vishnu, Abhishek, Walker, Ryan W, Young, Kristin L, Zubair, Niha, Acuña-Alonso, Victor, Ambite, Jose Luis, Barnes, Kathleen C, Boerwinkle, Eric, Bottinger, Erwin P, Bustamante, Carlos D, Caberto, Christian, Canizales-Quinteros, Samuel, Conomos, Matthew P, Deelman, Ewa, Do, Ron, Doheny, Kimberly, Fernández-Rhodes, Lindsay, Fornage, Myriam, Hailu, Benyam, Heiss, Gerardo, Henn, Brenna M, Hindorff, Lucia A, Jackson, Rebecca D, Laurie, Cecelia A, Laurie, Cathy C, Li, Yuqing, Lin, Dan-Yu, Moreno-Estrada, Andres, Nadkarni, Girish, Norman, Paul J, Pooler, Loreall C, Reiner, Alexander P, Romm, Jane, Sabatti, Chiara, Sandoval, Karla, Sheng, Xin, Stahl, Eli A, Stram, Daniel O, Thornton, Timothy A, Wassel, Christina L, Wilkens, Lynne R, Winkler, Cheryl A, Yoneyama, Sachi, Buyske, Steven, Haiman, Christopher A, Kooperberg, Charles, Le Marchand, Loic, Loos, Ruth JF, Matise, Tara C, North, Kari E, Peters, Ulrike, Kenny, Eimear E, and Carlson, Christopher S

Subjects
Humans, Body Height, Cohort Studies, Genetics, Medical, Multifactorial Inheritance, Minority Groups, African Continental Ancestry Group, Asian Continental Ancestry Group, Hispanic Americans, Women's Health, United States, Female, Male, Health Status Disparities, Genome-Wide Association Study, Health Equity, Genetics, Medical, General Science & Technology
Abstract

Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1-3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4-10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States-where minority populations have a disproportionately higher burden of chronic conditions13-the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities.

Published
2019

5. A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma

Author

Spear, Melissa L, Hu, Donglei, Pino-Yanes, Maria, Huntsman, Scott, Eng, Celeste, Levin, Albert M, Ortega, Victor E, White, Marquitta J, McGarry, Meghan E, Thakur, Neeta, Galanter, Joshua, Mak, Angel CY, Oh, Sam S, Ampleford, Elizabeth, Peters, Stephen P, Davis, Adam, Kumar, Rajesh, Farber, Harold J, Meade, Kelley, Avila, Pedro C, Serebrisky, Denise, Lenoir, Michael A, Brigino-Buenaventura, Emerita, Cintron, William Rodriguez, Thyne, Shannon M, Rodriguez-Santana, Jose R, Ford, Jean G, Chapela, Rocio, Estrada, Andrés Moreno, Sandoval, Karla, Seibold, Max A, Winkler, Cheryl A, Bleecker, Eugene R, Myers, Deborah A, Williams, L Keoki, Hernandez, Ryan D, Torgerson, Dara G, and Burchard, Esteban G

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Lung, Genetics, Asthma, Human Genome, Respiratory, Pharmacology & Pharmacy, Pharmacology and pharmaceutical sciences
Abstract

Short-acting β2-adrenergic receptor agonists (SABAs) are the most commonly prescribed asthma medications worldwide. Response to SABAs is measured as bronchodilator drug response (BDR), which varies among racial/ethnic groups in the United States. However, the genetic variation that contributes to BDR is largely undefined in African Americans with asthma. To identify genetic variants that may contribute to differences in BDR in African Americans with asthma, we performed a genome-wide association study (GWAS) of BDR in 949 African-American children with asthma, genotyped with the Axiom World Array 4 (Affymetrix, Santa Clara, CA) followed by imputation using 1000 Genomes phase III genotypes. We used linear regression models adjusting for age, sex, body mass index (BMI) and genetic ancestry to test for an association between BDR and genotype at single-nucleotide polymorphisms (SNPs). To increase power and distinguish between shared vs. population-specific associations with BDR in children with asthma, we performed a meta-analysis across 949 African Americans and 1830 Latinos (total = 2779). Finally, we performed genome-wide admixture mapping to identify regions whereby local African or European ancestry is associated with BDR in African Americans. We identified a population-specific association with an intergenic SNP on chromosome 9q21 that was significantly associated with BDR (rs73650726, p = 7.69 × 10-9). A trans-ethnic meta-analysis across African Americans and Latinos identified three additional SNPs within the intron of PRKG1 that were significantly associated with BDR (rs7903366, rs7070958 and rs7081864, p ≤ 5 × 10-8). Our results failed to replicate in three additional populations of 416 Latinos and 1615 African Americans. Our findings indicate that both population-specific and shared genetic variation contributes to differences in BDR in minority children with asthma, and that the genetic underpinnings of BDR may differ between racial/ethnic groups.

Published
2019

6. An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos

Author

Gignoux, Christopher R, Torgerson, Dara G, Pino-Yanes, Maria, Uricchio, Lawrence H, Galanter, Joshua, Roth, Lindsey A, Eng, Celeste, Hu, Donglei, Nguyen, Elizabeth A, Huntsman, Scott, Mathias, Rasika A, Kumar, Rajesh, Rodriguez-Santana, Jose, Thakur, Neeta, Oh, Sam S, McGarry, Meghan, Moreno-Estrada, Andres, Sandoval, Karla, Winkler, Cheryl A, Seibold, Max A, Padhukasahasram, Badri, Conti, David V, Farber, Harold J, Avila, Pedro, Brigino-Buenaventura, Emerita, Lenoir, Michael, Meade, Kelley, Serebrisky, Denise, Borrell, Luisa N, Rodriguez-Cintron, William, Thyne, Shannon, Joubert, Bonnie R, Romieu, Isabelle, Levin, Albert M, Sienra-Monge, Juan-Jose, Del Rio-Navarro, Blanca Estela, Gan, Weiniu, Raby, Benjamin A, Weiss, Scott T, Bleecker, Eugene, Meyers, Deborah A, Martinez, Fernando J, Gauderman, W James, Gilliland, Frank, London, Stephanie J, Bustamante, Carlos D, Nicolae, Dan L, Ober, Carole, Sen, Saunak, Barnes, Kathleen, Williams, L Keoki, Hernandez, Ryan D, and Burchard, Esteban G

Subjects
Biomedical and Clinical Sciences, Immunology, Human Genome, Clinical Research, Lung, Asthma, Genetics, Aetiology, 2.1 Biological and endogenous factors, Respiratory, Chromosome Mapping, Chromosomes, Human, Pair 18, Genetic Predisposition to Disease, Hispanic or Latino, Humans, Polymorphism, Single Nucleotide, Smad2 Protein, asthma exacerbations, admixture mapping, meta-analysis, Latinos, SMAD2, gene expression, targeted sequencing, rare variation, Allergy
Abstract

