Predicting Physical Features and Diseases by DNA Analysis: Current Advances and Future Challenges

The 'omics' era and its concomitant technological advances have brought great insight into genetics. One of the most promising fields within human genetics is the prediction of physical traits from analysis of genetic material. Besides the predictive potential of DNA, the traceability of pathogenic agents in the human body through molecular analysis is also a field to be further exploited. In this review, we aim to discuss specific aspects of phenotypic prediction by analysing DNA, with special emphasis on normal variation, and the application of a technology known as ‘Forensic DNA Phenotyping’ (FDP). We also suggest the term ‘Phenotype Informative Markers’ (PIMs) to designate any molecular markers responsible for normal or pathological human phenotypic variation. In addition, we raise some recommendations related to forensic genetics, the molecular diagnosis of human diseases, and the traceability of pathogens in the human body, giving special emphasis to the need for validation of these tests with strict protocols. Some relevant concerns about privacy, ethics, and legality of such predictions have also been discussed. Finally, we look at perspectives on the use of epigenetic tools, and quote some examples of what has been done in this specific field.Fil: Silva de Cerqueira, Caio Cesar. Scientific Police Of Sao Paulo State; BrasilFil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Hünemeier, Tábita. Universidade de Sao Paulo; BrasilFil: de Azevedo, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Quinto Sanchez, Mirsha Emmanuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Paschetta, Carolina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Cintas, Celia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: González, Marina Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Schüler-faccini, Lavinia. Universidade Federal do Rio Grande do Sul; Brasil. National Institute of Medical Genetics Population; BrasilFil: Bortolini, María Cátira. Universidade Federal do Rio Grande do Sul; BrasilFil: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentin

The effects of forest degradation on arboreal primates within Sikundur, the Gunung Leuser Ecosystem, Northern Sumatra

Abstract of a paper given at the 87th Annual Meeting of the American Association of Physical Anthropologists held at Austin, Texas, 11-14 April 201

A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation

We report a genome-wide association scan for facial features in B6,000 Latin Americans. We evaluated 14 traits on an ordinal scale and found significant association (P valueso5 10 8) at single-nucleotide polymorphisms (SNPs) in four genomic regions for three nose-related traits: columella inclination (4q31), nose bridge breadth (6p21) and nose wing breadth (7p13 and 20p11). In a subsample of B3,000 individuals we obtained quantitative traits related to 9 of the ordinal phenotypes and, also, a measure of nasion position. Quantitative analyses confirmed the ordinal-based associations, identified SNPs in 2q12 associated to chin protrusion, and replicated the reported association of nasion position with SNPs in PAX3. Strongest association in 2q12, 4q31, 6p21 and 7p13 was observed for SNPs in the EDAR, DCHS2, RUNX2 and GLI3 genes, respectively. Associated SNPs in 20p11 extend to PAX1. Consistent with the effect of EDAR on chin protrusion, we documented alterations of mandible length in mice with modified Edar funtion

Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.Instituto Multidisciplinario de Biología Celula

Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.Instituto Multidisciplinario de Biología Celula

Socioeconomic Status Is Not Related with Facial Fluctuating Asymmetry: Evidence from Latin-American Populations

The expression of facial asymmetries has been recurrently related with poverty and/or disadvantaged socioeconomic status. Departing from the developmental instability theory, previous approaches attempted to test the statistical relationship between the stress experienced by individuals grown in poor conditions and an increase in facial and corporal asymmetry. Here we aim to further evaluate such hypothesis on a large sample of admixed Latin Americans individuals by exploring if low socioeconomic status individuals tend to exhibit greater facial fluctuating asymmetry values. To do so, we implement Procrustes analysis of variance and Hierarchical Linear Modelling (HLM) to estimate potential associations between facial fluctuating asymmetry values and socioeconomic status. We report significant relationships between facial fluctuating asymmetry values and age, sex, and genetic ancestry, while socioeconomic status failed to exhibit any strong statistical relationship with facial asymmetry. These results are persistent after the effect of heterozygosity (a proxy for genetic ancestry) is controlled in the model. Our results indicate that, at least on the studied sample, there is no relationship between socioeconomic stress (as intended as low socioeconomic status) and facial asymmetries

O papel do gene ADRA2A no transtorno de déficit de atenção/ hiperatividade em adultos

