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606 results for “association genetics”
Data associated with: Minor genetic consequences of a major mass mortality: Short-term effects in Pisaster ochraceus
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Genetic diversity of Shaw's agave and soil associated microbes in Southern California preserve
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Data for "Accurate Estimation of Marker-Associated Genetic Variance and Heritability in Complex Trait Analyses"
<p>This data is associated with the manuscript titled "Accurate Estimation of Marker-Associated Genetic Variance and Heritability in Complex Trait Analyses".</p> <p>9 files are contained. These files contain the summary statistics from the linear mixed model analyses in the simulations</p> <p>data_fig1a - all data for recreating Figure 1A</p> <p>data_fig1b - all data for recreating Figure 1B</p> <p>data_fig1c - all data for recreating Figure 1C</p> <p>data_fig1d - all data for recreating Figure 1D</p> <p>data_fig1e - all data for recreating Figure 1E</p> <p>data_fig1f - all data for recreating Figure 1F</p> <p>data_fig2 - all data for recreating Figure 2</p> <p>data_fig3 - all data for recreating Figure 3</p> <p>data_fig4 - all data for recreating Figure 4</p>
Data from: Adaptation via pleiotropy and linkage: association mapping reveals a complex genetic architecture within the stickleback Eda locus
Genomic mapping of the loci associated with phenotypic evolution has revealed genomic "hotspots", or regions of the genome that control multiple phenotypic traits. This clustering of loci has important implications for the speed and maintenance of adaptation and could be due to pleiotropic effects of a single mutation or tight genetic linkage of multiple causative mutations affecting different traits. The threespine stickleback (<i>Gasterosteus aculeatus</i>) is a powerful model for the study of adaptive evolution because the marine ecotype has repeatedly adapted to freshwater environments across the northern hemisphere in the last 12,000 years. Freshwater ecotypes have repeatedly fixed a 16 kilobase haplotype on chromosome IV that contains Ectodysplasin (<i>Eda</i>), a gene known to affect multiple traits, including defensive armor plates, lateral line sensory hair cells, and schooling behavior. Many additional traits have previously been mapped to a larger region of chromosome IV that encompasses the <i>Eda</i> freshwater haplotype. To identify which of these traits specifically map to this adaptive haplotype, we made crosses of rare marine fish heterozygous for the freshwater haplotype in an otherwise marine genetic background. Further, we performed fine-scale association mapping in a fully interbreeding, polymorphic population of freshwater stickleback to disentangle the effects of pleiotropy and linkage on the phenotypes affected by this haplotype. Although we find evidence that linked mutations have small effects on a few phenotypes, a small 1.4 kb region within the first intron of <i>Eda</i> has large effects on three phenotypic traits: lateral plate count, and both the number and patterning of the posterior lateral line neuromasts. Thus, the <i>Eda</i> haplotype is a hotspot of adaptation in stickleback due to both a small, pleiotropic region affecting multiple traits as well as multiple linked mutations affecting additional traits.
Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations
<p>Data set linked to the paper, "Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations". Pre-print of the paper is here: <a href="https://doi.org/10.1101/2020.06.16.146803">https://doi.org/10.1101/2020.06.16.146803</a>.</p> <p> </p> <p>cross_cancer_sum_stats.txt.gz contains summary genome-wide association statistics for susceptibility to single cancers (breast (BR), prostate (PR), ovarian (OV), endometrial (EN), estrogen receptor (ER)-positive breast (POS), ER-negative breast (NEG), and high-grade serous ovarian (HGS) cancers) and from the cross-cancer meta-analysis (main [main] and subtype-focused [sub]). EA in the header refers to the effect allele, OA is the other allele, EAF is the effect allele frequency in the largest of the single cancer data sets (BR), IMPR2 is the imputation quality in the largest of the single cancer data sets (BR), SE is the standard error, PVAL is the P-value, RE2Cs1 is the RE2C statistic mean effect part, RE2Cs2 is the RE2C statistic heterogeneity part, RE2Cp* is the RE2C* P-value. More on RE2Cp* can be found here: <a href="http://software.buhmhan.com/RE2C/index.php?mid=contact&act=dispBoardWrite">http://software.buhmhan.com/RE2C/index.php?mid=contact&act=dispBoardWrite</a> and in <a href="https://academic.oup.com/bioinformatics/article/33/14/i379/3953957">https://academic.oup.com/bioinformatics/article/33/14/i379/3953957</a> SNP names in cross_cancer_sum_stats.txt.gz include the chromosome and build 37 position.</p> <p> </p> <p>main_tetrachoric_corr_matrix.txt and subtype_tetrachoric_corr_matrix.txt provide the tetrachoric correlation matrices used in the main and subtype-focused meta-analyses. These were also used to specify the cryptic.cor argument of the exh.abf function of MetABF. More on MetABF can be found here: <a href="https://github.com/trochet/metabf">https://github.com/trochet/metabf</a> and in <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/gepi.22202">https://onlinelibrary.wiley.com/doi/abs/10.1002/gepi.22202</a></p> <p> </p> <p>prior_sigmas_for_metabf.txt contains the values used to specify the prior.sigma argument of the exh.abf function in MetABF.</p> <p> </p> <p>The breast cancer data used are described in <a href="https://pubmed.ncbi.nlm.nih.gov/29059683/"><strong>PMID 29059683</strong></a> and can be downloaded from <a href="http://bcac.ccge.medschl.cam.ac.uk/bcacdata/oncoarray/oncoarray-and-combined-summary-result/gwas- summary-results-breast-cancer-risk-2017/">http://bcac.ccge.medschl.cam.ac.uk/bcacdata/oncoarray/oncoarray-and-combined-summary-result/gwas- summary-results-breast-cancer-risk-2017/</a> (this link also includes acknowledgements). The prostate cancer data are described in <a href="https://pubmed.ncbi.nlm.nih.gov/29892016/"><strong>PMID 29892016</strong></a> and can be downloaded from: <a href="http://practical.icr.ac.uk/blog/?page_id=8164">http://practical.icr.ac.uk/blog/?page_id=8164</a> (this link also includes acknowledgements). The ovarian cancer data used are described in <a href="https://pubmed.ncbi.nlm.nih.gov/28346442/"><strong>PMID 28346442</strong></a> and can be downloaded from <a href="https://www.ebi.ac.uk/gwas/studies/GCST004415">https://www.ebi.ac.uk/gwas/studies/GCST004415</a>. The endometrial cancer data are described in <a href="https://pubmed.ncbi.nlm.nih.gov/30093612/"><strong>PMID 30093612</strong></a> and can be downloaded from <a href="https://www.ebi.ac.uk/gwas/studies/GCST006464">https://www.ebi.ac.uk/gwas/studies/GCST006464</a>. These links point to the same data that form the basis of the cross_cancer_sum_stats.txt.gz file.</p> <p> </p> <p><strong>The sample size and precision of the data presented should preclude identification of any individual study participant. However, in downloading these data, you undertake not to attempt to identify individual study participant and not to re-post these data to a third-party website. Please cite the PMIDs highlighted above along with the appropriate acknowledements if you use the cross_cancer_sum_stats.txt.gz file.</strong></p> <p> </p> <p>If you have any questions about this repository, please email Siddhartha Kar at siddhartha dot kar at bristol dot ac dot uk</p>
Gene flow and climate-associated genetic variation in a vagile habitat specialist
