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1.
Nature ; 506(7487): 225-9, 2014 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-24522598

RESUMO

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 (14)C years before present (bp) (13,000 to 12,600 calendar years bp). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 (14)C years bp (approximately 12,707-12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.


Assuntos
Genoma Humano/genética , Indígenas Norte-Americanos/genética , Filogenia , Arqueologia , Ásia/etnologia , Osso e Ossos , Sepultamento , Cromossomos Humanos Y/genética , DNA Mitocondrial/genética , Emigração e Imigração/história , Europa (Continente)/etnologia , Fluxo Gênico/genética , Haplótipos/genética , História Antiga , Humanos , Lactente , Masculino , Modelos Genéticos , Dados de Sequência Molecular , Montana , Dinâmica Populacional , Datação Radiométrica
2.
Lancet ; 380(9844): 815-23, 2012 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-22763110

RESUMO

BACKGROUND: Osteoarthritis is the most common form of arthritis worldwide and is a major cause of pain and disability in elderly people. The health economic burden of osteoarthritis is increasing commensurate with obesity prevalence and longevity. Osteoarthritis has a strong genetic component but the success of previous genetic studies has been restricted due to insufficient sample sizes and phenotype heterogeneity. METHODS: We undertook a large genome-wide association study (GWAS) in 7410 unrelated and retrospectively and prospectively selected patients with severe osteoarthritis in the arcOGEN study, 80% of whom had undergone total joint replacement, and 11,009 unrelated controls from the UK. We replicated the most promising signals in an independent set of up to 7473 cases and 42,938 controls, from studies in Iceland, Estonia, the Netherlands, and the UK. All patients and controls were of European descent. FINDINGS: We identified five genome-wide significant loci (binomial test p≤5·0×10(-8)) for association with osteoarthritis and three loci just below this threshold. The strongest association was on chromosome 3 with rs6976 (odds ratio 1·12 [95% CI 1·08-1·16]; p=7·24×10(-11)), which is in perfect linkage disequilibrium with rs11177. This SNP encodes a missense polymorphism within the nucleostemin-encoding gene GNL3. Levels of nucleostemin were raised in chondrocytes from patients with osteoarthritis in functional studies. Other significant loci were on chromosome 9 close to ASTN2, chromosome 6 between FILIP1 and SENP6, chromosome 12 close to KLHDC5 and PTHLH, and in another region of chromosome 12 close to CHST11. One of the signals close to genome-wide significance was within the FTO gene, which is involved in regulation of bodyweight-a strong risk factor for osteoarthritis. All risk variants were common in frequency and exerted small effects. INTERPRETATION: Our findings provide insight into the genetics of arthritis and identify new pathways that might be amenable to future therapeutic intervention. FUNDING: arcOGEN was funded by a special purpose grant from Arthritis Research UK.


Assuntos
Osteoartrite/genética , Artroplastia de Substituição , Estudos de Casos e Controles , Feminino , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Desequilíbrio de Ligação , Masculino , Osteoartrite/cirurgia , Osteoartrite do Quadril/genética , Osteoartrite do Quadril/cirurgia , Osteoartrite do Joelho/genética , Osteoartrite do Joelho/cirurgia , Polimorfismo de Nucleotídeo Único
3.
Hum Hered ; 73(1): 47-51, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22261837

RESUMO

AIMS: Next-generation sequencing has opened the possibility of large-scale sequence-based disease association studies. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, we have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from 2 bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. METHODS: We used a weighted Z method that combines the probabilistic scores of PolyPhen-2 and SIFT. We defined 2 dataset pairs to train and test CAROL using information from the dbSNP: 'HGMD-PUBLIC' and 1000 Genomes Project databases. The training pair comprises a total of 980 positive control (disease-causing) and 4,845 negative control (non-disease-causing) variants. The test pair consists of 1,959 positive and 9,691 negative controls. RESULTS: CAROL has higher predictive power and accuracy for the effect of non-synonymous variants than each individual annotation tool (PolyPhen-2 and SIFT) and benefits from higher coverage. CONCLUSION: The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences.


Assuntos
Genômica/métodos , Anotação de Sequência Molecular/métodos , Software , Algoritmos , Humanos , Polimorfismo de Nucleotídeo Único , Curva ROC
4.
Clin Chem Lab Med ; 50(2): 255-60, 2011 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-22022988

RESUMO

The success of genome-wide association studies (GWAS) in identifying replicating associations has greatly contributed to understanding of the genetic aetiology of complex diseases. This review discusses and provides examples of the potential of GWAS findings to be translated into clinical practice, i.e., diagnosis, prediction, prognosis, novel treatments and response to treatment of common diseases. The biological insights afforded by newly-identified robust associations represent the largest, albeit indirect, translational contribution of GWAS.


