standOff, and the article is at its publisher via the link below. When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.| relation to other work | claim_relations | how this paper stands to another: agrees, contradicts, extends, qualifies |
| claim type | claim_type | the shape of the claim: existence, mechanism, method, critique, prediction, null |
| concept edge | concept_edges | an asserted relation between two concepts, with the sentence asserting it |
| concept | concepts | an idea the paper works with, quoted where the paper uses it |
| content tag | content_tags | a finding, definition, quantity, statistic or variable named in the paper |
| contribution | contribution | what the paper claims to add |
| control | controls | an experiment run to eliminate a rival explanation |
| limitation | limitations | what the paper says its evidence cannot support |
| mechanism | mechanisms | how the reported effect is said to come about |
| method | method | how the paper produced its evidence |
| object of study | object_of_study | what the paper is about — the thing it investigates |
| phenomenon | phenomenon | the effect or regularity under study |
| research question | research_question | the question the paper sets itself |
| sense | senses | a distinct use of a term, quoted where the paper fixes it |
| transfer | transfers | a method or concept carried in from another field |
Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; 2 of 2 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | tumour mutational burden as a biomarker - how it is counted, how little genome is enough to count it, and how it is distributed across cancer types Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | object_of_study | the paper's words | |
| research_question | whether a 1.1 Mb targeted panel can stand in for whole exome sequencing when measuring mutational burden, and what the burden looks like across a hundred thousand clinical specimens Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | research_question | the paper's words | |
| contribution | a validated targeted measurement of TMB, a downsampling analysis showing where it stops working, and the distribution of TMB across more than 100 tumour types Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | contribution | the paper's words | |
| claim_type | existence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_type | the paper's words | |
| phenomenon | a clinical category - high mutational burden - whose membership depends on an assay's size, a list of exclusions, and a threshold stated once in a figure caption Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | phenomenon | the paper's words | |
| method | omics-profiling Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: omics-profiling | method | the paper's words | |
| mechanisms | TMB is a rate estimated from a sample of the genome, so the fewer megabases read the noisier the estimate; the effect is worst where the underlying rate is low, because the expected count in the sampled region approaches zero Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | a synonymous change cannot itself create a neoantigen, but it is produced by the same mutational process that produced the nonsynonymous ones elsewhere, so counting it raises the sample size of the rate estimate without changing what the rate is about Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | with no normal tissue sequenced, inherited variants must be removed by matching against reference databases - so the filter's accuracy is the databases' coverage of the patient's ancestry Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[2] | 0.95 | the tagger's words |
| limitations | the germline filter depends on reference databases, so it will be least accurate for patients from ethnic backgrounds not well represented in them - stated by the authors Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[0] | 0.95 | the tagger's words |
| limitations | the MSI cut points were set by manual unsupervised clustering against a reference that was itself partly APPROXIMATED by the same pipeline's homopolymer indel counts Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[1] | 0.95 | the tagger's words |
| limitations | the accuracy figure rests on 29 specimens with matched whole exome sequencing; the two 0.98 correlations are the assay against itself and an in-silico subsetting Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[2] | 0.95 | the tagger's words |
| limitations | known mismatch-repair and replication genes account for less than 10% of high-TMB cases, so the molecular basis of most of the phenomenon is unexplained Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[3] | 0.95 | the tagger's words |
| limitations | the PMS2 promoter mutations are not shown to be causal, and the TOP2A association rests on eight cases Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[4] | 0.95 | the tagger's words |
| limitations | targeted profiling measures the burden but cannot identify the neoantigens the mechanism depends on, since those may occur in any gene Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[5] | 0.95 | the tagger's words |
| transfers | principal components analysis, carried from multivariate statistics to collapse 228 repeat-length measurements into a single MSI score that can be cut into categories Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | transfers[0] | 0.95 | the tagger's words |
| transfers | resampling simulation, carried from survey methodology to ask how small a genomic panel may be before the rate it estimates stops being the rate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | transfers[1] | 0.95 | the tagger's words |
| controls | the same biopsy specimens measured by both the targeted panel and whole exome sequencing, so the panel is checked against a different measurement rather than against itself Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the targeted panel's own gene selection as the explanation of the burden it reports - the same biopsy measured by a method that selects no genes gives a correlated answer · outcome: partial | controls[0] | 0.95 | the tagger's words |
| controls | 60 replicate pairs run through the same assay, separating precision from accuracy Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: assay noise as the explanation of the remaining disagreement with whole exome sequencing - the assay repeats itself at R2 0.98, so what is left is between methods and not within one · outcome: held | controls[1] | 0.95 | the tagger's words |
| controls | simulating the measurement at smaller panel sizes to find where sampling variance makes the estimate unusable, rather than asserting that 1.1 Mb is enough Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: sampling variance as a hidden contributor at the panel size actually used - the simulation measures it rather than assuming 1.1 Mb is enough, and names where it stops being enough · outcome: partial | controls[2] | 0.95 | the tagger's words |
| controls | an independent check on 8,917 TCGA exomes, comparing total mutations against those in the 315 assay genes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: this laboratory's own cohort and pipeline as the source of the agreement - the same comparison on 8,917 independently generated exomes reproduces it · outcome: held | controls[3] | 0.95 | the tagger's words |
