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Summary Several Bayesian methods have been proposed to borrow information dynamically from historical controls in clinical trials. In this note, we identify key features of the relationship between the first method proposed, the bias–variance method, which is strongly related to the commensurate prior approach, and a more recent and widely used approach called robust mixture priors (RMP). We focus on the two key terms that need to be chosen to define the RMP, namely $w$, the prior probability that the new trial differs systematically from the historical trial, and $s_v^2$, the variance of the vague component of the RMP. The relationship with Pocock’s prior reveals that different combinations of these two terms can express similar prior beliefs about the amount of information provided by the historical data. This demonstrates the value of fixing $s_v^2$, e.g., so the vague component is “worth one subject.” Prior belief about the relevance of the historical data is then driven by a single value, the prespecified weight $w$.

Skin fibrosis is a hallmark feature of systemic sclerosis. Skin biopsy transcriptomics and blister fluid proteomics give insight into the local environment of the skin. We have integrated these modalities with the aim of developing a surrogate for the modified Rodnan skin score (mRSS), using candidate genes and proteins from the skin and blister fluid as anchors to identify key analytes in the plasma.In this single-centre, prospective observational study at the Royal Free Campus, University College London, London, UK, transcriptional and proteomic analyses of blood and skin were performed in a cohort of patients with systemic sclerosis (n=52) and healthy controls (n=16). Weighted gene co-expression network analysis was used to explore the association of skin transcriptomics data, clinical traits, and blister fluid proteomic results. Candidate hub analytes were identified as those present in both blister and skin gene sets (modules), and which correlated with plasma (module membership0·7 and gene significance0·6). Hub analytes were confirmed using RNA transcript data obtained from skin biopsy samples from patients with early diffuse cutaneous systemic sclerosis at 12 months.We identified three modules in the skin, and two in blister fluid, which correlated with a diagnosis of early diffuse cutaneous systemic sclerosis. From these modules, 11 key hub analytes were identified, present in both skin and blister fluid modules, whose transcript and protein levels correlated with plasma protein concentrations, mRSS, and showed statistically significant correlation on repeat transcriptomic samples taken at 12 months. Multivariate analysis identified four plasma analytes as correlates of mRSS (COL4A1, COMP, SPON1, and TNC), which can be used to differentiate disease subtype.This unbiased approach has identified potential biological candidates that might be drivers of local skin pathogenesis in systemic sclerosis. By focusing on measurable analytes in the plasma, we generated a promising composite plasma protein biomarker that could be used for assessment of skin severity, case stratification, and as a potential outcome measure for clinical trials and practice. Once fully validated, the biomarker score could replace a clinical score such as the mRSS, which carries substantial variability.GlaxoSmithKline and UK Medical Research Council.

ObjectivesClinical heterogeneity is a cardinal feature of systemic sclerosis (SSc). Hallmark SSc autoantibodies are central to diagnosis and associate with distinct patterns of skin-based and organ-based complications. Understanding molecular differences between patients will benefit clinical practice and research and give insight into pathogenesis of the disease. We aimed to improve understanding of the molecular differences between key diffuse cutaneous SSc subgroups as defined by their SSc-specific autoantibodiesMethodsWe have used high-dimensional transcriptional and proteomic analysis of blood and the skin in a well-characterised cohort of SSc (n=52) and healthy controls (n=16) to understand the molecular basis of clinical diversity in SSc and explore differences between the hallmark antinuclear autoantibody (ANA) reactivities.ResultsOur data define a molecular spectrum of SSc based on skin gene expression and serum protein analysis, reflecting recognised clinical subgroups. Moreover, we show that antitopoisomerase-1 antibodies and anti-RNA polymerase III antibodies specificities associate with remarkably different longitudinal change in serum protein markers of fibrosis and divergent gene expression profiles. Overlapping and distinct disease processes are defined using individual patient pathway analysis.ConclusionsOur findings provide insight into clinical diversity and imply pathogenetic differences between ANA-based subgroups. This supports stratification of SSc cases by ANA antibody subtype in clinical trials and may explain different outcomes across ANA subgroups in trials targeting specific pathogenic mechanisms.

Diabetes self-care may become increasingly challenging as cognition declines. We sought to characterize glycated hemoglobin ARetrospective matched cohort study.Using a linkage between a primary care (Lambeth DataNet) and a secondary mental healthcare database, up to 5 individuals aged ≥65 y with preexisting T2D without dementia were matched to each individual with dementia based on age, sex, and general practice.Comparisons were made for HbAIn 725 incident dementia and 3154 matched comparators, HbAOur study has highlighted important differences in the monitoring, management, and control of diabetes in people with dementia. The effects of frailty and the extent of cognitive impairment on the ability to self-manage diabetes and on glycemic control may need to be considered in treatment guidelines and by primary care.

The complement system is an ancient and critical element of the innate immune system. The terminal step in the complement pathway, the membrane attack complex (MAC), has previously been linked to inflammasome activation and is linked to the pathogenesis of multiple diseases including rheumatoid arthritis and neurodegeneration. Using both metabolomic and proteomic approaches, here we show that in human monocyte-derived macrophages a sublytic concentration of MAC mediates a previously uncharacterised metabolic shift, mitochondrial dysfunction and upregulation of glycolysis-promoting genes. This skewing of metabolism coupled with mitochondrial dysfunction drives ROS-mediated NLRP3 inflammasome activation and subsequent gasdermin D activation and pro-inflammatory cytokine production and release. Together, these data elucidate a novel immunometabolic signalling cascade in MAC-stimulated human macrophages, the consequences of which have implications in considering much needed novel therapeutic options for diseases linked to aberrant complement activation

Liver enzyme concentrations are measured as safety end points in clinical trials to detect drug-related hepatotoxicity, but little is known about the epidemiology of these biomarkers in subjects without hepatic dysfunction who are enrolled in drug trials. We studied alanine and aspartate aminotransferase (ALT and AST) in subjects randomized to placebo who completed assessments over 36 mo in a cardiovascular outcome trial [the Stabilisation of Atherosclerotic Plaque by Initiation of Darapladib Therapy (“STABILITY”) trial; n = 4,264; mean age: 64.2 yr] or over 12 mo in three trials that enrolled only subjects with type 2 diabetes (T2D) [the DIA trials; n = 308; mean age: 62.4 yr] to investigate time-dependent relationships and the factors that might affect ALT and AST, including body mass index (BMI), T2D, and renal function. Multivariate linear mixed models examined time-dependent relationships between liver enzyme concentrations as response variables and BMI, baseline T2D status, hemoglobin A1clevels, and renal function, as explanatory variables. At baseline, ALT was higher in individuals who were men, 60 ml·min−1·1.73 m−2. ALT was not significantly associated with T2D at baseline, although it was positively associated with HbA1c. GFR had a greater impact on ALT than T2D. ALT concentrations decreased over time in subjects who lost weight but remained stable in individuals with increasing BMI. Weight change did not alter AST concentrations. We provide new insights on the influence of time, GFR, and HbA1con ALT and AST concentrations and confirm the effect of sex, age, T2D, BMI, and BMI change in subjects receiving placebo in clinical trials.NEW & NOTEWORTHY Clinical trials provide high-quality data on liver enzyme concentrations from subjects randomized to placebo that can be used to investigate the epidemiology of these biomarkers. The adjusted models show the influence of sex, age, time, renal function, type 2 diabetes, HbA1c, and body mass index on alanine aminotransferase and aspartate aminotransferase concentrations and their relative importance. These factors need to be considered when assessing potential signals of hepatotoxicity in trials of new drugs and in clinical trials investigating subjects with nonalcoholic fatty liver disease.

