Dashboard is the page where you will be right after log in.

A: Overall status of data you uploaded are shown according to the status of each sample(A).

B: Samples with low TAT are shown in Urgent Samples section(B).

C: In Activity section, you can see changes made on samples that are assigned to you(C).

'Projects' helps you creating and managing samples depends on the projects they belong.

You can set TAT, QC threshold and list of genes you are interested differently based on projects that you are working on.

While sample upload, you can choose a project that you want to include the sample to.

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↑ Please refer to the demo guide above.

Administrator accounts(Admin) can manage roles and permissions of other users.

Features on GEBRA may differ by the permission that each user is authorized.

Multiple Admins can co-exist in a single institution.

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↑ Please refer to the demo guide above.

In Settings-Gene Panel, users may make gene panels they want.

These gene panels are used to filter the variants in genes of interest.

Users can apply panels on a project level or on a sample level. Applied panels can be removed on a sample page.

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↑ Please refer to the demo guide above.

In Settings-QC, users may set different QC criteria.

Each QC criteria may be applied to different project.

If a sample in a project doesn't meet the QC criteria, QC tab on the sample page is highlighted with a red dot.

GEBRA leverages multiple callers for variant calling and filtering.

Variant types and callers for each type are listed below (Variant Type:Variant Callers).

· SNV/indel: GATK, Mutec2

· CNV: 3bCNV, MANTA, SMAfinder

· Inversion and breakend: MANTA

· Insertion: MELT, MANTA

· Repeat expansion: ExpansionHunter

· Region(Run) of Homozygosity: AutoMap

For more details, please refer to our white paper's '3billion’s Genomic Test Services' section (whitepaper 2024 link)

EVIDENCE, developed by 3billion, is a software for fast and accurate variant annotation.

Once variant calling is over, each variant files are by annotated by EVIDENCE, referring multiple databases and guidelines.

Classification of variant pathogenicity is based on the logics of ACMG/AMP guidelines.

For more details, please refer to our white paper's 'EVIDENCE' section (whitepaper 2024 link)

In 'See details' of each variant(only for SNV at the moment, other types of variants are under construction), users may change rules applied to the variant.

Logs of changed rules are recorded on the Knowledge Base of the institution and will be applied accordingly from the next analysis.

Users can check logs in the Knowledge Base on the Dashboard.

In Prioritized variant section, variants that went through multiple layers of filters are displayed.

Filters leverage bayesian score, applied rules/criteria, ClinVar, articles, etc.

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Move the variants of All Variants to priority.

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In All variants section, every variant except for variants with high population frequency(e.g. for SNV, BA1 applied variants are not shown in All variants section).

Priortized variants are also visible in this section.

Users can 'prioritize' (or move) variants from All variants to Proiritized section to generate a report, and if needed can leave a mark in 'See details'-'ACMG Classification'-'Edit'-'Prioritize this variant regardless of classification' to prioritize the variant automatically from next analysis.