BackgroundAsthma is a common but complex disease with racial/ethnic differences in prevalence, morbidity, and response to therapies.ObjectiveWe sought to perform an analysis of genetic ancestry to identify new loci that contribute to asthma susceptibility.MethodsWe leveraged the mixed ancestry of 3902 Latinos and performed an admixture mapping meta-analysis for asthma susceptibility. We replicated associations in an independent study of 3774 Latinos, performed targeted sequencing for fine mapping, and tested for disease correlations with gene expression in the whole blood of more than 500 subjects from 3 racial/ethnic groups.ResultsWe identified a genome-wide significant admixture mapping peak at 18q21 in Latinos (P = 6.8 × 10-6), where Native American ancestry was associated with increased risk of asthma (odds ratio [OR], 1.20; 95% CI, 1.07-1.34; P = .002) and European ancestry was associated with protection (OR, 0.86; 95% CI, 0.77-0.96; P = .008). Our findings were replicated in an independent childhood asthma study in Latinos (P = 5.3 × 10-3, combined P = 2.6 × 10-7). Fine mapping of 18q21 in 1978 Latinos identified a significant association with multiple variants 5' of SMAD family member 2 (SMAD2) in Mexicans, whereas a single rare variant in the same window was the top association in Puerto Ricans. Low versus high SMAD2 blood expression was correlated with case status (13.4% lower expression; OR, 3.93; 95% CI, 2.12-7.28; P

Published
2019

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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8. Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico

Author

Bravo-Lopez, Miriam, Villa-Islas, Viridiana, Arriaga, Carolina Rocha, Villaseñor-Altamirano, Ana B., Guzmán-Solís, Axel, Sandoval-Velasco, Marcela, Wesp, Julie K., Alcantara, Keitlyn, López-Corral, Aurelio, Gómez-Valdés, Jorge, Mejía, Elizabeth, Herrera, Alberto, Meraz-Moreno, Alejandro, de la Luz Moreno-Cabrera, Maria, Moreno-Estrada, Andrés, Nieves-Colón, Maria A., Olvera, Joel, Pérez-Pérez, Julia, Iversen, Katrine Højholt, Rasmussen, Simon, Sandoval, Karla, Zepeda, Gabriela, and Ávila-Arcos, María C.

Published
2020

9. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma

Author

Mak, Angel CY, White, Marquitta J, Eckalbar, Walter L, Szpiech, Zachary A, Oh, Sam S, Pino-Yanes, Maria, Hu, Donglei, Goddard, Pagé, Huntsman, Scott, Galanter, Joshua, Wu, Ann Chen, Himes, Blanca E, Germer, Soren, Vogel, Julia M, Bunting, Karen L, Eng, Celeste, Salazar, Sandra, Keys, Kevin L, Liberto, Jennifer, Nuckton, Thomas J, Nguyen, Thomas A, Torgerson, Dara G, Kwok, Pui-Yan, Levin, Albert M, Celedón, Juan C, Forno, Erick, Hakonarson, Hakon, Sleiman, Patrick M, Dahlin, Amber, Tantisira, Kelan G, Weiss, Scott T, Serebrisky, Denise, Brigino-Buenaventura, Emerita, Farber, Harold J, Meade, Kelley, Lenoir, Michael A, Avila, Pedro C, Sen, Saunak, Thyne, Shannon M, Rodriguez-Cintron, William, Winkler, Cheryl A, Moreno-Estrada, Andrés, Sandoval, Karla, Rodriguez-Santana, Jose R, Kumar, Rajesh, Williams, L Keoki, Ahituv, Nadav, Ziv, Elad, Seibold, Max A, Darnell, Robert B, Zaitlen, Noah, Hernandez, Ryan D, and Burchard, Esteban G

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Health Disparities, Precision Medicine, Lung, Genetics, Asthma, Human Genome, Pediatric, Minority Health, Biotechnology, 2.1 Biological and endogenous factors, Respiratory, Good Health and Well Being, Adolescent, Black or African American, Albuterol, Bronchodilator Agents, Child, Female, Genome-Wide Association Study, Hispanic or Latino, Humans, Male, Mexican Americans, Pharmacogenomic Variants, Polymorphism, Single Nucleotide, Race Factors, United States, albuterol, asthma, minority, NFKB1, Latinos, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Medical and Health Sciences, Respiratory System, Cardiovascular medicine and haematology, Clinical sciences
Abstract

RationaleAlbuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response.ObjectivesTo identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children.MethodsWe performed the first whole-genome sequencing pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR.Measurements and main resultsWe identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (P

Published
2018

10. Paths and timings of the peopling of Polynesia inferred from genomic networks

Author

Ioannidis, Alexander G., Blanco-Portillo, Javier, Sandoval, Karla, Hagelberg, Erika, Barberena-Jonas, Carmina, Hill, Adrian V. S., Rodríguez-Rodríguez, Juan Esteban, Fox, Keolu, Robson, Kathryn, Haoa-Cardinali, Sonia, Quinto-Cortes, Consuelo D., Miquel-Poblete, Juan Francisco, Auckland, Kathryn, Parks, Tom, Sofro, Abdul Salam M., Avila-Arcos, Maria C., and Sockell, Alexandra

Subjects
Polynesia -- Demographic aspects, Polynesians -- Distribution -- Genetic aspects, Company distribution practices, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth.sup.1, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys.sup.2-4. Here, using genome-wide data from merely 430 modern individuals from 21 key Pacific island populations and novel ancestry-specific computational analyses, we unravel the detailed genetic history of this vast, dispersed island network. Our reconstruction of the branching Polynesian migration sequence reveals a serial founder expansion, characterized by directional loss of variants, that originated in Samoa and spread first through the Cook Islands (Rarotonga), then to the Society (TÅtaiete ma) Islands (11th century), the western Austral (Tuha'a Pae) Islands and Tuamotu Archipelago (12th century), and finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua 'Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately ad 1200 via Mangareva. Analysis of genomic networks from 430 modern individuals across 21 Pacific island populations reveals the human settlement history of Polynesia., Author(s): Alexander G. Ioannidis [sup.1] [sup.2] , Javier Blanco-Portillo [sup.2] , Karla Sandoval [sup.2] , Erika Hagelberg [sup.3] , Carmina Barberena-Jonas [sup.2] , Adrian V. S. Hill [sup.4] [sup.5] , [...]

Published
2021
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11. A scoping review and critical evaluation of the methodological quality of clinical practice guidelines on nutrition in the preconception

Author

Ancira-Moreno, Mónica, primary, Burrola-Méndez, Soraya, additional, Muñoz-Manrique, Cinthya, additional, Omaña-Guzmán, Isabel, additional, Hoyos-Loya, Elizabeth, additional, Trejo-Domínguez, Alejandra, additional, Hernández-Cordero, Sonia, additional, Mazariegos, Mónica, additional, Smith, Natalia, additional, Tavano-Colaizzi, Loredana, additional, Mier-Cabrera, Jennifer, additional, Avendaño-Álvarez, Fermín, additional, Espino y Sosa, Salvador, additional, Muciño-Sandoval, Karla, additional, Ibarra-González, Lizeth, additional, and Medina-Avilés, Cristina, additional

Published
2023
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12. A global reference for human genetic variation

