Identifying Genomic Alterations in Stage IV Breast Cancer Patients using MammaSeq™: An International Collaborative Study
Authors: Shah Osama Shiraz , Soran Atilla , Sahin Mustafa , Ugras Serdar , Celik Esin , Lucas Peter C. , Lee Adrian V. 
Published: March 2020

Background

Identification of genomic alterations present in cancer patients may aid in cancer diagnosis and prognosis and may identify therapeutic targets. In this study, we aimed to identify clinically actionable variants present in stage IV breast cancer (BC) samples.

Materials and Methods

DNA was extracted from formalin fixed paraffin embedded (FFPE) 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 CRAVAT toolkit. SNVs were filtered to remove common polymorphisms and somatic variants. CNVkit was employed to identify copy number variations. The Precision Medicine Knowledgebase (PMKB) and OncoKB Precision Oncology Database were used to associate clinical significance with the identified variants.

Results

A total of 41 Turkish BC patient samples were sequenced (read depth of 94 – 13340, median of 1529). These samples were from patients diagnosed with various BC subtypes including invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC), apocrine BC and micropapillary BC. In total, 59 different alterations (49 SNVs and 10 CNVs) were identified. From these, 8 alterations (3 CNVs –ERBB2, FGFR1andARcopy number gains and 5 SNVs –IDH1.R132H,TP53.E204*,PI3KCA.E545K,PI3KCA.H1047R andPI3KCA.R88Q) were identified to have some clinical significance by PMKB and OncoKB. Moreover, the top five genes with most SNVs includedPIK3CA, TP53, MAP3K1, ATMandNCOR1. Additionally, copy number gains and losses were found inERBB2, GRB7, IGFR1, AR, FGFR1, MYCandIKBKB, andBRCA2, RUNX1andRB1respectively.

Conclusion

We identified 59 unique alterations in 38 genes in 41 stage IV BC tissue samples using MammaSeq™. Ten of these alterations were found to have some clinical significance by OncoKB and PKMB. This study highlights the potential use of cancer specific NGS panels in clinic to get better insight into the patient-specific genomic alterations.

Highlights

- 41 stage IV stage breast cancer patients of Turkish descent were sequenced using MammaSeq™

- 49 single nucleotide variations and 10 copy number variations identified

-PIK3CAandTP53mutations were present in 24% and 17% of the samples respectively

- 37% of the samples hadERBB2/GRB7gains and 7% had loss ofBRCA2/RB1locus

- Eight clinically significant alterations were identified

Micro Abstract

We performed targeted sequencing using DNA from FFPE samples of 41 stage IV breast cancer patients using MammaSeq™, a breast cancer gene specific targeted sequencing panel. In total, 49 single nucleotide variations (SNVs) and 10 copy number variations (CNVs) were identified. Eight alterations (3 CNVs –ERBB2, FGFR1andARcopy number gains and 5 SNVs –IDH1.R132H,TP53.E204*,PI3KCA.E545K,PI3KCA.H1047R andPI3KCA.R88Q) were identified to have clinical significance by PMKB and OncoKB databases.