A pragmatic suggestion for dealing with results for candidate genes obtained from genome wide association studies

<p>Abstract</p> <p>Background</p> <p>Researchers may embark on a genome-wide association study before fully investigating candidate regions which have been reported to produce evidence to suggest that they harbour susceptibility loci. If the genome wide study had not been carried out then results which demonstrated only modest statistical significance from candidate regions would be judged to be of interest and would stimulate further investigation. However if hundreds of thousands of markers are typed then inevitably very large numbers of such results will occur by chance and those from candidate regions may attract no special attention.</p> <p>Results</p> <p>An approach is proposed in which differential treatment is afforded to markers from candidate regions and from those that are routinely typed in the context of a genome wide scan. Different prior probabilities are assigned to the two types of marker. A likelihood ratio is derived from the reported <it>p </it>value for each marker, calculated as LR = e^{chiinv(1,p)/2}, and the posterior odds in favour of a true positive association are obtained. These odds can be used to rank the markers with a view to suggesting the regions in which further genotyping is indicated. We suggest that prior probabilities be specified such that a candidate marker significant at <it>p </it>= 0.01 and a routine marker significant at <it>p </it>= 0.00001 will yield similar values for the posterior odds. We show that this can be achieved by setting a value for prior probability of association to 0.1 for candidate markers and to 0.00018 for routine markers.</p> <p>Conclusion</p> <p>It is essential that formal procedures be adopted in order to avoid modestly positively results from candidate regions being swamped by the huge number of nominally significant results which will be obtained when very many markers are genotyped. Software to carry out the conversion from <it>p </it>values to posterior odds is available from <url>http://www.mds.qmul.ac.uk/statgen/grpsoft.html</url>.</p

A simple method for assessing the strength of evidence for association at the level of the whole gene

INTRODUCTION: It is expected that different markers may show different patterns of association with different pathogenic variants within a given gene. It would be helpful to combine the evidence implicating association at the level of the whole gene rather than just for individual markers or haplotypes. Doing this is complicated by the fact that different markers do not represent independent sources of information. METHOD: We propose combining the p values from all single locus and/or multilocus analyses of different markers according to the formula of Fisher, X = ∑(-2ln(p(i))), and then assessing the empirical significance of this statistic using permutation testing. We present an example application to 19 markers around the HTRA2 gene in a case-control study of Parkinson's disease. RESULTS: Applying our approach shows that, although some individual tests produce low p values, overall association at the level of the gene is not supported. DISCUSSION: Approaches such as this should be more widely used in assimilating the overall evidence supporting involvement of a gene in a particular disease. Information can be combined from biallelic and multiallelic markers and from single markers along with multimarker analyses. Single genes can be tested or results from groups of genes involved in the same pathway could be combined in order to test biologically relevant hypotheses. The approach has been implemented in a computer program called COMBASSOC which is made available for downloading

Digit ratio and autism spectrum disorders in the Avon Longitudinal Study of Parents and Children:a birth cohort study

OBJECTIVES: To investigate whether second-to-fourth digit ratio (2D:4D), a measure commonly used as a proxy for fetal testosterone exposure, is associated with autism spectrum disorders (ASDs), as predicted by the extreme male brain theory of autism. DESIGN: A birth cohort study. SETTING: The Avon Longitudinal Study of Parents and Children (ALSPAC). PARTICIPANTS: 6015 ALSPAC children with data on digit ratio, at least 1 outcome measure and information on potential confounding variables (parental occupational class, maternal education and age at digit ratio measurement). Digit ratio was measured by the photocopy and calliper method. OUTCOMES: ASD diagnosis (cases were identified previously by record linkage or maternal report) and 4 measures that combine optimally within ALSPAC to predict ASD: the Children's Communication Checklist (coherence subscale), the Social and Communication Disorders Checklist, a repetitive behaviour measure, and the Emotionality, Activity and Sociability scale (sociability subscale). These measures were dichotomised, with approximately 10% defined as the ‘risk’ group. RESULTS: Using logistic regression, we examined the association of 2D:4D with ASDs and 4 dichotomised ASD traits. Covariates were occupational class, maternal education and age at 2D:4D measurement. 2D:4D was not associated with ASDs in males (adjusted OR per 1 SD increase in mean 2D:4D, 0.88 (95% CI 0.65 to 1.21), p=0.435) or females (adjusted OR=1.36 (95% CI 0.81 to 2.28), p=0.245). Similar results were observed after adjustment for IQ. There was 1 weak association between reduced coherence and increased left 2D:4D in males, in the opposite direction to that predicted by the extreme male brain theory (adjusted OR=1.15 (95% CI 1.02 to 1.29), p=0.023). Given multiple comparisons, this is consistent with chance. CONCLUSIONS: In this population-based study, there was no strong evidence of an association between 2D:4D and ASD diagnosis or traits, although the CIs were wide. These results are not consistent with the extreme male brain theory

