Abstract 2961: First metastasis NGS analysis reveals new targets for personalized treatment in advanced breast cancer
Authors: callens celine , boulai anais , bernard virginie , baulande sylvain , legoix-ne patricia , salomon anne , chemlali walid , benhamo vanessa , brain etienne , campone mario , bachelot thomas , giachetti sylvie , bonneterre jacques , bidard francois-clement , servois vincent , comte aurelie , berger frederique , bieche ivan , sigal brigitte , cottu paul 
Published: August 2018

Abstract
Background Genomic profile of breast cancer (BC) metastases (M) may differ from that of the primary tumor (PT). Based on a multicenter prospective study (ESOPE, NCT 01956552) including 130 patients with biopsies of the first metastatic site, we report here the results of a matched, comparative PT/M targeted next generation sequencing (NGS) mutational analysis.
Methods 117 paired PT/M FFPE samples obtained before any treatment for either early or advanced BC were available for analysis. Targeted sequencing was done using Illumina Hiseq2500 technology with a custom made 91 BC associated genes panel. Sequence data were aligned to the human reference genome (hg19) using Bowtie2 algorithm. High mapping quality and at least 70% coverage were achieved for 69 paired PT/M. Median depth was 723 and 98 % of targets achieved 100X depth. SNVs and indels were called using GATK. We defined the pathogenicity of variants using several public databases. We only retained confirmed pathogenic variant and variant of unknown pathogenicity observed at a frequency lower than 0,1% in population and reported at least once in cbioportal/tumorportal.
Results Patient characteristics are representative of patients with first line metastatic BC (Comte et al, ASCO 2016#550). In 69 paired PT/M we retained 256 somatic variants (188 shared, 28 only in PT and 40 only in M) distributed in 47 genes and including 62 indels and 194 SNV. There were 128 distinct variants (33 indels and 95 SNV) classified pathogenic for 98 and of unknown pathogenicity for 30 of them. TP53, PIK3CA, CDH1, GATA3, MAP3K1, BRCA2, ERBB2, ESR1, NF1, PTEN, ARID1A, BRCA1 and EGFR are genes with the more frequently PT/M shared variants (mutated at least in 2 patients). Private mutations are seen mostly in NF1, PIK3CA, MAP3K1, NCOR1, TSC1 genes for PT and in TP53, LAMA2, PIK3CA, ESR1, NF1, MAP2K4 genes for M. ESR1 D538G mutation was detected for 3 PT/M pairs and 1 M. Beyond highly shared PIK3CA and TP53 variants, overall crude PT/M discordance rate was 42%. PT/M shared variants could be considered for targeted treatment in 48% patients. For 13% patients, sequencing M revealed at least one additional druggable target in PIK3CA, ALK, PTEN, SF3B1, NOTCH4, KDR, TSC2, POLE, ESR1 and CDKN2A genes. Examination of M private variants to find a site-specific pattern of metastatic spread suggested enrichment in MAPK (p=0.02) and PI3K (p&lt;0.0001) pathways mutations in liver M (n=30) when compared to other sites. Interestingly, all variants detected in bone M (n=8) were shared with PT.
Conclusion In this prospective multicenter study, the targeted mutational analysis showed that most metastatic samples at first relapse share majority of variants with their matched PT. Sequencing M showed additional druggable mutations in 13% of patients. Liver M had more variants in MAPK and PI3K pathways compared to other metastatic sites whereas bone M did not show a specific mutational pattern.
Citation Format: celine callens, anais boulai, virginie bernard, sylvain baulande, patricia legoix-ne, anne salomon, walid chemlali, vanessa benhamo, etienne brain, mario campone, thomas bachelot, sylvie giachetti, jacques bonneterre, francois-clement bidard, vincent servois, aurelie comte, frederique berger, ivan bieche, brigitte sigal, paul cottu. First metastasis NGS analysis reveals new targets for personalized treatment in advanced breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2961.