Cargando…

Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

BACKGROUND: Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow a consistent data analysis pipeline to achieve the highest possible accuracy an...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Christodoulou, Kyproula, Spyrou, George M., Kyriacou, Kyriacos, Hadjisavvas, Andreas
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2021
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080428/ https://www.ncbi.nlm.nih.gov/pubmed/33910496 http://dx.doi.org/10.1186/s12859-021-04144-1

Ejemplares similares

NGS Panel Testing of Triple-Negative Breast Cancer Patients in Cyprus: A Study of BRCA-Negative Cases
por: Zanti, Maria, et al.
Publicado: (2020)

In depth analysis of Cyprus-specific mutations of SARS-CoV-2 strains using computational approaches
por: Oulas, Anastasis, et al.
Publicado: (2021)

Combination of a 15-SNP Polygenic Risk Score and Classical Risk Factors for the Prediction of Breast Cancer Risk in Cypriot Women
por: Yiangou, Kristia, et al.
Publicado: (2021)

Multi-gene panel testing and association analysis in Cypriot breast cancer cases and controls
por: Zanti, Maria, et al.
Publicado: (2023)

Risk factors for breast cancer brain metastases: a systematic review
por: Koniali, Lola, et al.
Publicado: (2020)

The BRCA1 Variant p.Ser36Tyr Abrogates BRCA1 Protein Function and Potentially Confers a Moderate Risk of Breast Cancer
por: Christou, Charita M., et al.
Publicado: (2014)

Proteomic analysis in lupus mice identifies Coronin-1A as a potential biomarker for lupus nephritis
por: Nicolaou, Orthodoxia, et al.
Publicado: (2020)

Genetic Susceptibility to Systemic Sclerosis in the Greek-Cypriot Population: A Pilot Study
por: Chairta, Paraskevi, et al.
Publicado: (2020)

An investigation of breast cancer risk factors in Cyprus: a case control study
por: Hadjisavvas, Andreas, et al.
Publicado: (2010)

The mediterranean dietary pattern and breast cancer risk in Greek-Cypriot women: a case-control study
por: Demetriou, Christiana A, et al.
Publicado: (2012)

Alport syndrome: Proteomic analysis identifies early molecular pathway alterations in Col4a3 knock out mice
por: Nicolaou, Orthodoxia, et al.
Publicado: (2020)

Type 2 Diabetes Susceptibility in the Greek-Cypriot Population: Replication of Associations with TCF7L2, FTO, HHEX, SLC30A8 and IGF2BP2 Polymorphisms
por: Votsi, Christina, et al.
Publicado: (2017)

ngsComposer: an automated pipeline for empirically based NGS data quality filtering
por: Kuster, Ryan D, et al.
Publicado: (2021)

PathIN: an integrated tool for the visualization of pathway interaction networks()
por: Minadakis, George, et al.
Publicado: (2022)

Prediction of Parkinson’s Disease Risk Based on Genetic Profile and Established Risk Factors
por: Chairta, Paraskevi P., et al.
Publicado: (2021)

Observational study of health utilities in adult primary ciliary dyskinesia patients: preliminary data on associations with molecular diagnosis, clinical phenotype and HRQOL measures
por: Kouis, Panayiotis, et al.
Publicado: (2022)

Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19
por: Tomazou, Marios, et al.
Publicado: (2021)

Accuracy and efficiency of germline variant calling pipelines for human genome data
por: Zhao, Sen, et al.
Publicado: (2020)

Biomarkers of systemic lupus erythematosus identified using mass spectrometry‐based proteomics: a systematic review
por: Nicolaou, Orthodoxia, et al.
Publicado: (2016)

Development of Bioinformatics Pipeline for Analyzing Clinical Pediatric NGS Data
por: Crowgey, Erin L., et al.
Publicado: (2015)

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy
por: Tappeiner, Elias, et al.
Publicado: (2017)

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence
por: Blanca, Jose M, et al.
Publicado: (2011)

The Mutational Spectrum of Lynch Syndrome in Cyprus
por: Loizidou, Maria A., et al.
Publicado: (2014)

Molecular epidemiology of SARS-CoV-2 in Cyprus
por: Richter, Jan, et al.
Publicado: (2021)

Germline and somatic variants in ovarian carcinoma: A next-generation sequencing (NGS) analysis
por: Andrikopoulou, Angeliki, et al.
Publicado: (2022)

BRCA1 Mutation Analysis in 27 Cypriot Families with High Risk of Hereditary Breast and Ovarian Cancer
por: Hadjisavvas, A., et al.
Publicado: (1999)

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
por: Golosova, Olga, et al.
Publicado: (2014)

NEAT: a framework for building fully automated NGS pipelines and analyses
por: Schorderet, Patrick
Publicado: (2016)

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads
por: Lai, Binbin, et al.
Publicado: (2015)

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines
por: Kim, Baekdoo, et al.
Publicado: (2017)

Gene variants of adhesion molecules predispose to MS: A case-control study
por: Dardiotis, Efthimios, et al.
Publicado: (2019)

Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers
por: Chen, Jiayun, et al.
Publicado: (2019)

Intramuscular Evaluation of Chimeric Locked Nucleic Acid/2′OMethyl-Modified Antisense Oligonucleotides for Targeted Exon 23 Skipping in Mdx Mice
por: Georgiadou, Michaella, et al.
Publicado: (2021)

Identification of hereditary breast and ovarian cancer germline variants in Granada (Spain): NGS perspective
por: Molina-Zayas, María, et al.
Publicado: (2022)

Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut
por: Peng, Ze, et al.
Publicado: (2020)

Development of a high-resolution NGS-based HLA-typing and analysis pipeline
por: Wittig, Michael, et al.
Publicado: (2015)

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
por: Joo, Taewoon, et al.
Publicado: (2019)

Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform
por: Lin, Qun-ting, et al.
Publicado: (2023)

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
por: D'Antonio, Mattia, et al.
Publicado: (2015)

Analyzing Gene Expression Profiles from Ataxia and Spasticity Phenotypes to Reveal Spastic Ataxia Related Pathways
por: Kakouri, Andrea C., et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_diok991s4eh1j3hte8mc7qlkit