Methods for Handling Multiple Testing

Dysfluency in primary progressive aphasia: Temporal speech parameters

Analysing spontaneous speech in individuals experiencing fluency difficulties holds potential for diagnosing speech and language disorders, including Primary Progressive Aphasia (PPA). Dysfluency in the spontaneous speech of patients with PPA has mostly been described in terms of abnormal pausing behaviour, but the temporal features related to speech have drawn little attention. This study compares speech-related fluency parameters in the three main variants of PPA and in typical speech. Forty-three adults participated in this research, thirteen with the logopenic variant of PPA (lvPPA), ten with the non-fluent variant (nfvPPA), nine with the semantic variant (svPPA), and eleven who were healthy age-matched adults. Participants' fluency was assessed through a picture description task from which 42 parameters were computed including syllable duration, speaking pace, the duration of speech chunks (i.e. interpausal units, IPU), and the number of linguistic units per IPU and per second. The results showed that each PPA variant exhibited abnormal speech characteristics reflecting various underlying factors, from motor speech deficits to higher-level issues. Out of the 42 parameters considered, 37 proved useful for characterising dysfluency in the three main PPA variants and 35 in distinguishing among them. Therefore, taking into account not only pausing behaviour but also temporal speech parameters can provide a fuller understanding of dysfluency in PPA. However, no single parameter by itself sufficed to distinguish one PPA group from the other two, further evidence that dysfluency is not dichotomous but rather multidimensional, and that complementary multiparametric analyses are needed.

Sequence variants associated with resilient responses in growing pigs

The current work aimed to identify genomic regions and candidate genes associated with resilience in pigs. In previous work, we proposed the body weight deviation from the expected growth curve (ΔBW) and the increase of the positive acute-phase protein haptoglobin (ΔHP) after a vaccine challenge as resilience indicators which may be improved through selective breeding in pigs. Individuals with steady growth rate and minor activation of haptoglobin (high ΔBW and low ΔHP values) were considered resilient. In contrast, pigs with perturbed growth rate and high activation of haptoglobin (low ΔBW and high ΔHP values) were considered susceptible. Both ∆BW and ∆HP were simultaneously considered to select the most resilient (N = 40) and susceptible (N = 40) pigs. A genome-wide association study was carried out for the pigs' response classification to the challenge test using whole-genome sequence data (7,760,720 variants). Eleven associated genomic regions were identified, harbouring relevant candidate genes related to the immune response (such as pro- and anti-inflammatory responses) and growth pathways. These associated genomic regions harboured 41 potential functional mutations (frameshift, splice donor, splice acceptor, start loss and stop loss/gain) in candidate genes. Overall, this study advances our knowledge about the genetic determinism of resilience, highlighting its polygenic nature and strong relationship with immunity and growth.

Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology

Due to the complex nature of microbiome data, the field of microbial ecology has many current and potential uses for machine learning (ML) modeling. With the increased use of predictive ML models across many disciplines, including microbial ecology, there is extensive published information on the specific ML algorithms available and how those algorithms have been applied. Thus, our goal is not to summarize the breadth of ML models available or compare their performances. Rather, our goal is to provide more concrete and actionable information to guide microbial ecologists in how to select, run, and interpret ML algorithms to predict the taxa or genes associated with particular sample categories or environmental gradients of interest. Such microbial data often have unique characteristics that require careful consideration of how to apply ML models and how to interpret the associated results. This review is intended for practicing microbial ecologists who may be unfamiliar with some of the intricacies of ML models. We provide examples and discuss common opportunities and pitfalls specific to applying ML models to the types of data sets most frequently collected by microbial ecologists.

Genome-wide multimediator analyses using the generalized Berk-Jones statistics with the composite test

MOTIVATION

Mediation analysis is performed to evaluate the effects of a hypothetical causal mechanism that marks the progression from an exposure, through mediators, to an outcome. In the age of high-throughput technologies, it has become routine to assess numerous potential mechanisms at the genome or proteome scales. Alongside this, the necessity to address issues related to multiple testing has also arisen. In a sparse scenario where only a few genes or proteins are causally involved, conventional methods for assessing mediation effects lose statistical power because the composite null distribution behind this experiment cannot be attained. The power loss hence decreases the true mechanisms identified after multiple testing corrections. To fairly delineate a uniform distribution under the composite null, Huang (Genome-wide analyses of sparse mediation effects under composite null hypotheses. Ann Appl Stat 2019a;13:60-84; AoAS) proposed the composite test to provide adjusted P-values for single-mediator analyses.

RESULTS

Our contribution is to extend the method to multimediator analyses, which are commonly encountered in genomic studies and also flexible to various biological interests. Using the generalized Berk-Jones statistics with the composite test, we proposed a multivariate approach that favors dense and diverse mediation effects, a decorrelation approach that favors sparse and consistent effects, and a hybrid approach that captures the edges of both approaches. Our analysis suite has been implemented as an R package MACtest. The utility is demonstrated by analyzing the lung adenocarcinoma datasets from The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium. We further investigate the genes and networks whose expression may be regulated by smoking-induced epigenetic aberrations.

AVAILABILITY AND IMPLEMENTATION

An R package MACtest is available on https://github.com/roqe/MACtest.

Cognitive correlates of auditory hallucinations in schizophrenia spectrum disorders

Auditory hallucinations (AHs) are one of the central symptoms of schizophrenia spectrum disorders (SSD). Current cognitive models of AH implicate source monitoring, top-down processes, and inhibitory control. However, research combining these processes is limited. Our study aimed to examine how source monitoring bias, top-down processes, and inhibitory control contribute to AHs in individuals with SSD. Eighty seven patients (aged 18-45 years) with SSD were included in the analyses. Participants completed cognitive tasks assessing source monitoring (Action Memory Task), top-down processes (False Perception Task; FPT), and inhibitory control (Auditory Go/NoGo task). AH was positively associated with response bias on the FPT. Correlations between AH and the other cognitive tasks were nonsignificant. Source monitoring errors correlated positively with response bias measures and negatively with Hits on the FPT. PANSS total score was positively correlated with source monitoring bias and False Alarms on the Go/NoGo task. The severity of disorganized symptoms was related to Source Monitoring Errors and False Alarms in the Go/NoGo task. Negative symptoms were associated with Hits and False Alarms in the Go/NoGo task. Future studies are necessary to further elucidate the relationships between different cognitive processes that may be related to clinical symptoms of psychosis.

Genome-wide association study reveals novel genomic regions governing agronomic and grain quality traits and superior allelic combinations for Basmati rice improvement

BACKGROUND

Basmati is a speciality segment in the rice genepool characterised by explicit grain quality. For the want of suitable populations, genome-wide association study (GWAS) in Basmati rice has not been attempted.

MATERIALS

To address this gap, we have performed a GWAS on a panel of 172 elite Basmati multiparent population comprising of potential restorers and maintainers. Phenotypic data was generated for various agronomic and grain quality traits across seven different environments during two consecutive crop seasons. Based on the observed phenotypic variation, three agronomic traits namely, days to fifty per cent flowering, plant height and panicle length, and three grain quality traits namely, kernel length before cooking, length breadth ratio and kernel length after cooking were subjected to GWAS. Genotyped with 80K SNP array, the population was subjected to principal component analysis to stratify the underlying substructure and subjected to the association analysis using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model.

RESULTS

We identified 32 unique MTAs including 11 robust MTAs for the agronomic traits and 25 unique MTAs including two robust MTAs for the grain quality traits. Six out of 13 robust MTAs were novel. By genome annotation, six candidate genes associated with the robust MTAs were identified. Further analysis of the allelic combinations of the robust MTAs enabled the identification of superior allelic combinations in the population. This information was utilized in selecting 77 elite Basmati rice genotypes from the panel.

