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Research: Optical genome mapping enables accurate testing of large repeat expansions
- Bart van der Sanden,
- Kornelia Neveling,
- Syukri Shukor,
- Michael D. Gallagher,
- Joyce Lee,
- Stephanie L. Burke,
- Maartje Pennings,
- Ronald van Beek,
- Michiel Oorsprong,
- Ellen Kater-Baats,
- Eveline Kamping,
- Alide A. Tieleman,
- Nicol C. Voermans,
- Ingrid E. Scheffer,
- Jozef Gecz,
- Mark A. Corbett,
- Lisenka E.L.M. Vissers,
- Andy Wing Chun Pang,
- Alex Hastie,
- Erik-Jan Kamsteeg,
- and Alexander Hoischen
Genome Res. April 2025 35: 810-823; Published in Advance March 20, 2025, doi:10.1101/gr.279491.124
...expand or contract, causing genetic disorders, mainly when expanded. Traditional diagnostic methods for identifying these expansions, such as repeat-primed PCR and Southern blotting, are often labor-intensive, locus-specific, and are unable to precisely determine long repeat expansions. Sequencing...
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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
.... Any individuals with a positive diagnostic test result were excluded from the trial.View larger version: In this window In a new window Figure 1. Overview of the study and investigations performed. (SCA) spinocerebellar ataxia, (EH5) ExpansionHunter5, (RE) repeat expansion, (LP) likely pathogenic, (P...
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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
...then as olivopontocerebellar ataxias) would be caused by gene-specific repeat expansions (Caskey et al. 1992; Harper et al. 1992). Following the explanation of HDs genetic anticipation by a CAG expansion (Snell et al. 1993; Trottier et al. 1994), the connection was solidified, and it was predicted that SCAs, bipolar disorder...
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Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
...not include off-target locations for the other, potentially long repeats because the corresponding motifs (CAG and AAG) are common enough that we could not resolve which repeat the paired IRRs originated from. Figure 4 depicts the sizes of the longer repeat allele determined by ExpansionHunter. Each...
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REVIEW: The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases
- Karen Usdin
Genome Res. July 2008 18: 1011-1019; doi:10.1101/gr.070409.107
...the repeat is outside of the open reading frame (ORF) ( Table 1 ). Both coding and noncoding repeats can have significant impact. Open reading frame expansions In all repeat expansion diseases identified thus far in which the repeat is in an exon, the repeat unit is a triplet with the sequence CAG...
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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
...dystrophy 1 (DM1).SCA6 is caused by heterozygous expansion of the CAG repeat in the last exon of CACNA1A, which produces toxic proteins with a polyglutamine tract (Paulson et al. 2017). The repeat correlated with an intron (Chr 19: 13,208,054–13,208,755) usage in the cerebellum in our catalog (Q-value = 5...
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LETTER: Functional insights from the distribution and role of homopeptide repeat-containing proteins
- Noel G. Faux,
- Stephen P. Bottomley,
- Arthur M. Lesk,
- James A. Irving,
- John R. Morrison,
- Maria Garcia de la Banda,
- and James C. Whisstock
Genome Res. April 2005 15: 537-551; doi:10.1101/gr.3096505
...CAG repeats + CAA + CAG). In contrast, Machado-Joseph disease develops when the poly-Q repeat in ataxin-3 is 45 amino acids in length ( Cummings and Zoghbi 2000 ; Chow et al. 2004a ). The accumulation of the aggregated state in vivo appears to correlate with cell death and the onset of degenerative...
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RESEARCH: Identification and Chromosomal Localization of Human Genes Containing CAG/CTG Repeats Expressed in Testis and Brain
- Frédérique Bulle,
- Nuchanard Chiannilkulchai,
- André Pawlak,
- Jean Weissenbach,
- Gabor Gyapay,
- and Georges Guellaën
Genome Res. July 1, 1997 7: 705-715; doi:10.1101/gr.7.7.705
.... , Garnier J.-M. , Weber C. , Mandel J.L. , Cancel G. , Abbas N. , et al. ( 1996 ) Cloning of the gene for spinocerebellar ataxia 2 reveals a locus with high sensitivity to expanded CAG/glutamine repeats. Nature Genet. 14 : 285 – 291 . ↵ Jiang J.-X. , Lekanne Deprez R.H. , Zwarthoff E.C. , Riegman P...
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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
...read-level copy numbers, which we can use to examine an instance of somatic instability in this data set. De Luca et al. (2021) found that one of the expansion samples tested, NA20253, has three copy number peaks, namely, mosaic alleles, which they measured at 107, 134, and 175 CAG repeats...
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GENOME METHODS: Multivariate Analysis of Factors Influencing Repeat Expansion Detection
- Cecilia Zander,
- Jonas Thelaus,
- Kerstin Lindblad,
- Mikael Karlsson,
- Kjell Sjöberg,
- and Martin Schalling
Genome Res. October 1, 1998 8: 1085-1094; doi:10.1101/gr.8.10.1085
...M.-L. , Stevanin G. , Holmberg M. , Digre K. , Zander C. , Ehrsson H. , David G. , Benomar A. , Nikoskelainen E. , et al. ( 1996a ) An expanded CAG repeat sequence in spinocerebellar ataxia type 7. Genome Res. 6 : 965 – 971 . ↵ Lindblad K. , Lunkes A. , Maciel P. , Stevanin G. , Zander C...

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