transplant rejection

Is the transplanted organ being injured now?
512 draws (Python, shipped) · recomputed in 276 ms
headline

Informative molecules from graft luminal

6,456 (1,079–25,200) informative molecules of graft luminal reach the detector, against 1.0e5 needed.

  • Detection at the operating donor fraction of 10%, donor-fraction readout: 100% (100%–100%).
  • Limit of detection at 95%: 5.4% (2.7%–11.9%).
  • Feasibility ratio, achieved over required molecules: 0.0646 (0.0108–0.252).
  • The median draw carries fewer informative molecules than the assay class needs (1.0e5), so this is an architectural failure: no optimisation of depth fixes it.
requiredurothelium6,783 (1,134–26,478)renal tubule672 (112–2,625)leukocyte0.0717 (0.00346–1.06)hepatocyte0.0312 (0.00148–0.451)graft luminal6,456 (1,079–25,200)graft transrenal0.192 (0.00923–2.78)0.0010.010.11101001,00010,000informative molecules in the tube (GE)
Median, 25–75% box and 5–95% whisker over 512 draws. The target source is drawn solid.
funnel

From shedding to the detector

5.5e6 genome equivalents of graft luminal shed a day become 6,456 informative in the tube: 2.9 decades lost, the steepest drop at M1 in the collected urine, which keeps 3.25%.

under 60 bp60–100 bp100–170 bp170–300 bp300 bp and longer1,0001e51e7genome equivalents of the target source, log scaleunder 60 bp: 6.9e5 GE at M0 to 22,565 GE at M160–100 bp: 1.4e6 GE at M0 to 44,391 GE at M1100–170 bp: 1.8e6 GE at M0 to 58,218 GE at M1170–300 bp: 1.2e6 GE at M0 to 40,080 GE at M1300 bp and longer: 4.4e5 GE at M0 to 14,208 GE at M1−96.7%dilution: 50 mL of the day's urinekept 3.25% (1.85%–5.95%)under 60 bp: 22,565 GE at M1 to 22,565 GE at M260–100 bp: 44,391 GE at M1 to 44,391 GE at M2100–170 bp: 58,218 GE at M1 to 58,218 GE at M2170–300 bp: 40,080 GE at M1 to 40,080 GE at M2300 bp and longer: 14,208 GE at M1 to 14,208 GE at M20%no sieve on the luminal routekept 100% (100%–100%)under 60 bp: 22,565 GE at M2 to 68,492 GE at M360–100 bp: 44,391 GE at M2 to 63,551 GE at M3100–170 bp: 58,218 GE at M2 to 37,305 GE at M3170–300 bp: 40,080 GE at M2 to 9,257 GE at M3300 bp and longer: 14,208 GE at M2 to 857 GE at M3−<0.01%the nuclease: the leak below the gridkept 100% (100%–100%)under 60 bp: 68,492 GE at M3 to 24,040 GE at M460–100 bp: 63,551 GE at M3 to 33,923 GE at M4100–170 bp: 37,305 GE at M3 to 24,194 GE at M4170–300 bp: 9,257 GE at M3 to 6,572 GE at M4300 bp and longer: 857 GE at M3 to 626 GE at M4−48.2%void capture and the kit's recoverykept 51.8% (19.5%–116%)under 60 bp: 24,040 GE at M4 to 215 GE at M560–100 bp: 33,923 GE at M4 to 1,425 GE at M5100–170 bp: 24,194 GE at M4 to 3,143 GE at M5170–300 bp: 6,572 GE at M4 to 1,485 GE at M5300 bp and longer: 626 GE at M4 to 188 GE at M5−92.9%library conversion and the footprint gatekept 7.11% (2.46%–14.8%)M0 shed5.5e6 GE a dayM0 shed · under 60 bp: 12.6%, 6.9e5 GE a dayM0 shed · 60–100 bp: 24.7%, 1.4e6 GE a dayM0 shed · 100–170 bp: 32.4%, 1.8e6 GE a dayM0 shed · 170–300 bp: 22.3%, 1.2e6 GE a dayM0 shed · 300 bp and longer: 7.92%, 4.4e5 GE a dayM1 in the collected urine1.8e5 GEM1 in the collected urine · under 60 bp: 12.6%, 22,565 GEM1 in the collected urine · 60–100 bp: 24.7%, 44,391 GEM1 in the collected urine · 100–170 bp: 32.4%, 58,218 GEM1 in the collected urine · 170–300 bp: 22.3%, 40,080 GEM1 in the collected urine · 300 bp and longer: 7.92%, 14,208 GEM2 past the sieve1.8e5 GEM2 past the sieve · under 60 bp: 12.6%, 22,565 GEM2 past the sieve · 60–100 bp: 24.7%, 44,391 GEM2 past the sieve · 100–170 bp: 32.4%, 58,218 GEM2 past the sieve · 170–300 bp: 22.3%, 40,080 GEM2 past the sieve · 300 bp and longer: 7.92%, 14,208 GEM3 after the nuclease1.8e5 GEM3 after the nuclease · under 60 bp: 38.2%, 68,492 GEM3 after the nuclease · 60–100 bp: 35.4%, 63,551 GEM3 after the nuclease · 100–170 bp: 20.8%, 37,305 GEM3 after the nuclease · 170–300 bp: 5.16%, 9,257 GEM3 after the nuclease · 300 bp and longer: 0.477%, 857 GEM4 collected and extracted89,356 GEM4 collected and extracted · under 60 bp: 26.9%, 24,040 GEM4 collected and extracted · 60–100 bp: 38%, 33,923 GEM4 collected and extracted · 100–170 bp: 27.1%, 24,194 GEM4 collected and extracted · 170–300 bp: 7.36%, 6,572 GEM4 collected and extracted · 300 bp and longer: 0.701%, 626 GEM5 informative6,456 GEM5 informative · under 60 bp: 3.33%, 215 GEM5 informative · 60–100 bp: 22.1%, 1,425 GEM5 informative · 100–170 bp: 48.7%, 3,143 GEM5 informative · 170–300 bp: 23%, 1,485 GEM5 informative · 300 bp and longer: 2.91%, 188 GErequired 1.0e5
Each stop is the median over draws of the target source's genome equivalents, its width on a log scale, so equal tapers are equal factors wherever they happen. The whisker at each stop is the 5–95% spread. The ribbons carry the length classes through; the grey behind them is what the stage removed. Hover a ribbon or a stop for its numbers.
  • What gets through at M5: 25.4% shorter than 100 bp, 48.7% between 100 and 170 bp, 25.9% longer.
  • The neck against the requirement: 6,456 informative against 1.0e5 needed, the neck does not reach it at the median.
detection