CONCLUSION

This is the first ever GWAS study in Basmati rice which could generate valuable information usable for further breeding through marker assisted selection, including enhancing of heterosis.

Identification of New Genes and Genetic Variant Loci Associated with Breast Muscle Development in the Mini-Cobb F2 Chicken Population Using a Genome-Wide Association Study

Native chicken has become a favorite choice for consumers in many Asian countries recently, not only for its potential nutritional value but also for its deep ties to local food culture. However, low growth performance and limited meat production restrict their economic potential. Conducting a genome-wide association study (GWAS) for chicken-breast muscle development will help identify loci or candidate genes for different traits and potentially provide new insight into this phenotype in chickens and other species. To improve native chicken growth performance, especially breast muscle development, we performed a GWAS to explore the potential genetic mechanisms of breast muscle development in an F2 population constructed by reciprocal crosses between a fast-growing broiler chicken (Cobb500) and a slow-growing native chicken (Daweishan mini chicken). The results showed that 11 SNPs, which exceeded the 10% genome significance level (p = 1.79 × 10-8) were considered associated with breast muscle development traits, where six SNPS, NC_006126.5: g.3138376T>G, NC_006126.5: g.3138452A>G, NC_006088.5: g.73837197A>G, NC_006088.5: g.159574275A>G, NC_006089.5: g.80832197A>G, and NC_006127.5: g.48759869G>T was first identified in this study. In total, 13 genes near the SNPs were chosen as candidate genes, and none of them had previously been studied for their role in breast muscle development. After grouping the F2 population according to partial SNPs, significant differences in breast muscle weight were found among different genotypes (p < 0.05), and the expression levels of ALOX5AP, USPL1, CHRNA9, and EFNA5 among candidate genes were also significantly different (p < 0.05). The results of this study will contribute to the future exploration of the potential genetic mechanisms of breast muscle development in domestic chickens and also support the expansion of the market for native chicken in the world.

A Co-Association Network Analysis Reveals Putative Regulators for Health-Related Traits in Pigs

In recent years, the increase in awareness of antimicrobial resistance together with the societal demand of healthier meat products have driven attention to health-related traits in livestock production. Previous studies have reported medium to high heritabilities for these traits and described genomic regions associated with them. Despite its genetic component, health- and immunity-related traits are complex and its study by association analysis with genomic markers may be missing some information. To analyse multiple phenotypes and gene-by-gene interactions, systems biology approaches, such as the association weight matrix (AWM), allows combining genome wide association study results with network inference algorithms. The present study aimed to identify gene networks, key regulators and candidate genes associated to immunocompetence in pigs by integrating multiple health-related traits, enriched for innate immune phenotypes, using the AWM approach. The co-association network analysis unveiled a network comprised of 3,636 nodes (genes) and 451,407 edges (interactions), including a total of 246 regulators. From these, five genes (ARNT2, BRMS1L, MED12L, SUPT3H and TRIM25) were selected as key regulators as they were associated with the maximum number of genes with the minimum overlapping (1,827 genes in total). The five regulators were involved in pathways related to immunity such as lymphocyte differentiation and activation, platelet activation and degranulation, megakaryocyte differentiation, FcγR-mediated phagocytosis and response to nitric oxide, among others, but also in immunometabolism. Furthermore, we identified genes co-associated with the key regulators previously reported as candidate genes (e.g., ANGPT1, CD4, CD36, DOCK1, PDE4B, PRKCE, PTPRC and SH2B3) for immunity traits in humans and pigs, but also new candidate ones (e.g., ACSL3, CXADR, HBB, MMP12, PTPN6, WLS) that were not previously described. The co-association analysis revealed new regulators associated with health-related traits in pigs. This approach also identified gene-by-gene interactions and candidate genes involved in pathways related to cell fate and metabolic and immune functions. Our results shed new light in the regulatory mechanisms involved in pig immunity and reinforce the use of the pig as biomedical model.

Neurotranscriptomic changes associated with chick-directed parental care in adult non-reproductive Japanese quail

For many species, parental care critically affects offspring survival. But what drives animals to display parental behaviours towards young? In mammals, pregnancy-induced physiological transformations seem key in preparing the neural circuits that lead towards attraction (and reduced-aggression) to young. Beyond mammalian maternal behaviour, knowledge of the neural mechanisms that underlie young-directed parental care is severely lacking. We took advantage of a domesticated bird species, the Japanese quail, for which parental behaviour towards chicks can be induced in virgin non-reproductive adults through a sensitization procedure, a process that is not effective in all animals. We used the variation in parental responses to study neural transcriptomic changes associated with the sensitization procedure itself and with the outcome of the procedure (i.e., presence of parental behaviours). We found differences in gene expression in the hypothalamus and bed nucleus of the stria terminalis, but not the nucleus taeniae. Two genes identified are of particular interest. One is neurotensin, previously only demonstrated to be causally associated with maternal care in mammals. The other one is urocortin 3, causally demonstrated to affect young-directed neglect and aggression in mammals. Because our studies were conducted in animals that were reproductively quiescent, our results reflect core neural changes that may be associated with avian young-directed care independently of extensive hormonal stimulation. Our work opens new avenues of research into understanding the neural basis of parental care in non-placental species.

Nonparallel transcriptional divergence during parallel adaptation

How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies (Poecilia reticulata) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high- and low-predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high- and low-predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Exploring natural diversity of Medicago truncatula reveals physiotypes and loci associated with the response of seedling performance to nitrate supply

Seedling pre-emergence is a critical phase of development for successful crop establishment because of its susceptibility to environmental conditions. In a context of reduced use of inorganic fertilizers, the genetic bases of the response of seedlings to nitrate supply received little attention. This issue is important even in legumes where nitrate absorption starts early after germination, before nodule development. Natural variation of traits characterizing seedling growth in the absence or presence of nitrate was investigated in a core collection of 192 accessions of Medicago truncatula. Plasticity indexes to the absence of nitrate were calculated. The genetic determinism of the traits was dissected by genome-wide association study (GWAS). The absence of nitrate affected seed biomass mobilization and root/shoot length ratio. However, the large range of genetic variability revealed different seedling performances within natural diversity. A principal component analysis (PCA) carried out with plasticity indexes highlighted four physiotypes of accessions differing in relationships between seedling elongation and seed biomass partitioning traits in response to the absence of nitrate. Finally, GWAS revealed 45 associations with single or combined traits corresponding to coordinates of accessions on PCA, as well as two clusters of genes encoding sugar transporters and glutathione transferases surrounding loci associated with seedling elongation traits.

Clinical evaluation of atlas- and deep learning-based automatic segmentation of multiple organs and clinical target volumes for breast cancer

Manual segmentation is the gold standard method for radiation therapy planning; however, it is time-consuming and prone to inter- and intra-observer variation, giving rise to interests in auto-segmentation methods. We evaluated the feasibility of deep learning-based auto-segmentation (DLBAS) in comparison to commercially available atlas-based segmentation solutions (ABAS) for breast cancer radiation therapy. This study used contrast-enhanced planning computed tomography scans from 62 patients with breast cancer who underwent breast-conservation surgery. Contours of target volumes (CTVs), organs, and heart substructures were generated using two commercial ABAS solutions and DLBAS using fully convolutional DenseNet. The accuracy of the segmentation was assessed using 14 test patients using the Dice Similarity Coefficient and Hausdorff Distance referencing the expert contours. A sensitivity analysis was performed using non-contrast planning CT from 14 additional patients. Compared to ABAS, the proposed DLBAS model yielded more consistent results and the highest average Dice Similarity Coefficient values and lowest Hausdorff Distances, especially for CTVs and the substructures of the heart. ABAS showed limited performance in soft-tissue-based regions, such as the esophagus, cardiac arteries, and smaller CTVs. The results of sensitivity analysis between contrast and non-contrast CT test sets showed little difference in the performance of DLBAS and conversely, a large discrepancy for ABAS. The proposed DLBAS algorithm was more consistent and robust in its performance than ABAS across the majority of structures when examining both CTVs and normal organs. DLBAS has great potential to aid a key process in the radiation therapy workflow, helping optimise and reduce the clinical workload.

