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Bioinformatic Challanges in clinical diagnostic application of targeted next generation sequencing. Experience from Pheochromocytoma.

ABSTRACT: Bioinformatic Challanges in clinical diagnostic application of targeted next generation sequencing. Experience from Pheochromocytoma.

PROVIDER: PRJEB6521 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR532275_1.fastq.gz	Fastqsanger.gz
	ERR532275_2.fastq.gz	Fastqsanger.gz
	ERR532276_1.fastq.gz	Fastqsanger.gz
	ERR532276_2.fastq.gz	Fastqsanger.gz
	ERR532277_1.fastq.gz	Fastqsanger.gz

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Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma.

Project description:BackgroundRecent studies have demonstrated equal quality of targeted next generation sequencing (NGS) compared to Sanger Sequencing. Whereas these novel sequencing processes have a validated robust performance, choice of enrichment method and different available bioinformatic software as reliable analysis tool needs to be further investigated in a diagnostic setting.MethodsDNA from 21 patients with genetic variants in SDHB, VHL, EPAS1, RET, (n=17) or clinical criteria of NF1 syndrome (n=4) were included. Targeted NGS was performed using Truseq custom amplicon enrichment sequenced on an Illumina MiSEQ instrument. Results were analysed in parallel using three different bioinformatics pipelines; (1) Commercially available MiSEQ Reporter, fully automatized and integrated software, (2) CLC Genomics Workbench, graphical interface based software, also commercially available, and ICP (3) an in-house scripted custom bioinformatic tool.ResultsA tenfold read coverage was achieved in between 95-98% of targeted bases. All workflows had alignment of reads to SDHA and NF1 pseudogenes. Compared to Sanger sequencing, variant calling revealed a sensitivity ranging from 83 to 100% and a specificity of 99.9-100%. Only MiSEQ reporter identified all pathogenic variants in both sequencing runs.ConclusionsWe conclude that targeted next generation sequencing have equal quality compared to Sanger sequencing. Enrichment specificity and the bioinformatic performance need to be carefully assessed in a diagnostic setting. As acceptable accuracy was noted for a fully automated bioinformatic workflow, we suggest that processing of NGS data could be performed without expert bioinformatics skills utilizing already existing commercially available bioinformatics tools.

| S-EPMC4521794 | biostudies-literature

Copy number profiles of pheochromocytoma and paraganglioma

Project description:Until now, it is nearly impossible to diagnose malignancy of pheochromocytoma/paraganglioma with pathological examinations. The aim of the study is to find the genes which can be applied as a biomarker in the clinic to distinguish benign and malignant forms of pheochromocytoma/paraganglioma.

2014-08-17 | GSE60457 | GEO

Pheochromocytoma in rats with multiple endocrine neoplasia (MENX) shares gene expression patterns with human pheochromocytoma

Project description:MENX is a rat multiple endocrine neoplasia syndrome caused by a homozygous mutation of the Cdkn1b gene, encoding p27Kip1. Affected rats develop adrenomedullary hyperplasia which progresses to pheochromocytoma with time (incidence 100%), and to extra-adrenal pheochromocytoma (paraganglioma) (68%). We here report that hyperplasia and tumor have similar gene expression profiles, suggesting an early determination of the tumorigenic signature. Overexpressed genes in rat adrenal lesions are especially enriched in development/differentiation-associated genes.

2010-11-19 | GSE21006 | GEO

Copy number variation analysis of pheochromocytoma and paraganglioma

Project description:Cytogenetic analysis of 36 pheochromocytoma and four paraganglioma using high density arrays

2014-09-21 | GSE61594 | GEO

Gene expression profiling of pheochromocytoma (PCC)/paraganglioma (PGL) tumors

Project description:Transcriptional analysis of 84 primary pheochromocytoma (PCC)/paraganglioma tumors.

2010-12-31 | GSE19422 | GEO

Epigenome analysis of pheochromocytoma/paraganglioma samples

Project description:Genome wide DNA methylation profiling of pheochromocytoma/paraganglioma samples carrying different mutations. The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles.

2018-12-11 | GSE111336 | GEO

Copy number variation analysis of pheochromocytoma and paraganglioma

Project description:Cytogenetic analysis of 36 pheochromocytoma and four paraganglioma using high density arrays A series of 36 pheochromocytoma and four paraganglioma were analysed for genomic structural alterations using high density copy number arrays

2014-09-21 | E-GEOD-61594 | biostudies-arrayexpress

Gene expression profiling of pheochromocytoma (PCC)/paraganglioma (PGL) tumors

Project description:Transcriptional analysis of 84 primary pheochromocytoma (PCC)/paraganglioma tumors. 84 samples (primary pheochromocytoma (PCC)/paraganglioma tumors) were hybridized onto a cDNA microarray in order to investigate possible heterogeneity within these tumors

2010-12-31 | E-GEOD-19422 | biostudies-arrayexpress

Copy number profiles of pheochromocytoma and paraganglioma

2014-08-17 | E-GEOD-60457 | biostudies-arrayexpress

Expression profiles of pheochromocytoma and paraganglioma

Project description:Until now, it is nearly impossible to diagnose malignancy of peochormocytoma/paraganglioma with pathological examinations. The aim of the study is to find the genes which can be applied as a biomarker in the clinic to distinguish benign and malignant forms of pheochromocytoma/paraganglioma.

2014-08-17 | GSE60458 | GEO

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