<p>Previous work in landscape genetics suggests that geographic isolation is of greater importance to genetic divergence than variation in environmental conditions. This is intuitive when configurations of suitable habitat are the dominant factor limiting dispersal and gene flow, but has not been thoroughly examined for habitat specialists with strong dispersal capability. Here, we evaluate the effects of geographic and environmental isolation on genetic divergence in a vagile invertebrate with high habitat specificity and a discrete dispersal life stage: Dod's Old World swallowtail butterfly, <i>Papilio machaon dodi</i>. In Canada, <i>P. m. dodi </i>are generally restricted to eroding habitat along major river valleys where their larval host plant occurs. A series of causal and linear mixed effects models indicate that divergence of genome-wide single nucleotide polymorphisms is best explained by a combination of environmental isolation (variation in summer temperatures) and geographic isolation (Euclidean distance). Interestingly, least-cost path and circuit distances through a resistance surface parameterized as the inverse of habitat suitability were not supported. This suggests that, although habitat associations of many butterflies are specific due to reproductive requirements, habitat suitability and landscape permeability are not equivalent concepts due to considerable adult vagility. We infer that divergent selection related to variation in summer temperatures has produced two genetic clusters within <i>P. m. dodi</i>, differing in voltinism and diapause propensity. Within the next century, temperatures are predicted to rise by amounts greater than the present-day difference between regions of genetic clusters, potentially affecting the persistence of the northern cluster under continued climate change.</p>
Association of common genetic variants with brain microbleeds: A genome-wide association study
<p><strong>Objective:</strong> To identify common genetic variants associated with the presence of brain microbleeds (BMB).</p> <p><strong>Methods:</strong> We performed genome-wide association studies in 11 population-based cohort studies and 3 case-control or case-only stroke cohorts. Genotypes were imputed to the Haplotype Reference Consortium or 1000 Genomes reference panel. BMB were rated on susceptibility-weighted or T2*-weighted gradient echo magnetic resonance imaging sequences, and further classified as lobar, or mixed (including strictly deep and infratentorial, possibly with lobar BMB). In a subset, we assessed the effects of <em>APOE</em> ε2 and ε4 alleles on BMB counts. We also related previously identified cerebral small vessel disease variants to BMB.</p> <p><strong>Results: </strong>BMB were detected in 3,556 of the 25,862 participants, of which 2,179 were strictly lobar and 1,293 mixed. One locus in the <em>APOE</em> region reached genome-wide significance for its association with BMB (lead SNP rs769449; OR<sub>any BMB</sub> (95% CI)=1.33 (1.21-1.45); p=2.5x10-10). <em>APOE</em> ε4 alleles were associated with strictly lobar (OR (95% CI)=1.34 (1.19- 1.50); p=1.0x10-6) but not with mixed BMB counts (OR (95% CI)=1.04 (0.86-1.25); p=0.68). <em>APOE</em> ε2 alleles did not show associations with BMB counts. Variants previously related to deep intracerebral hemorrhage and lacunar stroke, and a risk score of cerebral white matter hyperintensity variants, were associated with BMB.</p> <p><strong>Conclusions: </strong>Genetic variants in the <em>APOE</em> region are associated with the presence of BMB, most likely due to the <em>APOE</em> ε4 allele count related to a higher number of strictly lobar BMB. Genetic predisposition to small vessel disease confers risk of BMB, indicating genetic overlap with other cerebral small vessel disease markers.</p>
Data from: Effects of parasitic sex-ratio distorters on host genetic structure in the Armadillidium vulgare-Wolbachia association
In the pill bug Armadillidium vulgare (Crustacea, Oniscidea) Wolbachia facilitates its spread through vertical transmission via the eggs by inducing feminization of genetic males. The spread of feminizing Wolbachia within and across populations is therefore expected to influence mtDNA genetic structure by hitchhiking. To test this hypothesis, we analysed nuclear and mtDNA genetic structure, and Wolbachia prevalence in 13 populations of the pill bug host. Wolbachia prevalence (ranging from 0 to 100% of sampled females) was highly variable among populations. All three Wolbachia strains previously observed in A. vulgare were present (wVulC, wVulM and wVulP) with wVulC being the most prevalent (9 out of 13 populations). The host showed a genetic structure on five microsatellite loci that is compatible with isolation by distance. The strong genetic structure observed on host mtDNA was correlated to Wolbachia prevalence: three mitotypes were in strong linkage disequilibrium with the three strains of Wolbachia. Neutrality tests showed that the mtDNA polymorphism is not neutral and we thus suggest that this unusual pattern of mtDNA polymorphism found in A. vulgare was due to Wolbachia.