Effectiveness of a Web-Based SUpport PRogram (SUPR) for Hearing Aid Users Aged 50+: Two-Arm, Cluster Randomized Controlled Trial

BACKGROUND

Hearing aid (HA) use is known to improve health outcomes for people with hearing loss. Despite that, HA use is suboptimal, and communication issues and hearing-related activity limitations and participation restrictions often remain. Web-based self-management communication programs may support people with hearing loss to effectively self-manage the impact of hearing loss in their daily lives.

OBJECTIVE

The goal of the research is to examine the short- and long-term effects of a web-based self-management SUpport PRogram (SUPR) on communication strategy use (primary outcome) and a range of secondary outcomes for HA users aged 50 years and older.

METHODS

Clients of 36 HA dispensing practices were randomized to SUPR (SUPR recipients; n=180 HA users) and 34 to care as usual (controls; n=163 HA users). SUPR recipients received a practical support booklet and online materials delivered via email over the course of their 6-month HA rehabilitation trajectory. They were encouraged to appoint a communication partner and were offered optional email contact with the HA dispensing practice. The online materials included 3 instruction videos on HA handling, 5 videos on communication strategies, and 3 testimonial videos. Care as usual included a HA fitting rehabilitation trajectory only. Measurements were carried out at baseline, immediately postintervention, 6 months postintervention, and 12 months postintervention. The primary outcome measure was self-reported use of communication strategies (3 subscales of the Communication Profile for the Hearing Impaired [CPHI]). Secondary outcome measures included self-reported personal adjustment to hearing loss (CPHI); use, satisfaction and benefit of HAs and SUPR (use questionnaire; International Outcome Inventory for Hearing Aids [IOI-HA], Alternative Interventions [IOI-AI]); recommendation of HA dispensing services; self-efficacy for HA handling (Measure of Audiologic Rehabilitation Self-Efficacy for Hearing Aids [MARS-HA]); readiness to act on hearing loss (University of Rhode Island Change Assessment adapted for hearing loss [URICA-HL]); and hearing disability (Amsterdam Inventory for Auditory Disability and Handicap [AIADH]).

RESULTS

Linear mixed model analyses (intention to treat) showed no significant differences between the SUPR and control group in the course of communication strategy use (CPHI). Immediately postintervention, SUPR recipients showed significantly higher self-efficacy for advanced HA handling than the controls, which was sustained at 12 months (MARS-HA; mean difference immediately postintervention: 5.3, 95% CI 0.3 to 10.4; P=.04). Also, SUPR recipients showed significantly greater HA satisfaction than controls immediately postintervention (IOI-HA; 0.3, 95% CI 0.09 to 0.5; P=.006), which was sustained at 12 months, and significantly greater HA use than the controls immediately postintervention (IOI-HA; 0.3, 95% CI 0.02 to 0.5; P=.03), which was not sustained at 12 months.

CONCLUSIONS

This study provides ground to recommend adding SUPR to standard HA dispensing care, as long-term, modest improvements in HA outcomes were observed. Further research is needed to evaluate what adjustments to SUPR are needed to establish long-term effectiveness on outcomes in the psychosocial domain.

TRIAL REGISTRATION

ISRCTN77340339; http://www.isrctn.com/ISRCTN77340339.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR2-10.1136/bmjopen-2016-015012.

Association of Single-Nucleotide Polymorphisms in ABCC5 Gene with Primary Angle Closure Glaucoma and the Ocular Biometric Parameters in a Northern Chinese Population

BACKGROUND

The rs1401999 gene in ABCC5 gene was the first locus confirmed by a genome-wide association study (GWAS) to be associated with both anterior chamber depth (ACD) and primary angle closure glaucoma (PACG); however, this locus was of obvious heterogeneity among different populations in the GWAS, and the conclusion has not been further verified by other studies. Therefore, this study was carried out to investigate whether the single-nucleotide polymorphisms (SNPs) in ABCC5 gene are associated with PACG and the ocular biometric parameters ACD and axial length (AL) in samples from northern China.

METHODS

Case-control association study included 500 PACG patients and 720 unrelated controls from northern China, and genotyping was performed for ten SNPs in ABCC5 gene using an improved multiplex ligation detection reaction technique. The association between these SNPs and risk of PACG was estimated by PLINK using a logistic regression model, while the association between genotypes and ocular biometric parameters was performed by SPSS using generalized estimation equation.

RESULTS

An SNP rs4148568 (p = 0.046) and a haplotype TCGGAG (p = 0.0364) in ABCC5 were associated with PACG, and rs4148568 was nominally associated with AL (β = 0.092, p = 0.08).

CONCLUSIONS

The SNP rs4148568 and a haplotype TCGGAG in ABCC5 contribute to PACG in northern Chinese people. In addition, rs4148568 might be associated with the AL, the variant allele of which may have effect of making the AL longer. Further studies are needed to elucidate the exact mechanism of ABCC5 in the progress of PACG.

Extreme mobility of the world's largest flying mammals creates key challenges for management and conservation

BACKGROUND

Effective conservation management of highly mobile species depends upon detailed knowledge of movements of individuals across their range; yet, data are rarely available at appropriate spatiotemporal scales. Flying-foxes (Pteropus spp.) are large bats that forage by night on floral resources and rest by day in arboreal roosts that may contain colonies of many thousands of individuals. They are the largest mammals capable of powered flight, and are highly mobile, which makes them key seed and pollen dispersers in forest ecosystems. However, their mobility also facilitates transmission of zoonotic diseases and brings them in conflict with humans, and so they require a precarious balancing of conservation and management concerns throughout their Old World range. Here, we analyze the Australia-wide movements of 201 satellite-tracked individuals, providing unprecedented detail on the inter-roost movements of three flying-fox species: Pteropus alecto, P. poliocephalus, and P. scapulatus across jurisdictions over up to 5 years.

RESULTS

Individuals were estimated to travel long distances annually among a network of 755 roosts (P. alecto, 1427-1887 km; P. poliocephalus, 2268-2564 km; and P. scapulatus, 3782-6073 km), but with little uniformity among their directions of travel. This indicates that flying-fox populations are composed of extremely mobile individuals that move nomadically and at species-specific rates. Individuals of all three species exhibited very low fidelity to roosts locally, resulting in very high estimated daily colony turnover rates (P. alecto, 11.9 ± 1.3%; P. poliocephalus, 17.5 ± 1.3%; and P. scapulatus, 36.4 ± 6.5%). This indicates that flying-fox roosts form nodes in a vast continental network of highly dynamic "staging posts" through which extremely mobile individuals travel far and wide across their species ranges.

CONCLUSIONS

The extreme inter-roost mobility reported here demonstrates the extent of the ecological linkages that nomadic flying-foxes provide across Australia's contemporary fragmented landscape, with profound implications for the ecosystem services and zoonotic dynamics of flying-fox populations. In addition, the extreme mobility means that impacts from local management actions can readily reverberate across jurisdictions throughout the species ranges; therefore, local management actions need to be assessed with reference to actions elsewhere and hence require national coordination. These findings underscore the need for sound understanding of animal movement dynamics to support evidence-based, transboundary conservation and management policy, tailored to the unique movement ecologies of species.