Author

Auton, Adam, Abecasis, Gonçalo R, Altshuler, David M, Durbin, Richard M, Bentley, David R, Chakravarti, Aravinda, Clark, Andrew G, Donnelly, Peter, Eichler, Evan E, Flicek, Paul, Gabriel, Stacey B, Gibbs, Richard A, Green, Eric D, Hurles, Matthew E, Knoppers, Bartha M, Korbel, Jan O, Lander, Eric S, Lee, Charles, Lehrach, Hans, Mardis, Elaine R, Marth, Gabor T, McVean, Gil A, Nickerson, Deborah A, Schmidt, Jeanette P, Sherry, Stephen T, Wang, Jun, Wilson, Richard K, Barnes, Kathleen C, Beiswanger, Christine, Burchard, Esteban G, Bustamante, Carlos D, Cai, Hongyu, Cao, Hongzhi, Gerry, Norman P, Gharani, Neda, Gignoux, Christopher R, Gravel, Simon, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S, Keinan, Alon, Kent, Alastair, Kerasidou, Angeliki, Li, Yingrui, Mathias, Rasika, Moreno-Estrada, Andres, Ossorio, Pilar N, Parker, Michael, Resch, Alissa M, Rotimi, Charles N, Royal, Charmaine D, Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H, Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Brooks, Lisa D, Felsenfeld, Adam L, McEwen, Jean E, Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A, Garrison, Erik P, Min Kang, Hyun, Marchini, Jonathan L, and McCarthy, Shane

Subjects
Human Genome, Genetics, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Datasets as Topic, Demography, Disease Susceptibility, Exome, Genetic Variation, Genetics, Medical, Genetics, Population, Genome, Human, Genome-Wide Association Study, Genomics, Genotype, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, INDEL Mutation, Internationality, Physical Chromosome Mapping, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Rare Diseases, Reference Standards, Sequence Analysis, DNA, Genomes Project Consortium, General Science & Technology
Abstract

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

Published
2015

13. Native American gene flow into Polynesia predating Easter Island settlement

Author

Ioannidis, Alexander G., Blanco-Portillo, Javier, Sandoval, Karla, Hagelberg, Erika, Miquel-Poblete, Juan Francisco, Moreno-Mayar, J. Víctor, and Rodríguez-Rodríguez, Juan Esteban

Subjects
Polynesia -- Social aspects -- Natural history, Genetic research, Population genetics -- Research -- Genetic aspects -- Social aspects, Gene flow -- Research -- Social aspects -- Genetic aspects, Native Americans -- Genetic aspects -- Natural history -- Research -- Social aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas.sup.1-6, while critics have argued that these botanical dispersals need not have been human mediated.sup.7. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South American populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui).sup.2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested.sup.8-12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian individuals with Native American individuals (around ad 1200) contemporaneous with the settlement of remote Oceania.sup.13-15. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia. Genomic analyses of DNA from modern individuals show that, about 800 years ago, pre-European contact occurred between Polynesian individuals and Native American individuals from near present-day Colombia, while remote Pacific islands were still being settled., Author(s): Alexander G. Ioannidis [sup.1] [sup.2] , Javier Blanco-Portillo [sup.2] , Karla Sandoval [sup.2] , Erika Hagelberg [sup.3] , Juan Francisco Miquel-Poblete [sup.4] , J. Víctor Moreno-Mayar [sup.5] , Juan [...]

Published
2020
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14. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos

Author

Pino-Yanes, Maria, Gignoux, Christopher R, Galanter, Joshua M, Levin, Albert M, Campbell, Catarina D, Eng, Celeste, Huntsman, Scott, Nishimura, Katherine K, Gourraud, Pierre-Antoine, Mohajeri, Kiana, O'Roak, Brian J, Hu, Donglei, Mathias, Rasika A, Nguyen, Elizabeth A, Roth, Lindsey A, Padhukasahasram, Badri, Moreno-Estrada, Andres, Sandoval, Karla, Winkler, Cheryl A, Lurmann, Fred, Davis, Adam, Farber, Harold J, Meade, Kelley, Avila, Pedro C, Serebrisky, Denise, Chapela, Rocio, Ford, Jean G, Lenoir, Michael A, Thyne, Shannon M, Brigino-Buenaventura, Emerita, Borrell, Luisa N, Rodriguez-Cintron, William, Sen, Saunak, Kumar, Rajesh, Rodriguez-Santana, Jose R, Bustamante, Carlos D, Martinez, Fernando D, Raby, Benjamin A, Weiss, Scott T, Nicolae, Dan L, Ober, Carole, Meyers, Deborah A, Bleecker, Eugene R, Mack, Steven J, Hernandez, Ryan D, Eichler, Evan E, Barnes, Kathleen C, Williams, L Keoki, Torgerson, Dara G, and Burchard, Esteban G

Subjects
Biomedical and Clinical Sciences, Immunology, Clinical Research, Human Genome, Genetics, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Adolescent, Adult, Black or African American, Child, Chromosome Mapping, Chromosomes, Human, Pair 14, DNA-Binding Proteins, Female, Genetic Loci, Genome, Human, Genome-Wide Association Study, Genotype, HLA-DQ alpha-Chains, Hispanic or Latino, Humans, Immunoglobulin E, Male, Polymorphism, Single Nucleotide, Transcription Factors, White People, IgE, genome-wide association study, admixture mapping, allergy, asthma, next-generation sequencing, Latinos, Hispanics, minority populations, Allergy
Abstract

BackgroundIgE is a key mediator of allergic inflammation, and its levels are frequently increased in patients with allergic disorders.ObjectiveWe sought to identify genetic variants associated with IgE levels in Latinos.MethodsWe performed a genome-wide association study and admixture mapping of total IgE levels in 3334 Latinos from the Genes-environments & Admixture in Latino Americans (GALA II) study. Replication was evaluated in 454 Latinos, 1564 European Americans, and 3187 African Americans from independent studies.ResultsWe confirmed associations of 6 genes identified by means of previous genome-wide association studies and identified a novel genome-wide significant association of a polymorphism in the zinc finger protein 365 gene (ZNF365) with total IgE levels (rs200076616, P = 2.3 × 10(-8)). We next identified 4 admixture mapping peaks (6p21.32-p22.1, 13p22-31, 14q23.2, and 22q13.1) at which local African, European, and/or Native American ancestry was significantly associated with IgE levels. The most significant peak was 6p21.32-p22.1, where Native American ancestry was associated with lower IgE levels (P = 4.95 × 10(-8)). All but 22q13.1 were replicated in an independent sample of Latinos, and 2 of the peaks were replicated in African Americans (6p21.32-p22.1 and 14q23.2). Fine mapping of 6p21.32-p22.1 identified 6 genome-wide significant single nucleotide polymorphisms in Latinos, 2 of which replicated in European Americans. Another single nucleotide polymorphism was peak-wide significant within 14q23.2 in African Americans (rs1741099, P = 3.7 × 10(-6)) and replicated in non-African American samples (P = .011).ConclusionWe confirmed genetic associations at 6 genes and identified novel associations within ZNF365, HLA-DQA1, and 14q23.2. Our results highlight the importance of studying diverse multiethnic populations to uncover novel loci associated with total IgE levels.

