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Method: Genetics-driven risk predictions leveraging the Mendelian randomization framework
- Daniel Sens,
- Liubov Shilova,
- Ludwig Gräf,
- Maria Grebenshchikova,
- Bjoern M. Eskofier,
- and Francesco Paolo Casale
Genome Res. September 2024 34: 1276-1285; Published in Advance September 27, 2024, doi:10.1101/gr.279252.124
...health outcomes are limited. To overcome this challenge, we introduce a novel framework, Predictive Risk modeling using Mendelian Randomization (PRiMeR), which utilizes genetic effects as supervisory signals to learn disease risk predictors without relying on longitudinal data. To do so, PRiMeR leverages...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...assessment, variant calling is the next step in the analysis. Detecting genomic alterations fosters our understanding of genomic differences between individuals and thus may also give insights into diseases or other important phenotypes. In general, genomic alterations can be classified into four different...
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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
.... Corresponding authors: smontgom@stanford.edu, mschatz@cs.jhu.edu, wheelerm@stanford.edu, ajbattle@jhu.eduAbstractRare structural variants (SVs)—insertions, deletions, and complex rearrangements—can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed...
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Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
...Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), 6500 HB Nijmegen, Netherlands ↵36 These authors contributed equally to this work. Corresponding author: alexander.hoischen@radboudumc.nlAbstractSolve-RD is a pan-European rare disease (RD) research...
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Method: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
- Nathan LaPierre,
- Boyang Fu,
- Steven Turnbull,
- Eleazar Eskin,
- and Sriram Sankararaman
Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123
...90095, USA; 3Department of Computational Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; 4Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA ↵5 These authors contributed equally to this work. Corresponding authors...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...with individual-level phenotype data are included in such studies, additional loci contributing to more nuanced parts of a phenotype will be found.View larger version: In this window In a new window Figure 1. Genomic analyses help resolve the genetics of shared human–canine traits. (A) Approximately 50...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...). To date, more than 4000 Mendelian disease genes have been identified, each contributing to a diverse array of human phenotypes (Boycott et al. 2013; https://mirror.omim.org/statistics/geneMap). These disease genes and associated phenotypes could provide insights into the evolutionary trajectory of human...
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Research: Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism
- Dale J. Annear,
- Geert Vandeweyer,
- Alba Sanchis-Juan,
- F. Lucy Raymond,
- and R. Frank Kooy
Genome Res. November/December 2022 32: 1967-1980; Published in Advance November 9, 2022, doi:10.1101/gr.277011.122
...with or directly linked to genetic disease. In total, of the 5989 STR loci that displayed deviation, 844 repeats were linked to 481 genes that may or are known to contribute toward autism, intellectual disability, neurodevelopmental delay, and neurodegenerative phenotypes.The largest expansion deviation observed...
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Method: Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance
- Christopher J. Yoon,
- Su Yeon Kim,
- Chang Hyun Nam,
- Junehawk Lee,
- Jung Woo Park,
- Jihyeob Mun,
- Seongyeol Park,
- Soyoung Lee,
- Boram Yi,
- Kyoung Il Min,
- Brian Wiley,
- Kelly L. Bolton,
- Jeong Ho Lee,
- Eunjoon Kim,
- Hee Jeong Yoo,
- Jong Kwan Jun,
- Ji Seon Choi,
- Malachi Griffith,
- Obi L. Griffith,
- and Young Seok Ju
Genome Res. November/December 2022 32: 2134-2144; Published in Advance December 6, 2022, doi:10.1101/gr.276794.122
...Mix can be applied to detect genomic abnormalities that deviate from Mendelian inheritance patterns, such as uniparental disomy (UPD) and chimerism. A -wide depth and variant allele frequency plot generated by TrioMix facilitates tracing the origin of Mendelian inheritance deviations. We showed that Trio...
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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
...These authors contributed equally to this review. Corresponding author: christopher.pearson@sickkids.caAbstractExpansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans...

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