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opencc-zeroSep 2021View details →

Allele frequency files for population genomic and phenotypic association analyses

Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. One challenge in studying the genetic architecture of local adaptation is to achieve high marker density to detect candidate genes in natural populations that often have small blocks of linkage disequilibrium. Here, we used low coverage whole-genome resequencing (lcWGR) to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts.

opencc-zeroOct 2021View details →

16S V4 raw read count data; 16S reads metadata; new MHC class II allele sequences

Pathogen-mediated selection at the major histocompatibility complex (MHC) is thought to promote MHC-based mate choice in vertebrates. Mounting evidence implicates odour in conveying MHC genotype, but the underlying mechanisms remain uncertain. MHC effects on odour may be mediated by odour-producing symbiotic microbes whose community structure is shaped by MHC genotype. In birds, preen oil is the primary source of body odour and similarity at MHC predicts similarity in preen oil composition. Hypothesizing that this relationship is mediated by symbiotic microbes, we characterized MHC genotype, preen gland microbial communities, and preen oil chemistry of song sparrows (Melospiza melodia). Consistent with the microbial mediation hypothesis, pairwise similarity at MHC predicted similarity in preen gland microbiota. Overall microbial similarity did not predict chemical similarity of preen oil, counter to this hypothesis. However, permutation testing identified a maximally predictive set of microbial taxa that best reflect MHC genotype, and another set of taxa that best predict preen oil chemical composition. The relative strengths of relationships between MHC and microbes, microbes and preen oil, and MHC and preen oil suggest that MHC may affect host odour both directly and indirectly. Thus, birds may assess MHC genotypes based on both host-associated and microbially-mediated odours.

opencc-zeroMar 2023View details →

Data for: Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle without understanding of genomic architecture for phenotypic traits. This study provides a high-resolution portrait of genomic variation in Chinook salmon (Oncorhynchus tshawytscha) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered dataset of ~13 million SNPs from low coverage whole genome resequencing of 53 populations (3,566 barcoded individuals), we contrasted patterns of genomic variation within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Allele frequency variation in GREB1L/ROCK1 was highly correlated with mean migration timing for early- and late-run populations within each of the lineages (r2 between 0.58–0.95; P < 0.001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream-type) compared to the other two major lineages which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

opennotspecifiedOct 2016View details →

Figure 3. Bayesian phylogenetic reconstruction for MHC class II in Diversity of MHC class II DRB alleles in the Eurasian population of the least weasel, Mustela nivalis (Mustelidae: Mammalia)

Figure 3. Bayesian phylogenetic reconstruction for MHC class II DRB alleles from Mustela nivalis and other species in Mustelidae, Felidae, and Canidae. Numbers near nodes are posterior probability values. Sequences from M. nivalis obtained in this study are in bold. GenBank accession numbers of previously published nucleotide sequences are in parentheses. Clades in Mustelidae are indicated by capital letters (A–G) to the right of the tree. The scale bar at the bottom shows branch length in substitutions per site. Abbreviations for species names are as follows: Cafa, Canis familiaris; Cala, Canis latrans; Calu, Canis lupus; Enlu, Enhydra lutris; Febi, Felis silvestris bieti; Feca, Felis catus; Fesi, Felis silvestris; Gugu, Gulo gulo; Meme, Meles meles; Muit, Mustela itatsi; Mulu, Mustela lutreola; Musi, Mustela sibirica; Nevi, Neovison vison; Tata, Taxidea taxus; Zaca, Zalophus californianus.

opennotspecifiedOct 2016View details →

Figure 2 in Diversity of MHC class II DRB alleles in the Eurasian population of the least weasel, Mustela nivalis (Mustelidae: Mammalia)

