Copy number alterations (CNAs) are common genetic features in cancer with prognostic and therapeutic implications. At our institutional Molecular Tumor Board we introduced an ultra low-coverage Whole Genome Sequencing (ulcWGS, <0.5x coverage) to estimate numerical karyotype and CNAs. We performed this technique on 128 solid tumor samples from 2018 to 2022. Here we report 3 exemplary cases in which we detected potentially targetable CNAs via ulcWGS.
DNA was extracted from microdissected Formalin-Fixed, Paraffin-Embedded tissue slides. ulcWGS libraries were prepared using the NEBNext Ultra II Kit (New England Biolabs, Ipswich, MA, USA). Sequencing was performed on an Illumina MiSeq Instrument and raw reads were analyzed with a proprietary read-depth based software developed recently for calculated karyotyping of Acute Myeloid Leukemia. We used immunohistochemistry (IHC) and targeted sequencing (VariantPlex, ArcherDX/Invitae, Boulder, CO, USA) (VP) to validate CNAs.
In patients reported in the table ulcWGS uncovered amplifications (amp) in FGFR1, ERBB2 and MDM2, respectively. In patient 1, IHC staining confirmed moderate to high (3+) membrane positivity for FGFR1, despite negativity of VP analysis. In patients 2 and 3, high-level amplifications were also confirmed via VP. Due to unavailability of clinical trials at the time of referral, just patient 2 received a matched therapy, particularly off-label trastuzumab deruxtecan (T-Dxd). At a 6-month follow-up, the patient showed a sustained stable disease on imaging and a tumor marker decrease.
Patients’ characteristics
Patient Histology Chromosomal regions Alteration Confirmatory assays Therapeutic implication 1 Luminal breast cancer 8(p11.23p11.1) FGFR1 amp IHC (3+) FGFR1 inhibitor 2 Rectal carcinoma 17(q12) ERBB2 amp IHC (3+), VP T-Dxd 3 Liposarcoma 12(q15q21.2) MDM2 amp IHC (positive nuclear staining), VP MDM2 inhibitor
ulcWGS is a sensitive low throughput assay compatible with benchtop sequencing instruments. The method can provide clinicians with highly relevant information that valuably adds to panel-based analyses in the context of precision oncology.
The authors.
Philipps University Marburg University Hospital Gießen and Marburg, Campus Marburg.
F. Rodepeter: Financial Interests, Personal, Invited Speaker: AstraZeneca. C. Denkert: Financial Interests, Personal, Advisory Board: MSD Oncology, Daiichi Sankyo, Molecular Health, AstraZeneca, Roche, Lilly; Financial Interests, Personal, Invited Speaker: Merck, AstraZeneca, VmScope digital pathology software; Financial Interests, Personal, Ownership Interest, Cofounder and shareholder of Sividon Diagnostics until 2016: Sividon Diagnostic; Financial Interests, Institutional, Funding: Roche; Financial Interests, Institutional, Research Grant: Myriad. E. Mack: Financial Interests, Personal, Invited Speaker: Roche, Boehringer Ingelheim; Financial Interests, Personal, Advisory Board: Roche. All other authors have declared no conflicts of interest.