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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...(Supplemental Fig. S6E).Among 18 patients without prior genetic diagnosis, we observed four patients with Watershed-SV prioritized gene-SV pairs in muscular disorder-related genes, one gene-SV posterior above 0.5, and three above 0.9 (Supplemental Table S6). Among them, a female patient (N10) with undiagnosed...
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Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
- Howard J. Womersley,
- Daniel Muliaditan,
- Ramanuj DasGupta,
- and Lih Feng Cheow
Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
...Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression Howard J. Womersley1,4, Daniel Muliaditan2,3,4, Ramanuj DasGupta3 and Lih Feng Cheow1,2 1Institute for Health Innovation and Technology, National University...
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Method: Bayesian estimation of cell type–specific gene expression with prior derived from single-cell data
- Jiebiao Wang,
- Kathryn Roeder,
- and Bernie Devlin
Genome Res. October 2021 31: 1807-1818; Published in Advance April 9, 2021, doi:10.1101/gr.268722.120
...and robustly by incorporating prior information to regularize the statistically challenging estimation we aim to achieve in this work. Distinguishing itself from other methods, bMIND is a powerful and flexible tool, suitable for estimation of CTS expression and for testing for differential expression...
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Research: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
- Alexandra J. Scott,
- Colby Chiang,
- and Ira M. Hall
Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
...and rare gene expression changes in up to 48 tissue types (Supplemental Table S1). This study expands on our prior analysis of SV in 147 human samples from the GTEx cohort with RNA-seq expression data from 13 different tissues (Chiang et al. 2017) and is the most comprehensive study of SV-eQTLs to date...
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Method: A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
- Daniel A. Skelly,
- Marnie Johansson,
- Jennifer Madeoy,
- Jon Wakefield,
- and Joshua M. Akey
Genome Res. October 2011 21: 1728-1737; Published in Advance August 26, 2011, doi:10.1101/gr.119784.110
...(ei) for gene i. As the dispersion ei approaches zero, the counts converge to binomially distributed. Finally, we place a two-component mixture prior on pi, ei pi; ei âj ; d̂; f ; g;h;p0 ; Beta â; âð Þ 3 Beta l; d̂ withprobabilityp0: Beta f ; gð Þ 3 Beta l;hð Þ withprobability 1 p0: The parameters...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...selection is a potent force shaping the amount and nature of genetic variation within species. Both theory and prior evidence predict that genomic regions that are significantly conserved across mammalian species should exhibit lower levels of intraspecies variation than the rest of the (LindbladToh et al...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
...as outgroup and vice versa experiments were performed as the pigeon is phylogenetically distant from the chicken and zebra finch. Two rounds of RACA were done for both species. The initial run was performed using the following parameters: WINDOWSIZE=10 RESOLUTION=150000 MIN_INTRACOV_ PERC=5. Prior...
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Perspective: The first five years of single-cell cancer genomics and beyond
- Nicholas E. Navin
Genome Res. October 2015 25: 1499-1507; doi:10.1101/gr.191098.115
...). These methods can now achieve >90% coverage of a single-cell , allowing mutations to be detected at base-pair resolution. nuc-seq and SNES take advantage of G2/M single cells that have duplicated their prior toWGA, providing four copies of the as input material and thereby reducing technical error rates (Wang...
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Research: Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato
- Nicola J. Nadeau,
- Mayté Ruiz,
- Patricio Salazar,
- Brian Counterman,
- Jose Alejandro Medina,
- Humberto Ortiz-Zuazaga,
- Anna Morrison,
- W. Owen McMillan,
- Chris D. Jiggins,
- and Riccardo Papa
Genome Res. August 2014 24: 1316-1333; Published in Advance May 13, 2014, doi:10.1101/gr.169292.113
...). Overall, the prospects for mapping individual phenotypic components and identifying epistatic relationships without prior knowledge are considerable, especially with larger sample sizes. The possibility of using hybrid zones for associationmapping has long been recognized (Kocher and Sage 1986), but few...
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Research: Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently
- Sophia David,
- Christophe Rusniok,
- Massimo Mentasti,
- Laura Gomez-Valero,
- Simon R. Harris,
- Pierre Lechat,
- John Lees,
- Christophe Ginevra,
- Philippe Glaser,
- Laurence Ma,
- Christiane Bouchier,
- Anthony Underwood,
- Sophie Jarraud,
- Timothy G. Harrison,
- Julian Parkhill,
- and Carmen Buchrieser
Genome Res. November 2016 26: 1555-1564; Published in Advance September 23, 2016, doi:10.1101/gr.209536.116
...PathO-Gen (Supplemental Fig. S2). Using a relaxed molecular clock model in BEAST, we estimated that the ST37 clone emerged in about 1979 (95% highest posterior density [HPD] intervals: L. pneumophila disease clones emerged recently Genome Research 1557 www..org 1968–1985) (Fig. 3), which is 3 yr prior...
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