Background/Aims The major antinuclear autoantibodies of systemic sclerosis (SSc) associate with different skin score trajectories and risk of internal organ manifestations. To elucidate molecular differences between ANA-defined subgroups, we utilised the prospective BIOPSY cohort of well-characterised SSc patients. Methods The prospectively collected BIOPSY cohort recruited 52 SSc patients (21 early dcSSc, 15 established dcSSc, 16 lcSSc) and 16 healthy controls (HC). 36 (69%) of the SSc patients are female. Mean disease duration in the early dcSSc cohort was 24 months (sd 12 months), and in established dcSSc was 11.3 years. ANA frequency in BIOPSY reflected the overall dcSSc population: anti-topoisomerase-1 (ATA) n = 14 (27%), anti-RNA pol III (ARA) n = 12 (23%) and other n = 26 (50%). Mean baseline skin score (MRSS) for early dcSSc was 21 (sd 11.2). At a group level mRSS peak was 21.9 (11.8) at 3 months and fell to 19.1(10.5) at 12 months. Serum biomarkers of ECM turnover and fibrosis were measured three monthly and genome-wide transcriptomic profiling of whole skin and whole blood performed by RNA-Seq. Statistical analysis used RStudio with ANOVA, and Tukey post-hoc test. Differential gene expression used the Bioconductor limma software, with standard thresholds for significance. Results At baseline, there were differences in soluble markers between clinical SSc sugroups and HC but not for major ANA subgroups. However, we found clear differences in early dcSSc analysed by major ANA subset for longitudinal change in serum markers of fibrosis and in whole skin gene expression, suggesting a mechanistic basis for the distinct clinical phenotypes associated with hallmark ANAs. During follow-up, significant differences were observed in HA, TIMP1, and PIIINP at 6 and 12 months (p < 0.05), with stable levels in ATA+ patients compared to progressively increased levels in the other subgroups. There were 564 significantly differentially expressed genes in skin between early dcSSc and HC. Unsupervised clustering differentiated patients with ARA and ATA positivity with early dcSSc. 54 genes were significantly differentially expressed in skin between ATA and ARA patients. Whilst 179 genes were differentially expressed in whole blood between early dcSSc compared with HC, no genes could significantly differentiate ATA from ARA. Functional analysis using HALLMARK pathway analysis identified both shared pathways associated with SSc across ANA groups (e.g. TGF beta signaling, IL6 JAK STAT3 signalling, inflammatory response), and pathways only upregulated in patients with ATA (e.g. Wnt beta catenin signaling, Notch signaling), and ARA (e.g. interferon gamma response, adipogenesis). Conclusion We have found significant differences in skin gene expression and longitudinal change in serum markers by autoantibody specificity in dcSSc. Our findings have implications for SSc pathogenesis and support stratification by ANA subgroup in clinical studies. Disclosure K.E. Clark: None. C. Campochiaro: None. E. Csomor: Corporate appointments; employee of GSK. A. Taylor: Corporate appointments; employee of GSK. K. Nevin: Corporate appointments; employee of GSK. N. Galwey: Corporate appointments; employee of GSK. M.A. Morse: Corporate appointments; employee of GSK. V.H. Ong: None. E. Derrett-Smith: None. N. Wisniacki: Corporate appointments; employee of GSK. S. Flint: Corporate appointments; employee of GSK. C.P. Denton: Consultancies; Actelion, GlaxoSmithKline, Bayer, Sanofi, lnventiva, Boehringer Ingelheim, Roche, Bristol Myers Squibb, CSL Behring, UCB, Leadiant Biosciences, Corbus, Servier, Arxx Therapeutics.

RORγt is an isoform of RORC, preferentially expressed in Th17 cells, that functions as a critical regulator of type 3 immunity. As murine Th17-driven inflammatory disease models were greatly diminished in RORC knock-out mice, this receptor was prioritised as an attractive therapeutic target for the treatment of several autoimmune diseases. Human genetic studies indicate a significant contributory role for RORC in several human disease conditions. Furthermore, genome-wide association studies (GWAS) report a significant association between inflammatory bowel disease (IBD) and the RORC regulatory variant rs4845604. To investigate if the rs4845604 variant may affect CD4+ T cell differentiation events, naïve CD4+ T cells were isolated from eighteen healthy subjects homozygous for the rs4845604 minor (A) or major (G) allele). Isolated cells from each subject were differentiated into distinct T cell lineages by culturing in either T cell maintenance medium or Th17 driving medium conditions for six days in the presence of an RORC inverse agonist (to prevent constitutive receptor activity) or an inactive diastereomer (control). Our proof of concept study indicated that genotype had no significant effect on the mean number of naïve CD4 T cells isolated, nor the frequency of Th1-like and Th17-like cells following six days of culture in any of the four culture conditions. Analysis of the derived RNA-seq count data identified genotype-driven transcriptional effects in each of the four culture conditions. Subsequent pathway enrichment analysis of these profiles reported perturbation of metabolic signalling networks, with the potential to affect the cellular detoxification response. This investigation reveals that rs4845604 genotype is associated with transcriptional effects in CD4+ T cells that may perturb immune and metabolic pathways. Most significantly, the rs4845604 GG, IBD risk associated, genotype may be associated with a differential detoxification response. This observation justifies further investigation in a larger cohort of both healthy and IBD-affected individuals.

BackgroundThe clinical context for using blood eosinophil (EOS) counts as treatment–response biomarkers in asthma and COPD requires better understanding of EOS distributions and ranges. We describe EOS distributions and ranges published in asthma, COPD, control (non-asthma/COPD) and general populations.MethodsWe conducted a comprehensive literature review and meta-analysis of observational studies (January 2008 to November 2018) that included EOS counts in asthma, severe asthma, COPD, control and general populations. Excluded studies had total sample sizes ResultsOverall, 91 eligible studies were identified, most had total-population-level data available: asthma (39 studies), severe asthma (12 studies), COPD (23 studies), control (seven studies) and general populations (14 studies); some articles reported data for multiple populations. Reported EOS distributions were right-skewed (seven studies). Reported median EOS counts ranged from 157–280 cells·µL−1 (asthma, 22 studies); 200–400 cells·µL−1 (severe asthma, eight studies); 150–183 cells·µL−1 (COPD, six studies); and 100–160 cells·µL−1 (controls, three studies); and 100–200 cells·µL−1 (general populations, six studies). The meta-analysis showed that observed variability was mostly between studies rather than within studies. Factors reportedly associated with higher blood EOS counts included current smoking, positive skin-prick test, elevated total IgE, comorbid allergic rhinitis, age ≤18 years, male sex, spirometric asthma/COPD diagnosis, metabolic syndrome and adiposity.ConclusionEOS distribution and range varied by study population, and were affected by clinical factors including age, smoking history and comorbidities, which, regardless of severity, should be considered during treatment decision-making.

