Lentiviral Integration Risk Track (2D)

Vector Design

Residual LTR enhancer/promoter strength 30%

Target-cell proliferation pressure 20%

Vector dose per batch 15 particles

Delivery

Live Readouts

Integrations

Genotoxic hits

Estimated clonal-dominance risk

0.0%

How it works

This is a 2D linearized-genome-track rendition of the same lentiviral integration-site model as the 3D chromatin-loop version: the 48-locus loop is unrolled onto a horizontal ruler, but distances between loci are still measured around the loop (circular distance), so the underlying math is identical, only the picture is flat.

P(integrate at bin i) = activity(i) / Σ activity(j)
risk(i) = E · exp( -(d / 1.2)² )
  E = enhancer strength (0–1), d = circular distance in loci to nearest oncogene
P(clonal dominance) = 1 − exp( −k · ΣE risk · (1 + 3·proliferation) ), k = 0.12

Genome track (top) — bar height = local transcriptional activity; red-ringed bars mark the four proto-oncogene TSS zones. Falling capsids land on their weighted-random target bin and stack as lollipop markers (green = safe, amber = borderline, red = genotoxic hit).
Risk time series (bottom) — plots the running clonal-dominance-risk percentage against every individual integration event, so you can watch the curve bend upward the moment a hot hit lands near an oncogene.
SIN (self-inactivating) design — deletes the U3 enhancer/promoter from the 3′ LTR; toggling it on caps residual enhancer strength at 15% of the slider value, mirroring modern clinical lentiviral vectors.
LTR-intact design — the historical (non-SIN, gammaretroviral-style) configuration used in the earliest X-SCID trials, where a strong LTR enhancer landing near LMO2 transactivated it and triggered leukemic clonal expansion in several patients.

This is a simplified, illustrative model of a real and well-documented safety mechanism in gene therapy — it is not a quantitative predictor for any specific clinical vector.

Chromatin locus (low activity) Chromatin locus (high activity) Proto-oncogene TSS zone Safe integration Genotoxic hit

Awaiting delivery…