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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...of variants related to craniofacial morphology and stature. Breed-enriched variants were prioritized according to gene constraint, which was calculated using a mutation model derived from trinucleotide substitution probabilities. Among the newly found variants is a splice-acceptor variant in PDGFRA associated...
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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
..., as confirmed by RNA analysis (Byrne et al. 2023). Similarly, a novel pathogenic sSNV in the WAS gene was found to disrupt splicing, thereby affecting protein expression (Sun et al. 2024). However, the functional relevance of most sSNVs remains unknown. In ClinVar (Landrum et al. 2020), sSNVs with a clear...
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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...estimator (LOFTEE), and (2) for nonsynonymous variants, they must be located within functional domains and either predicted as pathogenic by AlphaMissense or predicted as ambiguous by AlphaMissense with an ESM1b score below −10.This stringent selection resulted in five predicted pathogenic variants in CFM...
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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
...and cDNA sequencing, based on patient-derived DNA and RNA, to systematically evaluate deep intronic variation. We identified all variants across the full genomic loci of targeted genes, applied the in silico tools SpliceAI and Pangolin to predict variants of functional consequence, and then carried out...
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Research: Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides
- Sidi Zhang,
- Kaitlin E. Samocha,
- Manuel A. Rivas,
- Konrad J. Karczewski,
- Emma Daly,
- Ben Schmandt,
- Benjamin M. Neale,
- Daniel G. MacArthur,
- and Mark J. Daly
Genome Res. July 2018 28: 968-974; Published in Advance June 1, 2018, doi:10.1101/gr.231902.117
...://exac.broadinstitute.org) mapped to human reference (hg19) to scan for evidence of selection against variation in the near-splice-site regions. First, we tallied the number of A, T, C, and G's in the reference at each near-splice-site position across all canonical exons along with the number of variants observed in Ex...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci...
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Research: Exonic splice regulation imposes strong selection at synonymous sites
- Rosina Savisaar and
- Laurence D. Hurst
Genome Res. October 2018 28: 1442-1454; Published in Advance August 24, 2018, doi:10.1101/gr.233999.117
...of the evolutionary constraint under which they evolve. Current data are consistent both with a scenario of weak and diffuse constraint, enveloping large swaths of sequence, as well as with well-defined pockets of strong purifying selection. In the former case, natural selection on exonic splice enhancers (ESEs...
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Method: ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease
- Riccardo Sangermano,
- Mubeen Khan,
- Stéphanie S. Cornelis,
- Valerie Richelle,
- Silvia Albert,
- Alejandro Garanto,
- Duaa Elmelik,
- Raheel Qamar,
- Dorien Lugtenberg,
- L. Ingeborgh van den Born,
- Rob W.J. Collin,
- and Frans P.M. Cremers
Genome Res. January 2018 28: 100-110; Published in Advance November 21, 2017, doi:10.1101/gr.226621.117
...but no deleterious variants due to the PCR amplification of the insert when compared to the human reference GRCh37/hg19 assembly. Nevertheless, despite the use of a proofreading high-fidelity DNA polymerase, we found minor sequence variations (Supplemental Table S1).Selection of ABCA4 noncanonical splice site...
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Method: Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing data sets
- Perry Evans,
- Chao Wu,
- Amanda Lindy,
- Dianalee A. McKnight,
- Matthew Lebo,
- Mahdi Sarmady,
- and Ahmad N. Abou Tayoun
Genome Res. July 2019 29: 1144-1151; Published in Advance June 24, 2019, doi:10.1101/gr.240994.118
...and have equal or more population variation compared to expectation. With this knowledge, classifiers might flag a variant as pathogenic if it lies within a genomic region that selects against variants (Amr et al. 2017). Here, we examine three constraint metrics derived from ExAC or gnomAD. One...
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Research: HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo
- Jonathan M. Howard,
- Hai Lin,
- Andrew J. Wallace,
- Garam Kim,
- Jolene M. Draper,
- Maximilian Haeussler,
- Sol Katzman,
- Masoud Toloue,
- Yunlong Liu,
- and Jeremy R. Sanford
Genome Res. May 2018 28: 689-698; Published in Advance April 12, 2018, doi:10.1101/gr.229062.117
...-regulatory elements that compete with authentic exons for binding to splicing factors.To determine if changes in U2AF2 crosslinking correlated with HNRNPA1-dependent splicing regulation, we sequenced poly(A)+ selected RNA libraries from control and HNRNPA1 overexpression cells (Supplemental Table 16). Of the 267...

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