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CHU-ULg-Genetic-Diseases.

The purpose of this WEB page is to record all files used to / produced along the set-up of version 01 of the CUGD.

Infiles: Click here to download the Zip compressed folder.

Code n°1 Inputs/Outputs.

1. Test (used for validation): Click here to download the Zip compressed folder.

2. Full (800 gènes): Click here to download the Zip compressed folder.

Code n°2 Inputs/Outputs.

1. Test (used for validation): Click here to download the Zip compressed folder.

2. Full (800 gènes): Click here to download the Zip compressed folder.

Final (Codes n°1 & n°2) Exons (Test) tab delimited file: Click here to download the table.

Final (Codes n°1 & n°2) Exons (Full 800 gènes) tab delimited file: Click here to download the table.

Process Overview (pptx): Click Here.

QC Samples Review (Table): Click Here.

Some considerations/remarks.

As proposed here, the CUGD pipeline is closing to a FDA approval format (versioning, backups, codes annotations, multilevels cross-checks, CSV IQ/OQ validation datasets,...)

Validation of the final Genes Dataset remains whatever (by the end) on the side of clinicians / experts. The proposed approach is to:

define the genes compatible with diagnostics purposes (e.g. exclude genes with pseudogenes contaminating NGS data = Blast Flag)

review QC data per dataset (linked to the NGS kit in use) to evaluate the most efficient experimental approach.

Based on these Outcomes it is obvious that a new updated genes list for CUGD will be made and then processed again in this pipeline to record final outcomes.

Important (BioIT): Our estimations  about System Reqs (Ubuntu Linux Platform) are about 2.5 Mb / gene (RAM; 400 genes +/- 1 Gb) and run time of 5 genes / minute. (This FOR EACH of the 2 Perl codes).

BED TO BED.

Perl Code n°3: Providing Theortical Info by comparison of BED files. Remark: 2 output files are generated (1by2, 2by1) and ranked as provided from respective BED. Code, source BED files and a run LOG are archived.

Click Here to download (Zip file) a comparison (validation purposes) of a BED vs. itself.

Click Here to download (Zip file) comparison of BED HG19 CHU-ULg-Genetic-Diseases vs. Agilent ClearSeq Inherited Diseases (Improved; Leonor Palmeira)

Click Here to download (Zip file) comparison of BED HG38 CHU-ULg-Genetic-Diseases vs. Roche-KUL Genetic Diseases

Click Here to download (Zip file) comparison of BED HG19 CHU-ULg-Genetic-Diseases vs. Agilent WES V5

Click Here to download (Zip file) comparison of BED HG19 CHU-ULg-Genetic-Diseases vs. Agilent WES V6r2

Fichier MS-Excel pour Cliniciens (Blast search for homolgies): Click Here.

Code FetchGeneData: Input Files.

Common files:

1. Code: Click Here

2. BlastDB HG38 (zip file): Click Here

3. 800 Genes Genbank and FASTA (+ NCBI report) files:  Click Here

Test File( List of 20  selected genes): Click Here

CUGD v1.1 File (800 genes): Click Here

ZIP file outputs final version FetchGeneData: Click Here.

Evaluation of CUGD 800 genes vs HGNC genes HG38.7 (MS-Excel xlsx: click here)

LATEST VERSIONS/RUNS:

Output FetchGeneData (inclusive liftover BED exon + extended exons at 10) for CUGD800:  Click Here.

Output AddQCtoGeneData for CUGD800 normal exons vs 2 x Agilent Inherited Diseases & 2 x Agilent Whole Exomes & 1 x Roche: Click Here.

Output AddQCtoGeneData for CUGD800 extended exons vs 2 x Agilent Inherited Diseases & 2 x Agilent Whole Exomes & 1 x Roche: Click Here.