Question: Can I use the Targeted Gene Expression assay to detect specific polymorphisms?
Answer: We have not performed any in-house tests to determine whether the Targeted Gene Expression assay can be used to detect polymorphisms, such as indels or SNPs. In addition, SNP or indel calling from Targeted Gene Expression data will require additional bioinformatic expertise and is not part of the Cell Ranger or Space Ranger pipelines.
In theory, genotype-specific baits could be designed by entering a FASTA sequence for the region of the transcript that contains SNPs or indels as an “exogenous sequence” in the 10x Genomics Custom Panel Designer.
However, it is important to note that baits are likely to tolerate a few mismatches during hybridization. We have not specifically tested this in-house, but a report from Twist Biosciences suggests that baits may tolerate short indels or a few single mismatches in hybridization/capture-based enrichment assays. Therefore, it is possible that the same bait will hybridize to library fragments derived from wild-type transcripts as well as those derived from transcripts containing SNPs or short indels.
Another point to consider is that the Single Cell 3' or 5' Gene Expression libraries or Visium Spatial Gene Expression libraries that are used as input into the Targeted Gene Expression assay are generated by capturing the 3’ or 5' ends of transcripts. Therefore, if a SNP or indel lies far from the 3' or 5' end of the transcript, it may not be represented in the parent Single Cell or Spatial Gene Expression library, and therefore would also not be represented in the Targeted Library.
Note: The Targeted Gene Expression assay has been discontinued. For alternative options, please see: What options are there for performing a targeted enrichment for my gene expression libraries?
Products: Targeted Gene Expression