Association of common genetic variants with human skin color variation in Indian populations

A Cross-Sectional Assessment of Quantitative Epidermal Melanin and Erythema Indices among North Indians

Background

Remarkable diversity of skin tones among Indians ranging from pale pinkish to dark brown appears to be an ideal choice for the assessment of skin pigment variation.

Aim

The present study was designed to assess the variation observed in melanin and erythema indices among north Indians.

Material and Methods

Skin reflectance data (n = 574) was collected from six diverse populations of north India using DermaSpectrometer (DSM II ColorMeter) followed by statistical analysis to investigate the impact of geographical location and gender on constitutive skin pigmentation.

Results

The melanin index (MI) varied between 17.93 and 56.92 (Mean (M) = 35.80 ± 6.26) whereas the erythema index (EI) varied between 4.92 and 18.82 (M = 10.48 ± 2.68). MI and EI of females were found to be significantly lower than males (P < 0.001). Geographical location exhibited a significant association with MI and EI (P < 0.001). Furthermore, we have noted a positive correlation between MI and EI (P < 0.001).

Conclusion

The study has refined our understanding of skin pigmentation variation among north Indians in terms of significant association with geographical location {MI: F _(5,568) = 31.07, P < 0.001; EI: F _(5,568) = 73.37, P < 0.001} and gender {MI: t ₍₃₈₆₎ = -4.06, P < 0.001; EI: t ₍₃₈₆₎ = -11.96, P < 0.001} and rendered opportunities for further studies.

Leadership, gender, and colorism: Children in India use social category information to guide leadership cognition

Across the globe, women and racial minorities are underrepresented in leadership. We examined the development of 5-10-year-old children's leadership cognition in India, the world's largest democracy. This cultural context offered the opportunity to study the development of attitudes about gender and to extend examinations of children's conceptions of race to include colorism (the privileging of lighter skin). In Experiment 1, children completed a novel Election Task in which they saw a fictional class with 20 students varying in gender (boys, girls) and race/skin tone (darker-skinned South Asian [Dark-SA], lighter-skinned South Asian [Light-SA], Black, White). Children predicted who would be elected as President, Treasurer, Welcomer, and Notetaker. Children most often chose Light-SA and White students as President. When choosing Presidents, younger children showed an own-gender bias, but by age 9, both boys and girls primarily chose boy Presidents. Importantly, children's choices differed for the other class positions. Next, we asked children to draw a "leader." No boys drew a girl, and girls' drawings were mixed (52% drew girls). In Experiment 2, we replicated the drawing task findings and compared children's drawings of a leader to their drawings of a helper and a scientist. Children most often drew boys and men as leaders and scientists, but not as helpers, suggesting specificity of children's pro-male bias to male-stereotyped positions. Children's conceptions of leadership reflected a male bias and an association between lighter skin and status. This article is protected by copyright. All rights reserved.

Pervasive Selection against MicroRNA Target Sites in Human Populations

MicroRNA target sites are often conserved during evolution and purifying selection to maintain such sites is expected. On the other hand, comparative analyses identified a paucity of microRNA target sites in coexpressed transcripts, and novel target sites can potentially be deleterious. We proposed that selection against novel target sites pervasive. The analysis of derived allele frequencies revealed that, when the derived allele is a target site, the proportion of nontarget sites is higher than expected, particularly for highly expressed microRNAs. Thus, new alleles generating novel microRNA target sites can be deleterious and selected against. When we analyzed ancestral target sites, the derived (nontarget) allele frequency does not show statistical support for microRNA target allele conservation. We investigated the joint effects of microRNA conservation and expression and found that selection against microRNA target sites depends mostly on the expression level of the microRNA. We identified microRNA target sites with relatively high levels of population differentiation. However, when we analyze separately target sites in which the target allele is ancestral to the population, the proportion of single-nucleotide polymorphisms with high F_st significantly increases. These findings support that population differentiation is more likely in target sites that are lost than in the gain of new target sites. Our results indicate that selection against novel microRNA target sites is prevalent and, although individual sites may have a weak selective pressure, the overall effect across untranslated regions is not negligible and should be accounted when studying the evolution of genomic sequences.

Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil

BACKGROUND

Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SNPs) in pigmentation genes have been described in melanoma risk modulation, but knowledge in the field is still limited.

METHODS

In a case-control approach (107 cases and 119 controls), we investigated the effect of four pigmentation gene SNPs (TYR rs1126809, HERC2 rs1129038, SLC24A5 rs1426654, and SLC45A2 rs16891982) on melanoma risk in individuals from southern Brazil using a multivariate logistic regression model and multifactor dimensionality reduction (MDR) analysis.

RESULTS

Two SNPs were associated with an increased risk of melanoma in a dominant model: rs1129038AA and rs1426654AA [OR = 2.094 (95% CI: 1.106-3.966), P = 2.3 10^- 2 and OR = 7.126 (95% CI: 1.873-27.110), P = 4.0 10^- 3, respectively]. SNP rs16891982CC was associated with a lower risk to melanoma development in a log-additive model when the allele C was inherited [OR = 0.081 (95% CI: 0.008-0.782), P = 3 10^- 2]. In addition, MDR analysis showed that the combination of the rs1426654AA and rs16891982GG genotypes was associated with a higher risk for melanoma (P = 3 10^- 3), with a redundant effect.

CONCLUSIONS

These results contribute to the current knowledge and indicate that epistatic interaction of these SNPs, with an additive or correlational effect, may be involved in modulating the risk of melanoma in individuals from a geographic region with a high incidence of the disease.

Meta-analysis and prioritization of human skin pigmentation-associated GWAS-SNPs using ENCODE data-based web-tools

Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype. In the present study, which, to our knowledge, is the first of its kind, we tried to analyze and prioritize 519 non-coding SNPs and 24 3'UTR SNPs emerging from 14 different human skin pigmentation-related GWAS, primarily using several ENCODE-based web-tools like rSNPBase, RegulomeDB, HaploReg, etc., most of which incorporate experimentally validated evidences in their predictions. Using this comprehensive, in-silico, analytical approach, we successfully prioritized all the pigmentation-associated GWAS-SNPs and tried to annotate pigmentation-related functionality to them, which would pave the way for deeper understanding of the molecular basis of human skin pigmentation variations.