Degradation Index (DI)
Definition
The ratio of large-amplicon to small-amplicon Cq values in Quantifiler Trio or equivalent kits; a DI above ~3 indicates significant fragmentation of the template DNA.
- Kit
- Quantifiler Trio (or equivalent qPCR kits)
- Basis
- Large-amplicon vs small-amplicon Cq values
- Threshold
- DI above roughly 3 flags significant fragmentation
Common questions
Why does a large DI value matter for downstream STR typing?+
A high DI signals that the DNA template is fragmented, which predicts allele dropout and imbalanced peak heights at larger STR loci, so analysts may switch to a mini-STR or degraded-sample kit.
Why compare large and small amplicons instead of just total DNA yield?+
Total yield does not show whether the DNA is intact or fragmented; comparing amplification efficiency at a large target against a small target reveals fragmentation because degraded template amplifies poorly at longer targets.
Related terms
- A260/A280 Ratio
- Absorbance ratio at 260 nm and 280 nm used to assess nucleic acid purity. Values of 1.7-1.9 indicate pure DNA; lower values...
- Cq (Cycle Threshold)
- The PCR cycle at which fluorescence crosses a defined threshold; inversely proportional to starting template concentration and used to calculate DNA quantity...
- InnoQuant HY
- Human-specific qPCR quantitation kit with internal PCR control, providing autosomal and Y quantitation plus degradation index; widely used in Japanese and East...
- PicoGreen
- SYBR Green I-related fluorescent dye that intercalates specifically into double-stranded DNA, used for sensitive fluorometric quantitation in plate-reader or Qubit formats.
- Plexor HY
- Promega qPCR quantitation kit using isoguanosine/isocytidine quenching chemistry, providing autosomal and Y-chromosome quantitation with degradation index.
- QuantiBlot
- Human-specific slot-blot quantitation kit (Applied Biosystems) using a probe directed at the D17Z1 alpha-satellite repeat on chromosome 17.
- Quantifiler Trio
- Applied Biosystems qPCR kit reporting autosomal total DNA (small + large amplicon targets) and a Y-chromosome target, with a computed Degradation Index...