Data from: Local genetic structure in the critically endangered, cave-associated perennial herb Primulina tabacum (Gesneriaceae)
The local spatial genetic structures of cave-associated plants are seldom studied. Given that these plants are mainly confined to small areas in and around the entrances of caves, we hypothesized that they might lack genetic structures at local scales. To test this hypothesis, we sampled two large populations (named D and T) of a critically endangered perennial herb, Primulina tabacum, which is endemic to karst caves in southern China. We analysed nine microsatellite loci and sequenced four chloroplast DNA (cpDNA) intergenic spacer regions to study the genetic diversity and structure within and between both populations. Both populations have distinct genetic characteristics. Samples from two subpopulations in population D showed considerable genetic divergence. This is not consistent with the hypothesis that P. tabacum has a weak genetic structure at a local scale. However, 94% of the individuals in population T shared the same multilocus genotype, which indicates little genetic structure within this population. The contributions of seed flow, pollen flow and (sub)population history to the genetic diversity and structure in each and both populations are discussed. Our study is the first to investigate local genetic diversity and structure in a cave-associated plant, and provides valuable information for the sustainable conservation of such species.
Data from: Genetic architecture of traits associated with reproductive barriers in Silene: coupling, sex chromosomes and variation
The evolution of reproductive barriers and their underlying genetic architecture is of central importance for the formation of new species. Reproductive barriers can be controlled either by few large-effect loci suggesting strong selection on key traits, or by many small-effect loci, consistent with gradual divergence or with selection on polygenic or multiple traits. Genetic coupling between reproductive barrier loci further promotes divergence, particularly divergence with ongoing gene flow. In this study, we investigated the genetic architectures of ten morphological, phenological and life history traits associated with reproductive barriers between the hybridizing sister species Silene dioica and S. latifolia; both are dioecious with XY sex determination. We used quantitative trait locus (QTL) mapping in two reciprocal F2 crosses. One to six QTLs per trait, including 9 major QTLs (PVE > 20%) were detected, in total, on 11 of 12 linkage groups. We found strong evidence for coupling of QTLs for uncorrelated traits. QTL clusters occurred both on autosomes and on the sex chromosomes. Unexpectedly, QTLs detected in the two F2 crosses differed largely, despite limited phenotypic differences between them and sufficient statistical power. The widely dispersed genetic architectures of traits associated with reproductive barriers suggest gradual divergence or multifarious selection and coupling of the underlying QTLs likely promoted divergence with gene flow in this system. The low congruence of QTLs between the two crosses further points to variable and possibly redundant genetic architectures of traits associated with reproductive barriers, with important implications for the evolutionary dynamics of divergence and speciation.
Data from: Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice
Manual phenotyping of rice tillers is time consuming and labor intensive and lags behind the rapid development of rice functional genomics. Thus, automated, non-destructive phenotyping of rice tiller traits at a high spatial resolution and high-throughput for large-scale assessment of rice accessions is urgently needed. In this study, we developed a high-throughput micro-CT-RGB (HCR) imaging system to non-destructively extract 730 traits from 234 rice accessions at 9 time points. We could explain 30% of the grain yield variance from 2 tiller traits assessed in the early growth stages. A total of 402 significantly associated loci were identified by GWAS, and dynamic and static genetic components were found across the nine time points. A major locus associated with tiller angle was detected at nine time points, which contained a major gene TAC1. Significant variants associated with tiller angle were enriched in the 3'-UTR of TAC1. Three haplotypes for the gene were found and rice accessions containing haplotype H3 displayed much smaller tiller angles. Further, we found two loci contained associations with both vigor-related HCR traits and yield. The superior alleles would be beneficial for breeding of high yield and dense planting.
Data from: Genome-wide association analysis for blood lipid traits measured in three pig populations revealed a substantial level of genetic heterogeneity
Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS) in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC) for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption.
Data from: Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia.
Conservation of top predators has been emphasised as essential in an ecosystem due to their role in trophic chain regulation. Optimization of conservation strategies for these endangered marine top predators requires direct estimates of breeding patterns and connectivity, which are essential to understand their population dynamics. While there have been some attempts to investigate breeding patterns of reef sharks from litter reconstruction using molecular analyses, direct fine-scale migrations of female sharks for parturition as well as connectivity at a medium scale, such as between islands, remain mostly unknown. We used microsatellite DNA markers and a likelihood-based parentage analysis to determine breeding patterns of female blacktip reef sharks in Moorea (Society Islands, French Polynesia). Such an approach demonstrates that while most females gave birth at their home island, some migrated to specific nursery areas outside their home range, sometimes going to another island (up to 50 km across deep ocean). Analysis also revealed that females migrated to the same nursery on every birthing event. Many offspring showed a high level of inbreeding indicating an overall reduced population size, restricted movements and dispersal, or specific mating behaviour. Females represent the vectors that transport the genes at nursery grounds, and their fidelity should thus define reproductive units. As females seem to be philopatric, males could be the ones dispersing genes between metapopulations. These results highlight the need for conservation of coastal zones where female reef sharks seems to exhibit philopatry during the breeding season.
