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Immunodeficiency and autoinflammation extended analysis Code R-120

Immunodeficiencies are a group of disorders that impair the normal functioning of the immune system, making the individual more susceptible to infections. This heterogeneous group of diseases is represented by SCID, CVID, agammoglobulinemias, defects of innate immunity, neutrophil and lymphocyte defects as well as complement system deficits Autoinflammatory diseases are a group of disorders characterised by abnormal activation of the innate immune system, leading to recurrent episodes of inflammation without the presence of infection or autoantibodies typical of autoimmune diseases. These conditions are often hereditary and can occur in various organs and tissues of the body.
331 genes
SCID: 1-9/1,000,000 CVID: 1-5/50,000 Autoimmune diseases: 1-10/100,000 Haemophagocytic lymphohistiocytosis 1/50,000
Multigenic panel aimed at diagnosing SCID, CVID, agammoglobulinemias, innate immunity defects, neutrophil and lymphocyte defects as well as complement system deficiency, autoinflammatory diseases, Mediterranean fever, haemophagocytic lymphohistiocytosis

Method: NGS sequencing, determination of SNVs (Single Nucleotide Variants), small insertions and deletions and CNVs (Copy Number Variants).

Limits: The test is unable to determine the presence of underrepresented somatic events, balanced chromosomal rearrangements, nucleotide expansion events of repeat regions, CNVs <3 contiguous exons. <3 esoni contigui.

Some genes may have low coverage areas, where necessary or upon specific request, within the limits of methodological limitations, sequencing can be completed with alternative methods (Sanger).

Some genes may be duplicated in the genome (pseudogenes), which may invalidate the analysis. 

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Sample preparation

The sample of choice is blood.

Two purple cap tubes (K2DTA) with 4-5 ml of blood each for the adult or 1-2 ml for the child are sufficient.

  • Store at +4 degrees until dispatched; DO NOT FREEZE

  • Ship the sample at room temperature in the appropriate containers within 2-3 days.

  • The sample must arrive at the laboratory within 4 days​​

R&I Genetics can send doctors e-mails upon request info@rigenetics.comcomplete blood sampling kits, including shipping envelope.

The kit can be picked up at the address communicated by e-mail to info@rigenetics.com by a courier at R&I Genetics' expense.

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Reporting

The report will be available within 8-12 weeks after receipt of the sample for gene panel and single gene analysis; for exome or trio genome analysis the report will be available within 12-20 weeks.

The original report will be sent by courier to the requesting doctor and will be available and downloadable from the reserved area of our site by the same doctor.

R&I Genetics will keep the requesting physician informed of the analysis process by e-mail.

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Our analyses

R&I Genetics is a laboratory accredited with the National Health System specialising in the diagnosis of hereditary diseases, both rare and common.

We offer a full range of genetic analyses, ranging from single gene analysis to gene panels to exome and genome sequencing.

R&I Genetics actively collaborates with leading Italian hospital and university centres, guaranteeing a high level of expertise and support in genetic diagnosis.

 

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Technology

R&I Genetics uses Next Generation Sequencing (NGS) as well as CGH analysis, Sanger sequencing, MLPA analysis, to analyse patients' DNA. The identification of disease-causing variants can lead to a diagnosis, determine prognosis and help select the most appropriate treatments as well as define the risk of familial recurrence.

NGS technology enables an in-depth analysis of thousands of clinically relevant genes in a timeframe that facilitates clinical action and the possibility of performing almost all in-depth laboratory diagnostics, making R&I Genetics a benchmark for the diagnosis of rare genetic diseases.

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Innovative solutions

R&I Genetics offers a complete service of NGS (Next Generation Sequencing), CGH, MLPA, TP-PCR, QF-PCR and Sanger genetic testing performed entirely in its own laboratories, capable of meeting all clinical needs in the field of genetics.

R&I Genetics has been operating in Italy for over 20 years and has developed a unique know-how in the diagnosis of rare diseases with the creation of proprietary genotype-phenotype association databases that increase the diagnostic sensitivity of the tests offered.

R&I Genetics offers a complete service that includes sample analysis and, if necessary, sample collection, interpretation of variants, segregation in family members, preparation of the report with database and literature references, and electronic and paper submission of the report to the requesting physician.

R&I Genetics offers a technical support service to applicant doctors with trained operators.

