Searching journal content for articles similar to Roca et al. 18 (1): 77.

Displaying results 1-10 of 35

For checked items

view abstracts
download to citation manager

Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
Select this article
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...
Select this article
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...
Select this article
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...
Select this article
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...
Select this article
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...
Select this article
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...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Roca et al. 18 (1): 77.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: