Human pigmentation is a complex trait, probably involving more than 100 genes. Predicting phenotypes using SNPs present in those genes is important for forensic purpose. For this, the HIrisPlex tool ...was developed for eye and hair color prediction, with both models achieving high accuracy among Europeans. Its evaluation in admixed populations is important, since they present a higher frequency of intermediate phenotypes, and HIrisPlex has demonstrated limitations in such predictions; therefore, the performance of this tool may be impaired in such populations. Here, we evaluate the set of 24 markers from the HIrisPlex system in 328 individuals from Ribeirão Preto (SP) region, predicting eye and hair color and comparing the predictions with their real phenotypes. We used the HaloPlex Target Enrichment System and MiSeq Personal Sequencer platform for massively parallel sequencing. The prediction of eye and hair color was accomplished by the HIrisPlex online tool, using the default prediction settings. Ancestry was estimated using the SNP
for
ID 34-plex to observe if and how an individual’s ancestry background would affect predictions in this admixed sample. Our sample presented major European ancestry (70.5%), followed by African (21.1%) and Native American/East Asian (8.4%). HIrisPlex presented an overall sensitivity of 0.691 for hair color prediction, with sensitivities ranging from 0.547 to 0.782. The lowest sensitivity was observed for individuals with black hair, who present a reduced European contribution (48.4%). For eye color prediction, the overall sensitivity was 0.741, with sensitivities higher than 0.85 for blue and brown eyes, although it failed in predicting intermediate eye color. Such struggle in predicting this phenotype category is in accordance with what has been seen in previous studies involving HIrisPlex. Individuals with brown eye color are more admixed, with European ancestry decreasing to 62.6%; notwithstanding that, sensitivity for brown eyes was almost 100%. Overall sensitivity increases to 0.791 when a 0.7 threshold is set, though 12.5% of the individuals become undefined. When combining eye and hair prediction, hit rates between 51.3 and 68.9% were achieved. Despite the difficulties with intermediate phenotypes, we have shown that HIrisPlex results can be very helpful when interpreted with caution.
Leukocyte immunoglobulin (Ig)‐like receptors (LILR) LILRB1 and LILRB2 may play a pivotal role in maintaining self‐tolerance and modulating the immune response through interaction with classical and ...nonclassical HLA molecules. Although both diversity and natural selection patterns over HLA genes have been extensively evaluated, little information is available concerning the genetic diversity and selection signatures on the LILRB1/2 regions. Therefore, we identified the LILRB1/2 genetic diversity using next‐generation sequencing in a population sample from São Paulo State, Brazil. We identified 58 LILRB1 Single Nucleotide Variants (SNVs), which gave rise to 13 haplotypes, and 41 LILRB2 SNVs arranged into 11 haplotypes. Although we may not exclude as a possible effect of population structure, we found evidence of either positive or purifying selection on LILRB1/2 coding regions. Some residues in both proteins showed to be under the effect of positive selection, suggesting that amino acid replacements in these proteins resulted in beneficial functional changes. Finally, we have revealed that allelic variation (six and five amino acid exchanges in LILRB1 and LILRB2, respectively) affects the structure and/or stability of both molecules. Nonetheless, LILRB2 has shown higher average stability, with no D1/D2 residue affecting protein structure. Overall, our findings demonstrate that LILRB1 and LILRB2 are as polymorphic as HLA class Ib genes and provide strong evidence supporting the directional selection regime hypothesis.
•We have predicted pigmentation phenotypes for seven ancient Native Americans.•The HIrisPlex-S and Snipper systems were used for the predictions.•Except for a Karitiana sample, eye colors were ...predicted as intermediate/brown.•Except for a Karitiana sample, all individuals were predicted with black hair.•Snipper and HIrisPlex-S presented differences regarding skin color prediction.
Over the past few years, tools capable of predicting pigmentation phenotypes have been developed aiming to contribute for criminal and anthropological investigations. In this study, we used eight genetic systems to infer eye, hair, and skin color of ancient and contemporary Native Americans. To achieve this goal, we retrieved 61 SNPs from 42 samples available in free online repositories of DNA sequences. We performed pigmentation predictions using two freely available tools, HIrisPlex-S and Snipper, in addition to two other published models. This workflow made possible to predict all three phenotypes with at least one tool for 29 out of the 42 samples. Considering these 29 individuals, predictions for eye, hair, and skin color were obtained with HIrisPlex-S for 27, 28 and 27 individuals, respectively, while 24, 25 and 25 individuals had such predictions with Snipper. In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation.