Generalizability of SuperAlarm via Cross-Institutional Performance Evaluation

Bedside patient monitors are ubiquitous tools in modern critical care units to provide timely patient status. However, current systems suffer from high volume of false alarms leading to alarm fatigue, one of top technical hazards in clinical settings. Many studies are racing to develop improved algorithms towards precision patient monitoring, while little has been done to investigate the aspect of algorithm generalizability across different health institutions. Our group has been developing an evolving framework termed SuperAlarm that extracts multivariate patterns in data streams (monitor alarms, electronic health records and physiologic waveforms) of modern health enterprise to predict patient deterioration and has demonstrated great potential in mitigating alarm fatigue. In this study, we further investigate the generalizability of SuperAlarm by designing a comprehensive approach to achieve performance comparison in predicting in-hospital code blue (CB) events across two health institutions. SuperAlarm model trained with alarm data in one institution is tested on both internal and external test sets. Results show comparable performance with sensitivity up to 80% within one-hour window of events and over 90% in reduction of false alarms in both institutions. Cross-institutional performance agreement can be further improved by predicting a more stringent CB subtype (cardiopulmonary arrest), with internal sensitivity lying within 95% confident interval of external one up to 8-hour before event onset. The cross-institutional performance comparison offers first-hand knowledge on both advantages and challenges in generalizing a prediction algorithm across different institutions, which hold key information to guide the design of model training and deployment strategy.

Genetic Influences on Social Relationships: Sex Differences in the Mediating Role of Personality and Social Cognition

Objectives

In humans (and primates more generally), evolutionary fitness arises by two separate routes: conventional reproduction build around dyadic relationships and, reflecting the processes of group augmentation selection, how well individuals are embedded in their community. These processes are facilitated by a suite of genetically inherited neuroendocrines and neurotransmitters. It is not, however, known whether these effects are directly due to genetic factors or are mediated by aspects of personality, or whether there are sex differences in the way this is organised.

Methods

We examine whether dispositional factors related to the processing of social information, such as personality (Big 5 and Impulsivity), attachment style (Anxious and Avoidant dimensions) and sociocognitive capacity (emotion recognition) mediate associations between variation in receptor genes for oxytocin, vasopressin, beta-endorphin, dopamine, serotonin, testosterone and two core social relationship indices (the Sociosexual Orientation Index [SOI] and Support Network size).

Results

In men, variation in dopamine genes indirectly influences SOI through its effect on Impulsivity. In contrast, in women, variation in endorphin and vasopressin genes independently affect Openness to Experience, which mediates indirect effects of these genes on SOI. Moreover, endorphin gene variation also impacts on Network Size in women (but not men), via Extraversion.

Conclusions

These findings reveal that dispositional aspects of personality mediate some genetic effects on behaviour, thereby extending our understanding of how genetic and dispositional variation interact to determine individual differences in human sexual and social cognition and behaviour. The differences between the sexes seem to reflect differences in the two sexes’ social strategies.

TNFAIP3 genetic polymorphisms reduce ankylosing spondylitis risk in Eastern Chinese Han population

This study was conducted to clarify the associations of tumor necrosis factor-α induced protein 3 (TNFAIP3) and TNFAIP3-interacting protein 1 (TNIP1) genetic polymorphisms with ankylosing spondylitis (AS) susceptibility. Five single nucleotide polymorphisms (SNPs) in TNFAIP3 gene and four in TNIP1 gene were genotyped in 667 AS patients and 667 matched healthy controls. Genotypes and haplotype analysis were conducted by using SPSS 23.0 and Haploview 4.2 software. The T allele and CT genotype in TNFAIP3 rs10499194 were significantly associated with a reduced AS risk (T allele vs. C allele, OR = 0.619, 95% CI = 0.430–0.889, P = 0.009; CT vs. CC, OR = 0.603, 95% CI = 0.416–0.875, P = 0.007). However, no association remained significant after Bonferroni correction. The rs13207033^A- rs10499194^T haplotype of TNFAIP3 conferred a protective effect on AS susceptibility. Stratification analyses suggested that rs10499194 polymorphism decreased the risk of AS in the male subgroup, subgroup aged ≥ 29, HLA-B27 positive subgroup as well as the subgroups of BASFI < 4 and BASDAI < 4 (all P < 0.05). Furthermore, the functional annotation suggested a potential function of rs10499194 mutation. Our results demonstrated that TNFAIP3 rs10499194 polymorphism may be associated with a reduced risk of AS.

Understanding the Loss of Maternal Care in Avian Brood Parasites Using Preoptic Area Transcriptome Comparisons in Brood Parasitic and Non-parasitic Blackbirds

Parental care is critical for offspring survival in many species. However, parental behaviors have been lost in roughly 1% of avian species known as the obligate brood parasites. To shed light on molecular and neurobiological mechanisms mediating brood parasitic behavior, we compared brain gene expression patterns between two brood parasitic species and one closely related non-parasitic Icterid (blackbird) species. Our analyses focused on gene expression changes specifically in the preoptic area (POA), a brain region known to play a critical role in parental behavior across vertebrates. Using comparative transcriptomic approaches, we identified gene expression patterns associated with brood parasitism. We evaluated three non-mutually exclusive alternatives for the evolution of brood parasitism: (1) retention of juvenile-like (neotenic) gene expression, (2) reduced expression of maternal care-related genes in the POA, and/or (3) increased expression of genes inhibiting maternal care. We find evidence for neotenic expression patterns in both species of parasitic cowbirds as compared to maternal, non-parasites. In addition, we observed differential expression in a number of genes with previously established roles in mediating maternal care. Together, these results provide the first insight into transcriptomic and genetic mechanisms underlying the loss of maternal behavior in avian brood parasites.

Associations between neurochemical receptor genes, 2D:4D, impulsivity and relationship quality

The ratio between the second and fourth digits (2D:4D) has been widely used as a proxy for fetal exposure to androgens and has been linked to a number of sociosexual traits in humans. However, the role of genes in this equation remains unknown. Here (N = 474), we test, firstly, for associations between 2D:4D and single-nucleotide polymorphisms (SNPs) in nine neurochemical receptor genes (AR, OXTR, AVPR1A, OPRM1, DRD1/2, ANKK1, 5HTR1A/2A), and secondly, whether digit ratios mediate the relationship between genetic variation and sociosexuality. We demonstrate significant associations between AR, OPRM1 and AVPR1A and 2D:4D. Moreover, mediation analysis indicates that, in women, AR and OPRM1 variation drives digit ratios, which are related positively to impulsivity and, for OPRM1, negatively to romantic relationship quality. Although these findings are subject to multiple testing issues, this study provides preliminary evidence that in women genetic factors may affect both impulsivity and perceived relationship quality through influencing factors indexed by digit ratios.

