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opencc-zeroSep 2021View details →

VCF files of loci in approximate linkage equilibrium for two common spruce budworm larval parasitoids: Apanteles fumiferanae (Hymenoptera: Braconidae) and Glypta fumiferanae (Hymenoptera: Ichneumonidae)

Periodic and spatially synchronous outbreaks of insect pests have dramatic consequences for boreal and sub-boreal forests. Within these multitrophic systems, parasitoids can be stabilizing agents by dispersing toward patches containing higher host density (the so-called birdfeeder effect). However, we know little about the dispersal abilities of parasitoids in continuous forested landscapes, limiting our understanding of the spatiotemporal dynamics of host–parasitoid systems, and constraining our ability to predict forest resilience in the context of global changes. In this study, we investigate the spatial genetic structure and spatial variation in genetic diversity of two important species of spruce budworm larval parasitoids during outbreaks: Apanteles fumiferanae Viereck (Braconidae) and Glypta fumiferanae (Viereck) (Ichneumonidae). Using parasitoids sampled in 2014 from 26 and 29 locations across a study area of 350,000 km2, we identified 1,012 and 992 neutral SNP loci for A. fumiferanae (N = 279 individuals) and G. fumiferanae (N = 382), respectively. Using DAPC, PCA, AMOVA, and IBD analyses, we found evidence for panmixia and high genetic connectivity for both species, matching the previously described genetic structure of the spruce budworm within the same context, suggesting similar effective dispersal during outbreaks and high parasitoid population densities between outbreaks. We also found a significant negative relationship between genetic diversity and latitude for A. fumiferanae but not for G. fumiferanae, suggesting that northern range limits may vary by species within the spruce budworm parasitoid community. These spatial dynamics should be considered when predicting future insect outbreak severities in boreal landscapes.

opencc-zeroSep 2021View details →

Lampsilis siliquoidea and L. radiata seven microsatellite loci data set

The data set corresponds to genotypes of individuals belonging to Lampsilis siliquoidea and L. radiata which are two closely related freshwater mussel species [Bivalvia: Unionidae]. Individual genotypes consist of seven microsatellite loci developed by Eackles and King 2002. Genotypes were used to asses population genetic structure above and below waterfalls in the lower Great Lakes (USA) and to investigate the degree of hybridization between these two species.

opencc-zeroSep 2021View details →

Weak coupling among barrier loci and waves of neutral and adaptive introgression across an expanding hybrid zone

Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range-limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species' ranges, while putative cases of adaptive introgression had exceptionally wide clines with centers shifted towards one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per-generation dispersal between 200 and 400 meters, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range-limited species.

opencc-zeroNov 2022View details →

Genetic loci associated with winter survivorship in diverse lowland switchgrass populations: SNP read count data

High winter mortality is the most important factor limiting biomass yield of lowland switchgrass planted in the northern latitudes of North America. Due to the perennial growth habit and strong dependence on weather conditions to generate sufficient selection pressure to identify winter-hardy individuals, breeding of cold tolerant switchgrass cultivars requires many years. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 population with differential winter survivorship was used for BSA. A maximum of 10% of the individuals per population (8-20) was bulked to create survivor and non-survivor DNA pools. The DNA pools were evaluated using exome capture sequencing and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine QTL from tetraploid populations and seven QTL from octoploid populations. Some markers were identified in multiple populations that originated across a broad geographic landscape, while other markers were site-specific. QTL at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.

opencc-by-4.0Jun 2022View details →

Gaps and complex structurally variant loci in phased genome assemblies

Supplementary data including code for an science article 'Gaps and complex structurally variant loci in phased genome assemblies'.

opencc-zeroJan 2023View details →

Genotypes at 10 microsatellite loci for 8 perennial, polygyne colonies of Vespula squamosa

Many highly social species show plasticity in their social structure in response to different environmental conditions. For example, typical colonies of the yellowjacket wasp Vespula squamosa are headed by a single reproductive queen and survive for only a single season. However, in warmer climates, V. squamosa colonies sometimes persist for multiple years and can grow to extremely large size. We used genetic markers to understand patterns of reproduction and recruitment within these perennial colonies. We genotyped V. squamosa workers, pre-reproductive queens, and males from perennial colonies in the southeastern United States at 10 polymorphic microsatellite loci and one mitochondrial DNA locus. We found that V. squamosa from perennial nests were produced by multiple reproductives, in contrast to typical annual colonies. Relatedness of nestmates from perennial colonies was significantly lower than relatedness of nestmates from annual colonies. Our analyses of mitochondrial DNA indicated that most V. squamosa perennial colonies represented semi-closed systems whereby all individuals belonged to a single matriline despite the presence of multiple reproductive females. However, new queens recruited into perennial colonies apparently mated with non-nestmate males. Notably, perennial and annual colonies did not show significant genetic differences, supporting the hypothesis that perennial colony formation represents an instance of social phenotypic plasticity. Overall, our results indicate that perennial V. squamosa colonies show substantial changes to their social biology compared to typical annual colonies.

