Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis

Variation in body iron is associated with or causes diseases, including anaemia and iron overload. Here, we analyse genetic association data on biochemical markers of iron status from 11 European-population studies, with replication in eight additional cohorts (total up to 48,972 subjects). We find 11 genome-wide-significant (P<5 × 10(-8)) loci, some including known iron-related genes (HFE, SLC40A1, TF, TFR2, TFRC, TMPRSS6) and others novel (ABO, ARNTL, FADS2, NAT2, TEX14). SNPs at ARNTL, TF, and TFR2 affect iron markers in HFE C282Y homozygotes at risk for hemochromatosis. There is substantial overlap between our iron loci and loci affecting erythrocyte and lipid phenotypes. These results will facilitate investigation of the roles of iron in disease.

Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series.

PURPOSE: Recently, a 76-gene prognostic signature able to predict distant metastases in lymph node-negative (N(-)) breast cancer patients was reported. The aims of this study conducted by TRANSBIG were to independently validate these results and to compare the outcome with clinical risk assessment. EXPERIMENTAL DESIGN: Gene expression profiling of frozen samples from 198 N(-) systemically untreated patients was done at the Bordet Institute, blinded to clinical data and independent of Veridex. Genomic risk was defined by Veridex, blinded to clinical data. Survival analyses, done by an independent statistician, were done with the genomic risk and adjusted for the clinical risk, defined by Adjuvant! Online. RESULTS: The actual 5- and 10-year time to distant metastasis were 98% (88-100%) and 94% (83-98%), respectively, for the good profile group and 76% (68-82%) and 73% (65-79%), respectively, for the poor profile group. The actual 5- and 10-year overall survival were 98% (88-100%) and 87% (73-94%), respectively, for the good profile group and 84% (77-89%) and 72% (63-78%), respectively, for the poor profile group. We observed a strong time dependence of this signature, leading to an adjusted hazard ratio of 13.58 (1.85-99.63) and 8.20 (1.10-60.90) at 5 years and 5.11 (1.57-16.67) and 2.55 (1.07-6.10) at 10 years for time to distant metastasis and overall survival, respectively. CONCLUSION: This independent validation confirmed the performance of the 76-gene signature and adds to the growing evidence that gene expression signatures are of clinical relevance, especially for identifying patients at high risk of early distant metastases.

Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.

High blood pressure (BP) is more prevalent and contributes to more severe manifestations of cardiovascular disease (CVD) in African Americans than in any other United States ethnic group. Several small African-ancestry (AA) BP genome-wide association studies (GWASs) have been published, but their findings have failed to replicate to date. We report on a large AA BP GWAS meta-analysis that includes 29,378 individuals from 19 discovery cohorts and subsequent replication in additional samples of AA (n = 10,386), European ancestry (EA) (n = 69,395), and East Asian ancestry (n = 19,601). Five loci (EVX1-HOXA, ULK4, RSPO3, PLEKHG1, and SOX6) reached genome-wide significance (p < 1.0 × 10(-8)) for either systolic or diastolic BP in a transethnic meta-analysis after correction for multiple testing. Three of these BP loci (EVX1-HOXA, RSPO3, and PLEKHG1) lack previous associations with BP. We also identified one independent signal in a known BP locus (SOX6) and provide evidence for fine mapping in four additional validated BP loci. We also demonstrate that validated EA BP GWAS loci, considered jointly, show significant effects in AA samples. Consequently, these findings suggest that BP loci might have universal effects across studied populations, demonstrating that multiethnic samples are an essential component in identifying, fine mapping, and understanding their trait variability.

