4.8 Article

Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Genetics & Heredity

To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases

Fran Supek et al.

Summary: The nonsense-mediated mRNA decay (NMD) pathway has been extensively studied to accurately predict the degradation of mRNA with premature termination codons (PTCs). NMD plays a crucial role in disease identification and treatment, as well as in cancer immunotherapy.

TRENDS IN GENETICS (2021)

Article Oncology

Breast Cancer Patient Prognosis Is Determined by the Interplay between TP53 Mutation and Alternative Transcript Expression: Insights from TP53 Long Amplicon Digital PCR Assays

Annette Lasham et al.

Summary: This study focuses on assessing the expression of multiple TP53 transcripts in breast tumors from New Zealand patients and investigating the interplay with TP53 gene mutations. Mutations at TP53 splice sites were found to be associated with abnormal expression of specific transcripts, and the interaction between TP53 mutation status and transcript variant expression was significantly linked to patient outcome. The integration of mutation and transcript expression analysis provides valuable insights into the role of TP53 in cancer.

CANCERS (2021)

Article Biotechnology & Applied Microbiology

recount3: summaries and queries for large-scale RNA-seq expression and splicing

Christopher Wilks et al.

Summary: recount3 is a resource containing over 750,000 publicly available human and mouse RNA sequencing samples processed by the new Monorail analysis pipeline. Access to the data is facilitated through the recount3 and snapcount R/Bioconductor packages, along with complementary web resources. Monorail can process local and private data, allowing researchers to compare their results directly to any study in recount3.

GENOME BIOLOGY (2021)

Article Genetics & Heredity

Next-generation sequencing for the diagnosis of MYH9-RD: Predicting pathogenic variants

Loredana Bury et al.

HUMAN MUTATION (2020)

Article Multidisciplinary Sciences

Genomic basis for RNA alterations in cancer

Claudia Calabrese et al.

NATURE (2020)

Article Multidisciplinary Sciences

The mutational constraint spectrum quantified from variation in 141,456 humans

Konrad J. Karczewski et al.

NATURE (2020)

Article Multidisciplinary Sciences

Discovery of driver non-coding splice-site-creating mutations in cancer

Song Cao et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Predicting Splicing from Primary Sequence with Deep Learning

Kishore Jaganathan et al.

Article Biotechnology & Applied Microbiology

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing

Jun Cheng et al.

GENOME BIOLOGY (2019)

Article Genetics & Heredity

Annotation-free quantification of RNA splicing using LeafCutter

Yang I. Li et al.

NATURE GENETICS (2018)

Article Biochemistry & Molecular Biology

ClinVar: improving access to variant interpretations and supporting evidence

Melissa J. Landrum et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Genetics & Heredity

The Expanding Landscape of Alternative Splicing Variation in Human Populations

Eddie Park et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2018)

Article Biochemistry & Molecular Biology

A comprehensive characterization of cis-acting splicing-associated variants in human cancer

Yuichi Shiraishi et al.

GENOME RESEARCH (2018)

Article Genetics & Heredity

Integrating rare genetic variants into pharmacogenetic drug response predictions

Magnus Ingelman-Sundberg et al.

HUMAN GENOMICS (2018)

Letter Biotechnology & Applied Microbiology

Reproducible RNA-seq analysis using recount2

Leonardo Collado-Torres et al.

NATURE BIOTECHNOLOGY (2017)

Article Biotechnology & Applied Microbiology

IRFinder: assessing the impact of intron retention on mammalian gene expression

Robert Middleton et al.

GENOME BIOLOGY (2017)

Article Genetics & Heredity

Loss-of-Function Mutations in YY1AP1 Lead to Grange Syndrome and a Fibromuscular Dysplasia-Like Vascular Disease

Dong-chuan Guo et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2017)

Review Genetics & Heredity

Lessons from non-canonical splicing

Christopher R. Sibley et al.

NATURE REVIEWS GENETICS (2016)

Article Gastroenterology & Hepatology

Germline variants in Hamartomatous Polyposis Syndrome-associated genes from patients with one or few hamartomatous polyps

Anne Marie Jelsig et al.

SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY (2016)

Article Gastroenterology & Hepatology

Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome

Matthew B. Yurgelun et al.

GASTROENTEROLOGY (2015)

Article Genetics & Heredity

Intron retention is a widespread mechanism of tumor-suppressor inactivation

Hyunchul Jung- et al.

NATURE GENETICS (2015)

Article Medicine, General & Internal

ClinGen - The Clinical Genome Resource

Heidi L. Rehm et al.

NEW ENGLAND JOURNAL OF MEDICINE (2015)

Review Dermatology

Dystrophic epidermolysis bullosa: a review

Satoru Shinkuma

CLINICAL COSMETIC AND INVESTIGATIONAL DERMATOLOGY (2015)

Article Multidisciplinary Sciences

Comprehensive molecular profiling of lung adenocarcinoma

Eric A. Collisson et al.

NATURE (2014)

Review Multidisciplinary Sciences

Realizing the promise of cancer predisposition genes

Nazneen Rahman

NATURE (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

Transcriptome and genome sequencing uncovers functional variation in humans

Tuuli Lappalainen et al.

NATURE (2013)

Editorial Material Genetics & Heredity

The Genotype-Tissue Expression (GTEx) project

John Lonsdale et al.

NATURE GENETICS (2013)

Article Biochemistry & Molecular Biology

The Sequence Read Archive

Rasko Leinonen et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Hematology

Advances in the understanding of MYH9 disorders

Shinji Kunishima et al.

CURRENT OPINION IN HEMATOLOGY (2010)

Review Genetics & Heredity

Splicing in disease: disruption of the splicing code and the decoding machinery

Guey-Shin Wang et al.

NATURE REVIEWS GENETICS (2007)

Article Biochemical Research Methods

Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals

G Yeo et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2004)

Review Oncology

Dihydropyrimidine dehydrogenase and the efficacy and toxicity of 5-fluorouracil

ABP van Kuilenburg

EUROPEAN JOURNAL OF CANCER (2004)