Searching journal content for articles similar to Annear et al. 32 (11-12): 1967.

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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
..., Charen K, Hipp HS, Shubeck L, Amin A, He W, Nolin SL, Glicksman A, Tortora N, McKinnon B, et al. 2021. Refining the risk for fragile X–associated primary ovarian insufficiency (FXPOI) by FMR1 CGG repeat size. Genet Med 23: 1648–1655. doi:10.1038/s41436-021-01177-y ↵Benson G. 1999. Tandem repeats finder...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...validated an instance of oligogenic inheritance in CHD (Gifford et al. 2019), as well as speculated a role for oligogenic inheritance in other developmental disorders like autism spectrum disorder (Schaaf et al. 2011; Wenger et al. 2016). Although these studies discovered specific disease-causing gene...
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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
...of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; 3Department of Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA ↵4 These authors contributed equally to this work. Corresponding author: ekorb@pennmedicine.upenn.eduAbstractAutism...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...centenarians, AD patients, or HPRC individuals (Supplemental Fig. 9). Similarly, in the ataxin 2 (ATXN2) TR (Chr12:111,598,950–111,599,019), where interruptions in the CAG repeat with CAA motifs are associated with Spinocerebellar Ataxia Type 2 (SCA2), no reported pathogenic interruption patterns were detected...
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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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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...hybridization.GPF further categorizes alleles based on their inheritance patterns within a family. Mendelian alleles exhibit typical inheritance patterns from parents to offspring. De novo alleles arise in the child without being inherited from either parent. Omission refers to alleles that should logically...
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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: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...Extreme scrambling in marine planktonic Oikopleura dioica cryptic species Charles Plessy1,9, Michael J. Mansfield1,9, Aleksandra Bliznina1,10, Aki Masunaga1, Charlotte West1,11, Yongkai Tan1, Andrew W. Liu1, Jan Grašič1, María Sara del Río Pisula1, Gaspar Sánchez-Serna2,3, Marc Fabrega-Torrus2...
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Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
- Wouter De Coster,
- Ida Höijer,
- Inge Bruggeman,
- Svenn D'Hert,
- Malin Melin,
- Adam Ameur,
- and Rosa Rademakers
Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
...version: In this window In a new window Figure 3. pathSTR visualization of a sequence plot of the FMR1 repeat, showing colors for the most frequently seen motifs and gray for everything else, sorted by length. AGG motif interruptions (orange) between the CGG units (blue) can be observed.Length plots...
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