Tree of Sex: A database of sexual systems

The vast majority of eukaryotic organisms reproduce sexually, yet the nature of the sexual system and the mechanism of sex determination often vary remarkably, even among closely related species. Some species of animals and plants change sex across their lifespan, some contain hermaphrodites as well as males and females, some determine sex with highly differentiated chromosomes, while others determine sex according to their environment. Testing evolutionary hypotheses regarding the causes and consequences of this diversity requires interspecific data placed in a phylogenetic context. Such comparative studies have been hampered by the lack of accessible data listing sexual systems and sex determination mechanisms across the eukaryotic tree of life. Here, we describe a database developed to facilitate access to sexual system and sex chromosome information, with data on sexual systems from 11,038 plant, 705 fish, 173 amphibian, 593 non-avian reptilian, 195 avian, 479 mammalian, and 11,556 invertebrate species.

Directrius per a l'accessibilitat al contingut web, versió 1.0

Aquestes directrius expliquen com fer que el contingut web sigui accessible a persones amb discapacitats i s'adrecen a creadors de contingut (autors de pàgines web o dissenyadors de llocs web) i a creadors d'eines d'autor. L'objectiu principal d'aquestes directrius és promoure l'accessibilitat. Tanmateix, l'aplicació de les directrius facilitarà l'accés al contingut a tot tipus d'usuari, sigui quin sigui l'agent d'usuari usat (navegador web, navegador de veu, telèfon mòbil, ordinador de cotxe, etc.) o les condicions de l'entorn de consulta (entorns sorollosos, espais mal il·luminats, entorns en què no es poden usar les mans, etc.). L'aplicació d'aquestes directrius també ajudarà els usuaris a trobar la informació d'una manera més ràpida dins el web. Les directrius no pretenen desincentivar l'ús d'imatges, vídeo, etc., sinó que expliquen com fer que el contingut multimèdia sigui més accessible a una àmplia audiència.Aquest és un document de referència per a uns principis d'accessibilitat i idees de disseny. Algunes de les estratègies comentades tracten d'aspectes relatius a la internacionalització del web i a l'accés des de terminals mòbils. Tanmateix, el document se centra en l'accessibilitat i no tracta exhaustivament dels aspectes relacionats amb altres activitats del W3C. Si voleu més informació sobre aquests temes podeu consultar les pàgines inicials W3C Mobile Access Activity (per a l'accés des de terminals mòbils) i W3C Internationalization Activity (per als aspectes d'internacionalització).Aquest document està pensat per a ser estable en el temps i, per tant, no dóna informació específica sobre si els navegadors funcionen o no amb una determinada tecnologia, ja que aquesta informació varia molt ràpidament. Aquesta informació es pot trobar al web de la Web Accessibility Initiative ,WAI, (Iniciativa d'Accessibilitat Web) [WAI-UA-SUPPORT].Aquest document inclou un annex que organitza tots els punts de verificació ordenats per tema i per prioritat. Els punts de l'annex estan enllaçats a les respectives definicions en el document. Els temes recollits en l'annex inclouen les imatges, el contingut multimèdia, les taules, els marcs, els formularis i els scripts. L'annex es presenta en forma de taula o com a simple llista.Un document a part, amb el títol Techniques for Web Content Accessibility Guidelines 1.0 (Tècniques per a les directrius per a l'accessibilitat al contingut web, versió 1.0) ([TECHNIQUES]) explica com posar a la pràctica els punts citats fins aquí. El document de tècniques explica cada punt amb més detalls i dóna exemples usant el llenguatge d'etiquetatge d'hipertext (HTML), fulls d'estil en cascada (CSS), el llenguatge d'integració multimèdia sincronitzada (SMIL) o el llenguatge d'etiquetatge matemàtic (MathML). Aquest document també inclou tècniques per a provar o validar una pàgina web i un índex dels elements i atributs HTML amb les tècniques que els usen. El document de tècniques està pensat per a seguir de prop els canvis tecnològics i es preveu que s'actualitzi més sovint que les directrius.Nota: Algunes de les característiques descrites en les directrius no estan encara implementades en tots els navegadors o eines multimèdia; en concret pot ser que no es puguin utilitzar funcions noves d'HTML 4.0, de CSS1 o CSS2.Les Directrius per a l'accessibilitat al contingut web, versió 1.0 són part d'una col·lecció de directrius sobre accessibilitat publicades per la Web Accessibility Initiative, WAI (Iniciativa d'Accessibilitat Web). La col·lecció comprèn User Agent Accessibility Guidelines (Directrius d'accessibilitat per a agents d'usuari) [WAI-USERAGENT] i Authoring Tool Accessibility Guidelines (Directrius d'accessibilitat per a eines d'autor [WAI-AUTOOLS].

