Evidence map›Paper›PMID 35180879›Full record

ArticleBMC medical genomics2022

GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation.

Roozbeh Manshaei, Sean DeLong, Veronica Andric, Esha Joshi, John B A Okello, Priya Dhir, Cherith Somerville, Kirsten M Farncombe, Kelsey Kalbfleisch, Rebekah K Jobling and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC medical genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Article
  2. Review
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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

13 authors.

Roozbeh ManshaeiTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Sean DeLongTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Veronica Andric *Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Esha Joshi *Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
John B A OkelloTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Priya DhirTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Cherith SomervilleTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Kirsten M FarncombeTed Rogers Centre for Heart Research, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.
Kelsey KalbfleischTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Rebekah K JoblingTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Stephen W SchererThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Raymond H KimDivision of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada. raymond.kim@sickkids.ca.
S Mohsen HosseiniDepartment of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. smhosseini@mdanderson.org.ORCID 0000-0003-3626-9928

Funding

Wellcome Trust
6 · The paper itself

Abstract

backgroundVariant interpretation is the main bottleneck in medical genomic sequencing efforts. This usually involves genome analysts manually searching through a multitude of independent databases, often with the aid of several, mostly independent, computational tools. To streamline variant interpretation, we developed the GeneTerpret platform which collates data from current interpretation tools and databases, and applies a phenotype-driven query to categorize the variants identified in the genome(s). The platform assigns quantitative validity scores to genes by query and assembly of the genotype-phenotype data, sequence homology, molecular interactions, expression data, and animal models. It also uses the American College of Medical Genetics and Genomics (ACMG) criteria to categorize variants into five tiers of pathogenicity. The final output is a prioritized list of potentially causal variants/genes.

resultsWe tested GeneTerpret by comparing its performance to expert-curated genes (ClinGen's gene-validity database) and variant pathogenicity reports (DECIPHER database). Output from GeneTerpret was 97.2% and 83.5% concordant with the expert-curated sources, respectively. Additionally, similar concordance was observed when GeneTerpret's performance was compared with our internal expert-interpreted clinical datasets.

conclusionsGeneTerpret is a flexible platform designed to streamline the genome interpretation process, through a unique interface, with improved ease, speed and accuracy. This modular and customizable system allows the user to tailor the component-programs in the analysis process to their preference. GeneTerpret is available online at https://geneterpret.com .

Indexed as

GenomicsSoftwareGenetic VariationGenome, HumanHumansPhenotypeUnited StatesBioinformatic applicationCausative variantsDisease gene validityGene prioritizationGenome interpretationGenomic variantsGenotype–phenotype correlationVariant pathogenicity

Identifiers

PMID35180879
PMCPMC8857790

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LicenceCC BY
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Registered trials

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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.