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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
...of these variant classes in studies of human genetic diversity and in clinical settings (Fig. 1; Sanford Kobayashi et al. 2022; Mastrorosa et al. 2023; Oehler et al. 2023).View larger version: In this window In a new window Figure 1. Long-read sequencing facilitates accurate discovery of SVs and their breakpoints...
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Research: Actionable exomic incidental findings in 6503 participants: challenges of variant classification
- Laura M. Amendola,
- Michael O. Dorschner,
- Peggy D. Robertson,
- Joseph S. Salama,
- Ragan Hart,
- Brian H. Shirts,
- Mitzi L. Murray,
- Mari J. Tokita,
- Carlos J. Gallego,
- Daniel Seung Kim,
- James T. Bennett,
- David R. Crosslin,
- Jane Ranchalis,
- Kelly L. Jones,
- Elisabeth A. Rosenthal,
- Ella R. Jarvik,
- Andy Itsara,
- Emily H. Turner,
- Daniel S. Herman,
- Jennifer Schleit,
- Amber Burt,
- Seema M. Jamal,
- Jenica L. Abrudan,
- Andrew D. Johnson,
- Laura K. Conlin,
- Matthew C. Dulik,
- Avni Santani,
- Danielle R. Metterville,
- Melissa Kelly,
- Ann Katherine M. Foreman,
- Kristy Lee,
- Kent D. Taylor,
- Xiuqing Guo,
- Kristy Crooks,
- Lesli A. Kiedrowski,
- Leslie J. Raffel,
- Ora Gordon,
- Kalotina Machini,
- Robert J. Desnick,
- Leslie G. Biesecker,
- Steven A. Lubitz,
- Surabhi Mulchandani,
- Greg M. Cooper,
- Steven Joffe,
- C. Sue Richards,
- Yaoping Yang,
- Jerome I. Rotter,
- Stephen S. Rich,
- Christopher J. O’Donnell,
- Jonathan S. Berg,
- Nancy B. Spinner,
- James P. Evans,
- Stephanie M. Fullerton,
- Kathleen A. Leppig,
- Robin L. Bennett,
- Thomas Bird,
- Virginia P. Sybert,
- William M. Grady,
- Holly K. Tabor,
- Jerry H. Kim,
- Michael J. Bamshad,
- Benjamin Wilfond,
- Arno G. Motulsky,
- C. Ronald Scott,
- Colin C. Pritchard,
- Tom D. Walsh,
- Wylie Burke,
- Wendy H. Raskind,
- Peter Byers,
- Fuki M. Hisama,
- Heidi Rehm,
- Debbie A. Nickerson,
- and Gail P. Jarvik
Genome Res. March 2015 25: 305-315; Published in Advance January 30, 2015, doi:10.1101/gr.183483.114
..., substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...) encompass broad coverage of variant types and interpretations but fall short in elucidating the specific mechanisms by which sSNVs contribute to pathogenicity. Moreover, the sequence and structural properties of variants are widely used in the development of predictive models for sSNVs and demonstrate...
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Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...and disease-specific RTE dynamics in these diseases. A unified pipeline was developed to perform alignment, quantification, normalization, quality control, clustering, cell type annotation, and downstream analysis of these data sets (Fig. 1). Cell types were reannotated by mapping to the reference data set...
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Research: Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity
- Alexander Crits-Christoph,
- Nicholas Bhattacharya,
- Matthew R. Olm,
- Yun S. Song,
- and Jillian F. Banfield
Genome Res. February 2021 31: 239-250; Published in Advance December 23, 2020, doi:10.1101/gr.268169.120
...(Skinnider et al. 2017), but there are many known exceptions to this rule (Wenzel and Müller 2005), and the accuracies of these software predictions have not been formally assessed using a large training data set.Prediction of BGC metabolite function generally relies on contextual genes associated with BGCs...
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Research: RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus
- Kathrin Jansen,
- Noriko Shikama-Dorn,
- Moustafa Attar,
- Stefano Maio,
- Maria Lopopolo,
- David Buck,
- Georg A. Holländer,
- and Stephen N. Sansom
Genome Res. November 2021 31: 2022-2034; Published in Advance October 14, 2021, doi:10.1101/gr.275245.121
...that such transcripts can be produced by the same cell: single-cell RNA sequencing data revealed that the thyroid and nervous-system specific transcript isoforms of Calca were often produced together in individual mTEC (Supplemental Fig. 6D). We also assessed the representation of sets of tissue-restricted isoforms...
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