O TDAH (transtorno de déficit de atenção/ hiperatividade) é um transtorno multifatorial com herdabilidade de 76%. É mais prevalente na infância e adolescência (5,29%) do que na vida adulta (2,5%). Nos estudos sobre a genética do transtorno, os alvos mais visados têm sido genes da via das catecolaminas (que inclui o sistema noradrenérgico), em parte devido ao fato de que é o local de ação de psicoestimulantes usados no tratamento do TDAH. Uma recente meta-análise apresentou evidência de heterogeneidade na associação entre o polimorfismo DraI 1780 C>T do gene do receptor adrenérgico alfa-2A (ADRA2A) com o TDAH em crianças, sugerindo a necessidade de estudos adicionais para explicar as possíveis razões para esta heterogeneidade. No presente estudo, foi analisada a associação entre três polimorfismos (MspI -1291 C>G, HhaI -262 G>A e DraI 1780 C>T) do ADRA2A e o TDAH em adultos e variáveis relacionadas, tentando identificar possíveis fatores explicativos dos resultados conflitantes prévios. A amostra foi composta por 403 adultos com TDAH, diagnosticados de acordo com o DSM-IV e 232 controles provenientes do banco de sangue de Porto Alegre-RS. Os polimorfismos foram analisados pelas técnicas de PCR-RFLP e PCR-TaqMan (Applied Biosystems). A comparação das freqüências alélicas e genotípicas entre as amostras foi realizada por meio do teste do Qui-quadrado, e as associações com características de personalidade através da ANOVA. Todas as freqüências estavam em equilíbrio de HW e não foi encontrada nenhuma diferença significante entre as freqüências alélicas e genotípicas dos polimorfismos analisados entre os casos de TDAH e os controles. Entretanto, foi verificada associação dos polimorfismos MspI - 1291 C>G e DraI 1780 C>T com características de temperamento (Procura de Novidades, Evitação de Danos e Persistência). Além disso, o haplótipo contendo os alelos G-G-T (MspI-HhaI-DraI) apresentou escores mais baixos em Evitação de Danos e Persistência e mais elevados em Procura de Novidades quando comparado aos demais haplótipos. Concluindo, nossos resultados fornecem evidências sugestivas de que a associação entre polimorfismos no gene ADRA2A e dimensões de temperamento poderiam ser responsáveis pelos resultados conflitantes nos estudos de associação entre o ADRA2A e o TDAH. Futuros estudos genéticos em crianças com TDAH devem incluir a análise de variáveis de personalidade.The ADHD (Attention deficit hyperactivity disorder) is a multifatorial disorder with heritability of 76%. It is more prevalent in childhood and adolescence (5.29%) than adulthood (2.5%). In molecular genetic approaches to ADHD, the most obvious target has been the catecholamine pathway (including the noradrenergic system), in part because it is the locus of action of psychostimulants used to treat ADHD. A recent meta-analysis showed evidence for heterogeneity in the association between the DraI 1780 C>T polymorphism in the adrenergic receptor alpha-2A gene (ADRA2A) and childhood ADHD, suggesting the need for further research to explain the reasons for this heterogeneity. In present study, we investigated the association between three polymorphisms (-1291 C>G MspI, -262 G>A HhaI and 1780 C>T DraI) in the ADRA2A gene and ADHD in adults and related variables, trying to identify characteristics that could explain the previous conflicting findings. The sample included 403 ADHD adult patients that fulfilled diagnostic criteria for DSM-IV, and 232 controls. The polymorphisms were amplified with PCR-RFLP and PCR-TaqMan (Applied Biosystems). The genotype and allele frequency comparisons between ADHD patients and controls were performed with the Chi-square test, and the associations with personality characteristics by ANOVA. All frequencies were in Hardy-Weinberg equilibrium and no significant differences in allele and genotype frequencies of the polymorphisms were found between patients and controls. However, there was association between the MspI -1291 C>G and DraI 1780 C>T polymorphisms with temperament profiles (Novelty Seeking, Harm Avoidance, and Persistence). Additionally, the haplotype carrying the G-G-T alleles (MspI-HhaI-DraI) presented lower scores in Harm Avoidance and Persistence and higher in Novelty Seeking compared with other haplotypes. In conclusion, this study provides suggestive evidence that the association between ADRA2A gene polymorphisms and temperament dimensions could account for the conflicting results of association studies of ADRA2A and ADHD observed in children with ADHD. Future genetic studies in children with ADHD should include the analysis of personality variables

