Evidence map›Paper›PMID 33293579›Full record

ArticleCommunications biology2020

A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis.

Megan Shand, Jose Soto, Lee Lichtenstein, David Benjamin, Yossi Farjoun, Yehuda Brody, Yosef Maruvka, Paul C Blainey, Eric Banks

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.1field-weighted citation impact, top 60% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 1 institution in 1 country.

Megan ShandBroad Institute of Harvard and MIT, Cambridge, MA, USA. mshand@broadinstitute.org.ORCID 0000-0002-2507-6365
Jose SotoBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Lee LichtensteinBroad Institute of Harvard and MIT, Cambridge, MA, USA.
David BenjaminBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Yossi FarjounBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0002-7002-2868
Yehuda BrodyBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Yosef MaruvkaBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Paul C BlaineyBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0002-4889-8783
Eric BanksBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Broad Institute · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Existing cancer benchmark data sets for human sequencing data use germline variants, synthetic methods, or expensive validations, none of which are satisfactory for providing a large collection of true somatic variation across a whole genome. Here we propose a data set, Lineage derived Somatic Truth (LinST), of short somatic mutations in the HT115 colon cancer cell-line, that are validated using a known cell lineage that includes thousands of mutations and a high confidence region covering 2.7 gigabases per sample.

Indexed as

Genome, HumanDatabases, GeneticGene Expression Regulation, NeoplasticGenetic Predisposition to DiseaseHumansMutationNeoplasm ProteinsReproducibility of ResultsSoftwareNeoplasm Proteins

Identifiers

PMID33293579
PMCPMC7722876
OpenAlexW3111901767

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.