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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...methylation level in these bins (Methods). Then, we identified SV alleles and methylation bins within 100 kbp flanking sequence and performed 124.9 × 106 SVs act as methylation quantitative trait loci (SV-mQTL) tests (Supplemental Fig. S12). We detected 230,464 methylation bins that were in QTL with 76,677 SV...
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Erratum: Erratum: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 660; doi:10.1101/gr.281963.126
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...reads long enough to span and resolve complex or repetitive regions of the . Several groups have shown the power of long reads in detecting thousands of genomic and epigenomic features that were previously missed by short-read sequencing approaches. While these studies demonstrate how long reads can...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...performance across most loci when benchmarked against Digger-derived genotypes, with median precision exceeding 0.79 for all gene types except TRDV (Table 3). The notably low precision observed in TRDV resulted from the Digger annotation tool providing only TRDV2 allele annotations, whereas ImmunoTyper2...
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Research: Identification and validation of supervariants reveal novel loci associated with human white matter microstructure
- Shiying Wang,
- Ting Li,
- Bingxin Zhao,
- Wei Dai,
- Yisha Yao,
- Cai Li,
- Tengfei Li,
- Hongtu Zhu,
- and Heping Zhang
Genome Res. January 2024 34: 20-33; Published in Advance December 12, 2023, doi:10.1101/gr.277905.123
..., and anthropometric traits. These results are summarized in Supplemental Table S5. We highlight the colocalizations of SNPs contributing to three supervariants located in novel loci and with P-values lower than 0.05 in the meta-analysis of external validation data sets.Supervariant FXST_Chr8_25+ is composed of 344...
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Method: Highly accurate quantification of allelic gene expression for population and disease genetics
- Anna Saukkonen,
- Helena Kilpinen,
- and Alan Hodgkinson
Genome Res. August 2022 32: 1565-1572; Published in Advance July 6, 2022, doi:10.1101/gr.276296.121
..., Helsinki, 00014, Finland ↵6 These authors contributed equally to this work. Corresponding authors: helena.kilpinen@helsinki.fi, alan.hodgkinson@kcl.ac.ukAbstractAnalysis of allele-specific gene expression (ASE) is a powerful approach for studying gene regulation, particularly when sample sizes are small...
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Method: Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication
- Zihao Wang,
- Zhenquan Zhang,
- Songhao Luo,
- Tianshou Zhou,
- and Jiajun Zhang
Genome Res. January 2024 34: 106-118; Published in Advance January 3, 2024, doi:10.1101/gr.278631.123
...Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication Zihao Wang1,2,3, Zhenquan Zhang1,2,3, Songhao Luo1,2,3, Tianshou Zhou1,2 and Jiajun Zhang1,2 1Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...Gaps and complex structurally variant loci in phased assemblies David Porubsky1, Mitchell R. Vollger1, William T. Harvey1, Allison N. Rozanski1, Peter Ebert2,3, Glenn Hickey4, Patrick Hasenfeld5, Ashley D. Sanders6,7,8, Catherine Stober5, Human Pan Reference Consortium11, Jan O. Korbel5,9, Benedict...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...new mutation (Fig. 1A; Supplemental Datasets S1–S3). These mutations may occur at STRs for which both founders harbored the same allele or may occur at STRs that were already polymorphic in the founders. Mutations are scattered throughout the and do not cluster at any particular genomic location...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...is detected. This leaves large amounts of potentially interesting data unused. To the contrary, here we set out to explore inter-patient heterogeneity in ESR1 binding in more detail. We evaluate the biology underlying inter-tumor cistromic heterogeneity of ESR1, in relation to genomic locations and germline...

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