1:30-3:00pm

Round Table Discussion – cfDNA - #4

Measurement Technology Platforms – Analytical and Diagnostic Sensitivity and Specificity; Implications for Early-Cancer Detection

1. Whole Genome Sequencing

a) DNA somatic copy number alterations

b) Fragment endpoints

c) Fragment length

d) Allelic imbalance

2. Whole Genome Sequencing + Targeted NGS

a) Short and long fragment coverage characteristics

b) chromosomal arm copy number changes

c) mitochondrial copy numbers

d) small somatic variants

3. Targeted quantitative PCR

a) Single nucleotide variants

b) Small insertions and deletions

4. Methylation-specific sequencing

a) Whole genome bisulfite sequencing

b) Reduced representation bisulfite sequencing (RRBS) + Targeted NGS

c) Na-BS treatment + qRT-PCR

d) Na-BS treatment + non-targeted/targeted NGS

e) Immunoprecipitation enrichment + qRT-PCR or NGS

Preanalytical and Analytical Variables for cfDNA analysis

1. Mechanisms of shedding – pre-cancer vs cancer and indolent vs aggressive cancer
2. Stability of cfDNA and biological specimen to be analyzed – blood, saliva, urine, others
3. Blood collection tube (e.g., Streck or K2-EDTA) and volume requirements
4. QA/QC considerations
5. Single-organ site vs multi-cancer detection assays
6. Validation of methods and assays – reproducibility, cross-laboratory verification, generalizability
7. Cost

Computational and Bioinformatics tools and approaches

1. ML/DL/AI
2. Training, verification, and validation of analytical tools and pipelines
3. Data capture, storage, and sharing
4. Cost