The confidence score#

The final stage of database processing assigns a confidence score to each TCR:peptide:MHC complex, computed from the reported method entries.

The score evaluates TCR sequence confidence, identification confidence and verification confidence, by the following criteria:

  1. Ensuring TCR sequence is correctly identified according to method.sequencing and method.singlecell (1-3 points)

    • sanger - several cells sequenced (2+ cells sequenced according to method.frequency) - 2 points, otherwise 1

    • amplicon-seq - frequency is at least 0.01 - 3 points, otherwise 1. Where method.frequency.count is known it must also be at least 2 reads; where it is not (a float or a percentage carries no count) the frequency decides alone

    • single-cell - 3 points if performed

  2. Initial identification of TCR:pMHC is correct according to method.identification (0-1 point)

    • sort-based - frequency is higher than 0.1 according to method.frequency)

    • culture-based - frequency is higher than 0.5

    • limiting dilution/culture prior to sequencing - method.frequency is ambiguous here, check whether it is higher than 0.5

  3. Verification T-cell specificity (0-3 points)

    • direct method - 3 points, e.g. has PDB id (meta.structure.id is not empty) or some other method that directly evaluates TCR:pMHC binding

    • target stimulation-based - 2 points

    • staining-based - 1 points

    • If verification is performed, the TCR sequence is assumed to be known, so the score from part 1. is set to 3

The final score is the minimum of the part 1. score and the sum of the part 2. and part 3. scores.

Among records that point to the same unique complex entry, that is the same set of unique complex fields - independent submissions, replicas, and so on - the maximal score is taken.

score

description

0

Low confidence/no information - a critical aspect of sequencing/specificity validation is missing

1

Moderate confidence - no verification / poor TCR sequence confidence

2

High confidence - has some specificity verification, good TCR sequence confidence

3

Very high confidence - has extensive verification or structural data

Score rules#

The table below is rendered from vdjdb.score.confidence while this page builds.

frequency()

method.frequency as a fraction in [0, 1]. Unparseable or absent is 0.0.

cell_count()

The numerator of an n/m frequency. A percentage gives no cell count, so 0.

sequencing_score()

How much the sequence can be trusted: single cell > Sanger > amplicon depth.

row_score()

The per-row score, before the per-signature maximum.

The score is a maximum over the sample signature cdr3.alpha, v.alpha, j.alpha, cdr3.beta, v.beta, j.beta, species, mhc.a, mhc.b, mhc.class, antigen.epitope, so the same clonotype assayed twice takes the better of the two.