Dr Camilo Chacon-Duque

Dr Juan Chacon-Duque

Postdoctoral Researcher, GCRF Colombia

Department: Earth Sciences
Division: ES Vertebrates and Anthropology Palaeobiology

Summary

I am an Evolutionary Geneticist. My research focuses on the analysis of genetic and genomic data, from both contemporary and ancient DNA, to explore the evolutionary history of different species. I have contributed considerably to the development of statistical methods to increase the geographical resolution of genetic analyses in human populations from Latin America. As part of my role in the project GROW Colombia (funded by GCRF), I am working on the characterisation of spatial and temporal patterns of genetic diversity in different species from Colombia (my home country). For this purpose, I apply ancient DNA (aDNA) and Next-generation sequencing (NGS) approaches to study specimens from museum collections, aiming to understand better the evolution and ecology of these species. Currently, our signature species is the Andean bear. I am also involved in capacity building activities both in Colombia and the UK with GROW Colombia. This includes public engagement, science communication and training of researchers in aDNA and NGS, including laboratory techniques and bioinformatics.

Qualifications

Degrees

PhD, University College London, London, 2013 - 2018

MSc (High Distinction), Universidad de Antioquia, Medellin, 2010 - 2013

BSc (1st), Universidad de Antioquia, Medellin, 2004 - 2009

Employment history

Academic

Visiting Researcher, Instituto Alexander von Humboldt, Colombia, 2019 - ongoing

Teaching Assistant, University College London, United Kingdom, 2013 - 2017

Research Assistant, Universidad de Antioquia, Colombia, 2012 - 2013

COLCIENCIAS Young Researcher, Universidad de Antioquia, Colombia, 2011 - 2012

Teaching Assistant, Universidad de Antioquia, Colombia, 2010 - 2013

Research Assistant, Universidad de Antioquia, Colombia, 2009 - 2010

Non-academic

Population Geneticist, Living DNA, R&D, United Kingdom, 2017 - 2018

Publications

Schmid AB, Adhikari K, Ramirez-Aristeguieta LM, Chacón-Duque J-C, Poletti G, Gallo C, Rothhammer F, Bedoya G, Ruiz-Linares A, Bennett DL (2019) Genetic components of human pain sensitivity: a protocol for a genome-wide association study of experimental pain in healthy volunteers. BMJ Open, 9 (4) : e025530 - e025530. doi: 10.1136/bmjopen-2018-025530

Adhikari K, Mendoza-Revilla J, Sohail A, Fuentes-Guajardo M, Lampert J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Everardo P, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hunemeier T, Ramallo V, Schuler-Faccini L, Salzano FM, Gonzalez-José R, Bortolini M-C, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Tobin DJ, Fumagalli M, Balding D, Ruiz-Linares A (2019) A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia. Nature Communications, 10 (1) : doi: 10.1038/s41467-018-08147-0

Chacón-Duque J-C, Adhikari K, Fuentes-Guajardo M, Mendoza-Revilla J, Acuña-Alonzo V, Barquera R, Quinto-Sánchez M, Gómez-Valdés J, Everardo Martínez P, Villamil-Ramírez H, Hünemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Villena M, Vásquez R, Llop E, Sandoval JR, Salazar-Granara AA, Parolin M-L, Sandoval K, Peñaloza-Espinosa RI, Rangel-Villalobos H, Winkler CA, Klitz W, Bravi C, Molina J, Corach D, Barrantes R, Gomes V, Resende C, Gusmão L, Amorim A, Xue Y, Dugoujon J-M, Moral P, González-José R, Schuler-Faccini L, Salzano FM, Bortolini M-C, Canizales-Quinteros S, Poletti G, Gallo C, Bedoya G, Rothhammer F, Balding D, Hellenthal G, Ruiz-Linares A (2018) Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance. Nature Communications, 9 (1) : doi: 10.1038/s41467-018-07748-z

Useche YM, Ribeiro-Alves M, Restrepo B-N, Salgado DM, Narváez CF, Campo O, Avendaño E, Martínez C, Chacon-Duque JC, Bedoya G (2018) Single-Nucleotide Polymorphisms in NOD1, RIPK2, MICB, PLCE1, TNF, and IKBKE Genes Associated with Symptomatic Dengue in Children from Colombia. Viral Immunology, 31 (9) : 613 - 623. doi: 10.1089/vim.2018.0028

Adhikari K, Chacón-Duque JC, Mendoza-Revilla J, Fuentes-Guajardo M, Ruiz-Linares A (2017) The Genetic Diversity of the Americas, In: null, Annual Reviews : 277 - 296.

