Concordance of genotypes represented in VCF and gVCF files with those detected by the MI RISK Plus kit.

Genotyping of known SNPs from ClinVar using the VCF and gVCF file formats and the number of homozygous reference sites and no-calls based on WGS data.

The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population.

Genotyping of GWAS catalog sites using the VCF and gVCF file formats and the number of homozygous reference sites and no-calls based on WGS data.

Verticillium dahliae is an important soil-borne pathogen causing Verticillium wilt. It is also the primary causal agent of the Potato Early Dying, a disease complex involving the root-lesion nematode. Here, we report the whole-genome sequencing of 192 isolates of V. dahliae originating from the major potato production areas across Canada. Our results yielded a resource of 277,010 genetic variations that will be useful for genetic analyses and revealed the presence of two major lineages, both present in all provinces but exhibiting differences in regional prevalence., Filtered WGS reads (fastp) aligned on Verticillium dahliae reference (https://www.ncbi.nlm.nih.gov/assembly/95341/GCA_000150675.2) with BWA. VCF called with freebayes v1.3.6 and annotated with snpeff.,

Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease in cats, often leading to congestive heart failure, arterial thromboembolism, and sudden cardiac death. The genetics of feline HCM are poorly understood, and limited genetic discoveries remain breed or family-specific. We aimed to identify novel causative or disease-modifying variants in a large cohort of cats reflective of the general cat population. In a second cohort, we sought to characterize transcriptomic differences between HCM-affected cats and healthy controls. DNA was isolated from 138 domestic cats (109 HCM and 29 controls). No single or combination of variants of high, moderate, or modifying impact were identified in genome-wide analysis to cause or modify the disease severity of HCM. Several rare high and moderate-impact variants in genes associated with human HCM were detected in diseased cats. In a second cohort, left ventricular (LV), interventricular septal (IVS), and left atrial (LA) tissues..., WGS data generation A total of 1-2 mL of whole blood were collected from the cephalic, saphenous, or jugular vein into EDTA blood collection tubes. DNA was either isolated from whole blood or from buffy coats after whole blood centrifugation at 2000 rpm for 15 minutes. Genomic DNA isolation was performed using commercially available kits (Gentra Puregene Blood kit, QIAGEN, Hilden Germany; ArchivePure;5Prime) and by following the respective manufacturer’s protocol. High-quality unfragmented DNA was selected by a combination of 1% agarose gel visualization and spectrophotometric confirmation (a 260/280 ratio of ~1.8 and a concentration of > 50 ng/uL; NanoDrop One/One, Thermofisher, Waltham, GA, USA). Samples were stored at -20°C until ready for shipment to Theragen Bio Co., Ltd, Gyeonggi-do, Republic of Korea for WGS. Paired-end DNA libraries were generated with a TruSeq DNA Nano library prep kit. Samples were then pooled and sequenced at ~30x coverage on the Illumina NovaSeq6000 platf..., # Unraveling the genetics of feline hypertrophic cardiomyopathy: A multiomics study of 138 cats

Dataset DOI: 10.5061/dryad.cjsxksnjh

Description of the data and file structure

Data available

1. A population level vcf of polymorphic SNP and indel variants were called among 138 domestic cats with and without hypertrophic cardiomyopathy (HCM). The VCF was generated by mapping paired wgs fastq reads to the Fca126 reference genome with bwa mem and calling variants through GATK4 best practices. Variant annotations were generated with Ensembl's VEP based on Fca126 gene and exon boundaries.  The vcf file contains meta-information lines, followed by a header line specifying fixed fields per sample and subsequent data lines detail variants at genomic positions. The fixed fields include chromosome (CHROM), position (POS), identifier (ID), the reference base(s) (REF), alternate base(s) (ALT), quality (QUAL), filter status (FILTER), and additional information ...,

