Cargando…

Integrated bioinformatic pipeline using whole-exome and RNAseq data to identify germline variants correlated with cancer

Germline Variants (GVs) are effective in predicting cancer risk and may be relevant in predicting patient outcomes. Here we provide a bioinformatic pipeline to identify GVs from the TCGA lower grade glioma cohort in Genomics Data Commons. We integrate paired whole exome sequences from normal and tum...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sahu, Divya, Chatrath, Ajay, Ratan, Aakrosh, Dutta, Anindya
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Elsevier 2022
Materias:	Protocol
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8987392/ https://www.ncbi.nlm.nih.gov/pubmed/35403010 http://dx.doi.org/10.1016/j.xpro.2022.101273

Ejemplares similares

Germline variants predictive of tumor mutational burden and immune checkpoint inhibitor efficacy
por: Chatrath, Ajay, et al.
Publicado: (2021)

Protocol for integrative subtyping of lower-grade gliomas using the SUMO pipeline
por: Sienkiewicz, Karolina, et al.
Publicado: (2022)

The pan-cancer landscape of prognostic germline variants in 10,582 patients
por: Chatrath, Ajay, et al.
Publicado: (2020)

Practicality of identifying mitochondria variants from exome and RNAseq data
por: Zhang, Pan, et al.
Publicado: (2015)

Improving bioinformatic pipelines for exome variant calling
por: Ji, Hanlee P
Publicado: (2012)

Whole-exome identifies germline variants in families with obstructive sleep apnea syndrome
por: de Azevedo, Pedro Guimarães, et al.
Publicado: (2023)

Whole-Exome Sequencing Identifies Pathogenic Germline Variants in Patients with Lynch-Like Syndrome
por: dos Santos, Wellington, et al.
Publicado: (2022)

Germline Variants Associated with Nasopharyngeal Carcinoma Predisposition Identified through Whole-Exome Sequencing
por: Lee, Ning-Yuan, et al.
Publicado: (2022)

Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing
por: Cagirici, H. Busra, et al.
Publicado: (2021)

From Wet‐Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing
por: Laurie, Steve, et al.
Publicado: (2016)

sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data
por: Pogorelcnik, Romain, et al.
Publicado: (2018)

Protocol for unbiased, consolidated variant calling from whole exome sequencing data
por: Verrou, Kleio-Maria, et al.
Publicado: (2022)

Whole-Exome Sequencing Identifies a Novel Germline Variant in PTK7 Gene in Familial Colorectal Cancer
por: Miao, Beiping, et al.
Publicado: (2022)

Analysis workflow to assess de novo genetic variants from human whole-exome sequencing
por: Diab, Nicholas S., et al.
Publicado: (2021)

A three-caller pipeline for variant analysis of cancer whole-exome sequencing data
por: Liu, Ze-Kun, et al.
Publicado: (2017)

Whole Exome Sequencing Uncovers Germline Variants of Cancer-Related Genes in Sporadic Pheochromocytoma
por: Urbini, Milena, et al.
Publicado: (2018)

TMC-SNPdb: an Indian germline variant database derived from whole exome sequences
por: Upadhyay, Pawan, et al.
Publicado: (2016)

Whole-Exome Sequencing of Germline Variants in Non-BRCA Families with Hereditary Breast Cancer
por: Liu, Yaxuan, et al.
Publicado: (2022)

Detecting molecular subtypes from multi-omics datasets using SUMO
por: Sienkiewicz, Karolina, et al.
Publicado: (2022)

Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma
por: Pertesi, Maroulio, et al.
Publicado: (2019)

Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors
por: Sayaman, Rosalyn W., et al.
Publicado: (2022)

Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data
por: Kumaran, Manojkumar, et al.
Publicado: (2019)

Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite
por: Hafez, Ahmed Ibrahem, et al.
Publicado: (2023)

An improved burden-test pipeline for identifying associations from rare germline and somatic variants
por: Geng, Yu, et al.
Publicado: (2017)

Impact of concurrency on the performance of a whole exome sequencing pipeline
por: Dall’Olio, Daniele, et al.
Publicado: (2021)

Measuring the transcriptome-wide effects of aging on murine adipocytes using RNAseq
por: De Cauwer, Aurore, et al.
Publicado: (2023)

Whole-exome sequencing identifies variants in invasive pituitary adenomas
por: Lan, Xiaolei, et al.
Publicado: (2016)

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment
por: Li, Jason, et al.
Publicado: (2014)

Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools
por: Alganmi, Nofe, et al.
Publicado: (2023)

SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures
por: Kathuria, Kunal, et al.
Publicado: (2020)

Interactions of Monocytes, HIV, and ART Identified by an Innovative scRNAseq Pipeline: Pathways to Reservoirs and HIV-Associated Comorbidities
por: León-Rivera, Rosiris, et al.
Publicado: (2020)

Whole exome sequencing identifies novel germline variants of SLC15A4 gene as potentially cancer predisposing in familial colorectal cancer
por: Skopelitou, Diamanto, et al.
Publicado: (2022)

WEP: a high-performance analysis pipeline for whole-exome data
por: D'Antonio, Mattia, et al.
Publicado: (2013)

Correction to: Impact of concurrency on the performance of a whole exome sequencing pipeline
por: Dall’Olio, Daniele, et al.
Publicado: (2021)

Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants
por: Hynst, Jakub, et al.
Publicado: (2019)

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping
por: Ahmed, Zeeshan, et al.
Publicado: (2021)

A Novel ARMC5 Germline Variant in Primary Macronodular Adrenal Hyperplasia Using Whole-Exome Sequencing
por: Eghbali, Maryam, et al.
Publicado: (2022)

Novel Candidate loci and Pathogenic Germline Variants Involved in Familial Hematological Malignancies Revealed by Whole-Exome Sequencing
por: Andrés-Zayas, Cristina, et al.
Publicado: (2023)

Detection of germline variants with pathogenic potential in 48 patients with familial colorectal cancer by using whole exome sequencing
por: Singh, Ashish Kumar, et al.
Publicado: (2023)

Novel pathogenic variants and genes for myopathies identified by whole exome sequencing
por: Hunter, Jesse M, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_ananmga393ipummedt6qto23ap