Background The striking heterogeneity in skin fibrosis within systemic sclerosis (SSc) is likely to reflect differences between pro- and anti-fibrotic pathways and underlie the spontaneous regression of skin fibrosis observed in late stage diffuse SSc (dcSSc). We studied potential serum markers of profibrotic activity in SSc, aiming to understanding their relationship with progression of fibrosis as measured by the modified Rodnan skin score (MRSS) to improve stratification of patients likely to respond to fibrosis-targeted therapies Methods The BIOPSY cohort are well characterised patients recruited prospectively from across the scleroderma spectrum. Serum and plasma samples were collected from 67 participants were included in the analysis (21 early dcSSc ( Results Our results confirmed markers of collagen synthesis were significantly different between the patient subgroups (Pro-C6,Pro-C3,PIIINP), while markers of collagen degradation were not significantly altered (C3M,C6M,C4M2,C7M) (Table 1). Consistent with previous reports, the C3 fibrotic index (Pro-C3:C3M) and the ELF test also showed differentiation across subgroups. Across all tests, this difference was most significant between the early dcSSc subgroup compared with the other subgroups. There was significant upregulation of IL-6, MCP-1, and oncostatin M in SSc compared to HC. There were significant correlations between several candidate profibrotic serum markers and MRSS: Pro-C3, Pro C6, PIIINP, and IL6 (all p < 0.01). Conclusion Our results show the utility of extended patient cohorts to delineate fundamental biology in SSc. We identify key pro-fibrotic molecular markers upregulated in SSc and correlated these to extent of skin fibrosis. Markers of collagen III and collagen VI synthesis are particularly raised, especially in the early stages of the disease. However, markers of collagen degradation did not significantly differ between SSc subgroups and HCs. These promising cross-sectional data suggest that therapies targeting drivers of fibrosis are most likely to show benefit for skin in early dcSSc. This will be further explored longitudinally in the BIOPSY cohort. Disclosures K.E.N. Clark: None. C. Campochiaro: None. K. Nevin: Other; GSK employee. E. Csomor: Other; GSK employee. N. Galwey: Other; GSK employee. M. Morse: Other; GSK employee. N. Wisniacki: Other; GSK employee. S. Flint: Other; GSK employee. V.H. Ong: None. E. Derrett-Smith: None. C.P. Denton: Grants/research support; Actelion, GlaxoSmithKline, Bayer, Sanofi, lnventiva, Boehringer Ingelheim, Roche, Bristol Myers Squibb, CSL Behring, UCB, Leadiant Biosciences.

Objective: To identify phenotypic factors associated with the Short Physical Performance Battery (SPPB) and its individual sub-tests: standing balance, 4‑meter gait speed (4mGS) and 5-repetition sit-to-stand (5STS). Methods: The Evaluation of the Role of Inflammation in non-pulmonary disease manifestations in Chronic Airways disease (ERICA) study recruited adult participants with stable chronic obstructive pulmonary disease (COPD). Proportional odds models identified factors associated with the SPPB, and a principal component analysis (PCA) evaluated how much SPPB variance was explainable by each of its 3 sub-tests. Results: Of 729 enrolled participants, 717 (60% male, mean age 67 years) had full SPPB data. Overall, 76% of patients had some evidence of functional limitations (SPPB total score < 12). Scores < 4 were observed in 71%, 31%, and 22% of participants for the 5STS, 4mGS, and balance sub-tests, respectively. A longer 6-minute walk test and greater quadriceps maximal voluntary contraction decreased the odds of being in a lower score category for SPPB total score and for all 3 sub-tests. Aging, self-reported hypertension and higher dyspnea increased the odds, and being married decreased the odds of being in a lower category for total score. All sub-tests contributed equally to total score. Conclusion: Each of the 3 sub-tests contributed independent information to the SPPB, demonstrating their usefulness for assessing COPD when considered together rather than individually. The 5STS sub-test had the greatest variation in scores and may thus have the best discriminatory power for clinical COPD studies of lower limb performance where only one SPPB test is feasible.

International audience; P300/CBP-associated factor (PCAF) and general control nonderepressible 5 (GCN5) are closely related epigenetic proteins, each containing an acetyltransferase domain and a bromodomain. Consistent with reported roles for these proteins in immune function, we find that PCAF-deficient macrophages exhibit a markedly reduced ability to produce cytokines upon stimulation with lipopolysaccharide (LPS). Investigating the potential to target this pathway pharmacologically, we show that chemical inhibition of the PCAF/GCN5 bromodomains is insufficient to recapitulate the diminished inflammatory response of PCAF-deficient immune cells. However, by generating the first PCAF/GCN5 proteolysis targeting chimera (PROTAC), we identify small molecules able to degrade PCAF/GCN5 and to potently modulate the expression of multiple inflammatory mediators in LPS-stimulated macrophages and dendritic cells. Our data illustrate the power of the PROTAC approach in the context of multidomain proteins, revealing a novel anti-inflammatory therapeutic opportunity for targeting PCAF/GCN5.

Introduction: The SPPB was recommended as the measure of choice in trials of sarcopenia by the European Medicines Agency, but its role in COPD has not been fully established. Aims: Assess factors associated with total SPPB score, and whether it is a useful stratification tool for identifying physical limitation in COPD. Methods: 717 COPD subjects were recruited into the Evaluation of the Role of Inflammation in Chronic Airways disease (ERICA) study. A proportional odds model identified factors significantly associated with SPPB total score ( Results: Of the subjects (60% male, mean age 67y, mean FEV1%pred 52%), 75% had physical limitation (SPPB Conclusion: The study confirms the relevance of SPPB in COPD and enumerated the percentage of impaired individuals. SPPB total score correlates with important outcome measures such as 6MWD. All SPPB subscores are important when assessing physical limitation in COPD. Funding: A grant from Innovate UK. GSK, a consortium partner, made contributions in kind towards study management (PRJ2622).

Allele-specific analyses to understand frequency differences across populations, particularly populations not well studied, are important to help identify variants that may have a functional effect on disease mechanisms and phenotypic predisposition, facilitating new Genome-Wide Association Studies (GWAS). We aimed to compare the allele frequency of 11 asthma-associated and 16 liver disease-associated single nucleotide polymorphisms (SNPs) between the Estonian, HapMap and 1000 genome project populations. When comparing EGCUT with HapMap populations, the largest difference in allele frequencies was observed with the Maasai population in Kinyawa, Kenya, with 12 SNP variants reporting statistical significance. Similarly, when comparing EGCUT with 1000 genomes project populations, the largest difference in allele frequencies was observed with pooled African populations with 22 SNP variants reporting statistical significance. For 11 asthma-associated and 16 liver disease-associated SNPs, Estonians are genetically similar to other European populations but significantly different from African populations. Understanding differences in genetic architecture between ethnic populations is important to facilitate new GWAS targeted at underserved ethnic groups to enable novel genetic findings to aid the development of new therapies to reduce morbidity and mortality.

Used to detect liver disease and injury, baseline liver chemistry distributions were evaluated by age and gender in children without known liver disease. Baseline liver chemistries [alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and total bilirubin (TBIL)] were analyzed from 24 randomized controlled pediatric clinical trials. Using quantile regression, liver chemistry distributions were examined by age and gender; upper limit normal (ULN) ranges were compared to the 97.5th percentiles of the distributions for the specified ages and genders. 5410 subjects without known liver disease (0-18 years; 60% male) were studied. The median ALT varied little with age. In males age 5-18, the ALT 97.5th percentile increased from 34 to 63 IU/L. In both genders, the median and 97.5th percentile AST decreased with age. After age 9, ALP decreased. TBIL increased with age. Despite most liver chemistry 97.5th percentiles changing substantively with age and gender, the reference lab ULN generally changed minimally and did not correlate with the 97.5th percentile. Gender and age specific 97.5th percentile data should therefore be considered for the reference laboratory ULN in children to more accurately detect liver injury and disease.