Published
2015

15. Genetic ancestry influences asthma susceptibility and lung function among Latinos

Author

Pino-Yanes, Maria, Thakur, Neeta, Gignoux, Christopher R, Galanter, Joshua M, Roth, Lindsey A, Eng, Celeste, Nishimura, Katherine K, Oh, Sam S, Vora, Hita, Huntsman, Scott, Nguyen, Elizabeth A, Hu, Donglei, Drake, Katherine A, Conti, David V, Moreno-Estrada, Andres, Sandoval, Karla, Winkler, Cheryl A, Borrell, Luisa N, Lurmann, Fred, Islam, Talat S, Davis, Adam, Farber, Harold J, Meade, Kelley, Avila, Pedro C, Serebrisky, Denise, Bibbins-Domingo, Kirsten, Lenoir, Michael A, Ford, Jean G, Brigino-Buenaventura, Emerita, Rodriguez-Cintron, William, Thyne, Shannon M, Sen, Saunak, Rodriguez-Santana, Jose R, Bustamante, Carlos D, Williams, L Keoki, Gilliland, Frank D, Gauderman, W James, Kumar, Rajesh, Torgerson, Dara G, and Burchard, Esteban G

Subjects
Biomedical and Clinical Sciences, Immunology, Asthma, Genetics, Human Genome, Lung, Clinical Research, Respiratory, Adolescent, Adult, Child, Female, Genetic Predisposition to Disease, Hispanic or Latino, Humans, Male, Odds Ratio, Racial Groups, United States, Young Adult, Genetic admixture, Hispanics, childhood asthma, minority, pulmonary function, Childhood asthma, Minority, Pulmonary function, Allergy
Abstract

BackgroundChildhood asthma prevalence and morbidity varies among Latinos in the United States, with Puerto Ricans having the highest and Mexicans the lowest.ObjectiveTo determine whether genetic ancestry is associated with the odds of asthma among Latinos, and secondarily whether genetic ancestry is associated with lung function among Latino children.MethodsWe analyzed 5493 Latinos with and without asthma from 3 independent studies. For each participant, we estimated the proportion of African, European, and Native American ancestry using genome-wide data. We tested whether genetic ancestry was associated with the presence of asthma and lung function among subjects with and without asthma. Odds ratios (OR) and effect sizes were assessed for every 20% increase in each ancestry.ResultsNative American ancestry was associated with lower odds of asthma (OR = 0.72, 95% CI: 0.66-0.78, P = 8.0 × 10(-15)), while African ancestry was associated with higher odds of asthma (OR = 1.40, 95% CI: 1.14-1.72, P = .001). These associations were robust to adjustment for covariates related to early life exposures, air pollution, and socioeconomic status. Among children with asthma, African ancestry was associated with lower lung function, including both pre- and post-bronchodilator measures of FEV1 (-77 ± 19 mL; P = 5.8 × 10(-5) and -83 ± 19 mL; P = 1.1 x 10(-5), respectively) and forced vital capacity (-100 ± 21 mL; P = 2.7 × 10(-6) and -107 ± 22 mL; P = 1.0 x 10(-6), respectively).ConclusionDifferences in the proportions of genetic ancestry can partially explain disparities in asthma susceptibility and lung function among Latinos.

Published
2015

16. 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

17. Reconstructing the Population Genetic History of the Caribbean

Author

Moreno-Estrada, Andres, Gravel, Simon, Zakharia, Fouad, McCauley, Jacob L., Byrnes, Jake K., Gignoux, Christopher R., Ortiz-Tello, Patricia A., Martinez, Ricardo J., Hedges, Dale J., Morris, Richard W., Eng, Celeste, Sandoval, Karla, Acevedo-Acevedo, Suehelay, Martinez-Cruzado, Juan Carlos, Norman, Paul J., Layrisse, Zulay, Parham, Peter, Burchard, Esteban Gonzalez, Cuccaro, Michael L., Martin, Eden R., and Bustamante, Carlos D.

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

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean., Comment: 26 pages, 6 figures, and supporting information

Published
2013

18. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits

Author

Moreno-Estrada, Andrés, Gignoux, Christopher R, Fernández-López, Juan Carlos, Zakharia, Fouad, Sikora, Martin, Contreras, Alejandra V, Acuña-Alonzo, Victor, Sandoval, Karla, Eng, Celeste, Romero-Hidalgo, Sandra, Ortiz-Tello, Patricia, Robles, Victoria, Kenny, Eimear E, Nuño-Arana, Ismael, Barquera-Lozano, Rodrigo, Macín-Pérez, Gastón, Granados-Arriola, Julio, Huntsman, Scott, Galanter, Joshua M, Via, Marc, Ford, Jean G, Chapela, Rocío, Rodriguez-Cintron, William, Rodríguez-Santana, Jose R, Romieu, Isabelle, Sienra-Monge, Juan José, del Rio Navarro, Blanca, London, Stephanie J, Ruiz-Linares, Andrés, Garcia-Herrera, Rodrigo, Estrada, Karol, Hidalgo-Miranda, Alfredo, Jimenez-Sanchez, Gerardo, Carnevale, Alessandra, Soberón, Xavier, Canizales-Quinteros, Samuel, Rangel-Villalobos, Héctor, Silva-Zolezzi, Irma, Burchard, Esteban Gonzalez, and Bustamante, Carlos D

Subjects
Biological Sciences, Anthropology, Genetics, Human Society, Clinical Research, Human Genome, Black People, Genetic Variation, Genome, Human, Humans, Indians, North American, Mexican Americans, Mexico, Population, White People, General Science & Technology
Abstract

Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.

Published
2014

19. A genome-wide association study of bronchodilator response in Latinos implicates rare variants

Author

Drake, Katherine A, Torgerson, Dara G, Gignoux, Christopher R, Galanter, Joshua M, Roth, Lindsey A, Huntsman, Scott, Eng, Celeste, Oh, Sam S, Yee, Sook Wah, Lin, Lawrence, Bustamante, Carlos D, Moreno-Estrada, Andrés, Sandoval, Karla, Davis, Adam, Borrell, Luisa N, Farber, Harold J, Kumar, Rajesh, Avila, Pedro C, Brigino-Buenaventura, Emerita, Chapela, Rocio, Ford, Jean G, LeNoir, Michael A, Lurmann, Fred, Meade, Kelley, Serebrisky, Denise, Thyne, Shannon, Rodríguez-Cintrón, William, Sen, Saunak, Rodríguez-Santana, José R, Hernandez, Ryan D, Giacomini, Kathleen M, and Burchard, Esteban G

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Clinical Research, Patient Safety, Asthma, Genetics, Lung, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Respiratory, Adolescent, Adult, Albuterol, Bronchodilator Agents, Child, Forced Expiratory Volume, Genome-Wide Association Study, Genotype, Hispanic or Latino, Humans, Polymorphism, Single Nucleotide, Young Adult, Bronchodilator response, genome-wide association study, admixture mapping, Latinos, asthma, rare variants, BDR, GALA I, GALA II, GWAS, Genes-Environments & Admixture in Latino Americans, Genetics of Asthma in Latino Americans, Genome-wide association study, IGF, Insulin-like growth factor, LD, Linkage disequilibrium, MAF, Minor allele frequency, QC, Quality control, SABA, SLC, SNP, Short-acting β(2)-adrenergic receptor agonist, Single nucleotide polymorphism, Solute carrier, β(2)-Adrenergic receptor, β(2)AR, Immunology, Allergy
Abstract

