Identification of a novel locus associated with skin colour in African-admixed populations

Natalia Hernandez-Pacheco; Carlos Flores; Santos Alonso; Celeste Eng; Angel C.Y. Mak; Scott Hunstman; Donglei Hu; Marquitta J. White; Sam S. Oh; Kelley Meade; Harold J. Farber; Pedro C. Avila; Denise Serebrisky; Shannon M. Thyne; Emerita Brigino-Buenaventura; William Rodriguez-Cintron; Saunak Sen; Rajesh Kumar; Michael Lenoir; Jose R. Rodriguez-Santana; Esteban G. Burchard; Maria Pino-Yanes

doi:10.1038/srep44548

Identification of a novel locus associated with skin colour in African-admixed populations

Natalia Hernandez-Pacheco, Carlos Flores, Santos Alonso, Celeste Eng, Angel C.Y. Mak, Scott Hunstman, Donglei Hu, Marquitta J. White, Sam S. Oh, Kelley Meade, Harold J. Farber, Pedro C. Avila, Denise Serebrisky, Shannon M. Thyne, Emerita Brigino-Buenaventura, William Rodriguez-Cintron, Saunak Sen, Rajesh Kumar, Michael Lenoir, Jose R. Rodriguez-SantanaEsteban G. Burchard, Maria Pino-Yanes^*

^*Corresponding author for this work

Pediatrics

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

Abstract

Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10^-5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10^-14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10^-10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10^-9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.

Original language	English (US)
Article number	44548
Journal	Scientific reports
Volume	7
DOIs	https://doi.org/10.1038/srep44548
State	Published - Mar 16 2017

Funding

This work was supported in part by the Sandler Family Foundation, the American Asthma Foundation, the RWJF Amos Medical Faculty Development Program, Harry Wm. and Diana V. Hind Distinguished Professor in Pharmaceutical Sciences II, National Institutes of Health 1R01HL117004, R01Hl128439, National Institute of Health and Environmental Health Sciences R01 ES015794, R21ES24844, the National Institute on Minority Health and Health Disparities 1P60 MD006902, U54MD009523, 1R01MD010443 and the Tobacco-Related Disease Research Program under Award Number 24RT-0025. NH-P was funded by a fellowship from the Spanish Ministry of Education, Culture, and Sports (11608852). SSO was supported in part by the Flight Attendant Medical Research Institute.

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Hernandez-Pacheco, N., Flores, C., Alonso, S., Eng, C., Mak, A. C. Y., Hunstman, S., Hu, D., White, M. J., Oh, S. S., Meade, K., Farber, H. J., Avila, P. C., Serebrisky, D., Thyne, S. M., Brigino-Buenaventura, E., Rodriguez-Cintron, W., Sen, S., Kumar, R., Lenoir, M., ... Pino-Yanes, M. (2017). Identification of a novel locus associated with skin colour in African-admixed populations. Scientific reports, 7, Article 44548. https://doi.org/10.1038/srep44548

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title = "Identification of a novel locus associated with skin colour in African-admixed populations",

abstract = "Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10-5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10-14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10-10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10-9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.",

author = "Natalia Hernandez-Pacheco and Carlos Flores and Santos Alonso and Celeste Eng and Mak, {Angel C.Y.} and Scott Hunstman and Donglei Hu and White, {Marquitta J.} and Oh, {Sam S.} and Kelley Meade and Farber, {Harold J.} and Avila, {Pedro C.} and Denise Serebrisky and Thyne, {Shannon M.} and Emerita Brigino-Buenaventura and William Rodriguez-Cintron and Saunak Sen and Rajesh Kumar and Michael Lenoir and Rodriguez-Santana, {Jose R.} and Burchard, {Esteban G.} and Maria Pino-Yanes",

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Hernandez-Pacheco, N, Flores, C, Alonso, S, Eng, C, Mak, ACY, Hunstman, S, Hu, D, White, MJ, Oh, SS, Meade, K, Farber, HJ, Avila, PC, Serebrisky, D, Thyne, SM, Brigino-Buenaventura, E, Rodriguez-Cintron, W, Sen, S, Kumar, R, Lenoir, M, Rodriguez-Santana, JR, Burchard, EG & Pino-Yanes, M 2017, 'Identification of a novel locus associated with skin colour in African-admixed populations', Scientific reports, vol. 7, 44548. https://doi.org/10.1038/srep44548

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T1 - Identification of a novel locus associated with skin colour in African-admixed populations

AU - Hernandez-Pacheco, Natalia

AU - Flores, Carlos

AU - Alonso, Santos

AU - Eng, Celeste

AU - Mak, Angel C.Y.

AU - Hunstman, Scott

AU - Hu, Donglei

AU - White, Marquitta J.

AU - Oh, Sam S.

AU - Meade, Kelley

AU - Farber, Harold J.

AU - Avila, Pedro C.

AU - Serebrisky, Denise

AU - Thyne, Shannon M.

AU - Brigino-Buenaventura, Emerita

AU - Rodriguez-Cintron, William

AU - Sen, Saunak

AU - Kumar, Rajesh

AU - Lenoir, Michael

AU - Rodriguez-Santana, Jose R.

AU - Burchard, Esteban G.

AU - Pino-Yanes, Maria

PY - 2017/3/16

Y1 - 2017/3/16

N2 - Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10-5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10-14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10-10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10-9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.

AB - Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10-5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10-14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10-10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10-9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.

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Identification of a novel locus associated with skin colour in African-admixed populations

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