The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new ...approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology. Melanocortin-1 receptor (MC1R) is one of the most studied genes involved in pigmentation variation. As MC1R has already been suggested to affect melanogenesis and increase risk of developing melanoma, it constitutes one of the best models to understand how natural selection acts on pigmentation. Here we employed a locally developed pipeline to obtain genotype and haplotype data for MC1R from the raw sequencing data provided by the 1000 Genomes FTP site. We also compared such genotype data to Phase 3 VCF to evaluate its quality and discover any polymorphic sites that may have been overlooked. In conclusion, either the VCF file or one of the presently described pipelines could be used to obtain reliable and accurate genotype calling from the 1000 Genomes Phase 3 data.
Human leukocyte antigen-G (HLA-G) is a nonclassical Major Histocompatibility Complex (MHC) molecule with immunomodulatory function and restricted tissue expression. The genetic diversity of HLA-G has ...been extensively studied in several populations, however, the segment located upstream −1406 has not yet been evaluated. We characterized the nucleotide variation and haplotype structure of an extended distal region (−2635), all exons and the 3′UTR segment of HLA-G by next-generation sequencing (NGS) in a sample of 335 Brazilian individuals. We detected 29 variants at the HLA-G distal promoter region, arranged into 19 haplotypes, among which we identified sites that may influence transcription factor targeting. Although the variation pattern in the distal region resembled the one observed in the conventional promoter segment, molecular signature for balancing selection was observed in the promoter segment from −1406 to −1 (Tajima’s D = 2.315, P = 0.017), but not in this distal segment (D = 1.049, P = 0.118). Furthermore, the ancestry composition of this Brazilian population sample was determined by the analysis of SNPforID 34-plex ancestry informative marker (AIM) SNP panel. The distribution of HLA-G haplotypes was ancestry-dependent, corroborating previous findings and emphasizing the importance of considering the ancestry information in association studies.
•The SNPforID 52-plex system was analyzed in a Brazilian population sample (n = 340).•Next-generation sequencing was performed with the HaloPlex and MiSeq approaches.•On average, 50.5 genotypes were ...called in each sample.•Combined match probability of 6.48 × 10−21 and exclusion power of 0.9997 were found.•Admixture tools revealed predominant European contribution and low Amerindian input.
SNP analysis is of paramount importance in forensic genetics. The development of new technologies in next-generation sequencing allowed processing a large number of markers in various samples simultaneously. Although SNPs are less informative than STRs, they present lower mutation rates and perform better when using degraded samples. Some SNP systems were developed for forensic usage, such as the SNPforID 52-plex, from the SNPforID Consortium, containing 52 bi-allelic SNPs for human identification. In this paper we evaluated the informativeness of this system in a Brazilian population sample (n = 340). DNA libraries were prepared using a customized HaloPlex Target Enrichment System kit (Agilent Technologies, Inc.) and sequenced in the MiSeq Personal Sequencer platform (Illumina Inc.). The methodology presented here allowed the analysis of 51 out of 52 SNPforID markers. Allele frequencies and forensic parameters were estimated, revealing high informativeness: the combined match probability and power of exclusion were 6.48 × 10−21 and 0.9997, respectively. Population admixture analysis indicates high European contribution (more than 70%) and low Amerindian contribution (less than 10%) in our population, while individual admixture analyses were consistent with the majority of individuals presenting high European contribution. This study demonstrates that the 52-plex kit is suitable for forensic cases in a Brazilian population, presenting results comparable with those obtained using a 16 STR panel.
(1) Background: Vitiligo is characterized by white patches on the skin caused by loss of melanocyte activity or the absence of these cells. The available treatments minimize the symptoms by retarding ...the process of skin depigmentation or re-pigmenting the affected regions. New studies are required for a better comprehension of the mechanisms that trigger the disease and for the development of more efficient treatments. Studies have suggested an autoimmune feature for vitiligo, based on the occurrence of other autoimmune diseases in vitiligo patients and their relatives, and on the involvement of genes related to the immune response. (2) Methods: We evaluated, by massive parallel sequencing, polymorphisms of the
gene in vitiligo patients and control samples, to verify if variants of this gene could influence the susceptibility to vitiligo. (3) Results: We detected an association with non-segmental vitiligo regarding the haplotype Distal-010101a/G*01:01:01:01/UTR-1, adjusting for population stratification by using ancestry-informative markers (AIMs). (4) Conclusions: It remains unclear whether the
variants associated with vitiligo were detected because of the high linkage disequilibrium (LD) with HLA-A*02, or if the
variants previously reported as associated with vitiligo were detected because of the high LD with HLA-G*01:01:01:01/UTR-1, or if both genes jointly contribute to vitiligo susceptibility.