The association between cortisol, oxytocin, and immune cell mitochondrial oxygen consumption in postpartum women with childhood maltreatment

Childhood maltreatment (CM) is associated with an increased risk for the development of psychiatric and somatic diseases in later life. Individual risk and resilience factors may, however, influence how deep psychological stress gets under the skin. We hypothesized that the stress-related hormone cortisol and the attachment-related hormone oxytocin constitute biological factors that might moderate the biological sequelae and long-term health outcomes associated with CM. As biological outcome, we thereby focused on immunocellular oxygen consumption, which we previously found to be increased with a higher severity of CM experiences. In a study cohort of N = 49 postpartum women, we investigated the interaction between CM experiences, serum cortisol and plasma oxytocin levels, and the cellular oxygen consumption of intact peripheral blood mononuclear cells (PBMC) by high-resolution respirometry. Regression analyses revealed a significant interaction between the severity of CM experiences and cortisol as well as oxytocin on cellular oxygen consumption of PBMC three months postpartum: higher cortisol levels were thereby associated with an increase in oxygen consumption related to basal mitochondrial respiration and ATP turnover, while oxygen consumption related to basal mitochondrial respiration and ATP turnover were reduced with higher oxytocin levels in individuals with higher CM severity. These associations were not seen among women with no or low CM experiences. Together, the results suggest that cortisol and oxytocin might be associated with opposite effects on CM-related alterations in the bioenergetic profile of peripheral immune cells.

The Influence of Genetic Variation on Social Disposition, Romantic Relationships and Social Networks: a Replication Study

OBJECTIVES

Sociality is underpinned by a variety of neurochemicals. We previously showed, in a large healthy Caucasian sample, that genes for different neurochemicals are typically associated with differing social domains (disposition, romantic relationships and networks). Here we seek to confirm the validity of these findings by asking whether they replicate in other population samples.

METHODS

We test for associations between the same 24 Single Nucleotide Polymorphisms (SNPs) and measures of sociality as previously, in two smaller independent samples: Caucasian individuals with histories of mental illness (subclinical sample) (N = 140), and non-Caucasian individuals (N = 66). We also combined the relevant SNPs and social measures into 18 distinct neurochemical/social domain categories to examine the distribution of significant associations across these.

RESULTS

In the subclinical Caucasian sample, we confirm previous associations between (i) specific oxytocin and dopamine receptor gene SNPs and sexual attitudes and behavior, and (ii) two SNPs associated with dopamine receptor 2 and feelings of inclusion in the local community. In the non-Caucasian sample, we replicate the previous association between an oxytocin receptor SNP and anxious attachment. More generally, chi-squared tests indicated that the distribution of significant associations for each neurochemical across the three social domains did not differ significantly between the original sample and either of the new samples, except for oxytocin in the non-Caucasian sample.

CONCLUSIONS

These results corroborate both the SNP-specific and broader neurochemical associations with particular facets of sociality in two new populations, thereby confirming the validity of the previous findings.

What has GWAS done for HLA and disease associations?

The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations. Another layer of complexity is provided to the region by the extreme structural variation and copy number variations. While the HLA-B gene has the highest number of alleles, the HLA-DR/DQ subregion is structurally most variable and shows the highest number of disease associations. Reliance on a single reference sequence has complicated the design, execution and analysis of GWAS for the MHC region and not infrequently, the MHC region has even been excluded from the analysis of GWAS data. Here, we contrast features of the MHC region with the rest of the genome and highlight its complexities, including its functional polymorphisms beyond those determined by single nucleotide polymorphisms or single amino acid residues. One of the several issues with customary GWAS analysis is that it does not address this additional layer of polymorphisms unique to the MHC region. We highlight alternative approaches that may assist with the analysis of GWAS data from the MHC region and unravel associations with all functional polymorphisms beyond single SNPs. We suggest that despite already showing the highest number of disease associations, the true extent of the involvement of the MHC region in disease genetics may not have been uncovered.

Genetic modulation of atrial fibrillation risk in a Hispanic/Latino cohort

Atrial fibrillation (AF) is the most prevalent cardiac rhythm disorder worldwide but the underlying genetic and molecular mechanisms and the response to therapies is not fully understood. Despite a greater burden of AF risk factors in Hispanics/Latinos the prevalence of AF remains low. Over the last decade, genome-wide association studies have identified numerous AF susceptibility loci in mostly whites of European descent. The goal of this study was to determine if the top 9 single nucleotide polymorphisms (SNPs) associated with AF in patients of European descent also increase susceptibility to AF in Hispanics/Latinos. AF cases were prospectively enrolled in the University of Illinois at Chicago (UIC) AF Registry and control subjects were identified from the UIC Cohort of Patients, Family and Friends. AF cases and controls were genotyped for 9 AF risk SNPs at chromosome 1q21: rs13376333, rs6666258; chr1q24: rs3903239; chr4q25: rs2200733; rs10033464; chr10q22: rs10824026; chr14q23: rs1152591; chr16q22: rs2106261 and rs7193343. The study sample consisted of 713 Hispanic/Latino subjects including 103 AF cases and 610 controls. Among the 8 AF risk SNPs genotyped, only rs10033464 SNP at chromosome (chr) 4q25 (near PITX2) was significantly associated with development of AF after multiple risk factor adjustment and multiple testing (adj. odds ratio [OR] 2.27, 95% confidence interval [CI] 1.31–3.94; P = 3.3 x 10⁻³). Furthermore, the association remained significant when the analysis was restricted to Hispanics of Mexican descent (adj. OR 2.32, 95% CI 1.35–3.99; P = 0.002. We confirm for the first time the association between a chromosome 4q25 SNP and increased susceptibility to AF in Hispanics/Latinos. While the underlying molecular mechanisms by which the chr4q25 SNP modulates AF risk remains unclear, this study supports a genetic basis for non-familial AF in patients of Hispanic descent.

Identification of Disease-Related Genes Using a Genome-Wide Association Study Approach

Genome-wide association studies (GWAS) provide a hypothesis-free approach to discover genetic variants contributing to the risk of a certain disease or disease-related trait. Ongoing efforts to annotate the human genome have helped to localize disease-causing variants and point to mechanisms by which genetic variants might exert functional effects. By integrating bioinformatics approaches with in vivo and in vitro genomic strategies to predict and subsequently validate the functional roles of GWAS-identified variants, disease-related pathways can be characterized, providing new possibilities for therapeutic intervention. Here, we describe a basic workflow, from sample preparation to data analysis, for performing a GWAS to identify disease genes. We also discuss resources for the annotation and interpretation of GWAS results.

A Randomized Controlled Clinical Trial Comparing Belatacept With Tacrolimus After De Novo Kidney Transplantation

BACKGROUND

Belatacept, an inhibitor of the CD28-CD80/86 costimulatory pathway, allows for calcineurin-inhibitor free immunosuppressive therapy in kidney transplantation but is associated with a higher acute rejection risk than ciclosporin. Thus far, no biomarker for belatacept-resistant rejection has been validated. In this randomized-controlled trial, acute rejection rate was compared between belatacept- and tacrolimus-treated patients and immunological biomarkers for acute rejection were investigated.

METHODS

Forty kidney transplant recipients were 1:1 randomized to belatacept or tacrolimus combined with basiliximab, mycophenolate mofetil, and prednisolone. The 1-year incidence of biopsy-proven acute rejection was monitored. Potential biomarkers, namely, CD8CD28, CD4CD57PD1, and CD8CD28 end-stage terminally differentiated memory T cells were measured pretransplantation and posttransplantation and correlated to rejection. Pharmacodynamic monitoring of belatacept was performed by measuring free CD86 on monocytes.

RESULTS

The rejection incidence was higher in belatacept-treated than tacrolimus-treated patients: 55% versus 10% (P = 0.006). All 3 graft losses, due to rejection, occurred in the belatacept group. Although 4 of 5 belatacept-treated patients with greater than 35 cells CD8CD28 end-stage terminally differentiated memory T cells/μL rejected, median pretransplant values of the biomarkers did not differ between belatacept-treated rejectors and nonrejectors. In univariable Cox regressions, the studied cell subsets were not associated with rejection-risk. CD86 molecules on circulating monocytes in belatacept-treated patients were saturated at all timepoints.