Assuntos
Estudo de Associação Genômica Ampla , Predisposição Genética para Doença , Humanos
5.
Invest Ophthalmol Vis Sci ; 54(2): 1260-7, 2013 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-23322567

RESUMO

PURPOSE: Astigmatism is a common refractive error that reduces vision, where the curvature and refractive power of the cornea in one meridian are less than those of the perpendicular axis. It is a complex trait likely to be influenced by both genetic and environmental factors. Twin studies of astigmatism have found approximately 60% of phenotypic variance is explained by genetic factors. This study aimed to identify susceptibility loci for astigmatism. METHODS: We performed a meta-analysis of seven genome-wide association studies that included 22,100 individuals of European descent, where astigmatism was defined as the number of diopters of cylinder prescription, using fixed effect inverse variance-weighted methods. RESULTS: A susceptibility locus was identified with lead single nucleotide polymorphism rs3771395 on chromosome 2p13.3 (meta-analysis, P = 1.97 × 10(-7)) in the VAX2 gene. VAX2 plays an important role in the development of the dorsoventral axis of the eye. Animal studies have shown a gradient in astigmatism along the vertical plane, with corresponding changes in refraction, particularly in the ventral field. CONCLUSIONS: This finding advances the understanding of refractive error, and provides new potential pathways to be evaluated with regard to the development of astigmatism.


Assuntos
Astigmatismo/genética , Cromossomos Humanos Par 2 , Proteínas de Homeodomínio/genética , Polimorfismo de Nucleotídeo Único/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Austrália , Meio Ambiente , Feminino , Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Países Baixos , Fenótipo , Sistema de Registros/estatística & dados numéricos , Reino Unido , Adulto Jovem
6.
Nat Genet ; 42(10): 902-5, 2010 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-20835236

RESUMO

Myopia and hyperopia are at opposite ends of the continuum of refraction, the measure of the eye's ability to focus light, which is an important cause of visual impairment (when aberrant) and is a highly heritable trait. We conducted a genome-wide association study for refractive error in 4,270 individuals from the TwinsUK cohort. We identified SNPs on 15q25 associated with refractive error (rs8027411, P = 7.91 × 10⁻8). We replicated this association in six adult cohorts of European ancestry with a combined 13,414 individuals (combined P = 2.07 × 10⁻9). This locus overlaps the transcription initiation site of RASGRF1, which is highly expressed in neurons and retina and has previously been implicated in retinal function and memory consolidation. Rasgrf1(-/-) mice show a heavier average crystalline lens (P = 0.001). The identification of a susceptibility locus for refractive error on 15q25 will be important in characterizing the molecular mechanism responsible for the most common cause of visual impairment.


Assuntos
Cromossomos Humanos Par 15/genética , Predisposição Genética para Doença , Genoma Humano , Estudo de Associação Genômica Ampla , Miopia/genética , Adulto , Animais , Estudos de Casos e Controles , Estudos de Coortes , Feminino , Genótipo , Humanos , Masculino , Camundongos , Camundongos Knockout , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Estudos em Gêmeos como Assunto , ras-GRF1/genética , ras-GRF1/fisiologia
7.
Invest Ophthalmol Vis Sci ; 50(1): 126-31, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-18757506

RESUMO

PURPOSE: Twin studies have demonstrated a high heritability for refractive error of up to 90%, but some family studies have suggested up to one-third of population variance is attributable to the effects of shared family environment. This large twin study aimed to explore the role of shared environment in refractive error. METHODS: Refractive error was measured using autorefraction in 4602 subjects (1152 monozygotic and 1149 dizygotic twin pairs), aged between 16 and 82 years, recruited from the TwinsUK Adult Twin Registry. Maximum-likelihood methods were used to estimate the variance of genetic, environmental, and age variance components. RESULTS: Maximum likelihood model fitting estimate of the heritability from the best-fit model was 77% (95% confidence interval [CI], 68%-84%). Shared environmental effects explained 7% (95% CI, 0%-15%) and individual environmental effects explained 16% (95% CI, 15%-18%) of the spherical equivalent variance, respectively. Inclusion of age effects into the modeling reduced shared environmental effects to an estimated 2% of variation. CONCLUSIONS: Analysis of 2301 twin pairs confirms that the twin study design results in a very low estimate of shared family environmental effects in refractive error. Several factors may explain these differences; we believe the most likely is that twins are perfectly age matched and do not include cross-generation or cohort effects. This means twin study designs have more power to detect heritable effects in variance component models of myopia, whereas family studies have more power to detect shared environment effects.


Assuntos
Doenças em Gêmeos/genética , Meio Ambiente , Característica Quantitativa Herdável , Erros de Refração/genética , Gêmeos Dizigóticos/genética , Gêmeos Monozigóticos/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Predisposição Genética para Doença , Humanos , Masculino , Pessoa de Meia-Idade , Adulto Jovem
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