Data from: Genetic variation and association mapping for 12 agronomic traits in indica rice
Background: Increasing rice (Oryza sativa L.) yield is a crucial challenge for modern agriculture. The ideal plant architecture is considered to be critical to enhance rice yield. Elite plant morphological traits should include compact plant type, short stature, few unproductive tillers, thick and sturdy stems and erect leaves. To reveal the genetic variations of important morphological traits, 523 germplasm accessions were genotyped using the Illumina custom-designed array containing 5,291 single nucleotide polymorphisms (SNPs) and phenotyped in two independent environments. Genome-wide association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Results: In total, 126 and 172 significant loci were identified and these loci explained an average of 34.45 % and 39.09 % of the phenotypic variance in two environments, respectively, and 16 of 298 (~5.37 %) loci were detected across the two environments. For the 16 loci, 423 candidate genes were predicted in a 200-kb region (±100 kb of the peak SNP). Expression-level analyses identified four candidate genes as the most promising regulators of tiller angle. Known (NAL1 and Rc) and new significant loci showed pleiotropy and gene linkage. In addition, a long genome region covering ~1.6 Mb on chromosome 11 was identified, which may be critical for rice leaf architecture because of a high association with flag leaf length and the ratio of flag leaf length and width. The pyramid effect of the elite alleles indicated that these significant loci could be beneficial for rice plant architecture improvements in the future. Finally, 37 elite varieties were chosen as breeding donors for further rice plant architectural modifications. Conclusions: This study detected multiple novel loci and candidate genes related to rice morphological traits, and the work demonstrated that genome-wide association studies are powerful strategies for uncovering the genetic variations of complex traits and identifying candidate genes in rice, even though the linkage disequilibrium decayed slowly in self-pollinating species. Future research will focus on the biological validation of the candidate genes, and elite varieties will also be of interest in genome selection and breeding by design.
Data from: Predictability and irreversibility of genetic changes associated with flower color evolution in Penstemon barbatus
Two outstanding questions in evolutionary biology are whether, and how often, the genetic basis of phenotypic evolution is predictable; and whether genetic change constrains evolutionary reversibility. We address these questions by studying the genetic basis of red flower color in Penstemon barbatus. The production of red flowers often involves the inactivation of one or both of two anthocyanin pathway genes, Flavonoid 3',5'-hydroxylase (F3'5'h) and Flavonoid 3'-hydroxylase (F3'h). We used gene expression and enzyme function assays to determine that redundant inactivating mutations to F3'5'h underlie the evolution of red flowers in P. barbatus. Comparison of our results to previously characterized shifts from blue to red flowers suggests that the genetic change associated with the evolution of red flowers is predictable: when it involves elimination of F3'5'H activity, functional inactivation or deletion of this gene tends to occur; however, when it involves elimination of F3'H activity, tissue-specific regulatory substitutions occur and the gene is not functionally inactivated. This pattern is consistent with emerging data from physiological experiments indicating that F3'h may have pleiotropic effects and is thus subject to purifying selection. The multiple, redundant inactivating mutations to F3'5'h suggest that reversal to blue-purple flowers in this group would be unlikely.
