What do you recommend for starting input?
Twist recommends starting with 30 ng of starting input. 20-30 ng is a typical range for liquid biopsy assay.
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Synthetic Controls
cfDNA Pan-cancer
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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?