Avendaño-Tamayo E, Campo O, Chacón-Duque JC, Ramírez R, Rojas W, Agudelo-Flórez P, Bedoya G, Restrepo BN (null) Variants in the TNFA, IL6 and IFNG genes are associated with the dengue severity in a sample from Colombian population. Biomédica, 37 (4) : 486 - 486. doi: 10.7705/biomedica.v37i4.3305

Adhikari K, Mendoza-Revilla J, Chacón-Duque JC, Fuentes-Guajardo M, Ruiz-Linares A (2016) Admixture in Latin America. Current Opinion in Genetics & Development, 41 : 106 - 114. doi: 10.1016/j.gde.2016.09.003

Adhikari K, Fuentes-Guajardo M, Quinto-Sánchez M, Mendoza-Revilla J, Camilo Chacón-Duque J, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Pérez GM, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini M-C, Canizales-Quinteros S, Cheeseman M, Rosique J, Bedoya G, Rothhammer F, Headon D, González-José R, Balding D, Ruiz-Linares A (2016) A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation. Nature Communications, 7 (1) : doi: 10.1038/ncomms11616

Adhikari K, Fontanil T, Cal S, Mendoza-Revilla J, Fuentes-Guajardo M, Chacón-Duque J-C, Al-Saadi F, Johansson JA, Quinto-Sanchez M, Acuña-Alonzo V, Jaramillo C, Arias W, Barquera Lozano R, Macín Pérez G, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini M-C, Canizales-Quinteros S, Rothhammer F, Bedoya G, Gonzalez-José R, Headon D, López-Otín C, Tobin DJ, Balding D, Ruiz-Linares A (2016) A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features. Nature Communications, 7 (1) : doi: 10.1038/ncomms10815

Chacón-Duque JC, Adhikari K, Avendaño E, Campo O, Ramirez R, Rojas W, Ruiz-Linares A, Restrepo BN, Bedoya G (2014) African genetic ancestry is associated with a protective effect on Dengue severity in colombian populations. Infection, Genetics and Evolution, 27 : 89 - 95. doi: 10.1016/j.meegid.2014.07.003

Introduction

Summary

I am an Evolutionary Geneticist. My research focuses on the analysis of genetic and genomic data, from both contemporary and ancient DNA, to explore the evolutionary history of different species. I have contributed considerably to the development of statistical methods to increase the geographical resolution of genetic analyses in human populations from Latin America. As part of my role in the project GROW Colombia (funded by GCRF), I am working on the characterisation of spatial and temporal patterns of genetic diversity in different species from Colombia (my home country). For this purpose, I apply ancient DNA (aDNA) and Next-generation sequencing (NGS) approaches to study specimens from museum collections, aiming to understand better the evolution and ecology of these species. Currently, our signature species is the Andean bear. I am also involved in capacity building activities both in Colombia and the UK with GROW Colombia. This includes public engagement, science communication and training of researchers in aDNA and NGS, including laboratory techniques and bioinformatics.

Qualifications

Degrees

PhD, University College London, London, 2013 - 2018

MSc (High Distinction), Universidad de Antioquia, Medellin, 2010 - 2013

BSc (1st), Universidad de Antioquia, Medellin, 2004 - 2009

Employment history

Academic

Visiting Researcher, Instituto Alexander von Humboldt, Colombia, 2019 - ongoing

Teaching Assistant, University College London, United Kingdom, 2013 - 2017

Research Assistant, Universidad de Antioquia, Colombia, 2012 - 2013

COLCIENCIAS Young Researcher, Universidad de Antioquia, Colombia, 2011 - 2012

Teaching Assistant, Universidad de Antioquia, Colombia, 2010 - 2013

Research Assistant, Universidad de Antioquia, Colombia, 2009 - 2010

Non-academic

Population Geneticist, Living DNA, R&D, United Kingdom, 2017 - 2018

Publications

Publications

Schmid AB, Adhikari K, Ramirez-Aristeguieta LM, Chacón-Duque J-C, Poletti G, Gallo C, Rothhammer F, Bedoya G, Ruiz-Linares A, Bennett DL (2019) Genetic components of human pain sensitivity: a protocol for a genome-wide association study of experimental pain in healthy volunteers. BMJ Open, 9 (4) : e025530 - e025530. doi: 10.1136/bmjopen-2018-025530

