Although other methods exist for ultra high resolution gene typing, the Base5 Data Generator is different in a number of ways: A single assay for any or all multimegabase regions of interest (e.g. MHC, KIR, and NKC) containing 100s of genes Novel allele detection - we sequence each gene at single base resolution, which allows us to detect and report novel alleles Phasing information across the entire region - where other platforms can at most phase single genes, Base5’s Data Generator can phase across the entire region revealing multimegabase haplotypes, e.g. HLA-DRA alleles phased with HLA-DQB2 alleles and all HLA alleles in between. Minimal bias - bias-free enrichment, no amplification, no allele dropout, reference-free assembly, allele calling from de novo assembly.

Cultured cells (10 million +) Whole Blood (2 mL +)

The Data Generator platform is target agnostic, so we can target any or multiple regions of interest in the human genome. The ideal region size ranges from 50 kilobases to 5 megabases. We routinely target MHC (HLA), KIR, extended LRC, NKC, CYP2D6.

2-3 weeks from receipt of the samples

No, the Data Generator is suited for RUO.

Base5’s Insight Lens is a force multiplier to existing methods for short read sequencing data, including variant detection, HLA/KIR typing, imputation and GWAS fine-mapping. Insight Lens’ superior performance stems from the most complete pan-immunogenome reference constructed by the Data Generator. Furthermore, Data Generator customers can gain important context for their results with the Insight Lens pan-immunogenome graph. Base5’s Discovery Engine is currently in development, but is coming soon - it will take the field to a new era by leveraging unmatched data quality with machine learning powered analysis to find and interpret altogether new information.

Although, our current product offering are for human samples, the underlying technology is more widely applicable. Feel free to reach out if you want to hear more.

The imputation server accepts, preferably gzipped, VCF-files as well as 23andMe or Ancestry TXT-files. For VCF format, the imputation server accepts a gzipped VCF-file (recommended) or a VCF-file for a single chromosome (chromosome 6). Coordinates should be NCBI36, GRCh37 or GRCh38. You may further filter your VCF file to include only the MHC region (GRCh38 chr6:28509120-33481577 | GRCh37 chr6:28476897-33449354 | NCBI36 chr6:28585776-33556332). For 23andMe or Ancestry files, the imputation server accepts a gzipped TXT-file (recommended) or a TXT-file. Coordinates should be NCBI36, GRCh37 or GRCh38. This is indicated in the header of the file, where it will say assembly or reference build 36, 37, or 38, which corresponds to NCBI36, GRCh37 or GRCh38 respectively. You may filter the file to only contain chromosome 6.

We accept VCF files with 1 to 100 samples. Contact us if you would like to submit a job with more than 100 samples. 23andMe and Ancestry files contain one sample per file.

It typically takes just a couple of minutes before you receive an email with a link to your result. If you submit a lot of samples it may take up to 10 minutes. Your can view the status of your job in the jobs table.

When your job finishes you get an email with a link to download your results. You can also find the link to download your results in the jobs table. The link expires after 24 hours. The link will download a password protected compressed archive (zip). The password required to unzip the archive is provided in the email. If you are having trouble downloading the file, copy the link address of the download button and paste it into your browser. You may have some security settings preventing the download to go through directly.

Yes, you can use this file. It contains variant calls for the 7 NIST GIAB samples subset for the ThermoFisher PMDA array. You will need to select GRCh38 as the array built.

Yes, you can share the Early Access Program landing page and password with people in your network. Please keep in mind, however, that as stated in our terms of use we are not compliant for non-US samples at this moment.