Searching journal content for articles similar to Willems et al. 24 (11): 1894.

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  1. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...Institute, Kansas City, Missouri 64108, USA; 4Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec H3A 0G1, Canada Corresponding authors: david.lougheed@mail.mcgill.ca, guil.bourque@mcgill.caAbstractVariation in short tandem repeats (STRs) is implicated in Mendelian...
  2. Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    • Jonas A. Gustafson,
    • Sophia B. Gibson,
    • Nikhita Damaraju,
    • Miranda P.G. Zalusky,
    • Kendra Hoekzema,
    • David Twesigomwe,
    • Lei Yang,
    • Anthony A. Snead,
    • Phillip A. Richmond,
    • Wouter De Coster,
    • Nathan D. Olson,
    • Andrea Guarracino,
    • Qiuhui Li,
    • Angela L. Miller,
    • Joy Goffena,
    • Zachary B. Anderson,
    • Sophie H.R. Storz,
    • Sydney A. Ward,
    • Maisha Sinha,
    • Claudia Gonzaga-Jauregui,
    • Wayne E. Clarke,
    • Anna O. Basile,
    • André Corvelo,
    • Catherine Reeves,
    • Adrienne Helland,
    • Rajeeva Lochan Musunuri,
    • Mahler Revsine,
    • Karynne E. Patterson,
    • Cate R. Paschal,
    • Christina Zakarian,
    • Sara Goodwin,
    • Tanner D. Jensen,
    • Esther Robb,
    • The 1000 Genomes ONT Sequencing Consortium,
    • University of Washington Center for Rare Disease Research (UW-CRDR),
    • Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
    • William Richard McCombie,
    • Fritz J. Sedlazeck,
    • Justin M. Zook,
    • Stephen B. Montgomery,
    • Erik Garrison,
    • Mikhail Kolmogorov,
    • Michael C. Schatz,
    • Richard N. McLaughlin, Jr.,
    • Harriet Dashnow,
    • Michael C. Zody,
    • Matt Loose,
    • Miten Jain,
    • Evan E. Eichler,
    • and Danny E. Miller
    Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
    ...data challenging. To address this, the 1000 Genomes Project (1KGP) Oxford Nanopore Technologies Sequencing Consortium aims to generate LRS data from at least 800 of the 1KGP samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal...
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  3. Research: Natural variation in C. elegans short tandem repeats
    • Gaotian Zhang,
    • Ye Wang,
    • and Erik C. Andersen
    Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
    ...610081, P.R. China Corresponding author: erik.andersen@gmail.com, erik.andersen@northwestern.eduAbstractShort tandem repeats (STRs) represent an important class of genetic variation that can contribute to phenotypic differences. Although millions of single nucleotide variants (SNVs) and short indels have...
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  4. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...↵2 Present address: Admera Health, South Plainfield, NJ 07080, USA Corresponding author: andrew.sharp@mssm.eduAbstractShort tandem repeats (STRs) contribute significantly to genetic diversity in humans, including disease-causing variation. Although the effect of STR variation on gene expression has...
  5. Method: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
    • Keisha D. Carlson,
    • Peter H. Sudmant,
    • Maximilian O. Press,
    • Evan E. Eichler,
    • Jay Shendure,
    • and Christine Queitsch
    Genome Res. May 2015 25: 750-761; Published in Advance February 6, 2015, doi:10.1101/gr.182212.114
    ..., Washington 98195, USA Corresponding author: queitsch@u.washington.edu AbstractShort tandem repeats (STRs) are highly mutable genetic elements that often reside in regulatory and coding DNA. The cumulative evidence of genetic studies on individual STRs suggests that STR variation profoundly affects phenotype...
  6. Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
    ...tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci...
  7. Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
    • Maximilian O. Press,
    • Rajiv C. McCoy,
    • Ashley N. Hall,
    • Joshua M. Akey,
    • and Christine Queitsch
    Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
    ...author: queitsch@uw.eduAbstractShort tandem repeat (STR) mutations may comprise more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assessed this contribution across a collection of 96 strains of Arabidopsis thaliana...
  8. Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
    • Rashid Al-Abri and
    • Gamze Gürsoy
    Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
    ...with lengths that greatly exceed typical sequencing fragment sizes. When applied to data from the 1000 Genomes Project, ScatTR detects potential large TR expansions that other methods missed, highlighting its ability to better characterize -wide TR variation.Tandem repeats (TRs) are consecutively repeated...
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  9. Research: Discovery and genotyping of structural variation from long-read haploid genome sequence data
    • John Huddleston,
    • Mark J.P. Chaisson,
    • Karyn Meltz Steinberg,
    • Wes Warren,
    • Kendra Hoekzema,
    • David Gordon,
    • Tina A. Graves-Lindsay,
    • Katherine M. Munson,
    • Zev N. Kronenberg,
    • Laura Vives,
    • Paul Peluso,
    • Matthew Boitano,
    • Chen-Shin Chin,
    • Jonas Korlach,
    • Richard K. Wilson,
    • and Evan E. Eichler
    Genome Res. May 2017 27: 677-685; Published in Advance November 28, 2016, doi:10.1101/gr.214007.116
    ...samples. Am J Hum Genet 98: 116–126. ↵Carlson KD, Sudmant PH, Press MO, Eichler EE, Shendure J, Queitsch C. 2015. MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. Genome Res 25: 750–761. ↵Chaisson MJ, Tesler G. 2012. Mapping single molecule...
  10. Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
    • Alistair Miles,
    • Zamin Iqbal,
    • Paul Vauterin,
    • Richard Pearson,
    • Susana Campino,
    • Michel Theron,
    • Kelda Gould,
    • Daniel Mead,
    • Eleanor Drury,
    • John O'Brien,
    • Valentin Ruano Rubio,
    • Bronwyn MacInnis,
    • Jonathan Mwangi,
    • Upeka Samarakoon,
    • Lisa Ranford-Cartwright,
    • Michael Ferdig,
    • Karen Hayton,
    • Xin-zhuan Su,
    • Thomas Wellems,
    • Julian Rayner,
    • Gil McVean,
    • and Dominic Kwiatkowski
    Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
    ...Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum Alistair Miles 1 , 2 , Zamin Iqbal 3 , Paul Vauterin 1 , Richard Pearson 1 , 2 , Susana Campino 2 , Michel Theron 2 , Kelda...
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