CONCLUSIONS

Belatacept-based immunosuppressive therapy resulted in higher and more severe acute rejection compared with tacrolimus-based therapy. This trial did not identify cellular biomarkers predictive of rejection. In addition, the CD28-CD80/86 costimulatory pathway appeared to be sufficiently blocked by belatacept and did not predict rejection.

Single nucleotide polymorphisms of autophagy-related 16-like 1 gene are associated with ankylosing spondylitis in females: a case-control study

AIMS

To investigate the associations of autophagy-related 16-like 1 (ATG16L1) gene single nucleotide polymorphisms (SNPs) with ankylosing spondylitis (AS) in a Chinese Han population.

METHODS

Six hundred and forty-nine AS patients from the First Affiliation Hospital of Anhui Medical University and 628 matched controls were selected. Genotyping for five SNPs in the ATG16L1 gene (rs4663421, rs2241880, rs4663396, rs6758317 and rs6431655) was performed using the improved multiplex ligase detection reaction (iMLDR) method. Haplotypes were built after linkage disequilibrium (LD) analysis. All analyses were stratified by gender.

RESULTS

Significant differences in the genotype frequencies at rs4663421 were found between female AS patients and female controls (P = 0.033). The frequencies of allele G of rs4663421 and allele C of rs6758317 were lower in AS patients than controls (odds ratio [OR] = 0.391, 95% CI = 0.175-0.876, P = 0.019; OR = 0.499, 95% CI = 0.263-0.949, P = 0.032, respectively) in females. However, no association remained significant after Bonferroni correction. rs4663396 and rs6758317 have been tested in high LD, and were used to construct three haplotypes: ht1 (CC), ht2 (TT) and ht3 (CT). The frequency of ht2 (TT) haplotype was higher in AS patients than controls (OR = 2.003, 95% CI = 1.053-3.808, P = 0.032) in females; similarly, no association existed after Bonferroni correction.

CONCLUSIONS

Two SNPs (rs4663421 and rs6758317) and the TT haplotype of the ATG16L1 gene are possibly associated with AS susceptibility in a Chinese Han female population.

Joint Analysis of SNP-SNP-Environment Interactions for Chronic Dialysis by an Improved Branch and Bound Algorithm

In previous studies, both single-nucleotide polymorphism (SNP)-SNP or gene-gene (G × G) interactions and SNP-environmental factor (G × E) interactions were reported to partially account for "missing" heritability. However, (G × G) × E interactions were less commonly addressed. The purpose of this study was to develop a novel strategy to evaluate possible (G × G) × E interactions in D-loop-based chronic dialysis association. Using values from our previously published data set (704 controls and 193 cases) of 77 D-loop SNPs and 7 environmental factors (coronary heart disease, hypertension, diabetes mellitus, triglyceride, cholesterol, blood thiol, and TBARS levels), we compared the performances of G, G × G, G × E, and (G × G) × E. We found that the interactions of four individual SNPs previously associated with a significantly high risk of chronic dialysis [odds ratio (OR) = 1.56-4.93] with environmental factors (G × E) increased the risk of chronic dialysis (maximum OR = 35.43). We then used an improved branch and bound algorithm to identify combinations of two to four SNPs that were most highly associated with chronic dialysis (OR = 9.27-34.39). When the interactions of the two- and three-SNP combinations with environmental factors were evaluated, we found that the (G × G) × E effects increased the risk of chronic dialysis (maximum OR = 8.32-57.54 and OR = 12.52-57.81, respectively; adjusted OR = 8.67-81.81 and OR = 12.29-81.95, respectively). Taken together, the (G × G) × E interactions identified chronic dialysis-associated SNPs that would not have been found using G × G or G × E interactions, suggesting that (G × G) × E interactions may be helpful to solve the problems of missing heritability in association studies.

Association of candidate gene polymorphisms with clinical subtypes of preterm birth in a Latin American population

BackgroundPreterm birth (PTB) is the leading cause of neonatal mortality and morbidity. PTB is often classified according to clinical presentation as follows: idiopathic (PTB-I), preterm premature rupture of membranes (PTB-PPROM), and medically induced (PTB-M). The aim of this study was to evaluate the associations between specific candidate genes and clinical subtypes of PTB.MethodsTwenty-four single-nucleotide polymorphisms (SNPs) were genotyped in 18 candidate genes in 709 infant triads. Of them, 243 were PTB-I, 256 were PTB-PPROM, and 210 were PTB-M. These data were analyzed with a Family-Based Association.ResultsPTB was nominally associated with rs2272365 in PON1, rs883319 in KCNN3, rs4458044 in CRHR1, and rs610277 in F3. Regarding clinical subtypes analysis, three SNPs were associated with PTB-I (rs2272365 in PON1, rs10178458 in COL4A3, and rs4458044 in CRHR1), rs610277 in F3 was associated with PTB-PPROM, and rs883319 in KCNN3 and rs610277 in F3 were associated with PTB-M.ConclusionOur study identified polymorphisms potentially associated with specific clinical subtypes of PTB in this Latin American population. These results could suggest a specific role of such genes in the mechanisms involved in each clinical subtype. Further studies are required to confirm our results and to determine the role of these genes in the pathophysiology of clinical subtypes.

Vincristine-induced peripheral neuropathy in children with cancer: A systematic review

Vincristine-induced peripheral neuropathy (VIPN) is a dose-limiting side effect of vincristine (VCR) treatment in children, leading to diminished quality of life. Much remains unknown about the underlying mechanisms of VIPN. This review systematically summarizes the available literature concerning contributing factors of VIPN development in children. Studied factors include patient characteristics, VCR dose, administration method, pharmacokinetics, and genetic factors. Furthermore, this review reports on currently available tools to assess VIPN in children. In total, twenty-eight publications were included. Results indicate that Caucasian race, higher VCR dose, older age and low clearance negatively influence VIPN, although results regarding the latter two factors were rather conflicting. Moreover, genetic pathways influencing VIPN were identified. Furthermore, the studied tools to assess VIPN seriously impairs comparability across study results. Studying the factors and their interactions that seem to influence VIPN in children, should aid in personalized VCR treatment, thereby increasing VCR effectiveness while minimizing toxicity.

The allele combinations of three loci based on, liver, stomach cancers, hematencephalon, COPD and normal population: A preliminary study

The purpose of this study was to examine the specific allele combinations of three loci connected with the liver cancers, stomach cancers, hematencephalon and patients with chronic obstructive pulmonary disease (COPD) and to explore the feasibility of the research methods. We explored different mathematical methods for statistical analyses to assess the association between the genotype and phenotype. At the same time we still analyses the statistical results of allele combinations of three loci by difference value method and ratio method. All the DNA blood samples were collected from patients with 50 liver cancers, 75 stomach cancers, 50 hematencephalon, 72 COPD and 200 normal populations. All the samples were from Chinese. Alleles from short tandem repeat (STR) loci were determined using the STR Profiler plus PCR amplification kit (15 STR loci). Previous research was based on combinations of single-locus alleles, and combinations of cross-loci (two loci) alleles. Allele combinations of three loci were obtained by computer counting and stronger genetic signal was obtained. The methods of allele combinations of three loci can help to identify the statistically significant differences of allele combinations between liver cancers, stomach cancers, patients with hematencephalon, COPD and the normal population. The probability of illness followed different rules and had apparent specificity. This method can be extended to other diseases and provide reference for early clinical diagnosis.

Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses

Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.

A novel block at chromosome 12q24.1 is associated with coronary artery disease in Han Chinese populations

OBJECTIVE

The aim of this study was to refine the chromosomal region 12q24.1 associated with coronary artery disease in Han Chinese populations.

METHODS AND RESULTS

Twenty tagging single nucleotide polymorphisms covering 1.2 Mb of chromosomal 12q24.1 were selected and genotyped in three geographically isolated case-control populations consisting of 7076 coronary artery disease (CAD) patients and non-CAD participants. In addition to replication of the previous block (block 1), we identified a novel block (block 2) associated with CAD. In a combined analysis, the odds ratio (95% confidence interval, permuted P value) were 0.79 (0.72-0.86, 8.358×10) and 1.24 (1.13-1.36, 2.576×10) for haplotypes ATGGG and GCACA in block 1 and 1.22 (1.14-1.30, 6.484×10) and 0.82 (0.77-0.88, 6.484×10) for haplotypes GA and AG in block 2, respectively. Protective alleles of two index single nucleotide polymorphisms decreased the expression of NAA25 (P=0.034), but did not alter the expression of other genes within block 2.

CONCLUSION

We identified a novel block associated with CAD at chromosomal 12q24.

Quality of life effects of androgen deprivation therapy in a prostate cancer cohort in New Zealand: can we minimize effects using a stratification based on the aldo-keto reductase family 1, member C3 rs12529 gene polymorphism?

BACKGROUND

Androgen deprivation therapy (ADT) is an effective palliation treatment in men with advanced prostate cancer (PC). However, ADT has well documented side effects that could alter the patient's health-related quality of life (HRQoL). The current study aims to test whether a genetic stratification could provide better knowledge for optimising ADT options to minimize HRQoL effects.

METHODS

A cohort of 206 PC survivors (75 treated with and 131 without ADT) was recruited with written consent to collect patient characteristics, clinical data and HRQoL data related to PC management. The primary outcomes were the percentage scores under each HRQoL subscale assessed using the European Organisation for Research and Treatment of Cancer Quality of Life questionnaires (QLQ-C30 and PR25) and the Depression Anxiety Stress Scales developed by the University of Melbourne, Australia. Genotyping of these men was carried out for the aldo-keto reductase family 1, member C3 (AKR1C3) rs12529 single nucleotide polymorphism (SNP). Analysis of HRQoL scores were carried out against ADT duration and in association with the AKR1C3 rs12529 SNP using the generalised linear model. P-values <0 · 05 were considered significant, and were further tested for restriction with Bonferroni correction.

RESULTS

Increase in hormone treatment-related effects were recorded with long-term ADT compared to no ADT. The C and G allele frequencies of the AKR1C3rs12529 SNP were 53·4 % and 46·6 % respectively. Hormone treatment-related symptoms showed an increase with ADT when associated with the AKR1C3 rs12529 G allele. Meanwhile, decreasing trends on cancer-specific symptoms and increased sexual interest were recorded with no ADT when associated with the AKR1C3 rs12529 G allele and reverse trends with the C allele. As higher incidence of cancer-specific symptoms relate to cancer retention it is possible that associated with the C allele there could be higher incidence of unresolved cancers under no ADT options.

CONCLUSIONS

If these findings can be reproduced in larger homogeneous cohorts, a genetic stratification based on the AKR1C3 rs12529 SNP, can minimize ADT-related HRQoL effects in PC patients. Our data additionally show that with this stratification it could also be possible to identify men needing ADT for better oncological advantage.

CUSTOM-SEQ: a prototype for oncology rapid learning in a comprehensive EHR environment

BACKGROUND

As targeted cancer therapies and molecular profiling become widespread, the era of "precision oncology" is at hand. However, cancer genomes are complex, making mutation-specific outcomes difficult to track. We created a proof-of-principle, CUSTOM-SEQ: Continuously Updating System for Tracking Outcome by Mutation, to Support Evidence-based Querying, to automatically calculate and display mutation-specific survival statistics from electronic health record data.

METHODS

Patients with cancer genotyping were included, and clinical data was extracted through a variety of algorithms. Results were refreshed regularly and injected into a standard reporting platform. Significant results were highlighted for visual cueing. A subset was additionally stratified by stage, smoking status, and treatment exposure.

RESULTS

By August 2015, 4310 patients with a median follow-up of 17 months had sufficient data for survival calculation. As expected, epidermal growth factor receptor (EGFR) mutations in lung cancer were associated with superior overall survival, hazard ratio (HR) = 0.53 (P < .001), validating the approach. Guanine nucleotide binding protein (G protein), q polypeptide (GNAQ) mutations in melanoma were associated with inferior overall survival, a novel finding (HR = 3.42, P < .001). Smoking status was not prognostic for epidermal growth factor receptor-mutated lung cancer patients, who also lived significantly longer than their counterparts, even with advanced disease (HR = 0.54, P = .001).

INTERPRETATION

CUSTOM-SEQ represents a novel rapid learning system for a precision oncology environment. Retrospective studies are often limited by study of specific time periods and can lead to incomplete conclusions. Because data is continuously updated in CUSTOM-SEQ, the evidence base is constantly growing. Future work will allow users to interactively explore populations by demographics and treatment exposure, in order to further investigate significant mutation-specific signals.

Screening of intracerebral hemorrhage associated allele combinations at different loci using a novel association analysis

BACKGROUND

Genetic research has progressed along with scientific and technological developments. However, it is difficult to identify frequency differences in the allele combination at cross-loci.

OBJECTIVE

The purpose of this study was to examine the relationship between the presence of specific allele combinations of short tandem repeat (STR) loci and the onset of intracerebral hemorrhage (ICH) using a novel methodology.

METHODS

DNA samples were collected from patients with ICH, who were adult population. There were a total of 51 Chinese patients (102 chromosomes), comprising 30 males and 21 females. Alleles from short tandem repeat (STR) loci were determined using the STR Profiler Plus PCR amplification kit (15 STR loci). Statistically significant differences between observed and expected frequencies of allele combinations were identified. To further determine allele combinations related to the disease, analyses of patient age at disease onset for those carrying a specific allele combination were conducted. Finally, cross-validation of the two sets of analytical results was carried out.

RESULTS

A total of 1550 pairwise combinations were obtained by computer counting, of which eight pairs of alleles showed significant differences between the observed and expected frequencies (p<0.05, from 0.006 to 0.042). The p value for the cross-validation analysis was less than 0.05 for two pairs of alleles (D13S317-11 and vWA-17, p=0.021; D7S820-13 and D2S1338-18, p=0.023).

CONCLUSIONS

The study identified each population had a unique gene distribution and that distribution followed certain rules. ICH onset may be associated with this allele combinations (D13S317-11 and vWA-17; D7S820-13 and D2S1338-18). The new methodology used in this study could enable additional discoveries pertaining to the relationship between specific allele combinations at different loci and the onset of complex diseases.

Identification of Associations Between Prescribed Medications and Cancer: A Nationwide Screening Study

Purpose

We present a systematic screening for identifying associations between prescribed drugs and cancer risk using the high quality Danish nationwide health registries.

Methods

We identified all patients (cases) with incident cancer in Denmark during 2000–2012 (n = 278,485) and matched each case to 10 controls. Complete prescription histories since 1995 were extracted. Applying a two-phased case–control approach, we first identified drug classes or single drugs associated with an increased or decreased risk of 99 different cancer types, and further evaluated potential associations by examining specificity and dose–response patterns.