Blood eosinophil counts may be predictive of corticosteroid response in chronic obstructive pulmonary disease (COPD) patients. However, little is known about measurement stability, which is important for understanding the utility of blood eosinophil counts as a potential biomarker. We evaluated the stability of blood eosinophil counts over 1 year in a population-based cohort of patients with COPD in primary care. Patients were aged ≥ 40 years with forced expiratory volume in 1 second/forced vital capacity < 0.7 and ≥ 1 blood eosinophil measurement taken during a period of stable disease within 6 months of a COPD diagnosis code recorded between January 1, 2010 and December 31, 2012. Generalized linear mixed models were fitted to log-transformed data to estimate the between-(s2between) and within-patient (s2within) variance in eosinophil count; an intra-class correlation coefficient Ri was calculated (s2between/[s2between + s2within]). A sensitivity analysis was performed from which patients who were prescribed systemic corticosteroids or antibiotics at any time during follow-up were excluded. All models were adjusted for age, gender, smoking status, and asthma history. Overall, 27,557 patients were included in the full cohort (51.5% male, mean age [standard deviation] 71.1 [10.6] years) and 54% of patients had ≥ 2 eosinophil measurements (median 2 [interquartile range 1]) during follow-up. For the full cohort, Ri = 0.64, and in the sensitivity analysis subgroup, Ri = 0.70, mainly due to a decrease in s2within. For patients with COPD in primary care, eosinophil measurements demonstrated reasonable repeatability over 1 year, which increased after exclusion of patients who were prescribed systemic corticosteroids or antibiotics.

The worldwide emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis threatens to make this disease incurable. Drug resistance mechanisms are only partially understood, and whether the current understanding of the genetic basis of drug resistance in M. tuberculosis is sufficiently comprehensive remains unclear. Here we sequenced and analyzed 161 isolates with a range of drug resistance profiles, discovering 72 new genes, 28 intergenic regions (IGRs), 11 nonsynonymous SNPs and 10 IGR SNPs with strong, consistent associations with drug resistance. On the basis of our examination of the dN/dS ratios of nonsynonymous to synonymous SNPs among the isolates, we suggest that the drug resistance-associated genes identified here likely contain essentially all the nonsynonymous SNPs that have arisen as a result of drug pressure in these isolates and should thus represent a near-complete set of drug resistance-associated genes for these isolates and antibiotics. Our work indicates that the genetic basis of drug resistance is more complex than previously anticipated and provides a strong foundation for elucidating unknown drug resistance mechanisms.

Objective: The purpose of this study was to find loci for major depression via linkage analysis of a large sibling pair sample. Method: The authors conducted a genome-wide linkage analysis of 839 families consisting of 971 affected sibling pairs with severe recurrent major depression, comprising waves I and II of the Depression Network Study cohort. In addition to examining affected status, linkage analyses in the full data set were performed using diagnoses restricted by impairment severity, and association mapping of hits in a large case-control data set was attempted. Results: The authors identified genome-wide significant linkage to chromosome 3p25-26 when the diagnoses were restricted by severity, which was a maximum LOD score of 4.0 centered at the linkage marker D3S1515. The linkage signal identified was genome-wide significant after correction for the multiple phenotypes tested, although subsequent association mapping of the region in a genome-wide association study of a U.K. depression sample did not provide significant results. Conclusions: The authors report a genome-wide significant locus for depression that implicates genes that are highly plausible for involvement in the etiology of recurrent depression. Despite the fact that association mapping in the region was negative, the linkage finding was replicated by another group who found genome-wide-significant linkage for depression in the same region. This suggests that 3p25-26 is a new locus for severe recurrent depression. This represents the first report of a genome-wide significant locus for depression that also has an independent genome-wide significant replication.

The aim of this study was to identify whether age at onset (AAO) identifies Bipolar Disorder (BD) subtypes, and to test whether the subgroups were confirmed by different clinical profiles. Admixture analysis was applied to determine a model that best fit the observed distribution of AAO in 964 BD patients. Three distributions of AAO were identified, and age means were 16.1 (S.D. 4.2), 25.4 (S.D. 2.5) and 32.2 (S.D. 9.5) years. A significant increased rate of suicide attempts, Bipolar I (BD I) caseness, and depressive onset was observed in the early-onset group when compared to those with later-onset by means of χ². Findings from extant studies and our results are remarkably consistent in showing that BD can be subdivided into three groups based on AAO distributions, and that early-onset is associated with higher rates of suicide attempts.

Major depressive disorder (MDD) is a highly prevalent disorder with substantial heritability. Heritability has been shown to be substantial and higher in the variant of MDD characterized by recurrent episodes of depression. Genetic studies have thus far failed to identify clear and consistent evidence of genetic risk factors for MDD. We conducted a genome-wide association study (GWAS) in two independent datasets. The first GWAS was performed on 1022 recurrent MDD patients and 1000 controls genotyped on the Illumina 550 platform. The second was conducted on 492 recurrent MDD patients and 1052 controls selected from a population-based collection, genotyped on the Affymetrix 5.0 platform. Neither GWAS identified any SNP that achieved GWAS significance. We obtained imputed genotypes at the Illumina loci for the individuals genotyped on the Affymetrix platform, and performed a meta-analysis of the two GWASs for this common set of approximately half a million SNPs. The meta-analysis did not yield genome-wide significant results either. The results from our study suggest that SNPs with substantial odds ratio are unlikely to exist for MDD, at least in our datasets and among the relatively common SNPs genotyped or tagged by the half-million-loci arrays. Meta-analysis of larger datasets is warranted to identify SNPs with smaller effects or with rarer allele frequencies that contribute to the risk of MDD.

Background/objectives Muscle mass decreases with age, and heart failure (HF) patients may experience greater reductions due to pathophysiological processes associated with this disease. Reduced muscle mass may predispose HF patients to functional limitations and increased morbidity and mortality. This study estimated the associations between HF, low muscle mass (LMM), functional limitations and hospitalisation, as well as the combined effect of HF and LMM on these outcomes in a nationally representative sample. Design A cross-sectional survey. Setting the National Health and Nutrition Examination Survey 1999-2004. Subjects A total of 402 HF (weighted 3,994,205) and 7,061 non-HF participants (weighted 91,058,850), ≥45 years with dual-energy X-ray absorptiometry measurements. Methods the 20th percentile of the sex-specific distribution of lean appendicular mass residuals from linear regression with height and fat mass as predictors, served as the LMM cut-point. Logistic regression provided adjusted odds ratios (OR) and 95% confidence intervals (CI) for the association of HF and LMM with functional limitations and hospitalisation. Results There were statistically significant adjusted associations between HF and limitations in household chores, walking one-fourth of a mile and hospitalisation (OR (95% CI): 2.5 (1.7 -3.8), 1.9 (1.2 -3.0) and 1.6 (1.1 -2.4), respectively). LMM was significantly associated with limitations in household chores and walking one-fourth of a mile (OR (95% CI): 1.5 (1.2, 1.9) and 1.4 (1.2, 1.7), respectively). Interaction between HF and LMM was noted for the associations with functional limitations. Conclusions This hypothesis-generating study found a synergistic interaction between HF and LMM; the presence of LMM increased the negative effects of HF. HF patients may experience increased disease burden due to LMM.