opencc-zeroJan 2023View details →

Biomass data to accompany Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

<ul> <li>The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance.</li> <li>Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multi-level analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations.</li> <li>We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost.</li> <li>Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD and that the fitness cost associated with resistance in this species is likely a by-product of genetic-hitchhiking.</li> </ul>

opencc-by-4.0Feb 2023View details →

Germline Immunomodulatory Expression Quantitative Trait Loci (ieQTLs) Associated with Immune-Related Toxicity from Checkpoint Inhibition

Robert Ferguson1,2,3*, Vylyny Chat1,2,3*, Leah Morales1,2,3, Danny Simpson1,2,3, Kelsey Monson1,2,3, Elisheva Cohen1,2,3,Sarah Zusin1,2,3, Gabriele Madonna4, Mariaelena Capone4, Ester Simeone4, Anna Pavlick5, Jason Luke6,7, Thomas F Gajewski8,9,10, Iman Osman1,3,11,12, Paolo Antonio Ascierto4, Jeffrey Weber1,3,11, Tomas Kirchhoff1,2,3 1Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA 2Departments of Population Health and Environmental Medicine, New York University- Grossman School of Medicine, New York, NY, USA 3The Interdisciplinary Melanoma Cooperative Group, New York University-Grossman School of Medicine, New York, NY, USA 4Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy 5Division of Hematology & Medical Oncology, the Cutaneous Oncology Program, Weill Cornell Medicine and New York-Presbyterian, New York, USA 6Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA. 7UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA. 8Department of Pathology, University of Chicago, Chicago, IL, USA. 9Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA. 10Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA. 11Department of Medicine, New York University-Grossman School of Medicine, New York, NY, USA 12Ronald O. Perelman Department of Dermatology, New York University-Grossman School of Medicine, New York, NY, USA *These authors contributed equally to the work Corresponding author: Tomas Kirchhoff, PhD ABSTRACT Background: Immune-checkpoint inhibition (ICI) has improved clinical outcomes for metastatic melanoma patients, however, 65-80% of patients treated with ICI experience immune-related adverse events (irAEs). Given the plausible link of irAEs with underlying host immunity, we explored if germline genetic variants controlling the expression of 42 immunomodulatory genes were associated with the risk of irAEs in melanoma patients treated with the single-agent anti- CTLA-4 antibody ipilimumab (IPI). Methods: We identified 42 immunomodulatory expression quantitative trait loci (ieQTLs) most significantly associated with the expression of 382 immune-related genes. These germline variants were genotyped in IPI-treated melanoma patients, collected as part of a multiinstitutional collaboration. We tested the association of ieQTLs with irAEs in a discovery cohort of 95 patients followed by validation in an additional 97 patients. Results: We found that the alternate allele of rs7036417, a variant linked to increased expression of SYK, was strongly associated with an increased risk of grade 3-4 toxicity (OR= 7.46; 95% CI=2.65-21.03; p=1.43E-04). This variant was not associated with response (OR= 0.90; 95% CI=0.37-2.21; p=0.82). Conclusion: We report that rs7036417 associates with increased risk of severe irAEs, independent of IPI efficacy. SYK plays an important role in B-cell/T-cell expansion and increased pSYK has been reported in patients with autoimmune disease. The association between rs7036417 and IPI irAEs in our data suggests a role of SYK over-expression in irAE development. These findings support the hypothesis that inherited variation in immune-related pathways modulate ICI toxicity and suggest SYK as a possible future target for therapies to reduce irAEs.   Keywords: irAEs; germline variants; immune checkpoint inhibition; melanoma Funding: This research was funded by the Italian Ministry of Health (IT-MOH) through “Ricerca Corrente”, grants number M2/2 and L2-1.

opencc-by-4.0May 2023View details →

Identification of four novel loci associated with psychotropic drug-induced weight gain in a Swiss psychiatric longitudinal study: A GWAS analysis

