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Base5 Data Generator

Our Sample-to-Solution workflow delivers ground truth resolution in complex immunogenomic regions to enable better clinical outcomes



What We Consume

  • Large (200kb-4Mb) genomic  targets

  • Multiple targets in same tube (e.g. MHC + KIR, LRC, NKC) 


A Sample 

  • Cultured cells (10 million +)

  • Whole Blood (2 mL +)



Our 3-Stage Process

Bias free high molecular weight enrichment


High accuracy, 8kb -20kb+ reads 


Reference-free assembly and phasing 



What We Produce

All genomic sequencing information, including: 

  • Phased allele calls

  • Novel allele detection

  • Full length haplotypes 


Full-stack platform ~3 weeks turnaround time from sample delivery to report


Best foundation for any downstream analysis

Unprecedented resolution in the MHC/HLA locus 

Fully contiguous full length haplotype resolved de novo MHC assemblies for heterozygous samples 

  • Entire MHC locus assembled with single-base resolution for both haplotypes

  • 4-field allele resolution over 4.5mb assembled region

  • Phasing possible for allele calls over entire MHC region

  • Exact mapping for structural variants

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Unprecedented resolution in the KIR region

Fully contiguous phased KIR haplotypes for heterozygous samples

  • Entire 250kb KIR locus assembled and phased with single basepair resolution for both haplotypes

  • KIR allele calls at highest possible resolution (7-digits) including novel allele detection

  • Full phasing and haplotyping of all genes across the entire KIR locus

  • Exact mapping and characterization of structural variants such as gene-block tandem repeats

  • Full visibility into intergenic regions

  • No other methods reveal this level of clarity

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  • How is Base5's Data Generator different?
    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.
  • What kinds of samples can Base5’s Data Generator process?
    Cultured cells (10 million +) Whole Blood (2 mL +)
  • What regions can Base5’s Data Generator target?
    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.
  • What is the turn-around-time?
    2-3 weeks from receipt of the samples
  • Is Base5’s Data Generator CLIA certified?
    No, the Data Generator is suited for RUO.
  • What other products does Base5 offer?
    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.
  • Is Base5 Genomics restricted to human samples?
    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.

Want to Learn More?

We would love to meet with you and talk about how Base5 can supercharge your development capabilities.

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