Evidence map›Paper›PMID 40585303›Full record

ArticleNAR genomics and bioinformatics2025

MOLGENIS VIP: an end-to-end DNA variant interpretation pipeline for research and diagnostics configurable to support rapid implementation of new methods.

Willem T K Maassen, Lennart F Johansson, Bart Charbon, Dennis Hendriksen, Sander van den Hoek, Mariska K Slofstra, Renée Mulder, Martine T Meems-Veldhuis, Robert Sietsma, Henny H Lemmink and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in NAR genomics and bioinformatics, 2025. 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. medRxiv : the preprint server for health sciences · 2026
    Article
  3. Article
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

14 authors.

Willem T K MaassenGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.ORCID https://orcid.org/0000-0001-7086-0637
Lennart F JohanssonGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Bart CharbonGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Dennis HendriksenGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Sander van den HoekGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Mariska K SlofstraGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Renée MulderGenome Diagnostics, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Martine T Meems-VeldhuisGenome Diagnostics, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Robert SietsmaGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Henny H LemminkGenome Diagnostics, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Cleo C van DiemenGenome Diagnostics, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Mariëlle E van GijnGenome Diagnostics, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Morris A SwertzGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.
Kasper J van der VeldeGenomics Coordination Center, Department of Genetics, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, the Netherlands.ORCID https://orcid.org/0000-0002-0934-8375

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Achieving high yield in genetics research and genome diagnostics is a significant challenge because it requires a combination of multiple strategies and large-scale genomic analysis using the latest methods. Existing diagnostic software infrastructures are often unable to cope with high demands for versatility and scalability. We developed MOLGENIS VIP, a flexible, scalable, high-throughput, open-source, and "end-to-end" pipeline to process different types of sequencing data into portable, prioritized variant lists for immediate clinical interpretation in a wide variety of scenarios. VIP supports interpretation of short- and long-read sequencing data, using best-practice annotations and classification trees without complex IT infrastructures. VIP is developed within the long-living MOLGENIS open-source project to provide sustainability and has integrated feedback from a growing international community of users. VIP has undergone genome diagnostic laboratory testing and harnesses experiences from multiple Dutch, European, Canadian, and African diagnostic and infrastructural initiatives (VKGL, EU-Solve-RD, EJP-RD, CINECA, GA4GH). We provide a step-by-step protocol for installing and using VIP. We demonstrate VIP using 25 664 previously classified variants from the VKGL, and 18 and 41 diagnosed patients from a routine diagnostics and a Solve-RD research cohort, respectively. We believe that VIP accelerates causal variant detection and innovation in genome diagnostics and research.

Indexed as

Genetic VariationSoftwareHigh-Throughput Nucleotide SequencingHumansSequence Analysis, DNA

Identifiers

PMID40585303
PMCPMC12205968

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.