4.7 Article

dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations

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。
Article Genetics & Heredity

StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants

Andrew G. Sharo et al.

Summary: This article introduces a method called StrVCTVRE to distinguish between pathogenic and benign structural variants (SVs). By integrating multiple features and using a rare training set for classification, this method reduces about half of the SVs while maintaining a high sensitivity. It provides support for further investigation into unresolved cases and understanding new mechanisms of disease.

AMERICAN JOURNAL OF HUMAN GENETICS (2022)

Article Multidisciplinary Sciences

Automated prediction of the clinical impact of structural copy number variations

M. Gaziova et al.

Summary: Copy number variants (CNVs) play a crucial role in biological processes, but interpreting their effects is challenging. To relieve the burden on researchers, we developed a prediction method (ISV) based on boosted trees, achieving high accuracy and explainability in CNV predictions.

SCIENTIFIC REPORTS (2022)

Article Biotechnology & Applied Microbiology

TADA-a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs

Jakob Hertzberg et al.

Summary: Functional annotation-based prioritization of pathogenic CNVs is a promising approach to support clinical diagnostics and further the understanding of mechanisms controlling the disease impact of larger genomic alterations. Our method, TADA, demonstrates accurate prediction of pathogenic CNVs, outperforming current alternative methods, and producing a well-calibrated pathogenicity score.

GENOME BIOLOGY (2022)

Article Biotechnology & Applied Microbiology

AutoCNV: a semiautomatic CNV interpretation system based on the 2019 ACMG/ClinGen Technical Standards for CNVs

Chunna Fan et al.

Summary: AutoCNV is a semi-automatic automated CNV interpretation system developed based on the technical standards proposed by ACMG and ClinGen, which can automatically generate predictions on copy number loss and gain criteria in a fast and accurate manner, demonstrating high consistency with both reviewers and ClinGen-verified classifications during performance assessment.

BMC GENOMICS (2021)

Article Genetics & Heredity

X-CNV: genome-wide prediction of the pathogenicity of copy number variations

Li Zhang et al.

Summary: The research team developed the X-CNV computational framework, integrating multiple informative features to predict the pathogenicity of CNVs, outperforming other tools. They also proposed an MVP score to quantitatively measure the pathogenic effect of CNVs, demonstrating high discriminative power.

GENOME MEDICINE (2021)

Article Biochemistry & Molecular Biology

ClinVar: improvements to accessing data

Melissa J. Landrum et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

A structural variation reference for medical and population genetics

Ryan L. Collins 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

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Jill E. Moore et al.

NATURE (2020)

Article Multidisciplinary Sciences

ClassifyCNV: a tool for clinical annotation of copy-number variants

Tatiana A. Gurbich et al.

SCIENTIFIC REPORTS (2020)

Article Genetics & Heredity

A map of constrained coding regions in the human genome

James M. Havrilla et al.

NATURE GENETICS (2019)

Article Biochemistry & Molecular Biology

The UCSC Genome Browser database: 2019 update

Maximilian Haeussler et al.

NUCLEIC ACIDS RESEARCH (2019)

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

Structural variation in the 3D genome

Malte Spielmann et al.

NATURE REVIEWS GENETICS (2018)

Article Genetics & Heredity

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

Nilah M. Ioannidis et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2016)

Article Multidisciplinary Sciences

Analysis of protein-coding genetic variation in 60,706 humans

Monkol Lek et al.

NATURE (2016)

Review Genetics & Heredity

A copy number variation map of the human genome

Mehdi Zarrei et al.

NATURE REVIEWS GENETICS (2015)

Review Cell Biology

Three-dimensional genome architecture: players and mechanisms

Ana Pombo et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Medicine, General & Internal

ClinGen - The Clinical Genome Resource

Heidi L. Rehm et al.

NEW ENGLAND JOURNAL OF MEDICINE (2015)

Article Biochemistry & Molecular Biology

Haploinsufficiency predictions without study bias

Julia Steinberg et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

Joanna S. Amberger et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Psychiatry

Analysis of copy number variations at 15 schizophrenia-associated loci

Elliott Rees et al.

BRITISH JOURNAL OF PSYCHIATRY (2014)

Article Biochemistry & Molecular Biology

The Database of Genomic Variants: a curated collection of structural variation in the human genome

Jeffrey R. MacDonald et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation

Eugene Bragin et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

SIFT web server: predicting effects of amino acid substitutions on proteins

Ngak-Leng Sim et al.

NUCLEIC ACIDS RESEARCH (2012)

Letter Biochemical Research Methods

A method and server for predicting damaging missense mutations

Ivan A. Adzhubei et al.

NATURE METHODS (2010)

Article Biochemical Research Methods

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP plus

Eugene V. Davydov et al.

PLOS COMPUTATIONAL BIOLOGY (2010)