A new method (called New Relative Length) was developed for comparison of chromosome size when both paired and unpaired chromosomes are present. All chromosomes were used in the calculation. A method of graphical display of karyotype data (called a Karyotype Graph), plotting New Relative Length on the vertical axis and arm ratio on the horizontal axis was used to indicate sampling error, to pair chromosomes and to match similar chromosomes in related species. Terms for Chromosome Size were also defined namely Small, Medium or Large depending on New Relative Length as a proportion of total chromosome length. These terms could also be used to compare chromosomes within species and between related species.

Summary • Response to low temperature during early growth in cultivated chickpea (Cicer arietinum) and its wild progenitor C. reticulatum was investigated to clarify the evolutionary processes under domestication in this crop. • Parental lines and their F 2 and F 3 progeny were exposed to cold treatment (4°C) for 30°d after seed imbibition and compared with controls. • Cold treatment caused a 19-d advance in flowering time in wild chickpea, but only a 3-d advance in cultivated chickpea. It also promoted apical dominance of the main stem of the wild chickpea, whereas apical dominance was constitutive in the cultivated type. F 3 progeny showed significant genetic variation affecting the response of flowering time to low temperature. We suggest that selection against alleles conferring vernalization requirements was a major step in the evolution of cultivated chickpea. The reduced low-temperature response was fundamental both for the ancient conversion of chickpea from an autumn- to a spring-sown crop (‘summer crop’) in west Asia, and for its spread into the lower-latitude regions of India and east Africa. • Attempts to improve yield and/or resistance to biotic and abiotic stresses through introgression with wild chickpea species carry the risk of reintroducing vernalization sensitive alleles into the cultigen.

Assessments of the anatomy, porosity and profiles of radial O 2 loss from adventitious roots of 10 species in the Poaceae (from four subfamilies) and two species in the Cyperaceae identified a combination of features characteristic of species that inhabit wetland environments. These include a strong barrier to radial O 2 loss in the basal regions of the adventitious roots and extensive aerenchyma formation when grown not only in stagnant but also in aerated nutrient solution. Adventitious root porosity was greater for plants grown in stagnant compared with aerated solution, for all 10 species in the Poaceae. The ‘wetland root’ archetype was best developed in Oryza sativa and the two species of the Cyperaceae, in which the stele contributed less than 5% of the root cross-sectional area, the cells of the inner cortex were packed in a cuboidal arrangement, and aerenchyma was up to 35‐52%. Variations of this root structure, in which the proportional and absolute area of stele was greater, with hexagonal arrangements of cells in the inner cortex and varying in the extent of aerenchyma formation, were present in the other wetland species from the subfamilies Pooideae, Panicoideae and Arundinoideae. Of particular interest were Vetiveria zizanoides and V. filipes , wetland grass species from the tribe Andropogoneae (the same tribe as sorghum, maize and sugarcane), that had a variant of the root anatomy found in rice. The results are promising with regard to enhancing these traits in waterlogging intolerant crops.

The heritability of tolerance of wheat F3 lines to competition from annual ryegrass (Lolium rigidum), and its relationship to morphological traits, were determined using crosses between wheat cultivars with good and poor competitive ability. Forty F2-derived F3 lines from a cross between two late flowering varieties (Machete × Spear) and 40 from a cross between early flowering varieties (Wilgoyne × Gutha) were grown in the field with and without annual ryegrass. There was significant genetic variation between lines within each of the two populations in a number of aspects of plant growth and development, including yield in monoculture. The estimates of heritability for % yield loss due to competition were 0.25 and 0.57 in the two crosses respectively, indicating that selection for high tolerance to competition in the F3 generation or later should be effective. Fairly strong relationships between height and % yield loss and between leaf length and % yield loss suggest that these may be useful auxiliary traits when selecting for low % yield loss. However, differences between crosses in the magnitude and sign of genetic and phenotypic correlation between traits indicate that competitive ability is a complex character influenced by many factors.

Summary • Waterlogging tolerance and its physiological basis were evaluated in Lophopyrum elongatum (a species from a salt marsh habitat), Triticum aestivum (cv. Chinese Spring), their amphiploid, and disomic chromosome addition lines. • Growth in drained or waterlogged soil and aerated or deoxygenated stagnant nutrient solution were evaluated. Porosity, aerenchyma, rates of O2 consumption, radial O2 loss, and ethanolic fermentation in adventitious roots of selected genotypes were also measured. • L. elongatum was more tolerant of deoxygenated stagnant nutrient solution or waterlogged soil (0–48% reductions in growth, respectively) than ‘Chinese Spring’ (63–84% reductions), the amphiploid (49–81% reductions), or the addition lines (56–92% reductions). Roots of L. elongatum had a higher constitutive porosity than ‘Chinese Spring’, resulting in greater internal O2 movement in these roots when intact plants were first transferred to an O2-free root medium. This trait, as well as the slower growth and development of L. elongatum, might have contributed to its greater waterlogging tolerance. • Despite the differences between L. elongatum and ‘Chinese Spring’ in some traits, none of the Lophopyrum × wheat lines showed substantial improvement in waterlogging tolerance.

Aspects of growth and development were evaluated in the fast-developing annual Triticum aestivum L. 'Chinese Spring', the slow-developing perennial Lophopyrum elongatum Love, their amphiploid, and chromosome addition and substitution lines of L. elongatum into 'Chinese Spring'. Relative growth rates (RGR) of shoots of L. elongatum and the amphiploid were lower than those of 'Chinese Spring' (34 and 13% respectively) and main stem development was also slower. There was no diAerence in shoot RGR of any of the chromosome addition or substitution lines and that of 'Chinese Spring' when assessed between Haun stages 2.0 and 5.0. In contrast, several aspects of plant development were observed to diAer in the chromosome addition and substitution lines. Substituting E genome chromosomes (with the exceptions of 3E and 4E) for D genome chromosomes, or adding E genome chromosomes, slowed the rate of main stem development, at least up to Haun stage 5.0. Despite these diAerences in the rate of main stem development, the appearance of adventitious roots commenced at approximately Haun stage 2.0 in all genotypes. However, the numbers of adventitious roots and tillers at the 5.0 Haun stage diAered between some of the lines when compared to 'Chinese Spring'. Although incorporation of some L. elongatum chromosomes altered aspects of plant development, all lines showed more similarity to bread wheat than to L. elongatum, reflecting, in part, the greater genetic contribution made by bread wheat to these lines. # 2001 Annals of Botany Company

Nine species from the tribe Triticeae ‐ three crop, three pasture and three ‘wild’ wetland species ‐ were evaluated for tolerance to growth in stagnant deoxygenated nutrient solution and also for traits that enhance longitudinal O 2 movement within the roots. Critesion marinum (syn. Hordeum marinum ) was the only species evaluated that had a strong barrier to radial O 2 loss (ROL) in the basal regions of its adventitious roots. Barriers to ROL have previously been documented in roots of several wetland species, although not in any close relatives of dryland crop species. Moreover, the porosity in adventitious roots of C. marinum was relatively high: 14% and 25% in plants grown in aerated and stagnant solutions, respectively. The porosity of C. marinum roots in the aerated solution was 1·8‐5·4-fold greater, and in the stagnant solution 1·2‐2·8-fold greater, than in the eight other species when grown under the same conditions. These traits presumably contributed to C. marinum having a 1·4‐3 times greater adventitious root length than the other species when grown in deoxygenated stagnant nutrient solution or in waterlogged soil. The length of the adventitious roots and ROL profiles of C. marinum grown in waterlogged soil were comparable to those of the extremely waterlogging-tolerant species Echinochloa crus-galli L. (P. Beauv.). The superior tolerance of C. marinum , as compared to Hordeum vulgare (the closest cultivated relative), was confirmed in pots of soil waterlogged for 21 d; H. vulgare suffered severe reductions in shoot and adventitious root dry mass (81% and 67%, respectively), whereas C. marinum shoot mass was only reduced by 38% and adventitious root mass was not affected.

