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2. Neanderthal introgression in SCN9A impacts mechanical pain sensitivity

Author

Faux, Pierre, Ding, Li, Ramirez-Aristeguieta, Luis Miguel, Chacón-Duque, J. Camilo, Comini, Maddalena, Mendoza-Revilla, Javier, Fuentes-Guajardo, Macarena, Jaramillo, Claudia, Arias, William, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Barquera, Rodrigo, Everardo-Martínez, Paola, Quinto-Sánchez, Mirsha, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Silva de Cerqueira, Caio C., Hünemeier, Tábita, Ramallo, Virginia, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Poletti, Giovanni, Gallo, Carla, Rothhammer, Francisco, Rojas, Winston, Schmid, Annina B., Adhikari, Kaustubh, Bennett, David L., and Ruiz-Linares, Andrés

Published
2023
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3. Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape

Author

Li, Qing, Chen, Jieyi, Faux, Pierre, Delgado, Miguel Eduardo, Bonfante, Betty, Fuentes-Guajardo, Macarena, Mendoza-Revilla, Javier, Chacón-Duque, J. Camilo, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Jaramillo, Claudia, Arias, William, Barquera, Rodrigo, Everardo-Martínez, Paola, Sánchez-Quinto, Mirsha, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Silva de Cerqueira, Caio C., Hünemeier, Tábita, Ramallo, Virginia, Wu, Sijie, Du, Siyuan, Giardina, Andrea, Paria, Soumya Subhra, Khokan, Mahfuzur Rahman, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Rojas, Winston, Rothhammer, Francisco, Navarro, Nicolas, Wang, Sijia, Adhikari, Kaustubh, and Ruiz-Linares, Andrés

Published
2023
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4. 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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5. Inferring Long-Term and Short-Term Determinants of Genetic Diversity in Honey Bees: Beekeeping Impact and Conservation Strategies.

Author

Leroy, Thibault, Faux, Pierre, Basso, Benjamin, Eynard, Sonia, Wragg, David, and Vignal, Alain

Subjects
HONEYBEES, WHOLE genome sequencing, POLLINATION by bees, PLANT diversity, GENETIC variation, BEEKEEPING
Abstract

Bees are vital pollinators in natural and agricultural landscapes around the globe, playing a key role in maintaining flowering plant biodiversity and ensuring food security. Among the honey bee species, the Western honey bee (Apis mellifera) is particularly significant, not only for its extensive crop pollination services but also for producing economically valuable products such as honey. Here, we analyzed whole-genome sequence data from four Apis species to explore how honey bee evolution has shaped current diversity patterns. Using Approximate Bayesian Computation, we first reconstructed the demographic history of A. mellifera in Europe, finding support for postglacial secondary contacts, therefore predating human-mediated transfers linked to modern beekeeping. However, our analysis of recent demographic changes reveals significant bottlenecks due to beekeeping practices, which have notably affected genetic diversity. Black honey bee populations from conservatories, particularly those on islands, exhibit considerable genetic loss, highlighting the need to evaluate the long-term effectiveness of current conservation strategies. Additionally, we observed a high degree of conservation in the genomic landscapes of nucleotide diversity across the four species, despite a divergence gradient spanning over 15 million years, consistent with a long-term conservation of the recombination landscapes. Taken together, our results provide the most comprehensive assessment of diversity patterns in honey bees to date and offer insights into the optimal management of resources to ensure the long-term persistence of honey bees and their invaluable pollination services. [ABSTRACT FROM AUTHOR]

Published
2024
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11. 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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13. A Random Forests Framework for Modeling Haplotypes as Mosaics of Reference Haplotypes

Author

Faux, Pierre, Geurts, Pierre, and Druet, Tom

Subjects
random forests, supervised classification, lcsh:Genetics, lcsh:QH426-470, haplotype mosaic, Genetics, Molecular Medicine, imputation, extra-trees, Genetics (clinical), Original Research
Abstract

Many genomic data analyses such as phasing, genotype imputation, or local ancestry inference share a common core task: matching pairs of haplotypes at any position along the chromosome, thereby inferring a target haplotype as a succession of pieces from reference haplotypes, commonly called a mosaic of reference haplotypes. For that purpose, these analyses combine information provided by linkage disequilibrium, linkage and/or genealogy through a set of heuristic rules or, most often, by a hidden Markov model. Here, we develop an extremely randomized trees framework to address the issue of local haplotype matching. In our approach, a supervised classifier using extra-trees (a particular type of random forests) learns how to identify the best local matches between haplotypes using a collection of observed examples. For each example, various features related to the different sources of information are observed, such as the length of a segment shared between haplotypes, or estimates of relationships between individuals, gametes, and haplotypes. The random forests framework was fed with 30 relevant features for local haplotype matching. Repeated cross-validations allowed ranking these features in regard to their importance for local haplotype matching. The distance to the edge of a segment shared by both haplotypes being matched was found to be the most important feature. Similarity comparisons between predicted and true whole-genome sequence haplotypes showed that the random forests framework was more efficient than a hidden Markov model in reconstructing a target haplotype as a mosaic of reference haplotypes. To further evaluate its efficiency, the random forests framework was applied to imputation of whole-genome sequence from 50k genotypes and it yielded average reliabilities similar or slightly better than IMPUTE2. Through this exploratory study, we lay the foundations of a new framework to automatically learn local haplotype matching and we show that extra-trees are a promising approach for such purposes. The use of this new technique also reveals some useful lessons on the relevant features for the purpose of haplotype matching. We also discuss potential improvements for routine implementation.

