Evidence map›Paper›PMID 42025159›Full record

ArticleAmerican journal of human genetics2026

Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases.

Ben Weisburd, Egor Dolzhenko, Mark F Bennett, Matt C Danzi, Isaac R L Xu, Hope Tanudisastro, Bida Gu, Adam English, Laurel Hiatt, Tom Mokveld and 13 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in American journal of human genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

17 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

23 authors.

Ben WeisburdProgram in Medical and Population Genetics, Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. Electronic address: weisburd@broadinstitute.org.
Egor DolzhenkoPacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, USA. Electronic address: edolzhenko@pacificbiosciences.com.
Mark F BennettPopulation Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia.
Matt C DanziDr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
Isaac R L XuDr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
Hope TanudisastroCentre for Population Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
Bida GuDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Adam EnglishHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Laurel HiattUniversity of Utah, Department of Human Genetics, Salt Lake City, UT, USA.
Tom MokveldPacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, USA.
Guilherme De Sena BrandinePacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, USA.
Readman ChiuCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
Nehir Edibe KurtasProgram in Medical and Population Genetics, Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Helyaneh Ziaei JamDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Harrison BrandProgram in Medical and Population Genetics, Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Indhu-Shree Rajan-BabuDepartment of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Melanie BahloPopulation Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia.
Mark J P ChaissonDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
Stephan ZüchnerDr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
Melissa GymrekDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Harriet DashnowDepartment of Biomedical Informatics, University of Colorado Anschutz, Aurora, CO, USA.
Michael A EberlePacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, USA.
Heidi L RehmProgram in Medical and Population Genetics, Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Funding

Revealing new short tandem repeat variation in the human population across sequencing technologies: towards rare disease diagnosis and discoveryR00HG012796 · NHGRI · UNIVERSITY OF COLORADO DENVER · PI Harriet Dashnow · 2024 to 2026
$747k
NHGRI NIH HHS R00 HG012796
6 · The paper itself

Abstract

Tandem repeat (TR) catalogs are important components of repeat genotyping studies because they define the genomic coordinates and expected motifs of all TR loci being analyzed. In recent years, genome-wide studies have used catalogs ranging in size from fewer than 200,000 to over 7 million loci. These catalogs differed not only in which loci were included but often also in their definitions of TR locus boundaries and motifs. Now, with multiple groups developing public databases of TR variation in large population cohorts, there is a risk that the use of divergent repeat catalogs will lead to confusion, fragmentation, and incompatibility across resources. Here, we compare existing TR catalogs and discuss desirable features of a comprehensive genome-wide catalog. We then present a new, richly annotated catalog designed for genome-wide analyses and population datasets based on short-read or long-read samples. Additionally, using an algorithm that leverages long-read HiFi sequencing data, our catalog stratifies TRs into (1) isolated repeats suitable for repeat copy-number analysis and (2) variation clusters where TRs are embedded within wider polymorphic regions best studied through sequence-level analysis. We share the TR catalog, variation clusters, and annotations through the TRExplorer portal in order to support both the initial selection of TR loci for inclusion in an analysis and the subsequent interpretation of results.

Indexed as

Databases, GeneticGenetics, PopulationGenetic VariationGenome, HumanGenome-Wide Association StudyTandem Repeat SequencesAlgorithmsHumansHiFilong readsequencingshort readSTRstandem repeat catalogstandem repeatsVNTRs

Identifiers

PMID42025159
PMCPMC13277687

What OpenQuestion holds

Textmetadata
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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.