Data from: Genetic distance as an alternative to physical distance for definition of gene units in association studies
Background: Some association studies, as the implemented in VEGAS, ALIGATOR, i-GSEA4GWAS, GSA-SNP and other software tools, use genes as the unit of analysis. These genes include the coding sequence plus flanking sequences. Polymorphisms in the flanking sequences are of interest because they involve cis-regulatory elements or they inform on untyped genetic variants trough linkage disequilibrium. Gene extensions have customarily been defined as ± 50 Kb. This approach is not fully satisfactory because genetic relationships between neighbouring sequences are a function of genetic distances, which are only poorly replaced by physical distances. Results: Standardized recombination rates (SRR) from the deCODE recombination map were used as units of genetic distances. We searched for a SRR producing flanking sequences near the ± 50 Kb offset that has been common in previous studies. A SRR ≥ 2 was selected because it led to gene extensions with median length = 45.3 Kb and the simplicity of an integer value. As expected, boundaries of the genes defined with the ± 50 Kb and with the SRR ≥2 rules were rarely concordant. The impact of these differences was illustrated with the interpretation of top association signals from two large studies including many hits and their detailed analysis based in different criteria. The definition based in genetic distance was more concordant with the results of these studies than the based in physical distance. In the analysis of 18 top disease associated loci form the first study, the SRR ≥2 genes led to a fully concordant interpretation in 17 loci; the ± 50 Kb genes only in 6. Interpretation of the 43 putative functional genes of the second study based in the SRR ≥2 definition only missed 4 of the genes, whereas the based in the ± 50 Kb definition missed 10 genes. Conclusions: A gene definition based on genetic distance led to results more concordant with expert detailed analyses than the commonly used based in physical distance. The genome coordinates for each gene are provided to maintain a simple use of the new definitions.
Data from: Evolution of phenotype-environment associations by genetic responses to selection and phenotypic plasticity in a temporally autocorrelated environment
Covariation between population-mean phenotypes and environmental variables, sometimes termed a 'phenotype-environment association' (PEA), can result from phenotypic plasticity, genetic responses to natural selection, or both. PEAs can potentially provide information on the evolutionary dynamics of a particular set of populations, but this requires a full theoretical characterization of PEAs and their evolution. Here, we derive formulas for the expected PEA in a temporally fluctuating environment for a quantitative trait with a linear reaction norm. We compare several biologically relevant scenarios, including constant versus evolving plasticity, and the situation where an environment affects both development and selection but at different time periods. We find that PEAs are determined not only by biological factors (e.g., magnitude of plasticity, genetic variation), but also environmental factors, such as the association between the environments of development and of selection, and in some cases the level of temporal autocorrelation. We also describe how a PEA can be used to estimate the relationship between an optimum phenotype and an environmental variable (i.e., the environmental sensitivity of selection), an important parameter for determining the extinction risk of populations experiencing environmental change. We illustrate this ability using published data on the predator-induced morphological responses of tadpoles to predation risk.
Data from: Common genetic variation in ETV6 is associated with colorectal cancer susceptibility
Genome-wide association studies (GWAS) have identified multiple susceptibility loci for colorectal cancer, but much of heritability remains unexplained. To identify additional susceptibility loci for colorectal cancer, here we perform a GWAS in 1,023 cases and 1,306 controls and replicate the findings in seven independent samples from China, comprising 5,317 cases and 6,887 controls. We find a variant at 12p13.2 associated with colorectal cancer risk (rs2238126 in ETV6, P = 2.67 × 10-10). We replicate this association in an additional 1,046 cases and 1,076 controls of European ancestry (P = 0.034). The G allele of rs2238126 confers earlier age at onset of colorectal cancer (P = 1.98 × 10-6) and reduces the binding affinity of transcriptional enhancer MAX. The mRNA level of ETV6 is significantly lower in colorectal tumors than in paired normal tissues. Our findings highlight the potential importance of genetic variation in ETV6 conferring susceptibility to colorectal cancer.
Data from: A practical introduction to random forest for genetic association studies in ecology and evolution
Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here we explore the use of Random Forest (RF), a powerful machine learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild or non-model organisms. RF is becoming increasingly used in ecological and population genetics because, unlike traditional methods, it can efficiently analyze thousands of loci simultaneously and account for non-additive interactions. However, understanding both the power and limitations of Random Forest is important for its proper implementation and the interpretation of results. We therefore provide a practical introduction to the algorithm and its use for identifying associations between molecular markers and phenotypes, discussing such topics as data limitations, algorithm initiation and optimization, as well as interpretation. We also provide short R tutorials as examples, with the aim of providing a guide to the implementation of the algorithm. Topics discussed here are intended to serve as an entry point for molecular ecologists interested in employing Random Forest to identify trait associations in genomic data sets.
Data from: Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity
Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection, and identifying subtle signatures of polygenic adaptation. We used paired-end restriction-site associated-DNA sequencing data (6605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomics studies.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.