A cor da pele, olhos e cabelos são alguns dos traços fenotípicos mais aparentes quando nos referimos à identificação de características individuais. Essas características frequentemente são ...utilizadas na descrição de indivíduos em retratos falados usados em investigações policiais. Porém, em muitos casos as vítimas ou testemunhas não reconhecem o agressor, tornando inviável a produção desses retratos. Contudo, os vestígios biológicos deixados pelo criminoso poderiam ser utilizados na predição de suas características físicas, suprindo a falta ou complementando o retrato falado. Para que isso seja possível, é preciso conhecer as variáveis responsáveis pela formação desses fenótipos. No caso dos fenótipos de pigmentação há tanto um fator genético, quanto ambiental. Diversos genes participam da formação desses fenótipos, dentre eles está o gene MITF (Melanogenesis-associated transcription factor), um dos principais regulador da biossíntese de melanina nos melanócitos. Esse gene está fortemente associado às síndromes de Waadenburg e Tietz, as quais causam pigmentação anormal, principalmente na pele, e ao melanoma. No entanto, apesar do claro envolvimento do gene MITF na melanogênese, ainda não são conhecidas associações significativas de polimorfismos nesse gene com fenótipos de pigmentação. À vista disso, esse trabalho avaliou a relação da variabilidade do gene MITF com os fenótipos de pigmentação encontrados em uma amostra populacional do estado de São Paulo, por meio de sequenciamento de nova geração. Foram identificados 133 pontos de variação em toda a extensão do gene e sua região promotora, dos quais 21 estão associadas a pelo menos um fenótipo de pigmentação de pele, olhos ou cabelo. Adicionalmente foram encontradas associações com ao menos um fenótipo de pigmentação para 3 dos 17 haplótipos da região promotora, 7 dos 50 haplótipos da extensão que engloba a região 5UTR e codificante, e um dos 18 haplótipos encontrados na região 3UTR. Considerando os haplótipos encontrados para a extensão total do gene MITF e sua promotora, 20 dos 132 haplótipos encontrados estão associados a algum fenótipo de pigmentação. A maior parte das associações encontradas, tanto para alelos e genótipos quanto para haplótipos, são referentes a fenótipos mais escuros como cabelos castanhos escuros e pretos e pele escura. Associações com fenótipos mais claros, tais como olhos azuis e verdes e cabelos loiros e ruivos, também foram encontradas, porém envolvendo variantes e haplótipos de frequência baixa na população amostrada; tais associações, entretanto, representam achados falsos positivos. Os resultados confirmam a hipótese de que a variabilidade do gene MITF pode contribuir para a formação dos fenótipos de pigmentação de pele, olhos e cabelos dos indivíduos da população brasileira
Skin, eye and hair colors are some of the most noticeable phenotypes when referring to the identification of individual characteristics. These characteristics are often used to describe individuals in police sketches used in investigations. However, in many cases the victims or witnesses are unable to recognize the assaulter, making this sketches unfeasible. Nonetheless, biological traces left by the assaulter could be used to predict their physical characteristics, compensating or complementing these sketches. To make this possible, its necessary to know the variables responsible for the development of these traits. Pigmentation phenotype development relies on genetic and environmental aspects. A variety of genes contribute to the development of these phenotypes, among them MITF (Melanogenesis-associated transcription factor), one of the main regulators of melanin synthesis in melanocytes. This gene is strongly associated with Waardenburg and Tietz syndrome, which cause abnormal pigmentation, mostly in skin, and melanoma. Although MITFs clear involvement in melanogenesis, significant associations between this genes polymorphisms and pigmentation phenotypes are still unknown. Thus, this study evaluated the relation between MITF genetic variability and pigmentation phenotypes found in a population sample from the state of São Paulo, through next generation sequencing. There were identified 133 variation points through the whole gene and its promoter, from which 21 were associated with at least one skin, eye or hair pigmentation phenotype. Additionally, 3 of the 17 promoter haplotypes, 7 of the 50 haplotypes comprising the 5UTR and coding regions and one of the 18 3UTR haplotypes were associated with at least one pigmentation phenotype. Considering the haplotypes found for the whole gene and its promoter, 20 of the 132 haplotypes found were associated with at least one phenotype. The majority of the associations found for alleles, genotypes and haplotypes were related to darker phenotypes, like dark brown and black hair and dark skin. Associations with lighter phenotypes, like blue and green eyes and blonde and red hair, were also found, although involving variants and haplotypes with low frequencies in the studied population; these associations, however, represent false positives. The results corroborate the hypothesis that the MITF variability can contribute to the formation of pigmentation phenotypes in skin, eye and hair in the Brazilian population
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