Accessibilitat al web: panoràmica general

Es presenta el concepte d'accessibilitat al web com a sistema per a facilitar el treball a la xarxa per part de les persones discapacitades i millorar la usabilitat dels continguts. A partir de la Iniciativa per a l'Accessibilitat al Web (WAI) del World-Wide Web Consortium (W3C), aquest ha elaborat unes directrius que actualment estan en procés d'adopció pels diferents governs i empreses. Finalment es presenten diverses eines informàtiques i entitats de contacte que donen suport a aquestes actuacions.

Transapical aortic valve replacement in extreme-risk patients: outcome, risk factors and mid-term results.

OBJECTIVES: Transcatheter aortic valve replacement (TAVR) provides good results in selected high-risk patients. However, it is unclear whether this procedure carries advantages in extreme-risk profile patients with logistic EuroSCORE above 35%. METHODS: From January 2009 to July 2011, of a total number of 92 transcatheter aortic valve procedures performed, 40 'extreme-risk' patients underwent transapical TAVR (TA-TAVR) (EuroSCORE above 35%). Variables were analysed as risk factors for hospital and mid-term mortality, and a 2-year follow-up (FU) was obtained. RESULTS: The mean age was: 81 ± 10 years. Twelve patients (30%) had chronic pulmonary disease, 32 (80%) severe peripheral vascular disease, 14 (35%) previous cardiac surgery, 19 (48%) chronic renal failure (2 in dialysis), 7 (17%) previous stroke (1 with disabilities), 3 (7%) a porcelain aorta and 12 (30%) were urgent cases. Mean left ventricle ejection fraction (LVEF) was 49 ± 13%, and mean logistic EuroSCORE was 48 ± 11%. Forty stent-valves were successfully implanted with six Grade-1 and one Grade-2 paravalvular leakages (success rate: 100%). Hospital mortality was 20% (8 patients). Causes of death following the valve academic research consortium (VARC) definitions were: life-threatening haemorrhage (1), myocardial infarction (1), sudden death (1), multiorgan failure (2), stroke (1) and severe respiratory dysfunction (2). Major complications (VARC definitions) were: myocardial infarction for left coronary ostium occlusion (1), life-threatening bleeding (2), stroke (2) and acute kidney injury with dialysis (2). Predictors for hospital mortality were: conversion to sternotomy, life-threatening haemorrhage, postoperative dialysis and long intensive care unit (ICU) stay. Variables associated with hospital mortality were: conversion to sternotomy (P = 0.03), life-threatening bleeding (P = 0.02), acute kidney injury with dialysis (P = 0.03) and prolonged ICU stay (P = 0.02). Mean FU time was 24 months: actuarial survival estimates for all-cause mortality at 6 months, 1 year, 18 months and 2 years were 68, 57, 54 and 54%, respectively. Patients still alive at FU were in good clinical condition, New York Heart Association (NYHA) class 1-2 and were never rehospitalized for cardiac decompensation. CONCLUSIONS: TA-TAVR in extreme-risk patients carries a moderate risk of hospital mortality. Severe comorbidities and presence of residual paravalvular leakages affect the mid-term survival, whereas surviving patients have an acceptable quality of life without rehospitalizations for cardiac decompensation.

Genetic loci for retinal arteriolar microcirculation.

