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Comparing StrainSEEK® v2 to StrainSEEK® v1

The data from early and current versions of strainSEEK® are comparable in principle, but in reality it would be a huge effort and not very valuable.

StrainSEEK® V2, the current version we have been running since late 2017,  has some notable improvements over StrainSEEK® V1 (the first iteration of our sequencing panel) :
  1. The target capture in StrainSEEK® V2 uses an Agilent SureSelect probe-based capture instead of the amplicon-based capture used in StrainSEEK® V1. The probe-based captured reads are more random, and better represent the plant's genome.
  2. StrainSEEK® V2 samples are mapped to the Jamaican Lion reference, which is much more complete than the CanSat3 genome used for V1 samples. The Jamaican Lion reference genome also contains many interesting genes, such as CBDAS, THCAS, and many more. The Jamaican Lion reference makes mapping sequence reads to the right positions much easier and improves variant calling.
  3. StrainSEEK® V2 samples are analyzed using Illumina's Dragen Bio-IT platform. Dragen is based on Illumina's Field-Programmable Gate Array Technology, and it set the speed record for genomic analysis. It is also very accurate. In the 2018 PrecisionFDA Hidden Treasures – Warm Up Challenge, The DRAGEN Platform received the highest score in five out of six accuracy measures for whole-genome variant calling among platforms that recognized all 50 variants.
These upgrades make our analysis more robust, while also reducing the amount of post-analysis filtering we need to perform. However, the differences make it difficult to compare StrainSEEK V1 results to StrainSEEK V2 results. This is because the Dragen platform prefers probe-based capture to amplicon-based capture. We have asked Illumina to support amplicon-based analysis, and they agreed; however, they need time to implement. Until then, if a customer wants to compare a newly submitted sample to a previously sequenced StrainSEEK V1 sample (pre-2018), we would need to re-run the old sample, using the v2 probe-based capture so it can be analyzed with the Dragen platform. This would incur a cost and it would be dependent on us having enough genomic DNA material saved from the original extraction to re-process. Please contact support@medicinalgenomics.com for any additional questions.