2. How to submit

KVar submission: BioProject - BioSample - KVar

• BioProject : Summary of the conducted research project, which is mandatory to complete

• BioSample : Select the sample type of the biological specimen used in the research and insert the corresponding biological information

• KVar : The form for uploading variant data (SNPs or structural variants) with related metadata, including the option to specify the release date.

Data model

The KVar metadata framework is designed to describe all contextual information necessary to interpret variant data — from study design and population structure to experimental methods and submitted datasets.

Data model of KVar

• Study records the overall context of the submission, including the study variant type (SNP or SV), title, description, release information, submitter details (name, email, affiliation), and publication references (PubMed ID, DOI).

• SampleSet defines a biological or analytical group of samples, describing its size, population, and type (Case or Control). This unit serves as the basis for cohort-level or population-based comparisons.

• Sample provides specimen-level information, linking either to an existing BioSample accession or to a newly registered sample name, and includes the sample’s description and population metadata.

• Experiment captures technical and analytical details used for variant detection, including method and analysis type, reference assembly, detection platform, and methodological description.

• DataSet is the final variant object submitted to KVar, integrating information from related SampleSets and Experiments, and including variant type, molecular type, description, and linked variant file (VCF or Excel format).

  • Variant Call (SV) Refers to individual structural variant events (> 50 bp), including deletions (DEL), duplications (DUP), insertions (INS), inversions (INV), translocations (BND), and copy number variants (CNV).

  • Variant Region (SV) Defines a genomic region encompassing one or more Variant Calls that share overlapping coordinates or supporting evidence.

Pre-requisites

• Sequencing-based data only KVar accepts only sequencing-derived variation data (e.g., NGS or long-read sequencing). Data generated from hybridization-based detection methods such as microarrays are not accepted.

• Single variant type per Study Each Study can include only one variant type — either SNP or SV — to maintain data consistency.

  • When the study variant type is SNP, only variants ≤ 50 bp in length should be included in the variation file.

  • When the study variant type is SV, only variants > 50 bp should be included.

• Accepted file formats Variant files must be uploaded through GBox in either VCF or Excel (.xlsx) format. For VCF submissions, compressed files in .vcf.gz format are recommended. For detailed specifications, refer to the File Format Guide. For step-by-step instructions on file submission, please refer to KVar File Upload.

• Reference genome requirement (for human data) For human variant data, only datasets aligned to the GRCh38 reference genome are accepted. Submissions based on other reference assemblies will not be processed.

• Human-data compliance with the Bioethics and Safety Act In accordance with the Korean Bioethics and Safety Act, KVar does not accept individual-level genotypes or allele-frequency data for human subjects. All human submissions must report variant information at the cohort or population level only.

• BioProject restrictions Once a certificate for R&D outcomes has been issued, no additional submissions can be made under that BioProject. To register new data, please create a new BioProject and submit under that project.

• Updating existing records To update or correct an existing record, do not resubmit the data files. Instead, contact the KVar team at [e-mail] for assistance.

Contact KVar staff

Before contacting KVar staff for assistance please see our Frequently asked question. Please provide your submission's temporary ID in the form of DSUB#in your messages.

Email [e-mail] for help.