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. 2022 Apr 4;13:1791. doi: 10.1038/s41467-022-29487-y

Fig. 3. QASeq for longitudinal study of plasma samples from 15 ERBB2+ metastatic breast cancer patients.

Fig. 3

a Swimmer plot of clinical course and molecular findings of patients. QASeq identified cfDNA ERBB2 amplification or increase of ERBB2 ploidy relative to the previous point in 6 out of the 8 patients with progression within 6 months of plasma sampling. The other 2 patients (sample ID 2697 and 2366) were each reported with 4 progressions. Although ERBB2 amplification or increase of ERBB2 ploidy was also observed in these two patients, abnormal ERBB2 events are only associated with part of the progression. Between 5.6 and 8.3 ng DNA input was used based on availability. b ERBB2 ploidy and mutation allele frequency change in plasma sample of patients 2697 and 2366. Significant allele frequency changes in PIK3CA G1049R mutation in patient 2697 and in SNP rs1309838194 in patient 2366 were correlated with progression. c Categorization of patients based on QASeq abnormal molecular findings and disease progression. Chi-square test suggested that the QASeq result and progression are not statistically independent (p = 0.038). d Plasma ERBB2 ploidy normalization with tumor fraction to infer tumor ERBB2 ploidy. Tumor FISH results at three time points were collected in patient 1834. QASeq detected ERBB2 amplification in plasma 5 months earlier than FISH from tumor tissue. The inferred tumor ERBB2 ploidy by QASeq was consistent with the available tumor ploidy from FISH. The inferred tumor ERBB2 ploidy was generally stable in both of the two patients.