Published
2019
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14. MOESM3 of Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle

Author

Solé, Marina, Ann-Stephan Gori, Faux, Pierre, Bertrand, Amandine, Farnir, Frédéric, Gautier, Mathieu, and Druet, Tom

Abstract

Additional file 3. Figure S2. Comparison of genomic inbreeding coefficients estimated with different marker densities (LD panel in black, 50 K panel in red, BovineHD panel in green and WGS panel in blue) and for different base populations. Genomic inbreeding coefficients were estimated with the Mix14R model (13 HBD-classes model with pre-defined R k rates) for 634 Belgian Blue sires. Different base populations were obtained by selecting different thresholds T that determine which HBD-classes were considered in the estimation of F G-T (e.g., setting the base population approximately 0.5 * T generations in the past).

Published
2017
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15. MOESM2 of Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle

Author

SolĂŠ, Marina, Ann-Stephan Gori, Faux, Pierre, Bertrand, Amandine, FrĂŠdĂŠric Farnir, Gautier, Mathieu, and Druet, Tom

Abstract

Additional file 2. Boxplots of proportions of individual genomes associated with 13 HBD-classes with pre-defined R k rates (MIX14R model) in 11 cattle breeds of European origin using the BovineHD genotyping panel. The proportions correspond to individual genome-wide probabilities of belonging to each of the HBD-classes.

Published
2017
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18. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock

Author

Charlier, Carole, primary, Li, Wanbo, additional, Harland, Chad, additional, Littlejohn, Mathew, additional, Coppieters, Wouter, additional, Creagh, Frances, additional, Davis, Steve, additional, Druet, Tom, additional, Faux, Pierre, additional, Guillaume, François, additional, Karim, Latifa, additional, Keehan, Mike, additional, Kadri, Naveen Kumar, additional, Tamma, Nico, additional, Spelman, Richard, additional, and Georges, Michel, additional

Published
2016
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19. Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle

Author

Kadri, Naveen Kumar, primary, Harland, Chad, additional, Faux, Pierre, additional, Cambisano, Nadine, additional, Karim, Latifa, additional, Coppieters, Wouter, additional, Fritz, Sébastien, additional, Mullaart, Erik, additional, Baurain, Denis, additional, Boichard, Didier, additional, Spelman, Richard, additional, Charlier, Carole, additional, Georges, Michel, additional, and Druet, Tom, additional

Published
2016
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21. Prediction of eye, hair and skin colour in Latin Americans

Author

Palmal, Sagnik, Adhikari, Kaustubh, Mendoza-Revilla, Javier, Fuentes-Guajardo, Macarena, Silva de Cerqueira, Caio C., Bonfante, Betty, Chacón-Duque, Juan Camilo, Sohail, Anood, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Jaramillo, Claudia, Arias, William, Lozano, Rodrigo Barquera, Everardo-Martínez, Paola, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Hünemeier, Tábita, Ramallo, Virginia, Parolin, Maria-Laura, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Balding, David, Faux, Pierre, Ruiz-Linares, Andrés, Palmal, Sagnik, Adhikari, Kaustubh, Mendoza-Revilla, Javier, Fuentes-Guajardo, Macarena, Silva de Cerqueira, Caio C., Bonfante, Betty, Chacón-Duque, Juan Camilo, Sohail, Anood, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Jaramillo, Claudia, Arias, William, Lozano, Rodrigo Barquera, Everardo-Martínez, Paola, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Hünemeier, Tábita, Ramallo, Virginia, Parolin, Maria-Laura, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Balding, David, Faux, Pierre, and Ruiz-Linares, Andrés

Abstract

Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6,500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the p

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

Author

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

Abstract

To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.

23. Neanderthal introgression in SCN9A impacts mechanical pain sensitivity

Author

Faux, Pierre, Ding, Li, Ramirez-Aristeguieta, Luis Miguel, Chacón-Duque, J. Camilo, Comini, Maddalena, Mendoza-Revilla, Javier, Fuentes-Guajardo, Macarena, Jaramillo, Claudia, Arias, William, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Barquera, Rodrigo, Everardo-Martínez, Paola, Quinto-Sánchez, Mirsha, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Silva de Cerqueira, Caio C., Hünemeier, Tábita, Ramallo, Virginia, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Poletti, Giovanni, Gallo, Carla, Rothhammer, Francisco, Rojas, Winston, Schmid, Annina B., Adhikari, Kaustubh, Bennett, David L., Ruiz-Linares, Andrés, Faux, Pierre, Ding, Li, Ramirez-Aristeguieta, Luis Miguel, Chacón-Duque, J. Camilo, Comini, Maddalena, Mendoza-Revilla, Javier, Fuentes-Guajardo, Macarena, Jaramillo, Claudia, Arias, William, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Barquera, Rodrigo, Everardo-Martínez, Paola, Quinto-Sánchez, Mirsha, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Silva de Cerqueira, Caio C., Hünemeier, Tábita, Ramallo, Virginia, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Poletti, Giovanni, Gallo, Carla, Rothhammer, Francisco, Rojas, Winston, Schmid, Annina B., Adhikari, Kaustubh, Bennett, David L., and Ruiz-Linares, Andrés

Abstract

The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.

24. Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape

Author

Li, Qing, Chen, Jieyi, Faux, Pierre, Delgado, Miguel Eduardo, Bonfante, Betty, Fuentes-Guajardo, Macarena, Mendoza-Revilla, Javier, Chacón-Duque, J. Camilo, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Jaramillo, Claudia, Arias, William, Barquera, Rodrigo, Everardo-Martínez, Paola, Sánchez-Quinto, Mirsha, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Silva de Cerqueira, Caio C., Hünemeier, Tábita, Ramallo, Virginia, Wu, Sijie, Du, Siyuan, Giardina, Andrea, Paria, Soumya Subhra, Khokan, Mahfuzur Rahman, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Rojas, Winston, Rothhammer, Francisco, Navarro, Nicolas, Wang, Sijia, Adhikari, Kaustubh, Ruiz-Linares, Andrés, Li, Qing, Chen, Jieyi, Faux, Pierre, Delgado, Miguel Eduardo, Bonfante, Betty, Fuentes-Guajardo, Macarena, Mendoza-Revilla, Javier, Chacón-Duque, J. Camilo, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Jaramillo, Claudia, Arias, William, Barquera, Rodrigo, Everardo-Martínez, Paola, Sánchez-Quinto, Mirsha, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Silva de Cerqueira, Caio C., Hünemeier, Tábita, Ramallo, Virginia, Wu, Sijie, Du, Siyuan, Giardina, Andrea, Paria, Soumya Subhra, Khokan, Mahfuzur Rahman, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Rojas, Winston, Rothhammer, Francisco, Navarro, Nicolas, Wang, Sijia, Adhikari, Kaustubh, and Ruiz-Linares, Andrés

Abstract

We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10−8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.

25. 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, Bennett, David L, 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

Abstract

Repeated application of noxious stimuli leads to a progressively increased pain perception; this temporal summation is enhanced in and predictive of clinical pain disorders. Its electrophysiological correlate is "wind-up," in which dorsal horn spinal neurons increase their response to repeated nociceptor stimulation. To understand the genetic basis of temporal summation, we undertook a GWAS of wind-up in healthy human volunteers and found significant association with SLC8A3 encoding sodium-calcium exchanger type 3 (NCX3). NCX3 was expressed in mouse dorsal horn neurons, and mice lacking NCX3 showed normal, acute pain but hypersensitivity to the second phase of the formalin test and chronic constriction injury. Dorsal horn neurons lacking NCX3 showed increased intracellular calcium following repetitive stimulation, slowed calcium clearance, and increased wind-up. Moreover, virally mediated enhanced spinal expression of NCX3 reduced central sensitization. Our study highlights Ca2+efflux as a pathway underlying temporal summation and persistent pain, which may be amenable to therapeutic targeting.

26. Prediction of eye, hair and skin colour in Latin Americans

Author

Palmal, Sagnik, Adhikari, Kaustubh, Mendoza-Revilla, Javier, Fuentes-Guajardo, Macarena, Silva de Cerqueira, Caio C., Bonfante, Betty, Chacón-Duque, Juan Camilo, Sohail, Anood, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Jaramillo, Claudia, Arias, William, Lozano, Rodrigo Barquera, Everardo-Martínez, Paola, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Hünemeier, Tábita, Ramallo, Virginia, Parolin, Maria-Laura, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Balding, David, Faux, Pierre, Ruiz-Linares, Andrés, Palmal, Sagnik, Adhikari, Kaustubh, Mendoza-Revilla, Javier, Fuentes-Guajardo, Macarena, Silva de Cerqueira, Caio C., Bonfante, Betty, Chacón-Duque, Juan Camilo, Sohail, Anood, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Jaramillo, Claudia, Arias, William, Lozano, Rodrigo Barquera, Everardo-Martínez, Paola, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Hünemeier, Tábita, Ramallo, Virginia, Parolin, Maria-Laura, Gonzalez-José, Rolando, Schüler-Faccini, Lavinia, Bortolini, Maria-Cátira, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Balding, David, Faux, Pierre, and Ruiz-Linares, Andrés

Abstract

Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6,500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the p

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

Author

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

Abstract

To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.

28. A review of inversion techniques related to the use of relationship matrices in animal breeding.

Author

Faux, Pierre and Gengler, Nicolas

Subjects
ANIMAL breeding, INVERSIONS (Geometry), ANIMAL genetics, COVARIANCE matrices, EPISTASIS (Genetics), LOCUS (Genetics)
Abstract

Copyright of Biotechnologie, Agronomie, Societe et Environnement is the property of Les Presses Agronomiques de Gembloux and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2014

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