Frequently Asked Questions
Medical GeneticsGermline AnalysisSomatic OncologyTrio AnalysisPharmacogenomicsCarrier ScreeningPrenatal AnalysisMitochondrial DNAExome Analysis
General Information
Allelyn is an end-to-end genetic variant analysis platform running on NVIDIA DGX Spark or DGX Server. It takes FASTQ or VCF files from your sequencer and automatically performs alignment, variant calling, annotation, ACMG/AMP classification, and clinical report generation. The entire process is completed in your laboratory without needing a bioinformatician or cloud connection.
No, it is not mandatory. Allelyn supports both FASTQ and VCF formats. If you don't have your own NGS device, you can analyze VCF files obtained from external laboratories. If you have an NGS device, the entire pipeline runs automatically from the FASTQ file.
Illumina (MiSeq, NextSeq, NovaSeq), MGI (DNBSEQ-G400, DNBSEQ-T7), Ion Torrent, and all platforms producing standard FASTQ/VCF output are supported. No device-specific adapters are needed — standard FASTQ format is sufficient.
Allelyn supports 8 analysis types: Germline analysis, Somatic/Oncology analysis, Trio (family) analysis, Pharmacogenomics, Carrier screening, Prenatal analysis, Mitochondrial DNA analysis, and whole Exome analysis. Each analysis type includes automated classification with 28 ACMG/AMP criteria.
With the GPU-accelerated pipeline, a single patient panel analysis takes under 5 minutes, WES (whole exome) analysis approximately 15 minutes, and whole genome analysis 45 minutes. The annotation engine matches 50,000 variants against 15 reference databases in under 1 second.
Licensing & Solutions
Allelyn ONE runs on NVIDIA DGX Spark and is a desktop solution ideal for small to mid-size laboratories — compact enough to fit on any desk. Allelyn Server runs on NVIDIA DGX Server and is an enterprise solution designed for large hospitals and reference laboratories with high-volume analysis needs.
We operate on an annual license model. The license is device-based and offers unlimited tests — panel, exome, or genome. Monthly database updates and technical support are included. Contact us for a custom quote for your laboratory.
Security & Compliance
Yes, 100% safe. Allelyn operates completely offline — patient data never leaves the device. No data is sent to the cloud, internet, or external servers. The platform is fully compliant with KVKK (Turkish data protection law), GDPR, and HIPAA. ISO 15189 compliant audit trails are maintained.
No. Allelyn operates completely offline. All reference databases (ClinVar, gnomAD, COSMIC, dbSNP, OMIM, PharmGKB, SpliceAI, CADD, REVEL, AlphaMissense, etc.) are stored locally on the device. Database updates are delivered securely via USB or local network.
Technical Details
Device setup and staff training are completed within half a day. You can start analyzing the same day. During setup, all reference databases are loaded, pipeline configuration is done, and validation is performed with a sample analysis.
Allelyn integrates with 15 reference databases: ClinVar, gnomAD (v4), dbSNP, OMIM, COSMIC, PharmGKB, SpliceAI, CADD, REVEL, AlphaMissense, DANN, InterVar, Franklin, HGMD (licensed), and INFEVERS. All databases are regularly updated.
Allelyn generates ready-to-sign clinical reports in both Turkish and English. Reports are created in PDF format and can be directly presented to clinicians. They are fully compliant with HGVS nomenclature and ACMG/AMP classification standards.