BackgroundThe primary rescue medication to treat acute asthma exacerbation is the short-acting β₂-adrenergic receptor agonist; however, there is variation in how well a patient responds to treatment. Although these differences might be due to environmental factors, there is mounting evidence for a genetic contribution to variability in bronchodilator response (BDR).ObjectiveTo identify genetic variation associated with bronchodilator drug response in Latino children with asthma.MethodsWe performed a genome-wide association study (GWAS) for BDR in 1782 Latino children with asthma using standard linear regression, adjusting for genetic ancestry and ethnicity, and performed replication studies in an additional 531 Latinos. We also performed admixture mapping across the genome by testing for an association between local European, African, and Native American ancestry and BDR, adjusting for genomic ancestry and ethnicity.ResultsWe identified 7 genetic variants associated with BDR at a genome-wide significant threshold (P < 5 × 10(-8)), all of which had frequencies of less than 5%. Furthermore, we observed an excess of small P values driven by rare variants (frequency,

Published
2014

20. Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: The Genes-environments and Admixture in Latino Asthmatics (GALA II) study

Author

Kumar, Rajesh, Nguyen, Elizabeth A, Roth, Lindsey A, Oh, Sam S, Gignoux, Christopher R, Huntsman, Scott, Eng, Celeste, Moreno-Estrada, Andres, Sandoval, Karla, Peñaloza-Espinosa, Rosenda I, López-López, Marisol, Avila, Pedro C, Farber, Harold J, Tcheurekdjian, Haig, Rodriguez-Cintron, William, Rodriguez-Santana, Jose R, Serebrisky, Denise, Thyne, Shannon M, Williams, L Keoki, Winkler, Cheryl, Bustamante, Carlos D, Pérez-Stable, Eliseo J, Borrell, Luisa N, and Burchard, Esteban G

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Genetics, Lung, Asthma, Pediatric, Clinical Research, Adolescent, Allergens, Black People, Case-Control Studies, Child, Child, Preschool, Emigration and Immigration, Female, Gene-Environment Interaction, Hispanic or Latino, Humans, Hypersensitivity, Immediate, Male, Prevalence, Puerto Rico, Risk Factors, Skin Tests, United States, Latino, atopy, region of origin, genetic ancestry, immigration, kin test, aeroallergen, GALA II, Genes-environments and Admixture in Latino Asthmatics, OR, Odds ratio, SES, SNP, Single nucleotide polymorphism, Socioeconomic status, ZINB, Zero-inflated negative binomial, skin test, Immunology, Allergy
Abstract

BackgroundAtopy varies by ethnicity, even within Latino groups. This variation might be due to environmental, sociocultural, or genetic factors.ObjectiveWe sought to examine risk factors for atopy within a nationwide study of US Latino children with and without asthma.MethodsAeroallergen skin test responses were analyzed in 1830 US Latino subjects. Key determinants of atopy included country/region of origin, generation in the United States, acculturation, genetic ancestry, and site to which subjects migrated. Serial multivariate zero-inflated negative binomial regressions stratified by asthma status examined the association of each key determinant variable with the number of positive skin test responses. In addition, the independent effect of each key variable was determined by including all key variables in the final models.ResultsIn baseline analyses African ancestry was associated with 3 times (95% CI, 1.62-5.57) as many positive skin test responses in asthmatic participants and 3.26 times (95% CI, 1.02-10.39) as many positive skin test responses in control participants. Generation and recruitment site were also associated with atopy in crude models. In final models adjusted for key variables, asthmatic patients of Puerto Rican (exp[β] [95% CI], 1.31 [1.02-1.69]) and mixed (exp[β] [95% CI], 1.27 [1.03-1.56]) ethnicity had a greater probability of positive skin test responses compared with Mexican asthmatic patients. Ancestry associations were abrogated by recruitment site but not region of origin.ConclusionsPuerto Rican ethnicity and mixed origin were associated with degree of atopy within US Latino children with asthma. African ancestry was not associated with degree of atopy after adjusting for recruitment site. Local environment variation, represented by site, was associated with degree of sensitization.

Published
2013

22. A millennial history of sea level changes in the southwestern Atlantic

Author

Rubio-Sandoval, Karla Zurisadai, A. Shaw, Timothy, Horton, Ben, S. Khan, Nicole, Ferreira-Júnior, Augusto Luiz, J. Angulo, Rodolfo, C. Lessa, Guilherme, Cristina de Souza, Maria, Vacchi, Matteo, D. Ryan, Deirdre, Richiano, Sebastian, J. Gowan, Evan, Cerrone, Ciro, Stocchi, Paolo, Lorscheid, Thomas, Felis, Thomas, Petersen, Ann-Kathrin, and Rovere, Alessio

Abstract

Warmer temperatures and smaller-than-present ice sheets generally characterize interglacials. Determining the rates and geographic variability of relative sea-level (RSL) change during these periods provides insights into the future of the coastlines under warmer climatic conditions. Since the early 1940s, RSL studies along the southwestern Atlantic Coasts confirm the presence of several Last Interglacial (LIG, ~128-116 ka) and Holocene (HOL, 11 ka – to present) sea-level indicators. We use WALIS and HOLSEA templates to standardize and evaluate the quality and uncertainties of these published sea-level records. Our preliminary review produced more than 1000 standardized data points (55 LIG and 1177 HOL); more than 300 inconclusive data were rejected after being examined by quality control. Our data indicate that during the LIG, the paleo sea-level values range from ~5.6 to 20 m above sea level (a.s.l.) in the continental sector and from ~2 to 10 m a.s.l. in the Caribbean islands. Regarding the Holocene data, several sites show a mid-Holocene maximum transgression, with RSL rising 2-4 m above its present level, with a subsequent fall to its current position. This trend seems to be predominantly driven by glacial-isostatic adjustment processes. From our review, we identify that the coasts of Brazil, French Guiana, Suriname, Guyana, and Venezuela would benefit from a renewed study of Quaternary sea-level indicators. We also highlight that elevation measurements, sea-level interpretations, as well as chronological control at several locations may be improved by future research. This poster will be presented at GLOMAR/MARUM PhD Days 2023. Ph.D.

Published
2023
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23. 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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25. Quality Appraisal of Nutritional Guidelines to Prevent, Diagnose, and Treat Malnutrition in All Its Forms during Pregnancy

Author

Muñoz-Manrique, Cinthya, primary, Ancira-Moreno, Mónica, additional, Burrola-Méndez, Soraya, additional, Omaña-Guzmán, Isabel, additional, Hoyos-Loya, Elizabeth, additional, Hernández-Cordero, Sonia, additional, Trejo-Domínguez, Alejandra, additional, Mazariegos, Mónica, additional, Smith, Natalia, additional, Alonso-Carmona, Scarlett, additional, Mier-Cabrera, Jennifer, additional, Tavano-Colaizzi, Loredana, additional, Sánchez-Múzquiz, Belén, additional, Avendaño-Álvarez, Fermín, additional, Muciño-Sandoval, Karla, additional, Rodríguez-Moguel, Nadia C., additional, Padilla-Camacho, Magali, additional, Espino-y-Sosa, Salvador, additional, Ibarra-González, Lizeth, additional, and Medina-Avilés, Cristina, additional

Published
2022
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27. Warning labels on alcoholic beverage containers: a pilot randomized experiment among young adults in Mexico.

