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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
...Yaran Zhang1, Marc Hulsman1,2, Alex Salazar1, Niccolò Tesi1,2, Lydian Knoop1, Sven van der Lee1,2,3, Sanduni Wijesekera1, Jana Krizova1, Erik-Jan Kamsteeg4 and Henne Holstege1,2,3,5 1Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit...
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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
...9691 polymorphic STRs (pSTRs) had complete genotype data for more than 90% of the strains. Compared with the reference , the pSTRs showed more contraction than expansion. We found that STRs with different motif lengths were enriched in different genomic features, among which coding regions showed...
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Research: Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
- Meredith M. Course,
- Arvis Sulovari,
- Kathryn Gudsnuk,
- Evan E. Eichler,
- and Paul N. Valdmanis
Genome Res. August 2021 31: 1313-1324; Published in Advance July 9, 2021, doi:10.1101/gr.275560.121
...- sequencing. In addition, they are frequently located in noncoding or intergenic regions, which until recently have garnered less attention than genomic variants in coding regions. VNTRs, however, are highly mutable, suggesting that they play influential roles in evolutionary biology, and along with short...
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Research: Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
- Wilfried M. Guiblet,
- Michael DeGiorgio,
- Xiaoheng Cheng,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 2021 31: 1136-1149; Published in Advance June 29, 2021, doi:10.1101/gr.269589.120
...Selection and thermostability suggest G-quadruplexes are novel functional elements of the human Wilfried M. Guiblet1,8, Michael DeGiorgio2, Xiaoheng Cheng3, Francesca Chiaromonte4,5,6, Kristin A. Eckert5,7, Yi-Fei Huang3,5 and Kateryna D. Makova3,5 1Bioinformatics and Genomics Graduate Program...
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Research: Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis
- Ilias Georgakopoulos-Soares,
- Sandro Morganella,
- Naman Jain,
- Martin Hemberg,
- and Serena Nik-Zainal
Genome Res. September 2018 28: 1264-1271; Published in Advance August 13, 2018, doi:10.1101/gr.231688.117
...motifs are associated with increased mutability in cancer sGenomic features such as histone epigenetic marks and replication time domains have been shown to be predictive of the variation in distribution of somatic mutations (Schuster-Böckler and Lehner 2012; Polak et al. 2015). We thus explored whether...
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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
.... Indeed, we have argued that STRs are more likely than less mutable classes of genomic variation to exhibit epistasis (Press et al. 2014). In consequence, we expect that the associations described in the present study are an underestimate of STR effects on phenotype. Moreover, our data are constrained...
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Research: Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
- Tugce Bilgin Sonay,
- Tiago Carvalho,
- Mark D. Robinson,
- Maja P. Greminger,
- Michael Krützen,
- David Comas,
- Gareth Highnam,
- David Mittelman,
- Andrew Sharp,
- Tomàs Marques-Bonet,
- and Andreas Wagner
Genome Res. November 2015 25: 1591-1599; Published in Advance August 19, 2015, doi:10.1101/gr.190868.115
.... 2009; Gemayel et al. 2010). Our work shows that TRs, a type of sequence with unusually high mutability, are a relevant class of regulatory mutations that might contribute to such species differences. Methods Genomic sequence data We used a total of 83 samples sequenced with Illumina paired-end reads...
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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
...and more types of STRs, one may derive more precise predictions of sequencing error based on sequence composition, length, genomic position, and other features.However, even in this proof-of-principle study, some patterns emerged that inform our understanding of the mutability of STRs. First, as others...
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Research: NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits
- Piotr Dittwald,
- Tomasz Gambin,
- Przemyslaw Szafranski,
- Jian Li,
- Stephen Amato,
- Michael Y. Divon,
- Lisa Ximena Rodríguez Rojas,
- Lindsay E. Elton,
- Daryl A. Scott,
- Christian P. Schaaf,
- Wilfredo Torres-Martinez,
- Abby K. Stevens,
- Jill A. Rosenfeld,
- Satish Agadi,
- David Francis,
- Sung-Hae L. Kang,
- Amy Breman,
- Seema R. Lalani,
- Carlos A. Bacino,
- Weimin Bi,
- Aleksandar Milosavljevic,
- Arthur L. Beaudet,
- Ankita Patel,
- Chad A. Shaw,
- James R. Lupski,
- Anna Gambin,
- Sau Wai Cheung,
- and Pawel Stankiewicz
Genome Res. September 2013 23: 1395-1409; Published in Advance May 8, 2013, doi:10.1101/gr.152454.112
...NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits Piotr Dittwald 1 , 2 , 3 , 17 , Tomasz Gambin 1 , 4 , 17 , Przemyslaw Szafranski 1 , Jian Li 1 , Stephen...
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Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- Arkarachai Fungtammasan,
- Erin Walsh,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- and Kateryna D. Makova
Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
...A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? Arkarachai Fungtammasan 1 , 2 , 3 , Erin Walsh 3 , 4 , Francesca Chiaromonte 3 , 5 , 7 , Kristin A. Eckert 3 , 6 , 7...

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