Skip to main content

Table 2 Summary of publications evaluating quality of DNA samples

From: In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network

Measurement methodAnalytical techniqueEvaluated parameterQuality stratification thresholdOrganReferences
SpectrophotometryUV spectroscopy (A260) NanoDropQuantityPancreas, spleen, duodem, liver[41]
Fluorochrome binding and fluorometer (Qubit)QuantityPancreas, spleen, duodem, liver, sarcoma, breast, gastric, colorectal, prostate, lung adenocarcinoma[41,42,43,44,45]
UV spectroscopy (A260/280) NanoDropPurity1.8–2.1 optimal, < 1.8 or > 2.1 contamination with RNA proteins or othersLung adenocarcinoma, prostate[44, 45]
UV spectroscopy (A260/230) NanoDropPurity2–2.2 optimal, lower ratios may indicate presence of contaminantsProstate[44]
ElectrophoresisPulsed field gel electrophoresisFragmentationSize distribution between 12 and 300 kb[46]
Agarose gel, and capillary electrophoresis (DNA Integrity Number, DIN)Fragmentation Pancreas, spleen, duodenum, liver, sarcoma[41, 47, 48]
PCRMultiplex PCR and dHPLC/multiplex PCR and gel electrophoresisFunctionalityPresence of the 300- to 400-bp amplicon indicates optimal quality, amplicon sizes ranging from 102 to 300 bpBrain, colon and prostate[44, 49]
Multiplex PCR and gel electrophoresisFunctionalityThreshold not defined (amplicons between 268 and 1327 bp), optimal samples with amplification of 200 bp fragment or largerColon, uterine, myometrium and liver, breast[50, 51]
Multiplex PCR and microfluidic analysisFunctionalityA QC ratio above 0.20 indicates optimal quality, ratios below 0.20 suggests moderate or poor qualityLung[52]
Multiplex digital PCR (dPCR)FunctionalityValidation needed to establish stratification thresholdsLung[53]
 qPCRFunctionalityIncreasing 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 versaLiver, breast, tongue, prostate, sarcoma, lung adenocarcinoma, breast, gastric, colorectal[43, 45, 47, 54, 55]
Multiplex qPCRFunctionalitypercentage of functional templates (QFI, ranging from 0.03 to 24.5%), optimal > 3% to 6%Different sources[56]
  1. MF (somagen diagnostics) is a mixture of methanol and polyethylene glycol (90% and 10%, respectively)