Narrow arterioles in the retina have been shown to predict hypertension as well as other vascular diseases, likely through an increase in the peripheral resistance of the microcirculatory flow. In this study, we performed a genome-wide association study in 18,722 unrelated individuals of European ancestry from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium and the Blue Mountain Eye Study, to identify genetic determinants associated with variations in retinal arteriolar caliber. Retinal vascular calibers were measured on digitized retinal photographs using a standardized protocol. One variant (rs2194025 on chromosome 5q14 near the myocyte enhancer factor 2C MEF2C gene) was associated with retinal arteriolar caliber in the meta-analysis of the discovery cohorts at genome-wide significance of P-value <5×10(-8). This variant was replicated in an additional 3,939 individuals of European ancestry from the Australian Twins Study and Multi-Ethnic Study of Atherosclerosis (rs2194025, P-value = 2.11×10(-12) in combined meta-analysis of discovery and replication cohorts). In independent studies of modest sample sizes, no significant association was found between this variant and clinical outcomes including coronary artery disease, stroke, myocardial infarction or hypertension. In conclusion, we found one novel loci which underlie genetic variation in microvasculature which may be relevant to vascular disease. The relevance of these findings to clinical outcomes remains to be determined.

Taula de punts de verificació de les directrius per a l'accessibilitat al contingut de pàgines web, versió 1.0

El World-Wide Web Consortium (W3C), organisme encarregat de la normalització del web, va començar a preocupar-se fa uns anys dels problemes d'accessibilitat que poden presentar les pàgines web a les persones amb discapacitats. Com a resultat d'aquesta preocupació, va posar en marxa la Iniciativa sobre Accessibilitat al Web (WAI), amb el fi d'estudiar el tema i elaborar directrius d'actuació i altres materials d'ajuda. El document més important sorgit de la Iniciativa són les Directrius per a l'accessibilitat al contingut de pàgines web, versió 1.0, que ja va ser traduït al català en aquesta mateixa revista.2 Com a complement, el W3C ha publicat altres documents que volen facilitar-ne la implementació; en destaca el document que a continuació publiquem traduït, la Taula de punts de verificació de les Directrius per a l'accessibilitat al contingut de pàgines web, versió 1.0. La Taula de punts de verificació està pensada per actuar com un annex a les Directrius; sota la forma de llista de control (checklist) presenta un llistat classificat per nivells de prioritat de les pautes que s'haurien de seguir per crear pàgines web accessibles per tothom. La Taula vol ser, per tant, una eina ràpida per a la detecció manual dels problemes que puguin aparèixer, i que es descriuen amb més detalls a les Directrius.

Nivel de accesibilidad de las sedes web de las universidades españolas

El estudio presenta un análisis del nivel de accesibilidad de las webs de las universidades españolas según los indicadores de prioridad 1 de las Pautas de accesibilidad al contenido de la web, versión 1.0WCAG dentro de la Iniciativa WAI del World-Wide Web Consortium, y otros indicadores complementarios. Los resultados obtenidos nos indican que ninguna web universitaria española cumple en su totalidad este primer nivel y que queda pendiente una gran tarea de adaptación. [eng] This report presents an analysis of the accessibility level of websites in the Spanish universities considering level"A" of Web Contents Accessibility Guidelines 1.0 WCAG issued by the Web Accessibility Initiative working group in the Worlwide Web Consortium, and some additional criteria. The conclusions show that no Spanish university web reaches completely this first level and that there is still a hard work to do redesigning websites.

Genetic Variants of Serum Uric Acid and Gout: An Analysis of > 170,000 Individuals

