Structural variation detection by proximity ligation from FFPE tumor tissue

The clinical management and therapy of many solid tumor malignancies is dependent on detection of medically actionable or diagnostically relevant genetic variation. However, a principal challenge for genetic assays from tumors is the fragmented and chemically damaged state of DNA in formalin-fixed paraffin-embedded (FFPE) samples. From highly fragmented DNA and RNA there is no current technology for generating long-range DNA sequence data as is required to detect genomic structural variation or long-range genotype phasing. We have developed a high-throughput chromosome conformation capture approach for FFPE samples that we call "Fix-C", which is similar in concept to Hi-C. Fix-C enables structural variation detection from fresh and archival FFPE samples. We applied this method to 15 clinical adenocarcinoma and sarcoma specimens spanning a broad range of tumor purities. In this panel, Fix-C analysis achieves a 90% concordance rate with FISH assays - the current clinical gold standard. Additionally, we are able to identify novel structural variation undetected by other methods and recover long-range chromatin configuration information from these FFPE samples harboring highly degraded DNA. This powerful approach will enable detailed resolution of global genome rearrangement events during cancer progression from FFPE material, and inform the development of targeted molecular diagnostic assays for patient care.