Author

López-Olmedo, Nancy, Muciño-Sandoval, Karla, Canto-Osorio, Francisco, Vargas-Flores, Adriana, Quiroz-Reyes, Alai, Sabines, Arturo, Malo-Serrano, Miguel, Bautista-Arredondo, Sergio, Colchero, MArantxa, and Barrientos-Gutiérrez, Tonatiuh

Subjects
*WARNING labels, *YOUNG adults, *BEVERAGE containers, *PILOT projects, ALCOHOLIC beverage labeling
Abstract

Background: Little is known about the potential impacts of visible and up-to-date health warning labels on alcoholic beverage containers on a range of outcomes in low- and middle-income countries. We conducted an experimental study to test the potential impacts of visible health warning labels (on the principal panel of the package) on thinking about health risks, product attractiveness, visual avoidance, and intention to change alcohol use among students in Mexico aged 18–30 years. Methods: A double-blind, parallel-group, online randomized trial was conducted from November 2021 to January 2022 in 11 states in Mexico. In the control group, participants were presented with the image of a conventional beer can with a fictional design and brand. In the intervention groups, the participants observed pictograms with a red font and white backgrounds (health warning label in red—HWL red) or with a black font and yellow backgrounds (health warning label in yellow—HWL yellow), located at the top, covering around one-third of the beer can. We used Poisson regression models -unadjusted and adjusted for covariates- to assess differences in the outcomes across study groups. Results: Using intention-to-treat analysis (n = 610), we found more participants in groups HWL red and HWL yellow thought about the health risks from drinking beer compared to the control group [Prevalence Ratio (PR) = 1.43, CI95%:1.05,1.93 for HWL red; PR = 1.25, CI95%: 0.91, 1.71 for HWL yellow]. A lower percentage of young adults in the interventions vs control group considered the product attractive (PR 0.74, 95%CI 0.51, 1.06 for HWL red; PR 0.56, 95%CI 0.38, 0.83 for HWL yellow). Although not statistically significant, a lower percentage of participants in the intervention groups considered buying or consuming the product than the control group. Results were similar when models were adjusted for covariates. Conclusions: Visible health warning labels could lead individuals to think about the health risks of alcohol, reducing the attractiveness of the product and decreasing the intention to purchase and consume alcohol. Further studies will be required to determine which pictograms or images and legends are most contextually relevant for the country. Trial registration: The protocol of this study was retrospectively registered on 03/01/2023: ISRCTN10494244. [ABSTRACT FROM AUTHOR]

Published
2023
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28. A loss-of-function IFNAR1 allele in Polynesia underlies severe viral diseases in homozygotes

Author

Bastard, Paul, primary, Hsiao, Kuang-Chih, additional, Zhang, Qian, additional, Choin, Jeremy, additional, Best, Emma, additional, Chen, Jie, additional, Gervais, Adrian, additional, Bizien, Lucy, additional, Materna, Marie, additional, Harmant, Christine, additional, Roux, Maguelonne, additional, Hawley, Nicola L., additional, Weeks, Daniel E., additional, McGarvey, Stephen T., additional, Sandoval, Karla, additional, Barberena-Jonas, Carmina, additional, Quinto-Cortés, Consuelo D., additional, Hagelberg, Erika, additional, Mentzer, Alexander J., additional, Robson, Kathryn, additional, Coulibaly, Boubacar, additional, Seeleuthner, Yoann, additional, Bigio, Benedetta, additional, Li, Zhi, additional, Uzé, Gilles, additional, Pellegrini, Sandra, additional, Lorenzo, Lazaro, additional, Sbihi, Zineb, additional, Latour, Sylvain, additional, Besnard, Marianne, additional, Adam de Beaumais, Tiphaine, additional, Jacqz Aigrain, Evelyne, additional, Béziat, Vivien, additional, Deka, Ranjan, additional, Esera Tulifau, Litara, additional, Viali, Satupa‘itea, additional, Reupena, Muagututi‘a Sefuiva, additional, Naseri, Take, additional, McNaughton, Peter, additional, Sarkozy, Vanessa, additional, Peake, Jane, additional, Blincoe, Annaliesse, additional, Primhak, Sarah, additional, Stables, Simon, additional, Gibson, Kate, additional, Woon, See-Tarn, additional, Drake, Kylie Marie, additional, Hill, Adrian V.S., additional, Chan, Cheng-Yee, additional, King, Richard, additional, Ameratunga, Rohan, additional, Teiti, Iotefa, additional, Aubry, Maite, additional, Cao-Lormeau, Van-Mai, additional, Tangye, Stuart G., additional, Zhang, Shen-Ying, additional, Jouanguy, Emmanuelle, additional, Gray, Paul, additional, Abel, Laurent, additional, Moreno-Estrada, Andrés, additional, Minster, Ryan L., additional, Quintana-Murci, Lluis, additional, Wood, Andrew C., additional, and Casanova, Jean-Laurent, additional

Published
2022
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29. NIVELES DEL MAR DURANTE EL ÚLTIMO INTERGLACIAR (MIS 5e) EN EL ATLÁNTICO OCCIDENTAL: UN PERFIL DE BRASIL A HONDURAS

Author

Rubio-Sandoval, Karla Zurisadai, Rovere, Alessio, Cerrone, Ciro, Stocchi, Paolo, Lorscheid, Thomas, Felis, Thomas, Petersen, Ann-Kathrin, and Ryan, Deirdre

Subjects
ComputingMilieux_THECOMPUTINGPROFESSION, GeneralLiterature_INTRODUCTORYANDSURVEY, ComputingMilieux_COMPUTERSANDSOCIETY, ComputingMilieux_LEGALASPECTSOFCOMPUTING, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries)
Abstract

Poster on sea level changes during MIS 5e in a profile from Brazil to Honduras

Published
2022
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30. El Atlántico Suroccidental y la memoria de sus costas: Reconstruyendo los antiguos niveles del mar

Author

Rubio-Sandoval, Karla Zurisadai

Abstract

This is a presentation that was given in Spanish on the ongoing research about paleo sea-level changes in the southwest Atlantic. The talk took place on Wednesday 27th April at the Instituto Paleotológico de Geología y Paleotología in Puerto Madryn, Argentina. As part of the series of lectures organized by the same institute. The talk was attended by about 20 people.

Published
2022
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31. The Southwest Atlantic and its coastal memory: Reconstructing ancient sea levels along the Argentinian coasts

Author

Rubio-Sandoval, Karla Zurisadai

Abstract

Here, we present the preliminary results of a standardized review of Last Interglacial, and Holocene RSL data along the Argetinian coast, as well as preliminary observations of two field campaigns in the same region. The poster was presented during the Marum Retreat, a meeting organized by the Center for Marine Environmental Sciences of the University of Bremen, which was attended by more than 40 people.