Measuring elastic nonlinearity in a soft solid using a tilted acoustic radiation force for shear wave excitation

Excitation of multiple wave modes using shear wave elastography can result in additional information about the tissue's material characteristics and, potentially, improve disease diagnosis. Theoretically, tilting the acoustic radiation force excitation axis with respect to the material's symmetry axis should excite several wave modes in the material. In this work, we have experimentally demonstrated proof of concept in a uniaxially stretched phantom, while increasing the stretch level. Tilted acoustic radiation force experiments showed a clearly visible second wave mode across the stretch direction for larger stretches (>160%)

Characteristics and outcomes of neonates hospitalised with SARS-CoV-2 infection in the United Kingdom by variant: a prospective national cohort study

Objective Neonatal infection with wildtype SARS-CoV-2 is rare and good outcomes predominate. We investigated neonatal outcomes using national population-level data to describe the impact of different SARS-CoV-2 variants. Design Prospective population-based cohort study. Setting Neonatal, paediatric and paediatric intensive care inpatient care settings in the UK. Patients Neonates (first 28 days after birth) with confirmed SARS-CoV-2 infection who received inpatient care, March 2020 to April 2022. Neonates were identified through active national surveillance with linkage to national SARS-CoV-2 testing data, routinely recorded neonatal data, paediatric intensive care data and obstetric and perinatal mortality surveillance data. Outcomes Presenting signs, clinical course, severe disease requiring respiratory support are presented by the dominant SARS-CoV-2 variant in circulation at the time. Results 344 neonates with SARS-CoV-2 infection received inpatient care; breakdown by dominant variant: 146 wildtype, 123 alpha, 57 delta and 18 omicron. Overall, 44.7% (153/342) neonates required respiratory support; short-term outcomes were good with 93.6% (322/344) of neonates discharged home. Eleven neonates died: seven unrelated to SARS-CoV-2 infection, four were attributed to neonatal SARS-CoV-2 infection (case fatality 4/344, 1.2% 95% CI 0.3% to 3.0%) of which three were born preterm due to maternal COVID-19. More neonates were born very preterm (23/54) and required invasive ventilation (27/57) when delta variant was predominant, and all four SARS-CoV-2-related deaths occurred in this period. Conclusions Inpatient care for neonates with SARS-CoV-2 was uncommon. Although rare, severe neonatal illness was more common during the delta variant period, potentially reflecting more severe maternal disease and associated preterm birth. Trial registration number ISRCTN60033461

Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethiON platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150 bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from specific chromosomes of the long-read data achieved good specificity and sensitivity. However, results of somatic SNV calling highlight the need for the development of specialised joint calling algorithms. We find the comparative genome-wide performance of different tools varies significantly between structural variant types, and suggest long reads are especially advantageous for calling large somatic deletions and duplications. Finally, we highlight the utility of long reads for phasing clinically relevant variants, confirming that a somatic 1.6 Mb deletion and a p.(Arg249Met) mutation involving TP53 are oriented in trans

Assay strategies for the discovery and validation of therapeutics targeting <i>Brugia pahangi</i> Hsp90

The chemotherapy of lymphatic filariasis relies upon drugs such as diethylcarbamazine and ivermectin that largely target the microfilarial stages of the parasite, necessitating continued treatment over the long reproductive life span of the adult worm. The identification of compounds that target adult worms has been a long-term goal of WHO. Here we describe a fluorescence polarization assay for the identification of compounds that target Hsp90 in adult filarial worms. The assay was originally developed to identify inhibitors of Hsp90 in tumor cells, and relies upon the ability of small molecules to inhibit the binding of fluorescently labelled geldanamycin to Hsp90. We demonstrate that the assay works well with soluble extracts of Brugia, while extracts of the free-living nematode C. elegans fail to bind the probe, in agreement with data from other experiments. The assay was validated using known inhibitors of Hsp90 that compete with geldanamycin for binding to Hsp90, including members of the synthetic purine-scaffold series of compounds. The efficacy of some of these compounds against adult worms was confirmed in vitro. Moreover, the assay is sufficiently sensitive to differentiate between binding of purine-scaffold compounds to human and Brugia Hsp90. The assay is suitable for high-throughput screening and provides the first example of a format with the potential to identify novel inhibitors of Hsp90 in filarial worms and in other parasitic species where Hsp90 may be a target