Figure 2. Amino acid sequences deduced from the nucleotide sequences of part of Mustela nivalis MHC class II DRB exon 2. Identity with allele Muni-DRB*01 is indicated by dots. Numbers above the top sequence indicate codon positions in the β1-domain. Grey shading shows the antigen-binding site (ABS) predicted from data on the human gene HLA-DR1 (Brown et al., 1993). Asterisks indicate codons corresponding to sites under positive selection calculated from the mixed-effects model evolution (MEME) analysis. A triangle shows the recombination break point with the single break point recombination (SBP) method (see the text).

opennotspecifiedOct 2016View details →

Figure 1 in Diversity of MHC class II DRB alleles in the Eurasian population of the least weasel, Mustela nivalis (Mustelidae: Mammalia)

Figure 1. Map of Eurasia showing collecting localities (black circles) for 35 specimens of Mustela nivalis in this study. The sample size at each locality is indicated in parentheses.

opencc-by-4.0Jun 2023View details →

High-resolution KIR allele annotations for HPRC 47 assemblies and other reference genomes using SKIRT

Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the Structural KIR annoTator (SKIRT), to annotate, identify, and discover hundreds of novel alleles, more than a dozen structural variations among KIR genes, and all haplotypes carrying novel alleles, confirming KIR genetic diversity. The use of HPRC data needs to comply with the rules announced by HPRC.

opencc-zeroAug 2023View details →

Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation and a systematic review

Purpose: Searched for novel bi-allelic CRB1 mutations, then analyzed the CRB1 literature at the genotypic and phenotypic levels from 439 patients worldwide. Approach: We screened various variables such as the CRB1 mutation types, domains, exons, and genotypes and their relation with specific ocular phenotypes. An emphasis was given for the bi-allelic missense and nonsense mutations because of their high prevalence compared to other mutation types. Finally, we quantified the effect of various non-modifiable factors over the BCVA OU using multivariate linear regression models and identified genetic interactions. Results: We first identified a novel bi-allelic missense in the exon 9 of CRB1; c.2936G>A; p.(Gly979Asp) associated with RCD. CRB1 mutation type, exons, domains, and genotype distribution vary significantly according to Fundus characteristics, such as peripheral pigmentation and condition, optic disc, vessels, macular, and pigmentation (P<0.05). Of the 154 articles retrieved from PubMed, 96 studies with 439 bi-allelic CRB1 patients were included. Missense mutations were significantly associated with an absence of macular pigments, pale optic disc, and periphery pigmentation, resulting in a higher risk of RCD (P<0.05). In contrast, homozygous nonsense mutations were associated with macular pigments, periphery pigments, and a high risk of LCA (P<0.05) and increased BCVA OU (best-corrected visual acuity) levels. We found that age, mutation types, and inherited retinal diseases were critical determinants of BCVA OU as they significantly increased it by 33%, 26%, and 38%, respectively (P<0.05). Loss of function alleles additively increased the risk of LCA, with nonsense having a more profound effect than indels. Finally, our analysis showed that p.(Cys948Tyr) and p.(Lys801Ter) and p.(Lys801Ter); p.(Cys896Ter) might interact to modify BCVA OU levels. Conclusion: This meta-analysis updated the literature and identified genotype-phenotype associations in bi-allelic CRB1 patients.

opencc-zeroSep 2023View details →

Data from: Phormia regina allele report

Genetic structure of blow fly (Diptera: Calliphoridae) populations has remained elusive regardless of high relatedness within wild-caught samples. The aims of this research were to determine if the implementation of a high-resolution spatiotemporal sampling design would reveal latent genetic structure among blow fly populations and to elucidate environmental impacts on structure. Adult female black blow flies, Phormia regina (Meigen), were collected from nine urban parks in Indiana, USA over three years. Fly gut DNA was genotyped at six microsatellite loci, with subsequent amplification and sequencing of vertebrate mitochondrial DNA from the same source. Flies were also screened for vertebrate fecal metabolites. Latent clustering revealed four genetic groups which were interpreted as 11 distinct temporal populations. An analysis of molecular variance of temporal populations revealed stronger genetic differentiation (FST = 0.048, F'ST = 0.664) relative to geographic populations (FST = 0.009, F'ST = 0.241). Mean kinship within temporal populations was higher than expected in a panmictic population (R = 0.032 ± 0.088). Weather conditions (i.e., wind speed, precipitation, humidity, temperature) and vertebrate resource availability in the local environment significantly impacted the observed genetics of P. regina. Twenty-five vertebrate species were detected from flies, and 16% of flies collected in 2016 – 2017 tested positive for vertebrate feces, suggesting many varied resources are important for maintaining high gene flow among geographic populations. A complex interplay between biotic and abiotic factors, as well as the flies' own extensive dispersal abilities, seems to drive the strong temporal structure of this species in the Midwestern US.

