Fig. 2: Polyclonal resistance with co-enrichment of MAPK pathway and ESR1 mutations in advanced breast cancer.

a Association analysis for most frequent mutated genes with overall Fisher’s exact test two-sided p-values. Green genes showing mutual exclusivity, and purple showing co-occurrence with dark colours indicating significance following false discovery correction. b Frequency of MAPK pathway alterations comparing ESR1 mutant (77/265) vs ESR1 wild-type cancers overall (100/535) (left), ESR1 mutant (66/226) vs wild-type (59/289) in HR + HER2- cancers (middle), and within ESR1 mutant cancers between patients with single (27/138) and polyclonal ESR1 mutations (50/127) (right). p-values from two-sided Fisher’s exact test. c Example of polyclonal genomic resistance in a patient with multiple MAPK pathway and ESR1 mutations in ctDNA. Blue indicate dominant mutations with cancer fraction, and green subclonal mutations with cancer fraction. d Overall survival (OS) in patients with HR + HER2- disease who entered a treatment cohort in plasmaMATCH divided by combined ESR1 and MAPK pathway mutation status. ESR1 WT and MAPK WT, median 18.5 months, hazard ratio (HR) -. ESR1 mt and MAPK WT, median 17.7 months, HR 0.82, 95% confidence interval (CI) 0.40 to 1.69. ESR1 WT and MAPK mt, median 10.1 months, HR 1.65, 95% CI 0.56 to 4.88. ESR1 mt and MAPK mt, median 7.9 months, HR 1.65, 95% CI 0.84 to 3.23. p-value from log-rank test. HR > 1 indicate worse OS for that group. WT, wild-type; mt, mutant. e Mutational profile of ctDNA in plasmaMATCH (N = 725 patients with known breast cancer subtype) compared to published large metastatic breast cancer tissue sequencing dataset (MSKCC, N = 715 patients with known breast cancer subtype)¹¹. Red dots indicate significant change in frequency after false discovery adjusted two-sided Fisher’s exact test (HR + HER2-: ESR1 q < 0.0001, TP53 q = 0.0009). Included are genes with an incidence 1.5% in both data sets.