Cell-Free Dna Sequencing In Multiple Myeloma

Author

Russell IrwinFollow

Author ORCID Identifier

https://orcid.org/0000-0002-2446-004X

Date of Graduation

8-2022

Document Type

Thesis (MS)

Program Affiliation

Biomedical Sciences

Degree Name

Masters of Science (MS)

Advisor/Committee Chair

Michael Green

Committee Member

Robert Orlowski

Committee Member

Anirban Maitra

Committee Member

Michelle Hildebrandt

Committee Member

Michael Lorenz

Committee Member

Hans Lee

Abstract

Multiple myeloma (MM) is an incurable plasma cell dyscrasia. Recent advances in MM therapy, including CAR-T therapy, have increased survival and shown the value of assessing treatment response with great sensitivity, both in acute and long-term settings. Cell-free DNA, DNA fragments which are released into circulation as a part of normal cellular turnover, is a useful and dynamic biomarker in cancer patients due to the presence of circulating tumor DNA (ctDNA), which is readily identified using next generation sequencing. Here we report the analytical sensitivity, applicability, consistency, and prognostic ability of M5Seq, a novel hybrid capture panel designed for MM ctDNA. We performed in-silico validation of this panel and found high applicability (1,173/1,212 tumors with ≥1 variant covered, 97%, mode 6 variants covered). By sequencing serial dilutions of simulated cancer DNA in healthy donor DNA, we observed a limit of analytical sensitivity at 5x10^-5 and a limit of linearity at 10^-4. Then, we applied this method to the matched pre-treatment tumor and plasma samples of 10 newly diagnosed MM patients. We observed moderate concordance in the mutations detected in each compartment, consistent with existing literature. Based off these data, we applied M5Seq to plasma samples from 18 patients undergoing anti-BCMA chimeric antigen receptor T cell therapy (CAR-T). We observed similar concordance in the CAR-T cohort as in the newly diagnosed patients. In 14 evaluable patients, we observed no statistically significant decreases in variant allele fraction within two days of CAR-T infusion between patients achieving a complete response or better within 30 days of infusion as determined by IMWG criteria, as compared to those patients with stable or progressing disease. Furthermore, while we observed a slight overall survival advantage in patients with decreased VAF from baseline, this association did not meet the threshold for statistical significance.

Keywords

Multiple myeloma, CAR-T, MRD, kinetics, tumor burden, concordance, relapse