107.2026 Liquid biopsy testing service for the Department and Clinic of Marrow Transplantation, Oncology and Paediatric Hematology of the Medical University of Piastów Śląskie in Wrocław

… 1) Library preparation and sequencing a) whole genome sequencing, determination of methylation class and detection of residual cancer (MRD) b) sequencing on dedicated apparatus, in a validated process and quality control of this process; c) inclusion of internal controls - positive/negative controls. 2) Bioinformatics analysis a) Preliminary analysis, identification of principles and identification of variants; detection of fusion, single nucleotide variants (SNV) and copy number changes (CNV); a quantitative assessment of the ctDNA; assessment of minimum residual disease (MRD) with defined sensitivity thresholds; documentation of analytical processes, reference genomes and quality control indicators. 3) Reporting a) structured clinical reports summarizing detected changes, ctDNA levels, MRD status and quality control results; interpretation of results in the context of RMS biology and known molecular factors, indication of a positive/negative result; the notification of results that are clinically relevant or critical to the study. 4) Providing data a) providing all raw and processed data, including FASTQ, BAM/CRAM, VCF files and variant tables with annotations in pdf and csv formats b) secure data transfer, in accordance with the GDPR c) a specified lead time from the receipt of the sample to the preparation of the report; final delivery of a complete set of data at the end of a predetermined analysis period. 5) Communication and support a) readiness to provide technical clarifications and participation in data review and analysis meetings; b) limitations of the test - ongoing information to the contracting authority about factors that may affect the result. 6) Quality and compliance requirements (a) use of validated tests suitable for small-volume paediatric samples; ensuring full traceability of samples and documentation of analytical and poanalytical steps at each stage; c) ensuring compliance with the GDPR and applicable legislation on clinical trials. 7. Provision of results (a) provision of analytical results and quality control documentation for each sample; b) providing structured clinical reports containing, among others:  Patient and sample data – date of collection, date of receipt of the sample by the  laboratory Sample number/identifier and  report number Data of the commissioning physician/ centre Type of test material and type of test tube/anticoagulant  Method of analysis – name and version of the test (panel)  Quantitative assessment of the total ctDNA (e.g. ng/ul)  Gene and variant names (according to the HGVS nomenclature) together with the reference sequence  Assessment of the clinical classification variant (pathogenic, possibly pathogenic, VUS) % VAF (variant allele frequency)  Quantification or information on the absence of the monitored genetic marker  Interpretation of results in the context of RMS biology and known molecular factors, positive/negative indication;  Comparison with previous results (in case of assessment of another sample from the same patient), including assessment of dynamics/trend (e.g. molecular assessment of disease activity, growth/spa