A Genome-Wide Association Study of Skin and Iris Pigmentation among Individuals of South Asian Ancestry

Jonnalagadda, Manjari; Faizan, Muhammad Ashhad; Ozarkar, Shantanu; Ashma, Richa; Kulkarni, Shaunak; Norton, Heather L.; Parra, Esteban J.

doi:10.1093/gbe/evz057

Cited by 23 publications

(23 citation statements)

References 29 publications

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“…This is particularly so for hair and eye color, as the CANDELA sample has a highly skewed phenotypic distribution for these traits: 82% of individuals in the CANDELA sample are assigned to the darkest category for eye and 85% for hair color. This skewed phenotypic distribution is consistent with the fact that world-wide lightly pigmented eyes and hair are essentially Western Eurasian traits, while there is considerable variation in skin pigmentation outside Europe [23][24][25][26][27][28]. That is, the occurrence of lightly pigmented hair and eyes in the CANDELA sample is essentially a reflection of its partly European ancestry.…”

Section: Discussionsupporting

confidence: 73%

“…Among major continental populations, Europeans show the largest variation in eye and hair color, whereas the variation in skin color in Europeans is relatively lower compared to other continental regions such as Africa or South Asia [23][24][25][26][27][28]. The other continental regions have narrower variation in eye and hair color, mostly within the brown-black range;…”

Section: Introductionmentioning

confidence: 98%

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Prediction of Eye, Hair and Skin Color in Admixed Populations of Latin America

Palmal

Adhikari

Mendoza‐Revilla

et al. 2020

Preprint

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We report an evaluation of prediction accuracy for eye, hair and skin pigmentation based on genomic and phenotypic data for over 6,500 admixed Latin Americans (the CANDELA dataset). We examined the impact on prediction accuracy of three main factors: (i) The methods of prediction, including classical statistical methods and machine learning approaches, (ii) The inclusion of non-genetic predictors, continental genetic ancestry and pigmentation SNPs in the prediction models, and (iii) Compared two sets of pigmentation SNPs: the commonly-used HIrisPlex-S set (developed in Europeans) and novel SNP sets we defined here based on genome-wide association results in the CANDELA sample. We find that Random Forest or regression are globally the best performing methods. Although continental genetic ancestry has substantial power for prediction of pigmentation in Latin Americans, the inclusion of pigmentation SNPs increases prediction accuracy considerably, particularly for skin color. For hair and eye color, HIrisPlex-S has a similar performance to the CANDELA-specific prediction SNP sets. However, for skin pigmentation the performance of HIrisPlex-S is markedly lower than the SNP set defined here, including predictions in an independent dataset of Native American data. These results reflect the relatively high variation in hair and eye color among Europeans for whom HIrisPlex-S was developed, whereas their variation in skin pigmentation is comparatively lower. Furthermore, we show that the dataset used in the training of prediction models strongly impacts on the portability of these models across Europeans and Native Americans.

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Section: Discussionsupporting

confidence: 73%

Section: Introductionmentioning

confidence: 98%

Prediction of Eye, Hair and Skin Color in Admixed Populations of Latin America

Palmal

Adhikari

Mendoza‐Revilla

et al. 2020

Preprint

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“…Four of these genes are associated with reproduction traits: DST [ 42 , 43 ], RAB23 [ 44 ], KHDRBS2 [ 45 – 47 ], and TUBGCP5 [ 48 ]. The ROH island on BBU2 also contains three genes that are involved in skin pigmentation and eye disorders: LGSN [ 49 ], OCA2 [ 50 , 51 ], and HERC2 [ 52 ] and have been identified in selection signatures in buffalo [ 25 ] and in cattle [ 51 ]. Additional genes that map to this region are: PTPN18 , a gene involved in the regulation of the neuronal leptin and insulin signaling pathways [ 53 ] and is associated with feeding behavior in pigs [ 54 ], and AMER3 , which is involved in embryogenesis [ 55 ].…”

Section: Resultsmentioning

confidence: 99%

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events

et al. 2021

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Background Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types. Results The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction. Conclusions Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction.

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“…A further “negative control” experiment was conducted in UKB2. When repeating the analysis using the genetic loci (Supplementary Table 4 ) associated with eye colour 6 , 7 , there was no evidence of subgroups (Supplementary Fig. 5 ).…”

Section: Resultsmentioning

confidence: 99%

The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals

Strawbridge

Johnston

Bailey

et al. 2021

Sci Rep

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Understanding why individuals with severe mental illness (Schizophrenia, Bipolar Disorder and Major Depressive Disorder) have increased risk of cardiometabolic disease (including obesity, type 2 diabetes and cardiovascular disease), and identifying those at highest risk of cardiometabolic disease are important priority areas for researchers. For individuals with European ancestry we explored whether genetic variation could identify sub-groups with different metabolic profiles. Loci associated with schizophrenia, bipolar disorder and major depressive disorder from previous genome-wide association studies and loci that were also implicated in cardiometabolic processes and diseases were selected. In the IMPROVE study (a high cardiovascular risk sample) and UK Biobank (general population sample) multidimensional scaling was applied to genetic variants implicated in both psychiatric and cardiometabolic disorders. Visual inspection of the resulting plots used to identify distinct clusters. Differences between these clusters were assessed using chi-squared and Kruskall-Wallis tests. In IMPROVE, genetic loci associated with both schizophrenia and cardiometabolic disease (but not bipolar disorder or major depressive disorder) identified three groups of individuals with distinct metabolic profiles. This grouping was replicated within UK Biobank, with somewhat less distinction between metabolic profiles. This work focused on individuals of European ancestry and is unlikely to apply to more genetically diverse populations. Overall, this study provides proof of concept that common biology underlying mental and physical illness may help to stratify subsets of individuals with different cardiometabolic profiles.

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A Genome-Wide Association Study of Skin and Iris Pigmentation among Individuals of South Asian Ancestry

Cited by 23 publications

References 29 publications

Prediction of Eye, Hair and Skin Color in Admixed Populations of Latin America

Prediction of Eye, Hair and Skin Color in Admixed Populations of Latin America

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events

The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals

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