Findings

22,125 drug–cancer pairs underwent evaluation in the first phase. Of 4561 initial signals (i.e., drug–cancer associations), 3541 (78%) failed to meet requirements for dose–response patterns and specificity, leaving 1020 eligible signals. Of these, 510 signals involved the use of single drugs, and 33% (166 signals) and 67% (344 signals) suggested a reduced or an increased cancer risk, respectively. While a large proportion of the signals were attributable to the underlying conditions being treated, our algorithm successfully identified well-established associations, as well as several new signals that deserve further investigation.

Conclusion

Our results provide the basis for future targeted studies of single associations to capture novel carcinogenic or chemopreventive effects of prescription drugs.

•

We conducted a nationwide register-based screening study aimed at identifying potential drug–cancer associations.

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Screening initiatives using registry data may serve as an important tool for identification of drug–cancer associations.

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Future research should address the signals provided by our study, i.e. in studies of the single putative associations.

The use of prescription drugs may influence the risk of developing cancer. In this study, we sought to identify such effects by combining data from Danish nationwide health care registries on drug use and cancer occurrence. We compared drug use among 278,485 cancer patients to use among cancer-free control individuals. Thereby, we identified 1020 putative drug–cancer associations. Future research should address the signals provided by our study, either as studies focusing on single associations or as a replication of our study using other data sources.

Inter and intra-population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus, a rare freshwater fish in Scotland

This study revealed between-lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (FST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common-garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (FST = 0·001-0·024) and evidence of private alleles related to the basin structure of the lake. Within-lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.

Do reproduction and parenting influence personality traits? Insights from threespine stickleback

Although one of the hallmarks of personality traits is their consistency over time, we might expect personality traits to change during life history shifts. Becoming a parent is a major life history event, when individuals undergo dramatic behavioural and physiological changes. Here we employ a longitudinal experiment to ask whether personality changes in response to the experience of parenting in male threespine sticklebacks, Gasterosteus aculeatus. Life history theory predicts that males should be less risk averse after successfully parenting, and the neuroendocrinology of parenting suggests that parenting could reorganize the hormonal landscape and behaviour of fathers. We randomly assigned males to either an experimental group (reproduced and parented) or a control group (did not reproduce and parent), and repeatedly measured a personality trait ('boldness') and 11-ketotestosterone levels (11-kT, the major androgen in fishes) in individual males. In the control group, males became bolder over time. However, in the experimental group, boldness did not change. Furthermore, 11-kT changed dramatically in the experimental group, and changes in 11-kT in parents were associated with boldness after parenting ceased. Our study is one of the first to assess proximate and ultimate explanations for changes in personality as a function of reproduction and parenting.

Genome-Wide Association Studies and Liver Disease

Sequencing of the human genome has opened up many opportunities to learn about our own genetic susceptibilities to disease. In this Foreword to this issue of Seminars in Liver Disease, I provide some required background to understanding genome-wide association analyses in general, including a list of terms (Table 1) often used in such studies. Five areas of particular significance are then reviewed in detail in the articles that follow.

Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese

Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal-conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified.

Statistical determination of rainfall-runoff erosivity indices for single storms in the Chinese Loess Plateau

Correlation analysis is popular in erosion- or earth-related studies, however, few studies compare correlations on a basis of statistical testing, which should be conducted to determine the statistical significance of the observed sample difference. This study aims to statistically determine the erosivity index of single storms, which requires comparison of a large number of dependent correlations between rainfall-runoff factors and soil loss, in the Chinese Loess Plateau. Data observed at four gauging stations and five runoff experimental plots were presented. Based on the Meng’s tests, which is widely used for comparing correlations between a dependent variable and a set of independent variables, two methods were proposed. The first method removes factors that are poorly correlated with soil loss from consideration in a stepwise way, while the second method performs pairwise comparisons that are adjusted using the Bonferroni correction. Among 12 rainfall factors, I₃₀ (the maximum 30-minute rainfall intensity) has been suggested for use as the rainfall erosivity index, although I₃₀ is equally correlated with soil loss as factors of I₂₀, EI₁₀ (the product of the rainfall kinetic energy, E, and I₁₀), EI₂₀ and EI₃₀ are. Runoff depth (total runoff volume normalized to drainage area) is more correlated with soil loss than all other examined rainfall-runoff factors, including I₃₀, peak discharge and many combined factors. Moreover, sediment concentrations of major sediment-producing events are independent of all examined rainfall-runoff factors. As a result, introducing additional factors adds little to the prediction accuracy of the single factor of runoff depth. Hence, runoff depth should be the best erosivity index at scales from plots to watersheds. Our findings can facilitate predictions of soil erosion in the Loess Plateau. Our methods provide a valuable tool while determining the predictor among a number of variables in terms of correlations.

Distributions of allele combination in single and cross loci among patients with several kinds of chronic diseases and the normal population

Genetic research has progressed along with scientific and technological developments. However, it is difficult to identify frequency differences in a particular allele distribution at a single locus. Such differences can be identified by examining the allele combination distribution. We explored different mathematical methods for statistical analyses to assess the association between the genotype and phenotype. We investigated the frequency distributions of alleles, combinations of single-locus genes, and combinations of cross-loci genes at 15 loci using 447 blood samples of 200 normal subjects, 72 patients with chronic obstructive pulmonary resistance, 50 liver cancers, 75 stomach cancers and 50 hematencephalon and identified each population as having a unique gene distribution and that the distribution followed certain rules. The probability of illness followed different rules and had apparent specificity. Differences obtained using statistics of combinations of cross-loci genes are superior to single-locus gene statistics, and combinations of single-locus gene statistics are better than allelic statistics.

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates' recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X.

Population genetics of neotropical Culex quinquefasciatus (Diptera: Culicidae)

Background

Culex quinquefasciatus mosquitoes can be found in almost every major city of Brazil and are vectors of filariasis and several arboviruses. Microsatellite markers have been widely used to uncover the genetic structure of various groups of insect populations. The aim of this study was to glimpse the genetic structure of Cx. quinquefasciatus in Brazil.

Methods

Nine populations were sampled across Brazil (one of them from a laboratory colony - COL) and another one from Argentina and process regarding the variability of six microsatellite loci.

Results

The analyzed loci revealed moderate population genetic structure (mean F_st = 0.12). Dendrograms of genetic distances evidenced two major population clusters, respectively corresponding to the northern and southern populations. The hybrid population Cx. pipiens/quinquefasciatus (from La Plata, Argentina) and the colony population fell outside the major clusters. Those clusters were substructured and there was a significant correlation between genetic and geographic distances and environmental variables (r = 0.51; p > 0.001 and r = 0.46; p > 0.004).

Conclusions

Multilocus cluster Bayesian analysis confirmed that populations are mutually distinct, and the set of results point to genetic differences among populations. The presumable low gene flow among them may be due to the large geographic distances (>1000 km) and to the environmental heterogeneity of the sampled areas. The genetic structure observed in this study may lead to the best understanding of Cx. quinquefasciatus demographical diversity as well as their genetic variations patterns in Brazil so far unknown.

Paternal programming in sticklebacks

In a wide range of organisms, including humans, mothers can influence offspring via the care they provide. Comparatively little is known about the effects of fathering on offspring. Here, we test the hypothesis that fathers are capable of programming their offspring for the type of environment they are likely to encounter. Male threespine sticklebacks, Gasterosteus aculeatus, were either exposed to predation risk while fathering or not. Fathers altered their paternal behaviour when exposed to predation risk, and consequently produced adult offspring with phenotypes associated with strong predation pressure (smaller size, reduced body condition, reduced behavioural activity). Moreover, more attentive fathers produced offspring that showed stronger antipredator responses. These results are consistent with behaviourally mediated paternal programming: fathers can alter offspring phenotypes to match their future environment and influence offspring traits well into adulthood.