This synthetic dataset release has been generated in the context of the Better Project, funded by the European Union’s Horizon program and the UK Research and Innovation Program. The synthetic datasets mimic healthcare multimodal data (clinical and genomic) from different hospitals. It is intended to be reused for algorithm and pipeline testing for healthcare data management and analysis. The release includes healthcare data combining tabular data (in csv, tsv and xlsx format) and genomic resources in VCF format (Version 4.2 Specification). Three use cases are represented, with subfolders simulating data from distinct hospitals. Content: Use Case 1 condition: Hypotonia synthetic datasets: VCF files and tabular data (xlsx, tsv) description: For each of two hospitals, it is provided tabular data and VCF resources. Tabular data provides information on genomic, phenotypic, biological and clinical data (baseline and dynamic) according to domain rules. Regarding VCF resources, each dataset contains 300 patients, 50% of whom are affected by hypotonia and have a homozygote mutation overlapping the JUN gene region in the hg19 genome (chr1:59246463-59249719), and other random variants distributed throughout the genome. Use Case 2 condition: Inherited Retinal Diseases synthetic datasets: VCF files and tabular data (xlsx) description: For each of two hospitals, it is provided tabular data and VCF resources. Tabular data provides information on electrophysiological and visual field data according to standard clinical eye examination protocols. The dynamic clinical data has been generated to mimic patients showing different clinical progression depending on the affected gene. Measures are generated for both eyes, which may present differences in progression. Regarding VCF resources, each dataset contains 200 patients, of which 50% have mutations overlapping gene ABCA4 and 50% with mutations overlapping gene RPGR. Details on included variants for each gene extracted from ClinVar can be found in the ANNEX below. Use Case 3 condition: Autism Spectrum Disorder synthetic datasets: tabular data (csv and tsv) description: The generated dataset simulates patients with ASD, and provides information on demographic variables, neurodevelopmental and psychiatric comorbidities, family psychiatric history, bullying-related variables, abuse-related variables, sexual and gender-related descriptors, passive ideas of death, self-harm indicators and suicidal-intention-related features. Datasets have been generated with synthetic biases such as correlations and clusters to provide richness to the generated data. No VCF resources are included for this use case. ANNEX (UC2) The variants included in the VCF files for the ABCA4 gene are: ##fileformat=VCFv4.2 ##FORMAT=

Genetic testing, which is now a routine part of clinical practice and disease management protocols, is often based on the assessment of small panels of variants or genes. On the other hand, continuous improvements in the speed and per-base costs of sequencing have now made whole exome sequencing (WES) and whole genome sequencing (WGS) viable strategies for targeted or complete genetic analysis, respectively. Standard WGS/WES data analytical workflows generally rely on calling of sequence variants respect to the reference genome sequence. However, the reference genome sequence contains a large number of sites represented by rare alleles, by known pathogenic alleles and by alleles strongly associated to disease by GWAS. It’s thus critical, for clinical applications of WGS and WES, to interpret whether non-variant sites are homozygous for the reference allele or if the corresponding genotype cannot be reliably called. Here we show that an alternative analytical approach based on the analysis of both variant and non-variant sites from WGS data allows to genotype more than 92% of sites corresponding to known SNPs compared to 6% genotyped by standard variant analysis. These include homozygous reference sites of clinical interest, thus leading to a broad and comprehensive characterization of variation necessary to an accurate evaluation of disease risk. Altogether, our findings indicate that characterization of both variant and non-variant clinically informative sites in the genome is necessary to allow an accurate clinical assessment of a personal genome. Finally, we propose a highly efficient extended VCF (eVCF) file format which allows to store genotype calls for sites of clinical interest while remaining compatible with current variant interpretation software.

The American chestnut (Castanea dentata) is a functionally extinct tree species that was decimated by an invasive fungal pathogen in the early 20th century. An understanding of the genomic architecture of local adaptation in wild American chestnut was necessary in order to deploy locally adapted, disease-resistant American chestnut populations. Here, we characterize the genomic basis of climate adaptation in remnant wild American chestnut, develop new computational methods, and evaluate the adaptive genomic content captured within backcross breeding populations. Whole genome re-sequencing data of 356 trees from Sandercock et al. (2022) coupled with genotype-environment association methods identified 18483 climate associated loci.Methods: VCF file: The ~21 million SNP dataset from Sandercock et al. (2022) was first imputed using BEAGLE and filtered to remove SNPs with MAF < 0.05. Climate associated loci were then identified using RDA and LFMM2 genotype-environment association methods. Seed zone shape files: Three seed zones were identified using the ~18k climate associated loci. These regions partition the chestnut range into geographic seed zones that reflect relatively homogeneous areas with respect to multivariate adaptive genomic variation. These regions can be used to conserve germplasm ex situ and guide subsequent breeding crosses that lead to climate-matched restoration populations. gmbigxhorn.jtl.map.2022.csv is a genetic map generated from American chestnut backcross genotyping-by-sequencing data. R code for estimating the average migration distance for each seed zone under future climate change conditions.

