Medical Reporting at CENTOGENE
High-quality medical reporting is a key essential for building a partnership of trust.
CENTOGENE's philosophy is more than just producing technical DNA data. The extensive interpretation of clinical data delivered with our comprehensive medical reports includes differential diagnostic approaches as well as a detailed interpretation of key findings.
Sequencing and biomarker analysis has become a valuable approach for diagnostics of rare diseases. The increasing numbers of analyzed genes makes a clear, consistent and reproducible classification system mandatory.
What Are the Basics in Our Reporting?
- Detailed evaluation of patients and family history
- Detailed description of the genetic testing methods
- Clear results of identified variants following international best-practice guidelines (ACMG)1,2
- Comprehensive medical interpretation with differential diagnostic approaches if applicable
- References to publications supporting the medical and scientific results
- Recommendations for follow-up analyses for specific diseases
Classify variants to improve the understanding of their pathogenicity
ACMG guidelines define five classes regarding a Mendelian variant: pathogenic, likely pathogenic, uncertain significance, likely benign and benign1,2.
For some cases, disease-associated variants are reported if current medical literature and/or internal evidence supports an increased disease risk. Frequency of the variant, in silico predictions, conservation and published data with clinical information, segregation data or functional analyses among others, have all to be evaluated to classify the variants to the best of the available knowledge at the time of reporting. As knowledge on variant frequencies and annotations dramatically increases year by year, systematic and case-specific reevaluation of variants is an important step in improving our understanding of disease pathogenicity.
To strengthen this decisive topic CENTOGENE has created CentoMD®, a mutation database that includes detailed clinical information, frequency, geographic origin, etc.
The depth of available information in CentoMD® allows in many cases a pathogenic/likely pathogenic or benign/ likely benign classification exclusively based in CentoMD® data.
Thorough, uniform and comprehensive classification of variants based on a highly qualified and standardized curation workflow are hallmarks for the reporting at CENTOGENE. Such an approach guarantees you the best classification and basis for clinical interpretation of newly identified variants. In addition, reflecting our commitment to best and latest diagnostics to patients, we ensure that changes in variant classification will be proactively communicated by reclassification reports to all our past clinical cases as well.
For all NGS panels, all identified variants are classified according to our standardized system. Classes 1–5 are assigned based on publicly available databases (CentoMD®, HGMD, LOVD, UMD, etc.) as well as the huge internal database, according to a standard protocol. Available databases for previously reported variants are checked If the variant has not been reported to date, classification relies on data regarding the nature and frequency of the variant, in silico predictions and finally all available information regarding the zygosity and segregation of the identified variant in the patient’s family.
A complete list of all genes covered by CENTOGENE's NGS panels is available here.
Reporting of identified variants
In the final step, all identified variants along with their annotations have to undergo a medical evaluation regarding their possible relevance to the provided clinical symptoms and/or suspected diagnosis of the patient.
Whole exome sequencing (WES) and whole genome sequencing (WGS)
By WES analysis the protein-coding region of the human genome (exome; ~1%) is analyzed. This also includes those genes without any known involvement in human disease. In these cases filtering of the identified variants is performed using the above-mentioned workflow including all available information in public databases such as Online Mendelian Inheritance in Man (OMIM) and HGMD®, gene specific databases, publications (PubMed) and genotype-phenotype databases such as our CentoMD®.
Based on the standard guidelines and due to the diagnostic setting, only variants detected in genes with well-defined causation for human diseases are reported. From these, all relevant variants related to the phenotype of the patient are mentioned in the report. Pathogenicity of the variant(s) is discussed in light of the clinical information provided. Taking into account the clinical picture of the patient and family history of the disorder further diagnostic steps are recommended. Disease-associated polymorphisms with well-established clinical significance for the individual disease phenotype(s) are also reported. WGS is the most comprehensive method for analyzing the genome. In addition, enrichment artifacts and coverage issues are not a problem. It allows the interrogation of single-nucleotide variants (SNVs), insertion-deletion variants (INDELs), structural variants (SVs) and copy number variants (CNVs) in both the ~1% part of the genome that encodes protein sequences and the ~99% of remaining non-coding sequences. Reporting procedure of the WGS findings is similar to WES.
Dual genetic diagnosis is possible with WES and WGS
In these cases, two pathogenic or likely pathogenic genetic variants are associated with either non-overlapping clinical presentations or contributing to one major phenotype. In some occasions, it is necessary to discuss the case (before reporting) with the ordering clinician.
Secondary (incidental) findings
If requested by the clinician we also provide information on variants in genes not associated with the patient’s disease or symptoms but with medically actionable information available (incidental or secondary findings). We report variants in 73 selected genes according to the recommendations of the ACMG1,2
- Miller, D.T., Lee, K., Gordon, A.S. et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2021 update: a policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med (2021). doi.org/10.1038/s41436-021-01171-4
- Miller, D.T., Lee, K., Chung, W.K. et al. ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med (2021). doi.org/10.1038/s41436-021-01172-3
Since September 2019, medical reports for NGS tests of postnatal index patients include a tabular section of known gene variants in CentoMD® that have been classified pathogenic/likely pathogenic. This additional information facilitates genetic diagnosis in complex cases or in situations where clinical information might be missing. For more, see details and list of genes covered.