Relação genótipo -> fenótipo e a pigmentação humana : aspectos evolutivos e sua aplicação na genética forense

As populações brasileiras são caracterizadas por seus distintos (e extensos) padrões de mestiçagem. Justamente por apresentarem diferenças na proporção da herança genética africana, ameríndia e européia, é esperado que as conexões entre genótipos e fenótipos complexos como é o caso da cor de pele, olhos e cabelos, por exemplo, não sejam idênticas entre diferentes populações brasileiras, ou entre estas e aquelas encontradas em seus grupos ancestrais. Isto é corroborado pela consistente evidência de que grupos geográficos humanos diferem quanto ao background genético relacionado à pigmentação, refletindo-se, portanto, nas suas populações derivadas. Elucidar este background em amostras miscigenadas como a nossa é de fundamental importância para as áreas médica, evolutiva e forense. Na presente tese buscamos entender o que há de mais recente na literatura científica relacionada com a pigmentação humana, bem como produzir conhecimento de extrema relevância neste contexto em populações brasileiras com diferentes histórias demográficas. Para isto, estudamos o efeito de 18 SNPs com pigmentação da pele, olhos e cabelos na amostra de 563 voluntários brasileiros do consórcio internacional CANDELA (Consórcio para análise da diversidade e evolução latino-americana). Além disso, tentamos estabelecer um método de predição de fenótipos de pigmentação com a possível aplicação em genética forense e evolução humana. Na análise de associação dos 18 SNPs com fenótipos de pigmentação, observamos 3 (três) marcadores genéticos (HERC2rs1129038, SLC24A5rs1426654 e SLC45A2rs16891982) consistentemente associados com cor da pele, olhos e cabelos, nas distintas populações brasileiras investigadas. Este é o primeiro passo para compreender melhor o contexto biológico da produção de melanina e entender as relações genótipofenótipo da pigmentação em populações miscigenadas. Com a compreensão dos marcadores genéticos relacionados com pigmentação e também com o aperfeiçoamento do método de predição de fenótipos de pigmentação desenvolvido no presente trabalho, é possível dar o primeiro passo para a criação de uma metodologia de predição de fenótipos de cor da pele, olhos e cabelos em populações com histórias demográficas miscigenadas como a nossa, com possível aplicação nas áreas forense, médica e evolutiva.Brazilian populations are characterized by their distinct (and extensive) admixture patterns. Precisely because there are differences in the proportion of African, Amerindian and European genetic heritage, it is expected that the connections between genotypes and complex phenotypes such as skin, eyes and hair color, are not identical among different Brazilian populations, or between these and those found in their ancestral groups. This is corroborated by consistent evidence that human geographic groups differ in genetic background related to pigmentation, reflecting thus in the respectives populations derived. Elucidating this background in admixed samples such as ours is of fundamental importance to the medical, forensic and evolutionary fields. In this thesis we seek to understand what is latest in the scientific literature related to human pigmentation, as well as producing knowledge extremely relevant in this context in Brazilian populations with different demographic histories. For this, we studied the effect of 18 SNPs with pigmentation of the skin, eyes and hair in a sample of 563 Brazilian volunteers of the international consortium called CANDELA (Consortium for the analysis of the diversity and evolution of Latin America). Also, we try to establish a method for predicting pigmentation phenotypes with possible application in forensic genetics and human evolution. In association analysis of 18 SNPs with pigmentation phenotypes, we observed 3 (three) genetic markers (HERC2rs1129038, SLC24A5rs1426654 and SLC45A2rs16891982) consistently associated with skin, eye and hair color, in distinct Brazilian populations investigated. This is the first step to better understand the biological context of the production of melanin and know the connexions between genotype-phenotype of the pigmentation in admixed populations. With the understanding of the genetic markers related to pigmentation as well as with the improvement of the method of predicting phenotypes developed in the present work, it is possible to take the first step toward establishing a methodology for predicting phenotypes of skin, eye and hair color in populations with demographic histories like ours, with possible application in forensic, medical and evolutionary fields