Variant Calling Format (VCF) file used to produce Fig 3 in the associated manuscriptVariant Calling Format (VCF) files associated with the publication entitled: "Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies"

The increasing prevalence of vector-borne diseases around the world highlights the pressing need for an in-depth exploration of the genetic and environmental factors that shape the adaptability and widespread distribution of mosquito populations. This research focuses on Culex tarsalis, a principal vector for various viral diseases, including West Nile Virus (WNV). Through the development of a new reference genome and the examination of Restriction-Site Associated DNA sequencing (RAD-seq) data from over 300 individuals and 28 locations, we demonstrate that variables such as temperature, evaporation rates, and the density of vegetation significantly impact the genetic makeup of Cx. tarsalis populations. Among the alleles most strongly associated with environmental factors is a nonsynonymous mutation in a key gene related to circadian rhythms. These results offer new insights into the mechanisms of spread and adaptation in a key North American vector species, which is poised to beco..., Sample Collection Individual mosquitoes were trapped and collected from 28 different locations across the United States and Canada as part of the North American Mosquito Project (NAMP). All samples used in this study were collected in 2012 between the months of April and October. Genome Sequencing, Assembly, and Annotation An F4 population was used to generate the reference genome assembly, and high molecular weight DNA was extracted and sequenced on a Pacific Biosciences (PacBio) RS II (University of Delaware). Thirty-five SMRT cells were generated. The resulting reads provided 76X coverage of the ~790Mb Cx. tarsalis genome, and were assembled with MECAT. Gene annotation was completed by MAKER using EST and protein data from the Culex quinquefasciatus and Aedes aegypti mosquitoes. Sequences were downloaded from the NCBI Taxonomy database and both Trinotate and InterProScan were used for functional annotation of the MAKER predicted genes. The annotated assembly was ass..., , # Climate adaptation and genetic differentiation in the mosquito species Culex tarsalis

https://doi.org/10.5061/dryad.51c59zwh3

Description of the data and file structure

The data were stored in 8 different files.

1. bi_20missing_filtSNP_maf_005.recode.vcf

   File Details

   • File Name: bi_10missing_filtSNP_maf_005.recode.vcf
   • File Format: VCF (Variant Call Format) v4.2
   • Reference genome: culex.60x.contigs.fasta (from header ##reference=...)
   • Source software (inferred): GATK-style headers present (e.g., QD, MQ, FS, ReadPosRankSum, RGQ, PL, SB, END, NON_REF) suggest generation with GATK/HaplotypeCaller (gVCF→VCF workflow).
   • Samples: 7 individuals → 13-2, 13-3, 13-4, 13-5, 13-6, 13-7, 13-8

   Data Description

    -The VCF contains standard columns: * #CHROM – Contig/chromosome * POS – 1-based position * ID – Variant identifier * REF – Reference allele * ALT – Alternate allele...,

T-box transcription factor 1 Enables protein homodimerization activity and sequence-specific double-stranded DNA binding activity. Involved in several processes, including chordate embryonic development; parathyroid gland development; and soft palate development. Predicted to be active in chromatin and nucleus. Implicated in several diseases, including DiGeorge syndrome; congenital heart disease (multiple); hypoparathyroidism; sensorineural hearing loss; and velocardiofacial syndrome. Biomarker of congenital heart disease. This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene product shares 98% amino acid sequence identity with the mouse ortholog. DiGeorge syndrome (DGS)/velocardiofacial syndrome (VCFS), a common congenital disorder characterized by neural-crest-related developmental defects, has been associated with deletions of chromosome 22q11.2, where this gene has been mapped. Studies using mouse models of DiGeorge syndrome suggest a major role for this gene in the molecular etiology of DGS/VCFS. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.

The vcf genotype for paper "Genetic dissection of QTLs for starch content in four maize DH populations". four DH populations (SC1, SC2, SC3 and SC4) developed from F1 plants of crosses among eight corresponding parents (SC*-P*). ALL lines were genotyped with the GenoBaits Maize 1K marker panel that was developed by Mol Breeding Biotechnology Co., Ltd., Shijiazhuang, China (http://www.molbreeding.com/), based on genotyping by target sequencing platform in maize.

Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.

The dataset contains files with single nucleotide variants in VCF format for a total of 58 DNA samples originating from the Northern Sweden Population Health Study (NSPHS). For each of the 58 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. The NSPHS study was approved by the local ethics committee at the University of Uppsala (Regionala Etikprövningsnämnden, Uppsala, 2005:325 and 2016-03-09). All participants gave their written informed consent to the study including the examination of environmental and genetic causes of disease in compliance with the Declaration of Helsinki.

This dataset is one of 4 datasets included in the study "SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population" (http://identifiers.org/ega.study:EGAS50000000906).

Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.

Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.

Tursiops SNP datasetSNP genotype, vcf file. Mapped to the Tursiops truncatus genome (GCA_001922835.1).mappedQC.fil5.vcfTursiops ref_seqFForward reference sequencesTur_1.fastaTursiops ref_seqRReverse reference sequencesTur_2.fasta

Variant Calling Format (VCF) files associated with the publication entitled: "Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies"