AION requirements
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      1. AION guide
      2. AION - Instructions for Use
      3. AION requirements

      Variant type, genomic regions and sequencing technologies

      AION assumes best practices in secondary analysis. Specifically, we assume that trios and other pedigrees are jointly called.

      Variant types

      AION supports automatic prioritisation of WES and WGS data containing:

      • Single Nucleotide Variants (SNVs) and polymorphisms (SNPs)

      • Insertions or deletions (Indels). There is no explicit threshold for INDELs size as that depends on the secondary analysis pipeline. INDELs cannot be part of a CNV or SV (i.e. they need to contain REF and ALT fields with nucleotide data)

      • Copy Number Variations (CNVs) are supported. Input data must adhere to the VCF requirements page.

      • Structural Variations (SVs) are supported. Input data must adhere to the VCF requirements page.

      Genomic regions

      The supported regions for prioritisation are:

      • Coding regions

      • ±50bp around coding regions

      • Known variants from ClinVar outside of these regions are also included in the analysis

      This means that with WGS data, no deep intronic variants will be automatically prioritised. Instead, the results will cover approximately the same regions for WES and WGS data.

      AION supports gene panel data prioritisation as long as there is data within the supported regions.

      Sequencing technologies

      AION is optimized for Next Generation Sequencing (NGS) data from short-read platforms, particularly Illumina technology.  It is specifically designed to provide high-quality results when used with these technologies. However, the following limitations apply regarding other sequencing platforms:

      • Long-Read Platforms: Data from long-read sequencing technologies has not been fully tested with AION. If you intend to use long-read data, we recommend contacting our support team to troubleshoot potential issues and ensure high-quality results.
      • IonTorrent Platforms: While data from IonTorrent platforms and their derivatives are supported, they have been known to produce significant artifacts. We strongly advise users to filter their VCF data for common platform-specific artifacts before using it with AION. 
      • Artifact Detection: Different sequencing platforms generate distinct artifact profiles. AION’s quality control module includes tools to detect potential artifacts associated with specific sequencing technologies. See AION’s Limitations of use/ Contraindications section. 
      • Variant Filtering: While AION’s variant database excludes platform-related sequencing artifacts, we do not apply additional filtering to the quality of variants, relying instead on the thresholds set by the secondary analysis pipelines. These pipelines may vary between platforms, so users should ensure that their data has undergone proper quality filtering.
      • Ongoing Improvements: We are continuously working to improve platform support by incorporating data to fully differentiate between platforms, we are actively collecting and analyzing new information.

      For further details, including our control artifact list , and platform-specific artifact handling, please consult the relevant sections in the Instructions for Use (IFU, AION’s Limitations of use/ Contraindications).

      AION’s compatibility with certain sequencing platforms may evolve as we gather more data and feedback from users. We encourage users to remain in close communication to ensure optimal performance with their specific sequencing setup.