Biomarker assessments
tumor, sarcoma translocations
TUMOR
Serum IGF‐related proteins were assessed as an exploratory pharmacodynamic endpoint to demonstrate on‐target activity of ganitumab. Peripheral blood was collected prior to cycles 1, 2, and 4 in serum separator tubes. Serum was isolated, frozen, and batch shipped to Ansh Labs for testing using enzyme linked immunoassays for total IGF‐1, free IGF‐1, IGF‐2, and IGFBP‐3.Circulating tumor DNA (ctDNA) was also assessed as an exploratory aim. Samples were collected at baseline, on Day 15 of cycle 1, and prior to cycles 2, 3, 5, 7, 9, 11, and at end of therapy. All samples were drawn into EDTA or CellSave tubes and processed same day in this single‐center study. Samples were sequenced at the Broad Institute, Cambridge, MA. Total cell‐free DNA was extracted from plasma using QIAmp Circulating Nucleic Acid Kit (Qiagen). Libraries were prepped using a KAPA Hyper Prep Kit (Kapa Biosystems) with manual barcoded adapter ligation. Samples underwent ultra‐low‐pass whole‐genome sequencing (ULP‐WGS at 0.1–0.5× coverage) and analyzed on the Broad's ichorCNA algorithm for ctDNA quantification. All samples then underwent analysis with TranSS‐Seq, a custom hybrid‐capture assay. Sequencing libraries were enriched with a Twist Bioscience Hybrid Capture Kit with a validated custom bait set targeting intronic regions of genes commonly involved in sarcoma translocations, including 