Identifying Genomic Alterations in Patients With Stage IV Breast Cancer Using MammaSeq: An International Collaborative Study

• Published in: Clinical breast cancer Vol. 21; no. 3; pp. 210 - 217
• Main Authors: Shah, Osama Shiraz, Soran, Atilla, Sahin, Mustafa, Knapick, Beth A., Ugras, Serdar, Celik, Esin, Lucas, Peter C., Lee, Adrian V.
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 01-06-2021
• Subjects: Clinical genomics; Clinical utility; NGS panel; Targeted next generation sequencing; Turkish population; Clinical utility; NGS panel; Turkish population; Targeted next generation sequencing; Clinical genomics
• ISSN: 1526-8209; 1938-0666; 1938-0666
• DOI: 10.1016/j.clbc.2020.08.009

Identification of genomic alterations present in cancer patients may aid in cancer diagnosis, prognosis and therapeutic target discovery. In this study, we aimed to identify clinically actionable variants present in stage IV breast cancer (BC) samples.
DNA was extracted from formalin-fixed paraffin-embedded samples of BC (n = 41). DNA was sequenced using MammaSeq, a BC-specific next-generation sequencing panel targeting 79 genes and 1369 mutations. Ion Torrent Suite 4.0 was used to make variant calls on the raw data, and the resulting single nucleotide variants were annotated using the CRAVAT toolkit. Single nucleotide variations (SNVs) were filtered to remove common polymorphisms and germline variants. CNVkit was employed to identify copy number variations (CNVs). The Precision Medicine Knowledgebase (PMKB) and OncoKB Precision Oncology Database were used to associate clinical significance with the identified variants.
A total of 41 samples from Turkish patients with BC were sequenced (read depth of 94-13,340; median of 1529). These patients were diagnosed with various BC subtypes including invasive ductal carcinoma, invasive lobular carcinoma, apocrine BC, and micropapillary BC. In total, 59 different alterations (49 SNVs and 10 CNVs) were identified. From these, 8 alterations (3 CNVs – ERBB2, FGFR1, and AR copy number gains and 5 SNVs – IDH1.R132H, TP53.E204∗, PI3KCA.E545K, PI3KCA.H1047R, and PI3KCA.R88Q) were identified to have some clinical significance by PMKB and OncoKB. Moreover, the top 5 genes with the most SNVs included PIK3CA, TP53, MAP3K1, ATM, and NCOR1. Additionally, copy number gains and losses were found in ERBB2, GRB7, IGFR1, AR, FGFR1, MYC, and IKBKB, and BRCA2, RUNX1, and RB1, respectively.
We identified 59 unique alterations in 38 genes in 41 stage IV BC tissue samples using MammaSeqTM. Eight of these alterations were found to have some clinical significance by OncoKB and PKMB. This study highlights the potential use of cancer specific next-generation sequencing panels in clinic to get better insight into the patient-specific genomic alterations.
We performed targeted sequencing using DNA from formalin-fixed paraffin-embedded samples of 41 patients with stage IV breast cancer using MammaSeq, a breast cancer gene-specific targeted sequencing panel. In total, 49 single nucleotide variations and 10 copy number variations were identified. Eight alterations (3 copy number variations – ERBB2, FGFR1, and AR copy number gains and 5 single nucleotide variations – IDH1.R132H, TP53.E204∗, PI3KCA.E545K, PI3KCA.H1047R, and PI3KCA.R88Q) were identified to have clinical significance by the Precision Medicine Knowledgebase and OncoKB Precision Oncology databases.