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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...the usage of introns and 3′ splice sites. Our data highlighted a constrained window at canonical 3′ splice sites in which dynamic splice-site switches occurred in SF3B1-mutated patients. Using transcriptome-wide RNA-binding maps and molecular dynamics simulations, we showed multimodal SF3B1 binding at 3...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
..., such as correcting aberrant splicing and skipping exons that contain disease-causing mutations. In addition, manipulating alternative splicing, such as the suppression of endogenous “poison exons” containing premature termination codons (PTCs) and activation of cryptic splice sites, can provide a powerful means...
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Perspective: Functional genomics bridges the gap between quantitative genetics and molecular biology
- Tuuli Lappalainen
Genome Res. October 2015 25: 1427-1431; doi:10.1101/gr.190983.115
...-wide association studies, respectively, and eQTL is an abbreviation of expression quantitative trait loci. Lappalainen 1428 Genome Research www..org introduces a premature stop codon, is in close proximity to an annotated splice site, or disrupts a transcription factor binding site. Analysis of allelic expression...
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Research: BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies
- Guntram Borck,
- Friederike Hög,
- Maria Lisa Dentici,
- Perciliz L. Tan,
- Nadine Sowada,
- Ana Medeira,
- Lucie Gueneau,
- Holger Thiele,
- Maria Kousi,
- Francesca Lepri,
- Larissa Wenzeck,
- Ian Blumenthal,
- Antonio Radicioni,
- Tito Livio Schwarzenberg,
- Barbara Mandriani,
- Rita Fischetto,
- Deborah J. Morris-Rosendahl,
- Janine Altmüller,
- Alexandre Reymond,
- Peter Nürnberg,
- Giuseppe Merla,
- Bruno Dallapiccola,
- Nicholas Katsanis,
- Patrick Cramer,
- and Christian Kubisch
Genome Res. February 2015 25: 155-166; Published in Advance January 5, 2015, doi:10.1101/gr.176925.114
...candidate mutations to be pathogenic in an apparent isoform-specific context. BRF1 associates with BDP1 and TBP to form the transcription factor IIIB (TFIIIB), which recruits Pol III to target genes. We show that disease-causing mutations reduce Brf1 occupancy at tRNA target genes in Saccharomyces...
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Research: Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice
- Malte Spielmann,
- Naseebullah Kakar,
- Naeimeh Tayebi,
- Catherine Leettola,
- Gudrun Nürnberg,
- Nadine Sowada,
- Darío G. Lupiáñez,
- Izabela Harabula,
- Ricarda Flöttmann,
- Denise Horn,
- Wing Lee Chan,
- Lars Wittler,
- Rüstem Yilmaz,
- Janine Altmüller,
- Holger Thiele,
- Hans van Bokhoven,
- Charles E. Schwartz,
- Peter Nürnberg,
- James U. Bowie,
- Jamil Ahmad,
- Christian Kubisch,
- Stefan Mundlos,
- and Guntram Borck
Genome Res. February 2016 26: 183-191; Published in Advance January 11, 2016, doi:10.1101/gr.199430.115
.... Autozygosity mapping was performed as previously described (Borck et al. 2011). Exome sequencing Exome sequencing was performed in individual VI:3 in family 1. Briefly, genomic DNAwas enriched for exonic and adjacent splice site sequences with the SeqCap EZ human exome library v2.0 kit, and libraries were run...
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Methods: Mutation scanning by meltMADGE: Validations using BRCA1 and LDLR, and demonstration of the potential to identify severe, moderate, silent, rare, and paucimorphic mutations in the general population
- Khalid K. Alharbi,
- Mohammed A. Aldahmesh,
- Emmanuel Spanakis,
- Lema Haddad,
- Roslyn A. Whittall,
- Xiao-he Chen,
- Hamid Rassoulian,
- Matt J. Smith,
- Julie Sillibourne,
- Nicola J. Ball,
- Nikki J. Graham,
- Patricia J. Briggs,
- Iain A. Simpson,
- David I.W. Phillips,
- Deborah A. Lawlor,
- Shu Ye,
- Stephen E. Humphries,
- Cyrus Cooper,
- George Davey Smith,
- Shah Ebrahim,
- Diana M. Eccles,
- and Ian N.M. Day
Genome Res. July 2005 15: 967-977; doi:10.1101/gr.3313405
...region and a panel of 94 unrelated family breast cancer risk consultands previously screened in a clinical diagnostic laboratory. All 10 common polymorphisms, 15/15 previously identified disease-causing mutations, and three previously untested single base changes were identified. Assays of LDLR exons 3...
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Method: Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
- Yi-Fei Huang and
- Adam Siepel
Genome Res. August 2019 29: 1310-1321; Published in Advance June 27, 2019, doi:10.1101/gr.245522.118
...sites and improved shrinkage estimators for allele-specific selection coefficients.View larger version: In this window In a new window Figure 1. Overview of LASSIE. (A) For each potential protein-coding mutation, we collected 33 genomic features likely to be informative about natural selection...
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Method: A general framework for identifying oligogenic combinations of rare variants in complex disorders
- Vijay Kumar Pounraja and
- Santhosh Girirajan
Genome Res. May 2022 32: 904-915; Published in Advance March 17, 2022, doi:10.1101/gr.276348.121
...of comorbid features, including 1215 individuals with ID, 1825 with anxiety and depression, and 332 with schizophrenia features. We assessed for significant co-occurrences of two or more mutated genes with two or more of the above phenotypes (Fig. 4). Using one-tailed binomial tests to compare the observed...
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Method: Modeling Niemann–Pick disease type C in a human haploid cell line allows for patient variant characterization and clinical interpretation
- Steven Erwood,
- Reid A. Brewer,
- Teija M.I. Bily,
- Eleonora Maino,
- Liangchi Zhou,
- Ronald D. Cohn,
- and Evgueni A. Ivakine
Genome Res. December 2019 29: 2010-2019; Published in Advance November 21, 2019, doi:10.1101/gr.250720.119
...on Niemann–Pick disease type C (NPC) as an example. NPC is a fatal neurodegenerative disorder characterized by a lysosomal accumulation of unesterified cholesterol and glycolipids. In 95% of cases, NPC is caused by mutations in the NPC1 gene, for which more than 200 unique disease-causing variants have been...
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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
...incidence of variation in splice regions of intolerant and tolerant genes to characterize the deleteriousness of mutations at each individual near-splice sites (see Methods).Although different studies have focused on mutations in this region, none of them directly quantified the level of deleteriousness...

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