Summary In 1994, 407 L. sativus and 96 L. cicera lines were evaluated for phenology, seed yield and seed ODAP (a neurotoxin) concentration in the Mediterranean-type climate of south-western Australia. A selected number of lines from this study were grown at three sites in south-western Australia in 1995 and 1996, to examine genotype-environment interactions on seed yield and ODAP concentration in the seed of the two Lathyrus spp. Principal components analysis showed that L. sativus lines grown in 1995 and 1996 could be divided into two geographical origins: Indian sub-continent and Mediterranean/European. Those lines of Mediterranean/European origin were consistently higher yielding (both in 1994 and 1995/96), with much larger seeds and later phenology. In L. cicera seed yield was closely associated with greater mean seed weight and to a lesser extent with early phenology. The genotype-environment study indicated that higher yielding lines of both species generally responded to favourable environments; in the case of L. sativus the Mediterranean/European lines and for L. cicera the larger seeded, earlier phenology lines. For both species, genotype was the most important determinant of ODAP concentration and environment had less influence. Genotype-environment interactions had no effect on seed ODAP concentrations. In terms of seed yield, both species showed substantial potential in the environments tested. Further improvements in adaptation, seed yield and reduction in ODAP are possible in both species. Abbreviations: ODAP: 3-(-N-oxalyl)-L-2,3-diamino propionic acid

The extent and distribution of incompatibility between gene pools (Mesoamerican and Andean) and evolutionary classes (wild, landrace and bred) of the common bean (Phaseolus vulgaris) was explored by seeking anomalous values of highly heritable quantitative traits in the progeny of crosses. Clear incompatibility (no progeny or sterile or deformed progeny) was shown by 28 crosses in a 12-parent wild × bred diallel cross, and 37 crosses in a 12-parent landrace × bred diallel cross. Incompatibility was particularly common in the progeny of certain genotypes, but was not consistently associated with the division between gene pools or evolutionary classes. When crosses showing clear incompatibility were eliminated from the data, days to flowering, number of seeds per pod, log (weight per seed) and seed roundness in the F1 generation gave a good fit to an additive-dominance model, confirming that there is no overall tendency to incompatibility between the gene pools. There was a division between the gene pools with regard to log (weight per seed), as expected, but there was no such division, with regard either to the means of the parent lines or the distribution of the statistics V r and W r (which indicate the distribution of dominant alleles between genotypes), for the other quantitative variables. Differences between reciprocal crosses were strikingly widespread, and appeared generally to be due to cytoplasmic effects or cytoplasmic × nuclear interactions rather than maternal effects, indicating that the direction in which a cross is made may have a perceptible effect on the progeny that can be obtained from it.

Exposure to high temperature (30 °C) before or after exposure to low temperature (0, 4 or 8 weeks at 4 °C) consistently increased the number of leaf nodes at flowering and delayed flowering in a range of genotypes of spring rape (Brassica napus var. annua L.). Four days of prior exposure to high temperature had more effect than 2 d, and the effect of subsequent exposure to high temperature was maximized when exposure commenced 1 week after the end of the low-temperature treatment. In genotypes that showed a vernalization response (i.e. in which the number of leaf nodes at flowering was reduced or flowering was advanced by low temperature), this response was reduced or eliminated by either prior high-temperature treatment (antivernalization) or subsequent high-temperature treatment (devernalization). A biochemical model to account for these effects is proposed.

There are severe soil constraints for agriculture in many tropical regions of the world. Acidity and low levels of calcium are examples of them in the Brazilian Cerrados (Savannahs). They may prevent deep root growth of cultivated plants, exposing them to moisture stress during dry spells. This study aimed to develop a technique for screening soya bean varieties tolerant to low calcium based on root growth in nutrient solution. The results have shown varietal differences for tolerance to low-Ca stress. The method of screening for response to low-Ca is quick, non-destructive and can be employed in genetic studies and breeding programmes for efficient calcium utilisation by soya beans. It is expected that improved varieties for this character will lead to yield stability and contribute to develop sustainable farming systems in the savannahs.

We describe a method for applying geographical information systems (GIS) to exploring biodiversity in the wild relatives of crop species and illustrate its application to the wild common bean (Phaseolus vulgaris L.). We use the latitude, longitude and altitude of the location of origin of each accession in a germplasm collection of wild P. vulgaris, along with long-term monthly mean values of rainfall, temperature and diurnal temperature range for about 10000 stations throughout Latin America to produce maps indicating areas with ‘bean-favouring’ climates. In a test case, these identify a new suitable area in Colombia where wild P. vulgaris has been reported in the literature, and two more areas which are strong candidates on other grounds. Dividing the ‘bean-favouring’ climates into clusters identifies areas that have similar climates but are geographically remote, where we can expect to find wild beans with similar ecological adaptation. We discuss the implications of these results for conserving and improving the common bean, and the application of these methods to other species.

Cultivars of common bean (Phaseolus vulgaris L.) capable of yielding well at low levels of native or added phosphorus (P) are highly desirable in many tropical production systems. The objective of the present study was to identify geographical regions which might be sources of such genotypes. A total of 364 landraces, cultivars and wild genotypes, drawn from a broad geographic range, were divided on the basis of growth habit into four field trials, each comprising two levels of P, stressed and unstressed, on an infertile Andosol in Popayan, Colombia. The regression relationship between grain yield per plant in the presence and in the absence of stress was determined, and each genotype's deviation from this relationship was used as a measure of P-efficiency. There was highly significant variation in efficiency among genotypes in all growth habits, and in climbing beans there were consistent regional differences, superior genotypes being identified with greater frequency among those from Bolivia, West Mexico and South Mexico-West Guatemala. The latter region was promising for prostrate bush genotypes also. Wild beans in general performed relatively poorly; it appears that P-efficiency traits in P. vulgaris have been acquired during or after domestication. These results confirm that genetic differences in P-efficiency exist among common bean genotypes and suggest that these are related to geographic origin. Furthermore, the use of a representative sample of germplasm can help to identify segments of the gene bank that are especially promising as sources of desirable traits.