Background/Purpose: Gout is a common and excruciatingly painful inflammatory arthritis caused by hyperuricemia. In addition to various lifestyle risk factors, a substantial genetic predisposition to gout has long been recognized. The Global Urate Genetics Consortium (GUGC) has aimed to comprehensively investigate the genetics of serum uric acid and gout using data from _ 140,000 individuals of European-ancestry, 8,340 individuals of Indian ancestry, 5,820 African-Americans, and 15,286 Japanese. Methods: We performed discovery GWAS meta-analyses of serum urate levels (n_110,347 individuals) followed by replication analyses (n_32,813 different individuals). Our gout analysis involved 3,151 cases and 68,350 controls, including 1,036 incident gout cases that met the American College of Rheumatology Criteria. We also examined the association of gout with fractional excretion of uric acid (n_6,799). A weighted genetic urate score was constructed based on the number of risk alleles across urate-associated loci, and their association with the risk of gout was evaluated. Furthermore, we examined implicated transcript expression in cis (expression quantitative trait loci databases) for potential insights into the gene underlying the association signal. Finally, in order to further identify urate-associated genomic regions, we performed functional network analyses that incorporated prior knowledge on molecular interactions in which the gene products of implicated genes operate. Results: We identified and replicated 28 genome-wide significant loci in association with serum urate (P 5_10_8), including all previously-reported loci as well as 18 novel genetic loci. Unlike the majority of previouslyidentified loci, none of the novel loci appeared to be obvious candidates for urate transport. Rather, they were mapped to genes that encode for purine production, transcription, or growth factors with broad downstream responses. Besides SLC2A9 and ABCG2, no additional regions contained SNPs that differed significantly (P _ 5_10_8) between sexes. Urateincreasing alleles were associated with an increased risk of gout for all loci. The urate genetic risk score (ranging from 10 to 45) was significantly associated with an increased odds of prevalent gout (OR per unit increase, 1.11; 95% CI, 1.09-1.14) and incident gout (OR, 1.10; 95% CI, 1.08-1.13). Associations for many of the loci were of similar magnitude in individuals of non-European ancestry. Detailed characterization of the loci revealed associations with transcript expression and the fractional excretion of urate. Network analyses implicated the inhibins-activins signaling pathways and glucose metabolism in systemic urate control. Conclusion: The novel genetic candidates identified in this urate/gout consortium study, the largest to date, highlight the importance of metabolic control of urate production and urate excretion. The modulation by signaling processes that influence metabolic pathways such as glycolysis and the pentose phosphate pathway appear to be central mechanisms underpinned by the novel GWAS candidates. These findings may have implications for further research into urate-lowering drugs to treat and prevent gout.

A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.

BACKGROUND: The mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. More recently large initiatives such as the International Knockout Mouse Consortium (IKMC) are using the C57BL/6N mouse strain to generate null alleles for all mouse genes. Hence both strains are now widely used in mouse genetics studies. Here we perform a comprehensive genomic and phenotypic analysis of the two strains to identify differences that may influence their underlying genetic mechanisms. RESULTS: We undertake genome sequence comparisons of C57BL/6J and C57BL/6N to identify SNPs, indels and structural variants, with a focus on identifying all coding variants. We annotate 34 SNPs and 2 indels that distinguish C57BL/6J and C57BL/6N coding sequences, as well as 15 structural variants that overlap a gene. In parallel we assess the comparative phenotypes of the two inbred lines utilizing the EMPReSSslim phenotyping pipeline, a broad based assessment encompassing diverse biological systems. We perform additional secondary phenotyping assessments to explore other phenotype domains and to elaborate phenotype differences identified in the primary assessment. We uncover significant phenotypic differences between the two lines, replicated across multiple centers, in a number of physiological, biochemical and behavioral systems. CONCLUSIONS: Comparison of C57BL/6J and C57BL/6N demonstrates a range of phenotypic differences that have the potential to impact upon penetrance and expressivity of mutational effects in these strains. Moreover, the sequence variants we identify provide a set of candidate genes for the phenotypic differences observed between the two strains.