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Method of analysis

R&I Genetics uses next-generation sequencing (NGS) to analyse the DNA of patients. Alterations in the DNA sequence (called variants) can be harmful and cause serious medical conditions. Many inherited diseases are caused by DNA variants that originate in germ cells and are subsequently present in all cells of the human body. 

The identification of disease-causing variants can lead to a diagnosis, determine a patient's prognosis and help select the most appropriate treatments.

NGS technology enables a comprehensive analysis of thousands of clinically relevant target genes in a timeframe that facilitates clinical intervention. NGS sequencing detects different types of variants, such as nucleotide substitutions (point mutations) or nucleotide addition/removal (insertions and deletions). R&I Genetics has also implemented NGS searches for genetic events called 'copy number variations' (CNVs), i.e. deletions or insertions of nucleotide portions of significant size (often one or more exons) that cannot be detected by traditional methods.

R&I Genetics offers a complete service of complementary genetic testing such as CGH array, MLPA, TP-PCR, QF-PCR and Sanger sequencing, all performed entirely in its own laboratories, capable of meeting all clinical needs in the genetic field.

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Bioinformatics process

Analysing data from NGS sequencing is a complex process that requires IT and human resources, such as processing servers and specialised personnel, as well as advanced software. The automated and proprietary bioinformatics pipeline developed and used by R&I Genetics enables rapid, reliable and highly accurate results.

The bioinformatics analysis adopted, developed and validated by R&I Genetics, is based on the Broad Institute's BWA-GATK pipeline but with more efficient calculation algorithms and an enterprise-level software implementation provided by Sentieone/o Dragen.

In addition to incorporating state-of-the-art algorithms for quality control, alignment and variant calling, the pipeline also employs filtering steps to remove common variants based on allele frequencies in population cohorts. Furthermore, the functional consequence of amino acid changes is predicted using several in silico tools, increasing the accuracy in identifying potentially pathogenic variants.

To further support the variant interpretation process, results are compared to a comprehensive set of disease-related mutation databases, collected and curated in-house, as well as databases accessible from public sources or licensed from commercial vendors. In summary, our bioinformatics pipeline is designed to provide our requesting physicians with complete and accurate information in the shortest possible time.

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Interpretation

The final step in the analysis process is the interpretation of data and classification of variants. R&I Genetics' interpretation strategy consists of exome sequencing and the use of internally developed gene panels (virtual gene sets), which are targeted, in relation to the clinical phenotype, to search for variants in genes that may be the cause of a given genetic disease. The effectiveness of gene panels depends on the choice of genes and the construction strategy adopted.

The genes included in the different panels are chosen following a thorough analysis of the scientific literature and a detailed system based on the association of possible clinical phenotypes to different diseases and underlying molecular mechanisms developed by the R&I Genetics R&D team.

The panel construction strategy involves, where possible, specific sub-systems of genes that identify, for example, specific pathologies in correlation with each other according to hierarchical interactions.

In a diagnostic context, variant classification is essential for making informed clinical decisions. Proper classification of variants is crucial for proper patient management and obtaining the best possible results. Without a thorough interpretation and evaluation of sequencing data, the results of genomic analysis risk being meaningless.

R&I Genetics has developed a variant classification scheme that follows the guidelines and interpretation criteria established by the American College of Medical Genetics and Genomics (ACMG 2015, 2017 and subsequent supplements), the industry standard for clinical genetic diagnostic laboratories.

Our interpretation schemes have been validated with tens of thousands of rare disease patients. Variants are evaluated using population and gene/disease-specific databases, R&I Genetics' proprietary internal variant database, numerous public and commercial mutation databases, and the appropriate scientific literature. The patient's medical history and any identified variants are reviewed together with the relevant medical and genetic literature.

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The Report

The report, which is delivered exclusively to the requesting specialist physician, contains all the information that enables the clinician to interpret and evaluate the genetic data.

The results related to the clinical question are reported in the 'Primary outcome' section, followed by a technical commentary, analysis of the most significant literature and classification of variants according to ACMG.

In the 'Secondary result' section, any variants indicating the proband's carrier status are reported, which is very important for the patient's family.

Finally, the report contains all the genes analysed and the relevant technical analytical information to guarantee the quality level of the analysis conducted.