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Dataset results
29 results for “Variant genotypes”
Structural variant discovery and genotyping in next-generation sequencing data
<p>Code, logs, data, and summaries for detection and genotyping of genomic structural variants in the D.melanogaster Sussex LHM hemiclones (and one in-house reference line individual), using Genomestrip/2.0</p> <p>The unfiltered CNV pipleline results are lhm_gs.cnvs.raw.vcf.gz</p> <p>Filtered CNV results (including removal of bad samples) are filtered.goodS.lhm_gs.cnvs.raw.vcf.gz</p> <p>The file uploaded to NCBI dbVAR (which comprises of the filtered CNVs and indels >50bp from the HaplotypeCaller method) is lhm_sx16.dbVAR.vcf.gz</p> <p>The NCBI dbVAR accession number is nstd134. Code, logs and summary data are in the zipped archives, named accordingly. The archive reference_data.zip contains additional input files required for Genomestrip, including a shell script for making some of them. The file gstrip_lhm_RG_bams.list is also an input for Genomestrip, indicating bam file names and paths.</p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p> <p> </p>
i2QTL HipSci Structural Variant and Short Tandem Repeat Genotypes
<p>Here we provide structural variant and short tandem repeat variant calls from 204 HipSci donors as described in the manuscript Jakubosky et al. "Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats". </p> <p><a href="https://www.biorxiv.org/content/10.1101/713198v2">https://www.biorxiv.org/content/10.1101/713198v2</a></p> <p>Jakubosky D, Smith EN, D’Antonio M, Bonder MJ, Young Greenwald WW, Matsui H, D’Antonio-Chronowska A, (Hipsci), Stegle O, Montgomery SB, DeBoever C, Frazer KA. Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats. bioRxiv. January 2019:713198. doi:10.1101/713198.</p> <p> </p>
Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
<p>Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced‐representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (<i>Homarus americanus</i>) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs account for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic–environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in nonmodel species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.</p>
A specific IL6 polymorphic genotype modulates the risk of T. cruzi parasitemia while IL18, IL17A and IL1B variant profiles and HIV infection protect against cardiomyopathy in Chagas disease
<p><strong>Background:</strong> Chagas disease caused by Trypanosoma cruzi (T. cruzi) affects approximately six million individuals worldwide. Clinical manifestations are expected to occur due to the parasite persistence and host immune response. Herein we investigated potential associations between IL1B, IL6, IL17A or IL18 polymorphism profiles and cardiomyopathy or T. cruzi parasitemia, as well as the impact of HIV infection on cardiopathy.</p> <p><strong>Methods:</strong> 206 patients and 90 control individuals were analyzed. IL1B rs1143627 T>C, IL6 rs1800795 C>G, IL17A rs2275913 G>A, IL18 rs187238 C>G, and IL18 rs1946518 C>A SNVs were analyzed by real-time PCR and T. cruzi parasitemia by PCR.</p> <p><strong>Results: </strong>Our data revealed association between a cytokine gene polymorphism and parasitemia never previously reported. The IL6 rs1800795 CG genotype lowered the risk of positive parasitemia (OR=0.45, 95% CI 0.24–0.86, P=0.015). Original findings included associations between IL17A rs2275913 AA and IL18 s1946518 AA genotypes with decreased risk of developing cardiomyopathy (OR=0.27, 95% CI 0.07-0.97, P=0.044; and OR=0.35, 95% CI 0.14-0.87, P=0.023, respectively). IL18 rs1946518 AA and IL1B rs1143627 TC were associated with reduced risk for cardiomyopathy severity, including NYHA (New York Heart Association) class≥ 2 (OR=0.21, 95% CI 0.06-0.68, P=0.009; and OR=0.48, 95% CI 0.24-0.95, P=0.036, respectively) and LVEF (Left Ventricular Ejection Fraction) <45% for IL18 rs1946518 AA (OR=0.22, 95% CI 0.05-0.89, P=0.034). A novel, unexpected protective effect of HIV infection against development/progression of cardiomyopathy was identified, based on a lower risk of developing cardiopathy (OR=0.48, 95% CI 0.23‐0.96, P=0.039), NYHA class≥2 (OR=0.15, 95% CI 0.06‐0.39, P<0.001) and LVEF<45% (OR=0.03, 95% CI 0.00‐0.25, P=0.001). Digestive involvement was negatively associated with NYHA ≥2 and LVEF<45% (OR=0.20, 95% CI 0.09‐0.47, P<0.001; and OR=0.24, 95% CI 0.09-0.62, P=0.004, respectively).</p> <p><strong>Conclusions: </strong>Our data support a protective role of IL17A AA, IL18 AA and IL1B TC genotypes against development/progression of cardiomyopathy and a modulatory effect of the IL6 CG genotype on the risk of parasitemia in Chagas disease. Notably, HIV infection was shown to protect against development/progression of cardiopathy, potentially associated with a synergistic effect of HIV and HAART, attenuating a Th1-mediated response in the myocardium. This proposed hypothesis requires confirmation, however, in larger and more comprehensive future studies.</p>
Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
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A specific IL6 polymorphic genotype modulates the risk of T. cruzi parasitemia while IL18, IL17A and IL1B variant profiles and HIV infection protect against cardiomyopathy in Chagas disease
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A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
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Raw genotyped total called structural variant (SV)
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Data from: Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland
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Genotypes, variants and pedigree from a human parent-offspring trio (NA12878)
<p>This dataset includes whole genome sequencing data, produced at the French National Research Center for Human Genomics (CNRGH), with known pedigree information:<br> - The VCF file contains genotypes and variants from a CEU parent-offspring trio comprising NA12878 (child), NA12891 (father) and NA12892 (mother).<br> For each member, 150-bp paired-end whole genome sequencing data were generated on the Illumina HiSeq X system, from a PCR-free library (40x).<br> - The TFAM file contains pedigree information of this CEU parent-offspring trio.</p>
Data from: Variant files for genotypic and sex-reversed males
<p>X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, <i>Musca domestica</i>. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The up-regulation of the proto-Y allele may be favored in males because of this gene's function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.</p>
Genotype count for all coding variants in type I IFN genes investigated in 659 life-threatening COVID-19 patients and 534 asymptomatic/mild infected controls
<p>Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define LOF variants in 23 patients (3.5%), aged 17 to 77 years, underlying autosomal recessive or dominant deficiencies. We show that human fibroblasts with mutations affecting this pathway are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.</p>
Data from: Variant files for genotypic and sex-reversed males
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Genotype count for all coding variants in type I IFN genes investigated in 659 life-threatening COVID-19 patients and 534 asymptomatic/mild infected controls
Open the record for dataset details and reuse information.
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants (K5B)
GEO Series GSE252642. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis and atopic dermatitis
GEO Series GSE232341. Homo sapiens. 39 samples. Type: Expression profiling by high throughput sequencing; Other.
Unravelling Stargardt Disease (STGD1): Modelling Genotype-Phenotype Correlations and Unresolved Genetic Variants in iPSC-Derived Retinal Organoids
GEO Series GSE236097. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis and atopic dermatitis [MPRA]
GEO Series GSE232337. Homo sapiens. 29 samples. Type: Other.
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants (K6B)
GEO Series GSE252416. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing; Other.
A genotype-first approach identifies variants for orofacial clefts and other phenotypes in dogs
GEO Series GSE278600. Canis lupus familiaris. 308 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
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