Table 2 Summary of publications evaluating quality of DNA samples
Measurement method | Analytical technique | Evaluated parameter | Quality stratification threshold | Organ | References |
|---|---|---|---|---|---|
Spectrophotometry | UV spectroscopy (A260) NanoDrop | Quantity | – | Pancreas, spleen, duodem, liver | [41] |
Fluorochrome binding and fluorometer (Qubit) | Quantity | – | Pancreas, spleen, duodem, liver, sarcoma, breast, gastric, colorectal, prostate, lung adenocarcinoma | ||
UV spectroscopy (A260/280) NanoDrop | Purity | 1.8–2.1 optimal, < 1.8 or > 2.1 contamination with RNA proteins or others | Lung adenocarcinoma, prostate | ||
UV spectroscopy (A260/230) NanoDrop | Purity | 2–2.2 optimal, lower ratios may indicate presence of contaminants | Prostate | [44] | |
Electrophoresis | Pulsed field gel electrophoresis | Fragmentation | Size distribution between 12 and 300 kb | – | [46] |
Agarose gel, and capillary electrophoresis (DNA Integrity Number, DIN) | Fragmentation | Â | Pancreas, spleen, duodenum, liver, sarcoma | ||
PCR | Multiplex PCR and dHPLC/multiplex PCR and gel electrophoresis | Functionality | Presence of the 300- to 400-bp amplicon indicates optimal quality, amplicon sizes ranging from 102 to 300Â bp | Brain, colon and prostate | |
Multiplex PCR and gel electrophoresis | Functionality | Threshold not defined (amplicons between 268 and 1327Â bp), optimal samples with amplification of 200Â bp fragment or larger | Colon, uterine, myometrium and liver, breast | ||
Multiplex PCR and microfluidic analysis | Functionality | A QC ratio above 0.20 indicates optimal quality, ratios below 0.20 suggests moderate or poor quality | Lung | [52] | |
Multiplex digital PCR (dPCR) | Functionality | Validation needed to establish stratification thresholds | Lung | [53] | |
|  | qPCR | Functionality | Increasing qPCR ratio between frozen and FFPE tissue samples, 93 bp human GAPDH qPCR, detection of 18S5 rRNA by qPCR (CT-value < 38), qPCR using FFPE QC kit and PreSeq QC assay, Q-ratio (with a value between 0 and 1), in which 41 bp and 129 bp targets were amplified by qPCR (KAPA human genomic DNA quantification and QC Kit-KAPA Biosystems). High Q-ratio: less fragmentation and vice versa | Liver, breast, tongue, prostate, sarcoma, lung adenocarcinoma, breast, gastric, colorectal | |
Multiplex qPCR | Functionality | percentage of functional templates (QFI, ranging from 0.03 to 24.5%), optimal > 3% to 6% | Different sources | [56] |