Abstract P1-01-06: Whole-genome landscapes of 1,364 breast cancers with clinical outcomes

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Abstract Recent advancements in genomic technologies have become critical tools for deciphering the genetic complexities of cancer tissues, enabling precision medicine strategies aimed at improving patient clinical outcomes. Here we performed a comprehensive analysis of clinically annotated whole genome and whole transcriptome sequences from 1,364 breast cancer cases. Our investigation provides the most detailed genomic landscapes of breast cancer to date, which allowed us to comprehensively correlate genomic changes with clinical characteristics. Our findings include, but not limited to, (1) whole-genome-based homologous recombination deficiency profiles effectively predict responses to adjuvant chemotherapy and first-line CDK4/6 inhibitor treatment, (2) focal ERBB2 amplifications, often arising via extrachromosomal DNA mechanisms, are strongly associated with a positive response to neoadjuvant chemotherapy. Additionally, our study identified (3) recurrent copy number amplifications linked to patient survival, and (4) whole-genome-based intratumoral heterogeneity profiles that can predict patient survival as well as response to anti-HER2 therapies. Our work underscores the power of highly annotated whole-genome and transcriptome sequencing of a population-scale cancer cohorts for uncovering clinically relevant genomic mutations and novel molecular targets, thereby advancing precision oncology strategies for breast cancer. Citation Format: Ryul Kim,JongHan Yu, Joonoh Lim, Brian Baek-Lok Oh, Seok Jin Nam, Seok Won Kim, Jeong Eon Lee, Byung Joo Chae, Ji-Yeon Kim, Ga Eun Park, Bong Joo Kang, Pil Sun Baek, Soo Yeon Bae, Chang Ik Yoon, Young Joo Lee, Dooreh Kim, Kabsoo Shin, Ji Eun Lee, Jun Kang, Ahwon Lee, Erin Connolly-Strong, Sangmoon Lee, Bo Rahm Lee, Yuna Lee, Ki Jong Yi, Young Oh Kwon, In Hwan Chun, Junggil Park, Jihye Kim, Chahyun Choi, Jong Yeon Shin, Hyunjung Lee, Minji Kim, Hansol Park, Ilecheon Jeong, Boram Yi, Won-Chul Lee, Jeong Seok Lee, Woo Chan Park, Sung Hun Kim, Yoon-La Choi, Jeongmin Lee, Young Seok Ju, Yeon Hee Park. Whole-genome landscapes of 1,364 breast cancers with clinical outcomes [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P1-01-06.

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