Adhikari K, Mendoza-Revilla J, Sohail A, Fuentes-Guajardo M, Lampert J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Everardo P, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hunemeier T, Ramallo V, Schuler-Faccini L, Salzano FM, Gonzalez-José R, Bortolini M-C, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Tobin DJ, Fumagalli M, Balding D, Ruiz-Linares A (2019) A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia. Nature Communications, 10 (1) : doi: 10.1038/s41467-018-08147-0

Chacón-Duque J-C, Adhikari K, Fuentes-Guajardo M, Mendoza-Revilla J, Acuña-Alonzo V, Barquera R, Quinto-Sánchez M, Gómez-Valdés J, Everardo Martínez P, Villamil-Ramírez H, Hünemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Villena M, Vásquez R, Llop E, Sandoval JR, Salazar-Granara AA, Parolin M-L, Sandoval K, Peñaloza-Espinosa RI, Rangel-Villalobos H, Winkler CA, Klitz W, Bravi C, Molina J, Corach D, Barrantes R, Gomes V, Resende C, Gusmão L, Amorim A, Xue Y, Dugoujon J-M, Moral P, González-José R, Schuler-Faccini L, Salzano FM, Bortolini M-C, Canizales-Quinteros S, Poletti G, Gallo C, Bedoya G, Rothhammer F, Balding D, Hellenthal G, Ruiz-Linares A (2018) Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance. Nature Communications, 9 (1) : doi: 10.1038/s41467-018-07748-z

Useche YM, Ribeiro-Alves M, Restrepo B-N, Salgado DM, Narváez CF, Campo O, Avendaño E, Martínez C, Chacon-Duque JC, Bedoya G (2018) Single-Nucleotide Polymorphisms in NOD1, RIPK2, MICB, PLCE1, TNF, and IKBKE Genes Associated with Symptomatic Dengue in Children from Colombia. Viral Immunology, 31 (9) : 613 - 623. doi: 10.1089/vim.2018.0028

Adhikari K, Chacón-Duque JC, Mendoza-Revilla J, Fuentes-Guajardo M, Ruiz-Linares A (2017) The Genetic Diversity of the Americas, In: null, Annual Reviews : 277 - 296.

Avendaño-Tamayo E, Campo O, Chacón-Duque JC, Ramírez R, Rojas W, Agudelo-Flórez P, Bedoya G, Restrepo BN (null) Variants in the TNFA, IL6 and IFNG genes are associated with the dengue severity in a sample from Colombian population. Biomédica, 37 (4) : 486 - 486. doi: 10.7705/biomedica.v37i4.3305

Adhikari K, Mendoza-Revilla J, Chacón-Duque JC, Fuentes-Guajardo M, Ruiz-Linares A (2016) Admixture in Latin America. Current Opinion in Genetics & Development, 41 : 106 - 114. doi: 10.1016/j.gde.2016.09.003

Adhikari K, Fuentes-Guajardo M, Quinto-Sánchez M, Mendoza-Revilla J, Camilo Chacón-Duque J, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Pérez GM, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini M-C, Canizales-Quinteros S, Cheeseman M, Rosique J, Bedoya G, Rothhammer F, Headon D, González-José R, Balding D, Ruiz-Linares A (2016) A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation. Nature Communications, 7 (1) : doi: 10.1038/ncomms11616

Adhikari K, Fontanil T, Cal S, Mendoza-Revilla J, Fuentes-Guajardo M, Chacón-Duque J-C, Al-Saadi F, Johansson JA, Quinto-Sanchez M, Acuña-Alonzo V, Jaramillo C, Arias W, Barquera Lozano R, Macín Pérez G, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini M-C, Canizales-Quinteros S, Rothhammer F, Bedoya G, Gonzalez-José R, Headon D, López-Otín C, Tobin DJ, Balding D, Ruiz-Linares A (2016) A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features. Nature Communications, 7 (1) : doi: 10.1038/ncomms10815

Chacón-Duque JC, Adhikari K, Avendaño E, Campo O, Ramirez R, Rojas W, Ruiz-Linares A, Restrepo BN, Bedoya G (2014) African genetic ancestry is associated with a protective effect on Dengue severity in colombian populations. Infection, Genetics and Evolution, 27 : 89 - 95. doi: 10.1016/j.meegid.2014.07.003