Published
2022
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32. Molluscs as bioindicators of paleoclimate and paleoenvironment in sediments of neotropical aquatic ecosystems

Author

Rubio-Sandoval, Karla Zurisadai, SUAREZ MOZO, NANCY YOLIMAR, Ferreira-Júnior, Augusto Luiz, Correa-Metrio, Alexander, Simões, Nuno, Spotorno-Oliveira, Paula, Christo, Susete Wambier, Souza, Maria Cristina de, Angulo, Rodolfo Jose, Brenner, Mark, Rovere, Alessio, and Perez, Liseth

Abstract

Lake and marine sediments are used to explore past changes in climate and environment. Inferences about the past rely on analyses of physical, chemical and biological indicators such as mineral composition, element chemistry, stable isotopes in carbonates and organic matter, biomarkers, remains of algae (e.g. diatoms) and higher plants (pollen and macrofossils), as well as those of invertebrates such as cladocerans, foraminiferans, ostracodes and molluscs. We used sedimented mollusc remains (gastropods and bivalves) and geochemical data to infer Late Holocene environmental conditions in four aquatic ecosystems (fresh, brackish, marine) in the Neotropics. Study sites included Lake Nahá (Chiapas, Mexico), coastal Ría Lagartos Lagoon (Yucatán, Mexico), islands Belmonte (São Pedro and São Paulo archipelago, Brazil), and coastal Ilha do Mel (Paranaguá, Brazil). Short sediment cores were collected from Lake Nahá (60 cm) and Ría Lagartos Lagoon (25 cm), whereas multiple coastal surface deposits were retrieved from the Brazilian island sites. Core depth-age relationships were established using 210Pb and 137Cs, whereas age determination for the island samples was accomplished by radiocarbon dating. Molluscs in the four records were identified to species level and enumerated. The freshwater gastropod community in Lake Nahá was sensitive to changes in water level and trophic state, whereas the malacological assemblages in the coastal lagoon record show they responded to climate events such as hurricanes and recent human impacts (e.g. highway construction). Vermetid snails from the islands are indicators of past sea level changes. This study revealed differential responses of mollusc communities to climate and environmental change across distinct aquatic ecosystems in the Neotropics, but nevertheless illustrates their potential as reliable paleoclimate and paleoenvironmental indicators. Poster presented at World Congress of Malacology 2022

Published
2022
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33. Holocene sea-level change in the southwestern Atlantic: A standardized database

Author

Rubio-Sandoval, Karla Zurisadai, Rovere, Alessio, and Ryan, Deirdre

Abstract

Relative sea-level (RSL) studies along the southwestern Atlantic coasts confirm the presence of several Holocene sea-level index points in the facies of beach ridges, marine terraces, beach, lagoon and estuarine deposits, fixed biological indicators. Here, we present a standardized database of Holocene sea-level index points for this region, compiled using the HOLSEA template. We reviewed published data for the countries of Argentina, Uruguay, and Brazil. Our preliminary review produced 800 standardized datapoints and more than 1000 re-calibrated radiocarbon dates, providing an almost continuous south-to-north transect of sea-level data along the southwestern Atlantic. Our data compilation highlights that several sites show a mid-Holocene maximum transgression, with RSL rising 2-4m above its present level, with a subsequent fall to its modern position. This trend seems to be predominantly driven by glacio-isostatic processes. However, we also highlight that elevation measurements, sea-level interpretations, as well as the chronological control at several locations may be improved by future research. Poster presented at the conference PALSEA 2022

Published
2022
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34. Holocene sea-level trends in the southwestern Atlantic: A story behind the data

Author

Rubio-Sandoval, Karla Zurisadai

Abstract

Determinate the rates and geographic variability of Relative sea-level (RSL) change during the Holocene provides insights about the future of the coastlines under warmer climatic conditions. Since the early 1940s, RSL studies along the Southwestern Atlantic Coasts confirm the presence of several Holocene sea-level indicators. We use the HOLSEA template to standardize and evaluate the quality and uncertainties of these published sea-level records from the countries of Argentina, Uruguay, and Brazil. Our preliminary review produced 553 standardized datapoints (261 index points and 292 limiting data), and around 117 inconclusive data were considered as rejected after being examined by quality control. Our data indicates that several sites show a mid-Holocene maximum transgression, with RSL rising 2-4m above its present level, with a subsequent fall to its modern position. This trend seems to be predominantly driven by glacio-isostatic adjustment processes. We also highlight that elevation measurements, sea-level interpretations, as well as the chronological control at several locations may be improved by future research.

Published
2022
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35. OPTIMAL MEDICAL THERAPY IN PATIENTS WITH ACUTE CORONARY SYNDROME IN A MIDDLE-INCOME COUNTRY: A MULTICENTER REGISTRY

Author

Gil, Mariana, primary, Leal, Sofia, additional, Santis, Juan Carlos, additional, Ruano, Josue F. Samayoa, additional, Castro, Magda I. Ramos, additional, Leon, Elisa M. Anleu De, additional, Alvarado, Oscar F. Castro, additional, Overall, Paola, additional, Cifuentes, Luis A. Rodriguez, additional, Sandoval, Karla Y. Miranda, additional, Pineda, Juan P., additional, Andrade, Kevin O. Flores, additional, Reyes, Roberto A. Perez, additional, and Blas, Sofia W. Giron, additional

Published
2022
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36. GUATEMALA’S MULTICENTER ACUTE CORONARY SYNDROME REGISTRY

Author

Leal, Sofia, primary, Gil, Mariana, additional, Santis, Juan Carlos, additional, Ruano, Josue F. Samayoa, additional, de Leon, Elisa M. Anleu, additional, Castro, Magda I. Ramos, additional, Alvarado, Oscar F. Castro, additional, Overall, Paola, additional, Cifuentes, Luis A. Rodriguez, additional, Sandoval, Karla Y. Miranda, additional, Pineda, Juan P., additional, Andrade, Kevin O. Flores, additional, Reyes, Roberto A. Perez, additional, and Blas, Sofia W. Giron, additional

Published
2022
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37. Structure, Process, and Mortality Associated with Acute Coronary Syndrome Management in Guatemala’s National Healthcare System: The ACS-GT Registry

Author

Cornejo-Guerra, José Antonio, primary, Ramos-Castro, Magda Isabel, additional, Gil-Salazar, Mariana, additional, Leal-Wittkowsky, Sofia, additional, Santis-Mejía, Juan Carlos, additional, León, Elisa María Anleu-De, additional, Castro-Alvarado, Oscar Fernando, additional, López-Quiñónez, Boris Rudy Alexander, additional, Illescas-González, Edgar Alexander, additional, Overall-Salazar, Paola, additional, Rodríguez-Cifuentes, Luis Antonio, additional, Miranda-Sandoval, Karla Yesenia, additional, Pineda, Juan Pablo, additional, Flores-Andrade, Kevin Oneal, additional, Pérez-Reyes, Roberto Antonio, additional, Girón-Blas, Sofía Waleska, additional, and Samayoa-Ruano, Josué Fernando, additional

Published
2022
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38. Prenatal and Early Childhood Exposure to Lead and Repeated Measures of Metabolic Syndrome Risk Indicators From Childhood to Preadolescence

Author

Muciño-Sandoval, Karla, primary, Ariza, Ana Carolina, additional, Ortiz-Panozo, Eduardo, additional, Pizano-Zárate, María Luisa, additional, Mercado-García, Adriana, additional, Wright, Robert, additional, Maria Téllez-Rojo, Martha, additional, Sanders, Alison P., additional, and Tamayo-Ortiz, Marcela, additional

Published
2021
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40. 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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44. Supplementary Figures S1-S6 from Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico

Author

Bravo-Lopez, Miriam, Villa-Islas, Viridiana, Rocha, Carolina, Altamirano, Ana B. Villaseñor, Guzmán-Solís, Axel, Sandoval-Velasco, Marcela, Wesp, Julie K., Keitlyn Alcantara, Corral, Aurelio López, Valdés, Jorge Gómez, Mejía, Elizabeth, Herrera, Alberto, Moreno, Alejandro Meraz, Cabrera, Maria De La Luz Moreno, Moreno-Estrada, Andrés, Nieves-Colón, Maria A., Olvera, Joel, Pérez-Pérez, Julia, Iversen, Katrine Højholt, Rasmussen, Simon, Sandoval, Karla, Zepeda, Gabriela, and Ávila-Arcos, María C.