Summary statistics for the GWAS with different outcomes presented in the <a href="https://pubmed.ncbi.nlm.nih.gov/37173452/">publication</a>. PSYMETAB_GWAS_FREQ_CEU.BMI_change_1mo_all.glm - BMI change between 1 month vs baseline PSYMETAB_GWAS_FREQ_CEU.BMI_change_3mo_all.glm - BMI change between 3 months vs baseline PSYMETAB_GWAS_FREQ_CEU.BMI_change_6mo_all.glm - BMI change between 6 months vs baseline PSYMETAB_GWAS_FREQ_CEU.BMI_change_all.glm - BMI change between last follow-up time vs baseline PSYMETAB_GWAS_FREQ_CEU.BMI_slope_6mo_all.glm - BMI slope fitted for the first 6 months of followup data PSYMETAB_GWAS_FREQ_CEU.BMI_slope_all.glm - BMI slope fitted for all available follow-up data

opencc-by-4.0Sep 2023View details →

GWAS summary stats in "A web-based genome-wide association study reveals the susceptibility loci of common adverse events following COVID-19 vaccination in the Japanese population."

Summary stats of the genome-wide meta-analysis with METAL software in the article "A web-based genome-wide association study reveals the susceptibility loci of common adverse events following COVID-19 vaccination in the Japanese population."https://doi.org/10.1038/s41598-023-47632-5 Due to the absence of cases in either population, we were unable to perform GWAS for the following conditions. constipation at BNT162b1 1st dose dyspnea at BNT162b1 1st dose eczema (long-term rash) at BNT162b1 1st dose dyspnea at BNT162b1 2nd dose sneeze at mRNA-1273 1st dose dyspnea at mRNA-1273 1st dose

opencc-zeroOct 2023View details →

Phylogenetic relationships of Tilia (Malvaceae) inferred from multiple nuclear loci and plastid genomes

Premise of research. Tilia is a Eurasian-eastern North American disjunct plant genus with great economic and ecological importance. However, a robust phylogeny has not been established with a comprehensive taxon sampling and a large amount of data. Methodology. We obtained DNA sequences of plastomes and multiple nuclear loci using the anchored hybrid enrichment technique and next generation sequencing technology. Orthologous nuclear loci were inferred using tree-based methods. Phylogenetic analyses were performed using maximum parsimony, Bayesian, and coalescence-based species tree methods. Parentages of polyploids were inferred from the nuclear and plastid phylogenies. Pivotal results. Craigia yunnanensis is sister to Tilia, within which T. endochrysea endemic to southern China is the earliest lineage diverging followed by the European species T. platyphyllos. The European T. cordata and eastern Asian T. amurensis and T. kiusiana form a clade, while the North American T. americana is most closely related to the eastern and western Asian species complex including T. chingiana, T. mandshurica, T. oliver, and western Asian T. tomentosa. Significant incongruence exists between nuclear and plastid phylogenies. Conclusions. Our phylogenetic results suggest that there are six distinctive lineages or species complexes in the genus including 1) T. endochrysea, 2) T. platyphyllos, 3) T. kiusiana, 4) T. cordata and T. amurensis, 5) T. chingiana, T. miqueliana, T. oliveri, and 6) T. tomentosa, and T. americana. They may be divided into two sections (Trichophilyra and Tilia) and three subsections (Tilia, Lindnera, and Trabeculares). The prevalent incongruence between nuclear and plastid confirms the importance of ancient hybridization and introgression in the evolutionary history of the genus. Polyploid species in Eurasia and their corresponding diploid parental lineages may have formed a hybrid swarm in the region.

closedIPD-NOFeb 2026View details →

Testing the Leadership and Organizational Change for Implementation (LOCI) Intervention

ClinicalTrials.gov study NCT03042832. IPD Sharing: NO. Countries: 1. Publications: 2.

restrictedIPD-UNDECIDEDFeb 2026View details →

Autosomal Dominant Retinitis Pigmentosa: Prevalence of Known Genes Identification of New Loci / Genes

ClinicalTrials.gov study NCT01235624. IPD Sharing: Not stated. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

A Genome-Wide Scan For Quantitative Trait Loci of Serum Bilirubin - A Framingham Study

ClinicalTrials.gov study NCT00340509. IPD Sharing: Not stated. Countries: 1. Publications: 3.

closedIPD-NOFeb 2026View details →

Testing the LOCI Intervention

ClinicalTrials.gov study NCT03719651. IPD Sharing: NO. Countries: 1. Publications: 4.