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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...novo motif discoveryMotifScope uses a de novo motif discovery approach to enable the discovery of rare, possibly pathogenic motifs. In Figure 3A, we present the motif characterization results of a TR within intron 2 of RFC1 (Chr4:39,348,424–39,348,483), where biallelic AAGGG or GACAG repeat expansions...
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Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
...These authors contributed equally to this work. Corresponding authors: n.tesi@amsterdamumc.nl, a.n.salazar@amsterdamumc.nl, h.holstege@amsterdamumc.nlAbstractTandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization...
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Research: Alu insertion variants alter gene transcript levels
- Lindsay M. Payer,
- Jared P. Steranka,
- Maria S. Kryatova,
- Giacomo Grillo,
- Mathieu Lupien,
- Pedro P. Rocha,
- and Kathleen H. Burns
Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
..., Boston, MA 02215, USA Corresponding author: kathleenh_burns@dfci.harvard.eduAbstractAlu are high copy number interspersed repeats that have accumulated near genes during primate and human evolution. They are a pervasive source of structural variation in modern humans. Impacts that Alu insertions may have...
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Method: De novo reconstruction of satellite repeat units from sequence data
- Yujie Zhang,
- Justin Chu,
- Haoyu Cheng,
- and Heng Li
Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
...coordinate 227,746,662 and 228,024,151. The repeat unit is 2240 bp in length, composed of an AluY repeat, a 5S-RNA, and dinucleotide repeats. This is the only noncentromeric array in T2T-CHM13 longer than 100 kb.The SRF inference on the whole T2T-CHM13 (column “SRF/171 assembly” in Table 2) is close...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
.... 1991) and soon after revealed as a CGG expansion (Fu et al. 1991; Kremer et al. 1991; Pieretti et al. 1991; Verkerk et al. 1991). This was possible through using cytogenetics/FISH, coupled with somatic cell hybrids for FRAXA breakpoint mapping, Alu-PCR, and positional cloning, which together permitted...
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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
...of insertion and deletion counts stratified by size. The peak ∼300 bp represents Alu insertions or deletions, and the peak ∼6 kbp represents LINE insertions or deletions. (D) Cumulative novel SVs per sample. The frequency of new SVs observed increases when samples from individuals of African ancestry...
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Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
- Xiaofei Song,
- Christine R. Beck,
- Renqian Du,
- Ian M. Campbell,
- Zeynep Coban-Akdemir,
- Shen Gu,
- Amy M. Breman,
- Pawel Stankiewicz,
- Grzegorz Ira,
- Chad A. Shaw,
- and James R. Lupski
Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
...In a new window Figure 2. Diagram of the workflow used for predicting CNV-Alu pairs and AAMR hotspot genes in this study. Approximately 1.2 million Alus are documented in the “Repeating Elements by RepeatMasker” track at the UCSC Genome Browser. CNV-Alus are those with experimental evidence supporting...
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Research: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Xiao-Ou Zhang,
- Thomas R. Gingeras,
- and Zhiping Weng
Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
...data and characterized genomic and epigenetic signatures associated with their transcription profile and potential function as cell-type–specific enhancers.ResultsIdentification of primary Alu transcripts using RAMPAGE dataRAMPAGE uses several strategies to enrich for TSSs (Batut and Gingeras 2013...
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Research: Discovery of a new repeat family in the Callithrix jacchus genome
- Miriam K. Konkel,
- Brygg Ullmer,
- Erika L. Arceneaux,
- Sreeja Sanampudi,
- Sarah A. Brantley,
- Robert Hubley,
- Arian F.A. Smit,
- and Mark A. Batzer
Genome Res. May 2016 26: 649-659; Published in Advance February 25, 2016, doi:10.1101/gr.199075.115
...input, support, and helped write the manuscript. References Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 403–410. Arcot SS, Wang Z, Weber JL, Deininger PL, Batzer MA. 1995. Alu repeats: a source for the genesis of primate microsatellites.Genomics...
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Research: Mutagenesis of human genomes by endogenous mobile elements on a population scale
- Nelson T. Chuang,
- Eugene J. Gardner,
- Diane M. Terry,
- Jonathan Crabtree,
- Anup A. Mahurkar,
- Guillermo L. Rivell,
- Charles C. Hong,
- James A. Perry,
- and Scott E. Devine
Genome Res. December 2021 31: 2225-2235; Published in Advance November 12, 2021, doi:10.1101/gr.275323.121
...). This approach allowed us to perform MEI discovery on thousands of high-coverage Illumina s in days rather than months.We then used MELT and CloudMELT to perform MEI discovery on 57,919 human samples and identified 104,350 nonredundant MEIs (including 80,562 Alu, 16,525 L1, 6956 SVA, and 307 HERV-K insertions...

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