The Customized Genomic Analysis platform aims to offer the exhaustive analysis of Primary Immunodeficiency (PID) sequencing panels, whole exome sequencing (WES) and whole genome sequencing (WGS) in samples from patients with PIDs. This platform allows customers to benefit from the knowledge and experience of the Laboratory of Immunogenetics of Diseases (www.lighd.org) belonging to the Innate Immune Response Group, obtaining a report of the candidate genes responsible for pathology by filtering the list of variants provided by the mass sequencing tools.
Customers can provide their mass sequencing data for patients with PIDs in two ways: The raw sequencing data in FASTQ format or the list of annotated variants.
In case of delivering the data in FASTQ format the platform will do the bioinformatic processing of the raw sequence data until the list of annotated variants is obtained.
The list of annotated variants will be filtered in a personalized way according to the anonymous clinical data offered by the patient.
A report will be provided with the variants of the candidate genes causing the pathology, including the prediction of the deleteriousness of each one of them by means of The Mutation Significance Cutoffs (MSC) of human genes (Rockefeller University of New York).
Candidate gene variants will be validated by the platform through Sanger sequencing to confirm the existence of the change in the patient.
1) Genetic analysis from annotated variants of PID Sequencing Panel
An analysis of the responsible pathology candidate variants is performed based on the patient's anonymous clinical data. A report is provided with the variants, their allelic frequency and the deleteriousness prediction based on the MSC.
The analysis time is one week
2) Genetic analysis from annotated whole exome sequencing (WES) variants
An analysis of the candidate gene variants responsible for the pathology is performed based on the patient's anonymous clinical data. A report is provided with the variants, their allelic frequency and the deleteriousness prediction based on the MSC.
The analysis time is a month and a half
3) Genetic analysis from annotated whole genome sequencing (WGS) variants
An analysis of the candidate gene variants responsible for the pathology is performed based on the patient's anonymous clinical data. A report is provided with the variants, their allelic frequency and the deleteriousness prediction based on the MSC.
The analysis time is three months
4) Genetic analysis from raw data in FASQ format from PID Sequencing Panel
Annotation of the variants and analysis of the candidate variants responsible for the pathology is carried out based on the patient's anonymous clinical data. A report with the variants, their allelic frequency and the prediction of deleteriousness based on the MSC is delivered.
The analysis time is one week
5) Genetic analysis from raw data in whole exome sequencing (WES) FASQ format
Annotation of the variants and analysis of the variants of the candidate genes responsible for the pathology is carried out based on the patient's anonymous clinical data. A report with the variants, their allelic frequency and the prediction of deleteriousness based on the MSC is delivered.
The analysis time is a month and a half
6) Validation by Sanger sequencing of the selected variants
At the customer's request, the desired candidate variants can be validated by Sanger sequencing. For this purpose, the customer will provide the platform with 1 microgram of DNA or 3mL of blood in EDTA. A report will be sent with the image of the chromatography of the variant.
The analysis time is three months