El análisis de ADN como herramienta de la antropología forense

Como hemos visto en capítulos previos, uno de los objetivos de la Antropología Forense es auxiliar en la determinación de la identidad de un cadáver, a través del estudio de las variaciones cualitativas y cuantitativas de los caracteres humanos (Costa y Costa, 2011). Desde el siglo 19 se utiliza el sistema de huellas digitales (revisado en Hazarika y Russell, 2012) para la identificación civil y criminal de las personas. El análisis de ADN, más reciente, sólo se lleva a cabo en casos criminales más complejos, sobre todo cuando los exámenes dactiloscópico u odontológico no pueden aplicarse. En comparación con otros métodos, el análisis de ADN requiere mayor cantidad de tiempo y resulta más costoso. Además de la identificación criminal, existe una interesante discusión en la literatura científica sobre la utilización del perfil de ADN para la identificación de la población civil (Johnson y Williams, 2007)Fil: Silva de Cerqueira, Caio Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentin

Eficacia y seguridad del tratamiento con idursulfasa en pacientes con mucopolisacaridosis tipo II con y sin comparación con el placebo : revisión sistemática y metaanálisis

A mucopolissacaridose tipo II (MPS II) é uma doença genética de amplo espectro clínico, caracterizada por deficiência da enzima iduronato-2- sulfatase. Revisão sistemática avaliou a eficácia e segurança da terapia de reposição enzimática (TRE) com idursulfase (IDS) na MPS II. As bases de dados PubMed/MEDLINE, Embase, LILACS e Biblioteca Cochrane foram pesquisados até 30 de novembro de 2012. Apenas cinco estudos preencheram os critérios de inclusão (ensaios clínicos randomizados – ECRs, ECRs abertos ou séries de caso prospectivas, incluindo cinco ou mais pacientes e avaliando desfechos relevantes). Metanálise foi realizada para capacidade vital forçada (CVF; valores absolutos e em %) e para a distância percorrida no teste da caminhada dos seis minutos, com mudanças significativas em ambas as variáveis; também foi encontrado risco aumentado de reações leves relacionadas à infusão e de desenvolvimento de anticorpos IgG à IDS. Em face dos dados apresentados neste estudo, conclui-se que a TRE com IDS é segura e tem benefício potencial em MPS II, mas estudos adicionais são necessários.Mucopolysaccharidosis type II (MPS II) is a genetic disease of broad clinical spectrum, characterized by a deficiency of the enzyme iduronate- 2-sulfatase. The aim of this study was to assess whether enzyme replacement therapy (ERT) with idursulfase (IDS) for MPS II is effective and safe. PubMed/MEDLINE, Embase, LILACS, and Cochrane Library were searched until November 30, 2012. Only five articles met the inclusion criteria (randomized controlled trials – RCTs, or open-label trials/prospective case series including ≥ 5 patients and evaluating relevant outcomes). A meta-analysis was performed for forced vital capacity (FVC; absolute and %) and for distance walked on the 6-minute walking test (6MWT). there was a statistically significant increase, but not clinically relevant, in both variables; an increased risk for development of mild infusion-related reactions and IgG antibodies to IDS were also found. The data suggest that ERT with IDS is safe and has a potential benefit for MPS II patients, but further studies are required.La mucopolisacaridosis tipo II (MPS II) es una enfermedad genética de amplio espectro clínico, caracterizada por una deficiencia de la enzima iduronato-2-sulfatasa. El objetivo fue evaluar la seguridad y eficacia de la Terapia de Reemplazo Enzimático (TRE) con idursulfasa (IDS) en la MPS II. En las bases PubMed/MEDLINE, EMBASE, LILACS y Cochrane Library se inició la búsqueda hasta el 30 de noviembre de 2012. Sólo cinco estudios cumplieron los criterios de inclusión (ensayos controlados aleatorios –ECA, o ECA abiertos o series de casos prospectivo incluyendo ≥ 5 pacientes y evaluación de los resultados pertinentes). El metaanálisis se realizó para la capacidad vital forzada (FVC; absoluta y %) y la distancia caminada en 6 minutos, con cambios significativos en ambas variables; el riesgo también se encuentra aumentado por reacciones leves y anticuerpos IgG, relacionados con la infusión con IDS. El TRE con IDS es seguro y tiene un beneficio potencial en la MPS II, pero se necesitan estudios adicionales