Directrius per a l'accessibilitat al contingut web, versió 1.0. Recomanació de W3C, 5 de maig de 1999

Aquestes directrius expliquen com fer que el contingut web sigui accessible a persones ambdiscapacitats i s'adrecen a creadors de contingut (autors de pàgines web o dissenyadors de llocs web) ia creadors d'eines d'autor. L'objectiu principal d'aquestes directrius és promoure l'accessibilitat.Tanmateix, l'aplicació de les directrius facilitarà l'accés al contingut a tot tipus d'usuari, sigui quin siguil'agent d'usuari usat (navegador web, navegador de veu, telèfon mòbil, ordinador de cotxe, etc.) o les condicions de l'entorn de consulta (entorns sorollosos, espais mal il·luminats, entorns en què no es poden usar lesmans, etc.). L'aplicació d'aquestes directrius també ajudarà els usuaris a trobar la informació d'unamanera més ràpida dins el web. Les directrius no pretenen desincentivar l'ús d'imatges, vídeo, etc., sinóque expliquen com fer que el contingut multimèdia sigui més accessible a una àmplia audiència.Aquest és un document de referència per a uns principis d'accessibilitat i idees de disseny. Algunes deles estratègies comentades tracten d'aspectes relatius a la internacionalització del web i a l'accés desde terminals mòbils. Tanmateix, el document se centra en l'accessibilitat i no tracta exhaustivament delsaspectes relacionats amb altres activitats del W3C. Si voleu més informació sobre aquests temes podeuconsultar les pàgines inicials W3C Mobile Access Activity (per a l'accés des de terminals mòbils) i W3CInternationalization Activity (per als aspectes d'internacionalització). Aquest document està pensat per a ser estable en el temps i, per tant, no dóna informació específica sobre si els navegadors funcionen o no amb una determinada tecnologia, ja que aquesta informació varia molt ràpidament. Aquesta informació es pot trobar al web de la Web Accessibility Initiative ,WAI, (Iniciativa d'Accessibilitat Web) [WAI-UA-SUPPORT].Aquest document inclou un annex que organitza tots els punts de verificació ordenats per tema i perprioritat. Els punts de l'annex estan enllaçats a les respectives definicions en el document. Els temesrecollits en l'annex inclouen les imatges, el contingut multimèdia, les taules, els marcs, els formularis iels scripts. L'annex es presenta en forma de taula o com a simple llista. Un document a part, amb el títol Techniques for Web Content Accessibility Guidelines 1.0 (Tècniques per a les directrius per a l'accessibilitat al contingut web, versió 1.0) ([TECHNIQUES]) explica com posar a la pràctica els punts citats fins aquí. El document de tècniques explica cada punt amb més detalls i dóna exemples usant el llenguatge d'etiquetatge d'hipertext (HTML), fulls d'estil en cascada (CSS), el llenguatge d'integració multimèdia sincronitzada (SMIL) o el llenguatge d'etiquetatge matemàtic (MathML). Aquest document també inclou tècniques per a provar o validar una pàgina web i un índex Directrius per a l'accessibilitat al contingut web, versió 1.0 dels elements i atributs HTML amb les tècniques que els usen. El document de tècniques està pensat per a seguir de prop els canvis tecnològics i es preveu que s'actualitzi més sovint que les directrius.

The tomato genome sequence providies insights into fleshy fruit evolution

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

DNA mismatch repair gene MSH6 implicated in determining age at natural menopause.

The length of female reproductive lifespan is associated with multiple adverse outcomes, including breast cancer, cardiovascular disease and infertility. The biological processes that govern the timing of the beginning and end of reproductive life are not well understood. Genetic variants are known to contribute to ∼50% of the variation in both age at menarche and menopause, but to date the known genes explain <15% of the genetic component. We have used genome-wide association in a bivariate meta-analysis of both traits to identify genes involved in determining reproductive lifespan. We observed significant genetic correlation between the two traits using genome-wide complex trait analysis. However, we found no robust statistical evidence for individual variants with an effect on both traits. A novel association with age at menopause was detected for a variant rs1800932 in the mismatch repair gene MSH6 (P = 1.9 × 10(-9)), which was also associated with altered expression levels of MSH6 mRNA in multiple tissues. This study contributes to the growing evidence that DNA repair processes play a key role in ovarian ageing and could be an important therapeutic target for infertility.