Twenty cowpea ( Vigna unguiculata L. Walp.) genotypes, comprising Kenyan cultivars and Kenyan and introduced breedings lines, were grown in 15 replicated field trials carried out at three locations in semi-arid eastern Kenya over four seasons. Grain and straw yields and the carbon isotope discrimination (Δ) of this material were determined, and days to flowering and maturity observed. None of the seasons in which the trials were conducted was appreciably drier than the long term average for the sites, and some trials received excessive rain. Averaging the data for the 15 trials, one genotype yielded much less grain (77 g m −2 ) than the 19 others, whose yield ranged from 125 to 177 g m −2 (average 148 g m −2 ). Trial mean yield trials had a high straw Δ ( r = +0.567) and had received more rain between flowering and maturity ( r = +0.428) than lower yielding ones. Among genotypes, averaging over trials, the correlation coefficient ( r ) between grain yield and grain Δ was +0.394, and between grain yield and straw Δ, +0.460. Early genotypes had the highest grain Δ and straw Δ. The correlation among genotypes between date of flowering and grain Δ was −0.632 and with straw Δ, −0.502. When comparisons were made among trials, there was no clear relationship between the strength of the correlations among genotypes between grain yield and straw Δ or grain Δ and the degree of stress experienced by a trial (as indicated by the rainfall it had received). It appeared that this was because the variances of grain Δ and straw Δ were greater in the most droughted trials, whereas the variance of yield was greatest in the least droughted trials. It is concluded that the genetic correlation between grain yield and either grain Δ or straw Δ is unlikely to be strong enough to make either Δ a useful surrogate or adjunct in selecting for high yield in the segregating generations of a breeding programme for semi-arid eastern Kenya, but that Δ may be of value in the selection of parent genotypes.

Background Belimumab is a B-lymphocyte stimulator (BLyS)-specific inhibitor indicated for the treatment of adult patients with active, autoantibody-positive, systemic lupus erythematosus. Belimumab has also been shown to reduce anti-phospholipase A2 receptor (PLA2R) autoantibodies and proteinuria in a mechanistic study in primary membranous nephropathy (PMN) 1 . Here we report an interim analysis of B and T cell phenotypes in PMN subjects treated with belimumab to further elucidate the mechanism of action in autoantibody mediated disease. Objectives To characterize changes in B and T lymphocyte phenotypes in PMN patients treated with belimumab, as a comparison with known pharmacodynamic (PD) effects in SLE 2 , and to assess correlation with anti-PLA2R autoantibody. Methods 14 anti-PLA2R autoantibody positive PMN patients received 10mg/kg iv belimumab every 4 wks (or 2 wks) for up to 100 wks. 11 of these completed at least 28 wks treatment. Whole blood was collected at baseline, Wks 8, 16 and 28 for analysis of B and T-cell phenotypes by flow cytometry. Serum levels of anti-PLA2R antibodies were measured by ELISA (Euroimmun). Statistical analysis to identify PD-induced changes in lymphocyte subsets was carried out by paired t-test (2 tailed) against baseline. Correlations between anti-PLA2R antibody and B and T-cell subsets, either at a specific time point or in the linearised trend over time, were calculated using Pearson9s correlation coefficient (r). Results There was a significant reduction (-63%, p=0.002) in absolute numbers of naive B cells (CD19+ CD27-) at Wk 8 which was sustained through to Wk 28. There was a significant increase in absolute numbers of memory B cells (CD19+ CD27+) at Wk 8 (70%, p=0.023) which increased further through to Wk 28. Plasmablasts (or SLE subset, CD19lo CD38hi CD27hi) showed a trend at Wk 8 to decrease (-64%, p=0.20) but with high variance and low cell numbers. In addition, the expression (mean fluorescence intensity) of BAFF-R (B-cell activating factor receptor) on B-memory cells increased through Wk 28, while expression of TACI (transmembrane activator and calcium modulator and cyclophylin ligand interactor) decreased. Activated cells as identified by surface CD95 expression, decreased as a proportion of B-memory cells through Wk 28. No clear trend was seen in T-regulatory or T-activated cells. There was a significant negative correlation between decrease in absolute numbers of naive B-cells and immunological efficacy defined as level of anti-PLA2R antibody remaining at Wk 28 (r=-0.87, p=0.0005). Correlations were also seen between antibody and changes in proportion of B-memory CD95+ cells. Conclusions This mechanistic trial of belimumab in PMN has enabled a novel analysis of PD endpoints, confirming but also extending the PD effects previously reported in studies of SLE. Changes in B-cell subsets were associated with improvements in levels of autoantibody in PMN which in turn correlates with proteinuria. Further analysis of longer term anti-PLA2R antibody kinetics as related to early changes in B and T cell phenotypes may also be informative. References Willcocks L, Barrett C, Brenchley P et al. Nephrology Dialysis Transplantation. 2015; 30 (Supplement 3): iii32–iii33. Stohl W, Hiepe F, Latinis KM et al. Arthritis & Rheumatism. 2012;64(7):2328–2337. Acknowledgement This study was funded by GSK (study sponsor) (BEL116472, NCT01610492). Disclosure of Interest C. Barrett Shareholder of: GlaxoSmithKline, Employee of: GlaxoSmithKline, R. Henderson Shareholder of: GlaxoSmithKline, Employee of: GlaxoSmithKline, N. Galwey Shareholder of: GlaxoSmithKline, Employee of: GlaxoSmithKline, S. Flint Grant/research support from: GlaxoSmithKline, A. Gibson Shareholder of: GlaxoSmithKline, Employee of: GlaxoSmithKline, C. Savage Shareholder of: GlaxoSmithKline, Employee of: GlaxoSmithKline

A series of field experiments was undertaken in order to determine whether resistance to bean common mosaic virus (BCMV) could be incorporated into genotypes of the common bean (Phaseolus vulgaris L.) suitable for cultivation in Zimbabwe without recourse to backcrossing. Six inbred genotypes carrying the resistance-conferring alleles at the loci I and Bc-3 were crossed with five locally-adapted inbred genotypes. The first experiment comprised F3 progeny rows, each derived from a single unselected F2 plant, the second, F3 bulks selected for resistance, and the third, a comparison of selected and unselected F2-derived F4 lines. The number of days to flowering and to maturity, the incidence of mosaic and necrosis symptoms, seed yield and seed size were recorded. There was evidence that late flowering and maturity were associated with BCMV resistance in some crosses, though not strongly enough to present an obstacle to plant breeding. The incidence of virus symptoms and seed yield were influenced by genetic factors additional to the major resistance genes, and variation in seed yield was present not only between bulk populations of crosses, but also between single-row plots of lines within crosses. This indicates that early-generation selection for yield in the presence of BCMV, even among progeny selected for BCMV-resistace, is likely to be effective. However, the variation in yield among F4 lines was least in the highest-yielding crosses, which may represent a limit to successful selection for yield. Seed size was partly under additive genetic control, but there was also evidence of non-allelic interactions. There was no association between large seed size, preferred by consumers, and susceptibility to BCMV in the progeny, indicating that the association between these characters in the parent lines is fortuitous and will not present an obstacle to plant breeding. It is noted that a considerable amount of useful genetic information can be obtained without recourse to elaborate crossing schemes, provided that unselected progeny are included in experiments as controls. The evidence presented indicates that resistance to BCMV can be combined with appropriate values of maturity date, yield and seed size without the need for backcrossing.

