BaseSpace Variant Interpreter FAQs

Yes, but only after validating the BaseSpace Variant Interpreter software per institution, local, state, and federal guidelines before using it.

BaseSpace Interpreter and BaseSpace Hub use the same logon credentials for authentication, so logging on to 1 application logs you on to the other. After logging on to BaseSpace Interpreter, your account automatically links to your BaseSpace Hub account to allow import and viewing of variant call files stored there.

BaseSpace Variant Interpreter is a web-based application. To make sure that you can access it through your company firewall, open port 443.

BaseSpace Variant Interpreter is a Software as a Service (SaaS) solution that is accessed through a web browser, so installation is not necessary. The minimum system standards are: Chrome version 49, Firefox version 45, and Internet Explorer 11, or later.

A knowledge base content entry in BaseSpace Knowledge Network is defined as an association between a genetic biomarker (such as a variant), and a phenotypic content (such as a disease). Each association can contain multiple pieces of evidence (such as a publication, clinical trial, or statistical measure) to support the association.

No, BaseSpace Knowledge Network provides Research Use Only content that is focused on expediting interpretation of variants.

Each content entry in BaseSpace Knowledge Network is stamped with an entry date parameter, indicating the creation date of the curated entry.

The first release of BaseSpace Knowledge Network contains content curated by the Illumina Scientific Research Curation team. For more information on the content and the process that generated it, see BaseSpace Knowledge Network.

BaseSpace Variant Interpreter uses the following annotation sources: dbSNP, Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, 1000 Genomes, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), PolyPhen, and SIFT.

No, BaseSpace Variant Interpreter does not currently support direct comparison of analysis results from two different samples.

No. The software uses the following default classification schemes for tumor and germline samples:

• Somatic analysis—FDA guidance available, general guidance available, inclusion criteria for clinical trial, and other reportable variant.
• Germline analysis—Pathogenic, Likely Pathogenic, Variant of Unknown Significance (VUS), Likely Benign, and Benign. These categories follow ACMG guidelines.

No. For germline variants, the software uses a simple rule set to predict the classification:

• Variants are automatically ranked and prioritized based on their annotations, predicted consequence (loss of function, missense, or noncoding) and population allele frequency (using the highest frequency from ExAC, 1000 Genomes, and EVS).
• Variants are typically assigned the ClinVar pathogenicity unless the variant is greater than 5% population frequency, in which case they are assigned Benign per ACMG guidelines.
• Variants without ClinVar entries that are common (over 1% population frequency) are assigned Likely Benign.
• Variants without ClinVar entries that are uncommon (less than 1% population allele frequency) are assigned Likely Pathogenic if loss-of-function (frameshift, stop-gained or essential splice), VUS if a missense or near-splice, and Likely Benign if noncoding.

This pathogenicity autoscoring is only a suggestion. Review these predictions, the provided annotations, and all evidence for the variant before assigning your final interpretation.

When both alleles of a heterozygous position are different from the reference, as in a tri-allelic position, the variants are split into 2 lines and both variants are annotated.

No. BaseSpace Variant Interpreter does not support comparisons of two or more groups of samples. Use BaseSpace Cohort Analyzer for cohort or population analysis.

Batch uploads from a network or local directory are limited to 100 files or 10 GB, whichever is greater. There are no limits on importing files from BaseSpace Sequence Hub.