Subjects
stomatognathic diseases
Abstract

The ‘red complex’ is an aggregate of three oral bacteria (Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient Tannerella forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from Pre-Hispanic to Colonial period in Mexico. We recovered 12 partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules'.

Published
2020
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45. A Review of Last Interglacial Sea-Level Indicators in the Southern Western Atlantic: State-of-the-art and future perspectives

Author

Rubio-Sandoval, Karla Zurisadai, Ryan, Deirdre, Vacchi, Matteo, RICHIANO, Sebastian, and Rovere, Alessio

Abstract

We use the World Atlas of Last Interglacial Shorelines (WALIS) database to standardize and evaluate the quality of the sea-level record and its uncertainties. Using WALIS, we reviewed published data for the countries of Brazil, French Guiana, Surinam, Guyana, Venezuela, Colombia, as well as the islands Bonaire, Curaçao and Aruba, documenting and standardizing both geological and chronological information. While not all the reviewed papers fulfilled the database standards (e.g. missing or unclear information), the review allowed us to estimate the current state-of-the-art. Sea-level indicators are well preserved in the Southern Western Atlantic providing an almost continuous record between the states. Despite this and the relative sea-level indicators variety, there are main gaps related to the accuracy of elevation measurements and the reliability of chronology; uncertainties that hinder our ability to precisely estimate effects causing departures from eustasy. Improve our knowledge of sea-level changes during the LIG is a key to assess the future of the coastlines under warmer climatic conditions.

Published
2020
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46. Description of the samples analyzed in this study and the data obtained from Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico

Author

Bravo-Lopez, Miriam, Villa-Islas, Viridiana, Rocha, Carolina, Altamirano, Ana B. Villaseñor, Guzmán-Solís, Axel, Sandoval-Velasco, Marcela, Wesp, Julie K., Keitlyn Alcantara, Corral, Aurelio López, Valdés, Jorge Gómez, Mejía, Elizabeth, Herrera, Alberto, Moreno, Alejandro Meraz, Cabrera, Maria De La Luz Moreno, Moreno-Estrada, Andrés, Nieves-Colón, Maria A., Olvera, Joel, Pérez-Pérez, Julia, Iversen, Katrine Højholt, Rasmussen, Simon, Sandoval, Karla, Zepeda, Gabriela, and Ávila-Arcos, María C.

Subjects
stomatognathic diseases
Abstract

The ‘red complex’ is an aggregate of three oral bacteria (Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient Tannerella forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from Pre-Hispanic to Colonial period in Mexico. We recovered 12 partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules'.

Published
2020
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47. An integrated map of genetic variation from 1,092 human genomes

Author

McVean, Gil A., Altshuler, David M., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Donnelly, Peter, Eichler, Evan E., Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Green, Eric D., Hurles, Matthew E., Knoppers, Bartha M., Korbel, Jan O., Lander, Eric S., Lee, Charles, Lehrach, Hans, Mardis, Elaine R., Marth, Gabor T., Nickerson, Deborah A., Schmidt, Jeanette P., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Dinh, Huyen, Kovar, Christie, Lee, Sandra, Lewis, Lora, Muzny, Donna, Reid, Jeff, Wang, Min, Wang, Jun, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Li, Zhuo, Liu, Xiao, Lu, Yao, Ma, Xuedi, Su, Zhe, Tai, Shuaishuai, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Yin, Ye, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Zhou, Yan, Lander, Eric S., Gabriel, Stacey B., Gupta, Namrata, Flicek, Paul, Clarke, Laura, Leinonen, Rasko, Smith, Richard E., Zheng-Bradley, Xiangqun, Bentley, David R., Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, Sudbrak, Ralf, Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Sherry, Stephen T., McVean, Gil A., Mardis, Elaine R., Wilson, Richard K., Fulton, Lucinda, Fulton, Robert, Weinstock, George M., Durbin, Richard M., Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, Yu, Fuli, Bainbridge, Matthew, Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Sabo, Aniko, Wang, Yi, Yu, Jin, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Qin, Nan, Shao, Haojing, Wang, Bingqiang, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Garrison, Erik P., Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Lee, Charles, Griffin, Lauren, Hsieh, Chih-Heng, Mills, Ryan E., Shi, Xinghua, von Grotthuss, Marcin, Zhang, Chengsheng, Daly, Mark J., DePristo, Mark A., Banks, Eric, Bhatia, Gaurav, Carneiro, Mauricio O., del Angel, Guillermo, Genovese, Giulio, Handsaker, Robert E., Hartl, Chris, McCarroll, Steven A., Nemesh, James C., Poplin, Ryan E., Schaffner, Stephen F., Shakir, Khalid, Yoon, Seungtai C., Lihm, Jayon, Makarov, Vladimir, Jin, Hanjun, Kim, Wook, Cheol Kim, Ki, Korbel, Jan O., Rausch, Tobias, Beal, Kathryn, Cunningham, Fiona, Herrero, Javier, McLaren, William M., Ritchie, Graham R. 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Published
2012
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48. Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes

Author

Ávila-Arcos, María C, primary, McManus, Kimberly F, primary, Sandoval, Karla, primary, Rodríguez-Rodríguez, Juan Esteban, primary, Villa-Islas, Viridiana, primary, Martin, Alicia R, primary, Luisi, Pierre, primary, Peñaloza-Espinosa, Rosenda I, primary, Eng, Celeste, primary, Huntsman, Scott, primary, Burchard, Esteban G, primary, Gignoux, Christopher R, primary, Bustamante, Carlos D, primary, and Moreno-Estrada, Andrés, primary

Published
2019
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50. Reseña del libro de Rita Segato 'La guerra contra las mujeres'

Author

Núñez Sandoval, Karla Jhoana

Abstract

El libro reúne, a través de siete ensayos, el trabajo que Rita Segato ha venido desarrollando en la última década con la finalidad de analizar las olas crecientes de violencia contra las mujeres, y, más específicamente, contra los cuerpos femeninos o feminizados. Que se han dado en distintos puntos del globo, pero que de alguna manera se manifestaron con una gran fuerza y brutalidad en Ciudad Juárez, México.

Published
2019

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