Twenty locally-adapted but genetically diverse cowpea genotypes were grown in 17 replicated trials in a range of sites and seasons in the drylands of eastern Kenya, and the discrimination against the heavy isotope of carbon (with a mass of 13) (Δ) was determined in grain and straw samples. Most genotypes gave similar, low grain yields in the environments which subjected the plants to drought stress, but high yielding and low yielding genotypes were clearly distinct in the less stressful environments. The converse pattern was found for Δ: the genotypes were all very similar in the non-stressful (high-Δ) environments, but in the stressful environments, low-Δ (drought susceptible) and high-Δ (drought avoiding) genotypes were clearly distinct. This pattern was clearest for straw Δ, but was also apparent for grain Δ. The early-maturing genotypes, which escaped terminal drought, were generally those with the most stable and highest Δ, but in the case of straw Δ there were statistically significant deviations from this relationship. It is concluded that Δ provides a reliable measure of the specific response of cowpea genotypes to drought, which may be of value in breeding programs provided that carbon isotope discrimination can be measured reasonably economically.

Neuroticism is a moderately heritable personality trait considered to be a risk factor for developing major depression, anxiety disorders and dementia. We performed a genome-wide association study in 2,235 participants drawn from a population-based study of neuroticism, making this the largest association study for neuroticism to date. Neuroticism was measured by the Eysenck Personality Questionnaire. After Quality Control, we analysed 430,000 autosomal SNPs together with an additional 1.2 million SNPs imputed with high quality from the Hap Map CEU samples. We found a very small effect of population stratification, corrected using one principal component, and some cryptic kinship that required no correction. NKAIN2 showed suggestive evidence of association with neuroticism as a main effect (p < 10(-6)) and GPC6 showed suggestive evidence for interaction with age (p approximately = 10(-7)). We found support for one previously-reported association (PDE4D), but failed to replicate other recent reports. These results suggest common SNP variation does not strongly influence neuroticism. Our study was powered to detect almost all SNPs explaining at least 2% of heritability, and so our results effectively exclude the existence of loci having a major effect on neuroticism.

Quinoa (Chenopodium quinoa Willd.) is an annual grain crop which was a staple food in the Andes before the Spanish conquest of South America, and which in recent years has attracted renewed interest for its high nutritional value. It has a higher protein content and a better balanced protein composition than do cereals, supplying high levels of lysine, histidine and methionine + cystine. Quinoa starch has much smaller granules than do cereal starches, has a lower amylose content and is more viscous. These differences should make it suitable for some specialised industrial uses, including manufacture of a carbohydrate-based cream substitute. The grain of most varieties also contains saponins, bitter compounds which have to be removed by washing or abrasion before consumption, but which are biologically active in several potentially valuable ways. Cultivation of quinoa in Europe will require the development of short, non-branched, early maturing varieties with large, white, low-saponin seeds. Quinoa is tolerant of drought and low soil fertility, and may be of value in Europe as a break between cereal crops and after potato crops. When grown in the areas to which it is best adapted, it should be able to compete with cereals in both human diets and animal rations.

Heterogeneity is observed in the patterns of cognition in Alzheimer’s disease (AD). Such heterogeneity might suggest the involvement of different etiological pathways or different host responses to pathology. A total of 627 subjects with mild/moderate AD underwent cognitive assessment with the Mini-Mental State Examination (MMSE) and the Dementia Rating Scale-2 (DRS-2). Latent class analysis (LCA) was performed on cognition subscale data to identify and characterize cognitive subgroups. Clinical, demographic, and genetic factors were explored for association with class membership. LCA suggested the existence of four subgroups; one group with mild and another with severe global impairment across the cognitive domains, one group with primary impairments in attention and construction, and another group with primary deficits in memory and orientation. Education, disease duration, age, Apolipoprotein E-ε4 (APOE ε4) status, gender, presence of grasp reflex, white matter changes, and early or prominent visuospatial impairment were all associated with class membership. Our results support the existence of heterogeneity in patterns of cognitive impairment in AD. Our observation of classes characterized by predominant deficits in attention/construction and memory respectively deserves further exploration as does the association between membership in the attention/construction class and APOE ε4 negative status. (JINS, 2010, 16, 233–243.)

p-Values from tests of significance can be combined using the Sidak correction (or the closely related Bonferroni correction) or Fisher's method, but both these methods require that the p-values combined be independent when all null hypotheses tested are true. In this paper adjustments to these methods are proposed, using a new eigenvalue-based measure of the effective number of independent tests to which the actual tests performed are equivalent, and are compared with adjustments proposed by previous authors. The adjusted methods are evaluated using a sample of 726 Alzheimer's disease (AD) cases and 707 group-matched controls, genotyped at 84,975 single-nucleotide polymorphism loci in 2,000 randomly chosen genes. The tests for genetic association with AD at loci within each gene are combined. The number of loci tested per gene varies from 2 to 994. The adjusted combined p-values agree well with the significance of the combined p-values determined empirically by random permutation of the data (Sidak correction: r=0.990; Fisher's method: r=0.994). This indicates that the combined p-values can be used to assess the relative strength of evidence for association of these genes with AD. The adjustment proposed here is a refinement of that of Nyholt ([2004] Am. J. Hum. Genet. 74:765–769), giving improved agreement with the results of random permutation. The improvement obtained is similar to that given by the refinement proposed by Li and Ji ([2005] Heredity 95:221–227). It is concluded that the concept of an effective number of tests is a valid approximation that allows p-values to be combined in a highly informative way. Genet. Epidemiol. 33:559–568, 2009. © 2009 Wiley-Liss, Inc.

Genome-wide association studies (GWAS) testing several hundred thousand SNPs have been performed in multiple sclerosis (MS) and other complex diseases. Typically, the number of markers in which the evidence for association exceeds the genome-wide significance threshold is very small, and markers that do not exceed this threshold are generally neglected. Classical statistical analysis of these datasets in MS revealed genes with known immunological functions. However, many of the markers showing modest association may represent false negatives. We hypothesize that certain combinations of genes flagged by these markers can be identified if they belong to a common biological pathway. Here we conduct a pathway-oriented analysis of two GWAS in MS that takes into account all SNPs with nominal evidence of association ( P < 0.05). Gene-wise P -values were superimposed on a human protein interaction network and searches were conducted to identify sub-networks containing a higher proportion of gen es associated with MS than expected by chance. These sub-networks, and others generated at random as a control, were categorized for membership of biological pathways. GWAS from eight other diseases were analyzed to assess the specificity of the pathways identified. In the MS datasets, we identified sub-networks of genes from several immunological pathways including cell adhesion, communication and signaling. Remarkably, neural pathways, namely axon-guidance and synaptic potentiation, were also over-represented in MS. In addition to the immunological pathways previously ident- ified, we report here for the first time the potential involvement of neural pathways in MS susceptibility.

Multiple sclerosis (MS), a chronic disorder of the central nervous system and common cause of neurological disability in young adults, is characterized by moderate but complex risk heritability. Here we report the results of a genome-wide association study performed in a 1000 prospective case series of well-characterized individuals with MS and group-matched controls using the Sentrix® HumanHap550 BeadChip platform from Illumina. After stringent quality control data filtering, we compared allele frequencies for 551 642 SNPs in 978 cases and 883 controls and assessed genotypic influences on susceptibility, age of onset, disease severity, as well as brain lesion load and normalized brain volume from magnetic resonance imaging exams. A multi-analytical strategy identified 242 susceptibility SNPs exceeding established thresholds of significance, including 65 within the MHC locus in chromosome 6p21.3. Independent replication confirms a role for GPC5, a heparan sulfate proteoglycan, in disease risk. Gene ontology-based analysis shows a functional dichotomy between genes involved in the susceptibility pathway and those affecting the clinical phenotype.