Sporadic Creutzfeldt-Jakob Disease in 2 Plasma Product Recipients, United Kingdom

Sporadic Creutzfeldt-Jakob disease (sCJD) has not been previously reported in patients with clotting disorders treated with fractionated plasma products. We report 2 cases of sCJD identified in the United Kingdom in patients with a history of extended treatment for clotting disorders; 1 patient had hemophilia B and the other von Willebrand disease. Both patients had been informed previously that they were at increased risk for variant CJD because of past treatment with fractionated plasma products sourced in the United Kingdom. However, both cases had clinical and investigative features suggestive of sCJD. This diagnosis was confirmed in both cases on neuropathologic and biochemical analysis of the brain. A causal link between the treatment with plasma products and the development of sCJD has not been established, and the occurrence of these cases may simply reflect a chance event in the context of systematic surveillance for CJD in large populations

Land management explains major trends in forest structure and composition over the last millennium in California's Klamath Mountains

For millennia, forest ecosystems in California have been shaped by fire from both natural processes and Indigenous land management, but the notion of climatic variation as a primary controller of the pre-colonial landscape remains pervasive. Understanding the relative influence of climate and Indigenous burning on the fire regime is key because contemporary forest policy and management are informed by historical baselines. This need is particularly acute in California, where 20th-century fire suppression, coupled with a warming climate, has caused forest densification and increasingly large wildfires that threaten forest ecosystem integrity and management of the forests as part of climate mitigation efforts. We examine climatic versus anthropogenic influence on forest conditions over 3 millennia in the western Klamath Mountains—the ancestral territories of the Karuk and Yurok Tribes—by combining paleoenvironmental data with Western and Indigenous knowledge. A fire regime consisting of tribal burning practices and lightning were associated with long-term stability of forest biomass. Before Euro-American colonization, the long-term median forest biomass was between 104 and 128 Mg/ha, compared to values over 250 Mg/ha today. Indigenous depopulation after AD 1800, coupled with 20th-century fire suppression, likely allowed biomass to increase, culminating in the current landscape: a closed Douglas fir–dominant forest unlike any seen in the preceding 3,000 y. These findings are consistent with precontact forest conditions being influenced by Indigenous land management and suggest large-scale interventions could be needed to return to historic forest biomass levels

Resting EEG periodic and aperiodic components predict cognitive decline over 10 years

Measures of intrinsic brain function at rest show promise as predictors of cognitive decline in humans, including EEG metrics such as individual alpha peak frequency (IAPF) and the aperiodic exponent, reflecting the strongest frequency of alpha oscillations and the relative balance of excitatory:inhibitory neural activity, respectively. Both IAPF and the aperiodic exponent decrease with age and have been associated with worse executive function and working memory. However, few studies have jointly examined their associations with cognitive function, and none have examined their association with longitudinal cognitive decline rather than cross-sectional impairment. In a preregistered secondary analysis of data from the longitudinal Midlife in the United States (MIDUS) study, we tested whether IAPF and aperiodic exponent measured at rest predict cognitive function (N = 235; age at EEG recording M = 55.10, SD = 10.71) over 10 years. The IAPF and the aperiodic exponent interacted to predict decline in overall cognitive ability, even after controlling for age, sex, education, and lag between data collection timepoints. Post-hoc tests showed that “mismatched” IAPF and aperiodic exponents (e.g., higher exponent with lower IAPF) predicted greater cognitive decline compared to “matching” IAPF and aperiodic exponents (e.g., higher exponent with higher IAPF; lower IAPF with lower aperiodic exponent). These effects were largely driven by measures of executive function. Our findings provide the first evidence that IAPF and the aperiodic exponent are joint predictors of cognitive decline from midlife into old age and thus may offer a useful clinical tool for predicting cognitive risk in aging