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• What is your background cfDNA made from?
• Could there be some mutation ‘contaminants’ coming from the background DNA as well?
• Is your background cfDNA limited supply?
• How do you perform quality control on the reference standards?
• Are these control oligos, RNA, what is in it/ components?
• How do you design the ctDNA/ variant list?
• What is the molecular structure of the 3′ and 5′ termini?
• Were the mutations in the standards confirmed by NGS as well, as with digital PCR as it says in the document?
• Recommendations for diluting the controls?
• Can’t find indel or other hard to detect variants?
• What reagents (e.g, library prep) do you use for the liquid biopsy workflow?
• What do you recommend for starting input?
• Do you recommend pooling this control with a patient sample after library prep, before NGS?
• The variant (COSM214499) is always high in 0% in NGS QC results, why?
• For NGS QC, do you use target capture sequence for the 456 variants, or use a whole genome sequence?
• 456 variants are all in one tube, or subsets?
• What are the kit configurations of the cfDNA standards?