Detection probability against donor fraction

The curve says where the assay starts to work; the band says how sure the priors are of it.

00.20.40.60.81donor-fraction readout (median, 5–95%)operating pointprobability of detection0.0050.010.020.050.10.20.5donor fraction
Median with the 5–95% band over draws, at the current collection and assay. The graft's own share of the mapped molecules is 46.4% (46.4%–46.4%); detection is a rise above the stable baseline.
00.250.50.751donor-fraction readoutoperating pointshare of draws0.020.050.10.2limit of detection at 95% (donor fraction)
Cumulative share of draws whose 95% limit of detection lies below each donor fraction. Draws that never reach 95% are counted as unreachable.
cascade

Where the molecules of graft luminal go

The largest single loss at the medians is M5 informative (post-footprint), which removes 92.8% of what reaches it.

M1 shed and diluted3,589 (2,039–6,572)M2 past the sieve3,589 (2,039–6,572)M3 after the nuclease3,589 (2,039–6,571)M4 collected and extracted1,787 (602–5,762)M5 informative (post-footprint)129 (21.6–504)20501002005001,0002,0005,000genome equivalents per mL of urine
Each stage's total for the target source, in GE/mL. M3 only redistributes mass over length, so its loss is the sub-detectable leak; the footprint gate at M5 is where a long amplicon costs the most.
  • Extracted DNA yield, all sources: 12.9 (4.34–41.5) ng/mL.
  • Median fragment length of the extracted population: 65 (50–80) bp.
length

What the nuclease and the footprint leave

The population after M3 sits far below the footprint for most of its molecules; the informative population is the tail the assay can still read.

00.020.040.060.080.1after the nuclease (M3) (median, 5–95%)informative (M5) (median, 5–95%)footprintshare of molecules per bin2004006008001,000fragment length (bp)
Weighted mean over draws of each draw's normalised molecule-count profile for the target source.
design

Collected volume against assay footprint

Each cell replays the same draws through one design; the comparison is between designs, not between samplings.

volume \ footprint30 bp45 bp60 bp90 bp
10 mL100%
100%–100%
3,631 mol.		100%
100%–100%
2,676 mol.		100%
100%–100%
2,095 mol.		100%
100%–100%
1,107 mol.
25 mL100%
100%–100%
5,603 mol.		100%
100%–100%
4,359 mol.		100%
100%–100%
3,319 mol.		100%
100%–100%
1,792 mol.
50 mL100%
100%–100%
8,329 mol.		100%
100%–100%
6,456 mol.		100%
100%–100%
4,967 mol.		100%
100%–100%
2,777 mol.
100 mL100%
100%–100%
12,215 mol.		100%
100%–100%
9,747 mol.		100%
100%–100%
7,059 mol.		100%
100%–100%
3,776 mol.

Detection at the operating point: median, 5–95% range, and the median informative molecules. Green clears the target at the 5% quantile, amber clears it only at the median, red has too few molecules for the assay class. The current design is outlined. Every other control applies to every cell.

method

How this page computes

  • The chain M0 to M6 runs in this page in JavaScript, checked against the Python model on fixed draws to a relative 1e-8 on every stage and readout.
  • The 512 shipped draws are Python's, seeds 0 to 511, with their post-nuclease states solved at build time. Volume, kit, footprint, chemistry, platform, tumour volume, injury and urine output are downstream or linear, so they recompute in the page.
  • Hold, temperature, preservative, pH, filtration and proteinuria change the nuclease input, so the page re-solves the fragmentation master equation for every draw in a pool of workers, by the action of the matrix exponential on each draw's own profiles.
  • A prior edit reweights the draws by the ratio of the new density to the old, which is exact but thins the sample; the effective sample size says by how much. Fresh draws sample the edited priors in the page and re-solve.