# Longitudinal genomic profiling of chemotherapy-related CHIP variants in patients with ovarian cancer

## TL;DR

This study tracks changes in rare blood cell mutations in ovarian cancer patients before and after chemotherapy, revealing how treatment affects these mutations and their potential role in future blood cancers.

## Contribution

The study introduces an ultra-deep sequencing method to detect low-frequency CHIP variants in ovarian cancer patients and shows how chemotherapy alters their frequency.

## Key findings

- Post-chemotherapy samples showed fewer low-frequency CHIP mutations, suggesting chemotherapy exerts selective pressure on hematopoietic clones.
- A large number of novel low-frequency candidate CHIP mutations were identified in cfDNA from ovarian cancer patients.
- Some CHIP variants were enriched after chemotherapy and may serve as predictive markers for therapy-related myeloid neoplasia.

## Abstract

Clonal hematopoiesis (CH) is characterized by the presence of hematopoietic stem cells (HSCs) with the potential of clonally expanding and giving rise to hematological malignancies. Clonal hematopoiesis of indeterminate potential (CHIP) is the outgrowth of a single HSC clone with an acquired somatic mutation in the absence of hematological abnormalities. CHIP variants occur with a variant allele frequency (VAF) of at least 2% in peripheral blood. This definition does not account for less frequent mutations that give rise to hematopoietic clones. Previous studies indicate an association between CH and secondary hematologic malignancies in cancer patients who receive chemotherapy.

To discover novel candidate CHIP mutations, including those with extremely low VAFs, we performed an in-depth characterization of low-frequency CHIP variants in a highly selected group of patients with high-grade serous ovarian cancer (HGSC) before and after neoadjuvant chemotherapy (NACT). We performed comprehensive ultra-high-depth whole-exome sequencing of circulating free DNA (cfDNA) and matched white blood cell (WBC) DNA from pre- (n=9) and post-NACT (n=9) samples from HGSC patients who had excellent response (ER; n=4) or poor response (PR; n=5) to NACT.

Variants present in both the WBC DNA and cfDNA from a patient were considered candidate CHIP variants. We identified 93,088 candidate CHIP variants in 13,780 genes. Compared with pre-NACT samples, post-NACT samples tended to have fewer CHIP mutations with VAFs of less than 5%, which may reflect the negative selective pressure of chemotherapy on rare hematopoietic clones. Finally, we identified CHIP variants in tumor samples matched to the liquid biopsies.

Our innovative sequencing approach enabled the discovery of a large number of novel low-frequency candidate CHIP mutations, whose frequency and composition are affected by chemotherapy, in the cfDNA of patients with HGSC. The CHIP variants that were enriched after chemotherapy, if validated, might become essential predictive markers for therapy-related myeloid neoplasia.