Methods – KiTu1

Sample Material

For diagnostic profiling of solid tumors, we accept sections taken from FFPE (formalin-fixed, paraffin-embedded) tumor tissue blocks. The pathologist must determine the tumor type and tumor cell percentage before sending the sample to our laboratory. The recommended tumor cell percentage is at least 30%.

Our diagnostic service is accredited for FFPE tumor tissue samples. However, with the KiTu1 panel, it is also possible to analyze germline mutations from a blood sample. Please contact us for more information about this option.

DNA Extraction

DNA is extracted from FFPE tissue sections using a commercially available kit designed for this purpose. The concentration, purity, and quality of the isolated double-stranded DNA are verified prior to genetic analysis.

Next-Generation Sequencing (NGS)

Targeted next-generation sequencing of 53 genes is performed on the extracted DNA. NGS libraries are prepared using an automated library preparation system (Magnis NGS Prep System, Agilent) and a hybridization-based SureSelect X HT2 kit (Agilent).

NGS sequencing relies on massive parallel sequencing, where millions of short DNA fragments are amplified simultaneously. Samples are sequenced on the Illumina NextSeq 2000 platform. Sequencing data is processed using our in-house bioinformatics pipeline.

Genes Included in the Test

The test covers the following 53 genes:

ALK, ARID1A, ARID5B, ATM, BARD1, BRAF, BRCA1, BRCA2, BRIP1, CDK12, CDKN2A, CHEK1, CHEK2, CTNNB1, DICER1, EGFR, EPCAM, ERBB2, FANCL, FGFR2, FGFR3, KEAP1, KIT, KRAS, MET, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, NFE2L2, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PDGFRA, PIK3CA, PMS2, POLE, PPP2R2A, PTEN, RAD50, RAD51B, RAD51C, RAD51D, RAD54L, RET, ROS1, SMARCA4, STK11, TP53

The analysis includes the protein-coding regions (exons) and 10 base pairs of intronic sequence on both sides of each exon (splice sites). The test is designed to detect single nucleotide variants (SNVs) and small insertions and deletions. It does not detect large insertions/deletions, complex structural changes at the gene or chromosome level, translocations, gene fusions, variants outside the target regions, or technically challenging regions such as long repetitive sequences.

Interpretation of Results

Sequenced DNA fragments are aligned to the human reference genome (GRCh38) to identify base differences. Observed variants are compared against public and cancer-specific databases (e.g., ClinVar, COSMIC, gnomAD) and published literature to assess pathogenicity. Variants are classified according to AMP/ASCO/CAP consensus guidelines (Li et al., 2017).

Analysis Report

The report includes pathogenic or likely pathogenic variants and variants of uncertain significance (VUS) with a variant allele frequency (VAF) of 5% or higher. In certain cases, pathogenic variants with VAF below 5% may also be reported if sequencing depth is sufficient. Variants classified as likely benign or benign are not reported. Variant classification may change as new information becomes available; in such cases, we will notify the submitting clinician.

The report specifies the average sequencing depth and coverage percentage at ≥100× depth for each sample. For each detected variant, VAF and local sequencing depth are reported. A separate appendix provides gene-level average depth and coverage at 100× and 250× depth.

Reports are delivered to the submitting unit within 10 business days.

References

Li, M.M., Datto, M., Duncavage, E.J., Kulkarni, S., Lindeman, N.I., Roy, S., Tsimberidou, A.M., Vnencak-Jones, C.L., Wolff, D.J., Younes, A., and Nikiforova, M.N., 2017. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. Journal of Molecular Diagnostics, 19 (1), p. 4 – 23. https://doi.org/10.1016/j.jmoldx.2016.10.002.