opencc-zeroOct 2023View details →

Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population

Interest in the genetic basis of variation in skin pigmentation in Native American populations led us to seek indigenous populations of the Western Hemisphere with African and minimal European admixture to study the effect of Native American ancestry on skin color. Admixture analysis from DNA collected from 458 individuals in the Kalinago territory of the Commonwealth of Dominica showed shared ancestry with East Asians at K=3 and 55% Native American, 32% African, and 11% European ancestry at K=6, the highest Native American ancestry of Caribbean populations. Skin pigmentation was 20 to 80 melanin units, averaging 46. Three albino individuals were homozygous for multi-nucleotide polymorphism OCA2NW273KV of African origin, whose population allele frequency was 0.03 and single allele effect size was -8 melanin units. Hypopigmenting allele frequencies for SLC24A5A111T and SLC45A2L374F were 0.14 and 0.05, whose single allele effect sizes were -6 and -3, respectively. Skin color plots of individuals lacking known hypopigmenting alleles suggests that Native American Ancestry reduced pigmentation by more than 20 melanin units (low and high estimates 21.8 and 28.5). Shared ancestry with East Asians at K=3 suggests potential sharing of one or more pigmentation alleles.

Interest of CALR Allele Burden in Diagnosis and Follow-up of Patients With CALR Mutated Myeloproliferative Syndromes (CALRSUIVI)

ClinicalTrials.gov study NCT04942080. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Sensitivity of Short and Long Allele Carriers of the 5-HTTLPR to Environmental Threat Post Hydrocortisone Administration

ClinicalTrials.gov study NCT01710202. IPD Sharing: Not stated. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Fatty Acid Metabolism in Carriers of Apolipoprotein E Epsilon 4 Allele: Determining the Blood-to-brain Link

ClinicalTrials.gov study NCT04279743. IPD Sharing: NO. Countries: 1. Publications: 0.

Brain Changes by Rivastigmine According to Butyrylcholinesterase Alleles

ClinicalTrials.gov study NCT02063269. IPD Sharing: Not stated. Countries: 1. Publications: 15.

Comparison of Obesity Alleles Among Diverse Demographic Patients

ClinicalTrials.gov study NCT01396096. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Comparison of Platelet Inhibition With Adjunctive Cilostazol Versus High Maintenance-Dose Clopidogrel According to Hepatic Cytochrome 2C19 Allele (CYP2C19) Polymorphism

ClinicalTrials.gov study NCT00891670. IPD Sharing: Not stated. Countries: 1. Publications: 2.

The Occurrence of the ApoE4 Allele in Agitated In-Patients With Late-Onset Alzheimer's Disease

ClinicalTrials.gov study NCT01329536. IPD Sharing: Not stated. Countries: 1. Publications: 6.

Association of HY-restricting HLA Class II Alleles, Sex of Firstborn Child, and Pregnancy Outcome in RPL Patients

ClinicalTrials.gov study NCT05342948. IPD Sharing: Not stated. Countries: 1. Publications: 2.

Percentage of BRAFV600E Alleles and Outcome in Thyroid Carcinoma

ClinicalTrials.gov study NCT04664413. IPD Sharing: UNDECIDED. Countries: 1. Publications: 7.