GenerateReports

GenerateReports: Sequencing data becomes clear and actionable

While new DNA sequencing technologies make it possible to better characterize tumors, they generate a large volume of data that must be interpreted.

GenerateReports is a bioinformatics platform for analyzing raw next-generation sequencing data in a clinical report that clearly summarizes the main sequencing results.

Its design allows:

a retrospective analysis of biological samples as part of research projects
interpretation of samples on a daily basis as part of a diagnostic activity

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GenerateReports is above all a modular tool allowing you to create bioinformatics processing chains depending on the nature of the constructions of the sequencing libraries (targeted panels, exomes, capture, amplicon, etc.) and the biological questions asked (diagnosis/research, tumor/ctDNA sequencing, etc.).

it is accreditation assistance to the diagnosis of high-throughput sequencing (NGS) technology by enabling fine-grained control of bioinformatics pipeline versions and their dependencies.

GenerateReports integrates the notion of a list of variants to enable personalized bioinformatics analyses.

Software Features Technical Specifications Resources

Software Features

Sequencing report for each Sample

For each sequenced sample, a detailed report is generated, providing a complete and transparent view of the results obtained. This report includes the following elements:

Sample identification data
Quality control on the scale of the Run
Specific quality control of the sample
The list of genetic variations detected and annotated
Variations in gene copy number
Experimental traceability and bioinformatics traceability information.

Schéma fonctionnel GenerateReports

Database

All data is also aggregated in a database allowing retrospective consultation of results at the following scale:

of a sample or a variant
of a complete project
of a cohort of patients
of an experiment

Variation lists can be created by biologists, making it possible to create documents, custom filters and certain automated analyses.

The database also allows the storage of external experimental validations to confirm the results obtained by high-throughput sequencing.

The software allows the insertion of data from various sequencing platforms.

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Technical Specifications

Library Compatibility	QIAseq (QIAGEN) AmpliSeq (Illumina) SureSelect (Agilent) Twist (Twist Biosciences) For other bookstores, contact us
Sequenced data type	Gene panels Whole Exome Sequencing (WES) Whole Genome Sequencing (WGS)
Variants detected	Single Nucleotide Polymorphisms (SNPs) Insertion & Deletion (INDEL) Mid-sized INDEL (~100b) Panel/exome/whole genome Copy Number Variant (CNVs)
Material compatibility	Sequencer Illumina® ThermoFisher ION S5 Sequencers
Supported data formats	FASTQ file
Databases used	1000G ExAC ESP6500siv2 CG46
Prediction scores used	ADA_score RF_score Score SIFT Score PolyPhen LRT MutationTaster MutationAssessor FATHMM PROVEAN VEST3 MetaSVM MetaLR MCAP CADD fathmm_MKL_coding GERP Interpro_domain

Results Obtained

Resources

Publications Related to GenerateReports

References

UMI-VarCal, Sater V, Bioinformatics, January 30, 2020, Read the Article

A recurrent clonally distinct Burkitt lymphoma case, Sater V, Leukemia, February 14, 2019, Read the Article

Somatic mutations of cell-free circulating DNA, Michel M, Clinical Cancer Research, August 1, 2018, Read the Article

Non-invasive monitoring of diffuse large B-cell lymphoma, Bohers E, Blood Advances, August 14, 2018, Read the Article

Biological and Clinical Relevance of Associated Genomic Alterations, Mareschal S, Oncotarget, December 6, 2016, Read the Article

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