| controls | cohort filtering declared in advance - duplicates removed, coverage floor, and a minimum of 50 specimens before a cancer type is analysed at all Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: duplicate specimens and under-covered samples as contributors to the reported distribution · outcome: held | controls[4] | 0.95 | the tagger's words |
| controls | checking whether more than the first principal component of the MSI score was needed Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: further principal components as carriers of microsatellite signal the one-dimensional score discards - none of the others explains more than 4% of the variance · outcome: held | controls[5] | 0.95 | the tagger's words |
| concepts | TMB Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: TMB | concepts[0] | 0.95 | the paper's words |
| concepts | mutation load Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: mutation load | concepts[1] | 0.95 | the paper's words |
| concepts | biomarker Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: biomarker | concepts[2] | 0.95 | the paper's words |
| concepts | Synonymous mutations Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Synonymous mutations | concepts[3] | 0.95 | the paper's words |
| concepts | MSI-High Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MSI-High | concepts[4] | 0.95 | the paper's words |
| concepts | MSI score Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MSI score | concepts[5] | 0.95 | the paper's words |
| concepts | CGP Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: CGP | concepts[6] | 0.95 | the paper's words |
| concepts | WES Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: WES | concepts[7] | 0.95 | the paper's words |
| concepts | neoantigens Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: neoantigens | concepts[8] | 0.95 | the paper's words |
| concepts | percentage deviation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: percentage deviation | concepts[9] | 0.95 | the paper's words |
| concepts | germline polymorphisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: germline polymorphisms | concepts[10] | 0.95 | the paper's words |
| concepts | effect size Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: effect size | concepts[11] | 0.95 | the paper's words |
| senses | "high TMB" - AS USED throughout the abstract, results, discussion and conclusions: an unquantified clinical category of patients who might benefit from immunotherapy Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[0] | 0.95 | the tagger's words |
| senses | "high TMB" - AS DEFINED: more than 20 mutations per megabase. The threshold appears once in the paper, in the caption of Fig. 3, and nowhere in the prose Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[1] | 0.95 | the tagger's words |
| senses | agreement of targeted CGP with whole exome - AS ACCURACY: R2 = 0.74, from 29 specimens where both measurements were made on the same biopsy Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[2] | 0.95 | the tagger's words |
| senses | agreement of targeted CGP with whole exome - AS PRECISION: R2 = 0.98, the assay against itself on 60 replicate pairs. The paper labels this one precision, and it is the number that looks like agreement without being it Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[3] | 0.95 | the tagger's words |
| claim_relations | qualifies → PD-1/PD-L1 expression by immunohistochemistry as the companion diagnostic for checkpoint inhibitors Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | extends → whole exome measurement of tumour mutational burden, by showing a 1.1 Mb targeted panel reproduces it Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[1] | 0.95 | the tagger's words |
| claim_relations | qualifies → neoantigen load as the predictor of immunotherapy response - correlated, but with no recurrent neoantigens found that predict response Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[2] | 0.95 | the tagger's words |
| concept_edges | MSI-High —part-of→ TMB Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 0.85 · the relation stated: MSI-High samples are largely a subset of the high-TMB population, and not the reverse | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | mutation load —same-as→ TMB Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 0.9 · the relation stated: one quantity under two names, given in apposition at first use also in: mutation load · TMB | concept_edges[1] | 0.95 | the tagger's words |
| content_tags | Targeted sequencing identifies high-TMB specimens well, but deviation rises at intermediate TMB, especially below 0.5 Mb sequenced. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[0] | 0.95 | the tagger's words |
| content_tags | 83% of MSI-High samples have high TMB but only 16% of high-TMB samples are MSI-High - two markers of genomic instability that do not substitute for each other Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[1] | 0.95 | the tagger's words |
| content_tags | the overlap between MSI-High and high TMB depends on the cancer type - near-total in gastrointestinal cancers, rare in melanoma Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[2] | 0.95 | the tagger's words |
| content_tags | known mismatch-repair and replication mutations account for under 10% of high-TMB cases Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | the number of somatic, coding, base substitution and indel mutations per megabase of genome examined, with synonymous alterations counted and seven classes of alteration excluded Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: TMB | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | more than 20 mutations per megabase - stated once, in the caption of Fig. 3, for a category used throughout the article Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: high TMB | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | the first principal component of the means and variances of repeat lengths at 114 intronic homopolymer loci, projected onto one dimension Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MSI score | content_tags.definitions[2] | 0.95 | the tagger's words |
| content_tags | the panel size below which measurement variance increases significantly Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[0] | 0.95 | the tagger's words |
| content_tags | MSI-High samples that also had high TMB Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[1] | 0.95 | the tagger's words |
| content_tags | high-TMB samples classified as MSI-High - the converse, and much smaller Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[2] | 0.95 | the tagger's words |
| content_tags | the initial clinical cohort, filtered to 92,439 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[3] | 0.95 | the tagger's words |
| content_tags | R2 = 0.74 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: R2 = 0.74 | content_tags.statistics[0] | 0.95 | the tagger's words |
| content_tags | R2 = 0.98 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: R2 = 0.98 | content_tags.statistics[1] | 0.95 | the tagger's words |
| content_tags | principal components analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: principal components analysis | content_tags.statistics[2] | 0.95 | the tagger's words |
| content_tags | false discovery rate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: false discovery rate | content_tags.statistics[3] | 0.85 | the tagger's words |
| content_tags | percentage deviation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: percentage deviation | content_tags.variables[0] | 0.95 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.