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  6. My reference genome was assembled from fragment DNA sequencing, and is highly polymorphic (with possible unidentified SNPs in the flanking regions to my SNPs of interest). Would Flex-Seq work?

FAQ

My reference genome was assembled from fragment DNA sequencing, and is highly polymorphic (with possible unidentified SNPs in the flanking regions to my SNPs of interest). Would Flex-Seq work?

Generally, compared to other targeted genotyping methods, Flex-Seq is more tolerant of known or unknown SNPs in the probe binding region. However the quantity and location of the variants can have a negative impact on probe hybridization, and can lead to increased missing data.
When the flanking SNPs are unknown, and suspected to be high, we would recommend a trial study using the fragmented draft reference genome to assess the project feasibility. In terms of probe design, a mismatch that is located in the middle of the probe is typically acceptable.