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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
...haplotype reads from participant P1 (Fig. 4A) demonstrated a repeating pattern across the array from the proximal (R1) to distal (R5) repeat. Aligning methylation frequencies of individual CpGs within the 5U haplotype from participant P1 with the annotated features of the 3.3 kb KpnI-KpnI repeat showed...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...55421, USA Corresponding author: jshaw@ds.dfci.harvard.eduAbstractReconstructing exact haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling sequencing errors requires specialized...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...cynomolgus macaques (O'Connor et al. 2010). Another study demonstrated reduced CD4+ T cell counts in SHIV-infected cynomolgus macaques that exhibit a particular MHC class II haplotype (M2), containing two functional DRB genes (Borsetti et al. 2012; Wiseman et al. 2013). Similarly, correlations of HLA...
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Research: Large haplotypes highlight a complex age structure within the maize pan-genome
- Jianing Liu and
- R. Kelly Dawe
Genome Res. March 2023 33: 359-370; Published in Advance February 28, 2023, doi:10.1101/gr.276705.122
...performed hierarchical clustering using SNPs within cenhaps to interpret relative divergence in an all-by-all manner. The results confirm the deep separation of major haplotype groups and demonstrate that the majority of modern cenhap diversity evolved in the recent past (Fig. 4A; Supplemental Fig. S17...
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Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
- Benjamin Davies,
- Gang Zhang,
- Daniela Moralli,
- Samy Alghadban,
- Daniel Biggs,
- Chris Preece,
- Peter Donnelly,
- and Anjali Gupta Hinch
Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
.... thaliana, although synapsis and segregation of homologous chromosomes remain defective (Da Ines et al. 2012; Lao et al. 2013).View larger version: In this window In a new window Figure 1. Methodology of mapping recombination intermediates using Dmc1 knockout hybrid founders. (A) Key steps in mammalian...
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Research: Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
- Lujia Chen,
- Xiangduo Kong,
- Kevin G. Johnston,
- Ali Mortazavi,
- Todd C. Holmes,
- Zhiqun Tan,
- Kyoko Yokomori,
- and Xiangmin Xu
Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
...92697, USA ↵8 These authors contributed equally to this work. Corresponding authors: tanz@hs.uci.edu, kyokomor@uci.edu, xiangmix@uci.eduAbstractFacioscapulohumeral muscular dystrophy (FSHD) is linked to abnormal derepression of the transcription activator DUX4. This effect is localized to a low...
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Research: 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy
- Alice Cortesi,
- Matthieu Pesant,
- Shruti Sinha,
- Federica Marasca,
- Eleonora Sala,
- Francesco Gregoretti,
- Laura Antonelli,
- Gennaro Oliva,
- Chiara Chiereghin,
- Giulia Soldà,
- and Beatrice Bodega
Genome Res. June 2019 29: 883-895; Published in Advance May 16, 2019, doi:10.1101/gr.233288.117
...to this work. Corresponding author: bodega@ingm.orgAbstractDespite increasing insights in structure organization, the role of DNA repetitive elements, accounting for more than two thirds of the human , remains elusive. Facioscapulohumeral muscular dystrophy (FSHD) is associated with deletion of D4Z4 repeat...
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Research: Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes
- Leen Abu-Safieh,
- May Alrashed,
- Shamsa Anazi,
- Hisham Alkuraya,
- Arif O. Khan,
- Mohammed Al-Owain,
- Jawahir Al-Zahrani,
- Lama Al-Abdi,
- Mais Hashem,
- Salwa Al-Tarimi,
- Mohammed-Adeeb Sebai,
- Ahmed Shamia,
- Mohamed D. Ray-zack,
- Malik Nassan,
- Zuhair N. Al-Hassnan,
- Zuhair Rahbeeni,
- Saad Waheeb,
- Abdullah Alkharashi,
- Emad Abboud,
- Selwa A.F. Al-Hazzaa,
- and Fowzan S. Alkuraya
Genome Res. February 2013 23: 236-247; Published in Advance October 26, 2012, doi:10.1101/gr.144105.112
...M, Hashem M, Hardcastle AJ, Al-Hazzaa SA, Alkuraya FS. 2012. RP1 and retinitis pigmentosa: Report of novel mutations and insight into mutational mechanism. British J Ophthalmol 96: 1018–1022. Autozygome/exome analysis in retinal dystrophy Genome Research 245 www..org Aldahmesh MA, Safieh LA, Alkuraya H, Al...
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Method: Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
- Paul J. Norman,
- Steven J. Norberg,
- Lisbeth A. Guethlein,
- Neda Nemat-Gorgani,
- Thomas Royce,
- Emily E. Wroblewski,
- Tamsen Dunn,
- Tobias Mann,
- Claudia Alicata,
- Jill A. Hollenbach,
- Weihua Chang,
- Melissa Shults Won,
- Kevin L. Gunderson,
- Laurent Abi-Rached,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2017 27: 813-823; Published in Advance March 30, 2017, doi:10.1101/gr.213538.116
...characterized and ordered final sequence (Fig. 2A). Although the methods we used to generate scaffolds were entirely de novo, the final stage of scaffold orientation was guided by a reference sequence based on the published COX haplotype (described inMethods). To demonstrate that our approach could capture...
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Research: SORBS2 transcription is activated by telomere position effect–over long distance upon telomere shortening in muscle cells from patients with facioscapulohumeral dystrophy
- Jérôme D. Robin,
- Andrew T. Ludlow,
- Kimberly Batten,
- Marie-Cécile Gaillard,
- Guido Stadler,
- Frédérique Magdinier,
- Woodring E. Wright,
- and Jerry W. Shay
Genome Res. December 2015 25: 1781-1790; Published in Advance September 10, 2015, doi:10.1101/gr.190660.115
...SORBS2 transcription is activated by telomere position effect–over long distance upon telomere shortening in muscle cells from patients with facioscapulohumeral dystrophy Jérôme D. Robin 1 , Andrew T. Ludlow 1 , Kimberly Batten 1 , Marie-Cécile Gaillard...

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