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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...cosegregates with breast, ovarian, pancreatic, and prostate cancer in three generations of two extended families (Fig. 1A). The variant creates a 74 bp pseudoexon in intron 16 with a stop at codon 1673 (Fig. 1B). The families are not closely related, but both trace their ancestry in the 19C to the same region...
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Method: A complete pedigree-based graph workflow for rare candidate variant analysis
- Charles Markello,
- Charles Huang,
- Alex Rodriguez,
- Andrew Carroll,
- Pi-Chuan Chang,
- Jordan Eizenga,
- Thomas Markello,
- David Haussler,
- and Benedict Paten
Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
...tasks of gene discovery is the detection of variants in highly polymorphic, repetitive, and incompletely represented regions of the , exactly where pan graphs can potentially extend accuracy and precision.We first describe VG-Pedigree, a software workflow for mapping and variant calling high...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
..., France; 5Clareo Biosciences, Louisville, Kentucky 40222, USA ↵6 These authors contributed equally to this work. Corresponding authors: andreas.lossius@medisin.uio.no, corey.watson@louisville.eduAbstractGenetic diversity within the human immunoglobulin heavy-chain (IGH) locus influences the expressed...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...and epigenetic status, including DNA methylation of the monomeric units constituting young mouse L1 promoters. Locus-specific L1 methylation dynamics during development may therefore elucidate and explain spatiotemporal niches of endogenous retrotransposition but remain unresolved. Here, we interrogate...
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Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
...Resolving complex duplication variants in autism spectrum disorder using long-read sequencing Jesper Eisfeldt1,2, Edward J. Higginbotham3,4, Felix Lenner5, Jennifer Howe3,4, Bridget A. Fernandez6,7, Anna Lindstrand1,2, Stephen W. Scherer3,4,8 and Lars Feuk5 1Department of Molecular Medicine...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...@pennmedicine.upenn.eduAbstractAutism spectrum disorder (ASD) is a highly heterogenous neurodevelopmental disorder with numerous genetic risk factors. Notably, a disproportionate number of risk genes encode transcription regulators including transcription factors and proteins that regulate chromatin. Here, we test the function of nine such ASD...
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Method: A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome
- Fan Gao,
- Xuedong Pan,
- Elissa B. Dodd-Eaton,
- Carlos Vera Recio,
- Matthew D. Montierth,
- Jasmina Bojadzieva,
- Phuong L. Mai,
- Kristin Zelley,
- Valen E. Johnson,
- Danielle Braun,
- Kim E. Nichols,
- Judy E. Garber,
- Sharon A. Savage,
- Louise C. Strong,
- and Wenyi Wang
Genome Res. August 2020 30: 1170-1180; Published in Advance August 18, 2020, doi:10.1101/gr.249599.119
...of criterion 2 at a cutoff age (provided next to the stars). The gray dotted lines show the range of cutoff ages, 45–65, where a partial AUC is calculated for criterion 1.We also compared our method with two simple criterion-based prediction models that do not require the collection of extended pedigree data...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...from 44,190 breakpoints (Supplemental Data S3), including 22 called by MELT or TranSurVeyor, and one additional de novo locus. In total, we identified and PCR-validated 26 de novo MEIs, including eight L1, seven SVA, and 11 Alu insertions in 16 of 33 CEPH pedigrees (Table 1; Fig. 1; Supplemental Table...
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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
...disorders (Lucá et al. 2013; McNulty et al. 2018). Finally, it is possible that there is an advantage to keeping around a locus that promotes STR variability in general as a source of new and potentially adaptive changes upon which evolution can act (Kashi and King 2006). Although we did not assess...
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Research: Identifying multiple causative genes at a single GWAS locus
- Michael J. Flister,
- Shirng-Wern Tsaih,
- Caitlin C. O'Meara,
- Bradley Endres,
- Matthew J. Hoffman,
- Aron M. Geurts,
- Melinda R. Dwinell,
- Jozef Lazar,
- Howard J. Jacob,
- and Carol Moreno
Genome Res. December 2013 23: 1996-2002; Published in Advance September 4, 2013, doi:10.1101/gr.160283.113
...of bipolar disorder identifies a new susceptibility locus near ODZ4. Nat Genet 43: 977–983. Takaluoma K, Hyry M, Lantto J, Sormunen R, Bank RA, Kivirikko KI, Myllyharju J, Soininen R. 2007. Tissue-specific changes in the hydroxylysine content and cross-links of collagens and alterations in fibril morphology...

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