Characterizing Molecular Variants and Clinical Utilization of Next-generation Sequencing in Advanced Breast Cancer

Abstract

Women with advanced breast carcinomas have few therapeutic options. Recent advances in genomic profiling represent a new paradigm of cancer classification and treatment, but experience with genomic testing in a clinical setting remains limited. We retrospectively determined the genomic variants and correlate these with histology [histomorphologic subtype, nuclear grade, standard immunohistochemistry (IHC)] and clinical utilization (ordering, turnaround time, report review, and targeted therapy). Among 48 patients, 2 showed no genetic alterations, 11 (23%) showed variants of unclear significance only and 35 (73%) showed variant(s) affecting function (VaF) and/or variants of unclear significance. Overall, 119 variants were observed in 20 of 50 tested genes. Each patient had a unique molecular profile, with numerous (n=58) variants not previously reported in breast cancer. VaF detected in more than 2 patients included: TP53 (n=21), PIK3CA (n=20), and FGFR1 (n=3). VaF comprised 46 single nucleotide variants (79%), 7 amplifications (12%), 3 frameshifts (5%), 1 insertion (2%), and 1 deletion (2%). The tested samples had very high Ki67 index (average 57%±23%) and approximately half were hormone receptor and HER2 negative (25/46, 54%). Metastatic breast carcinomas showed a higher average VaF versus breast-localized tumors (1.3±0.99 vs. 0.18±0.60, P<0.05). Next-generation sequencing reports were promptly reported and reviewed (average 1 to 2 d) and 7 (∼25%) of potentially eligible patients received targeted therapy. Advanced breast cancers show unique landscapes of genetic variants. Most testing was done in late disease, often in metastatic and receptor-negative carcinomas. Next-generation sequencing results were promptly reported and reviewed, but the utilization of targeted therapies was limited.

Targeted mutation detection in breast cancer using MammaSeq™

“…Typically, NGS diagnostics are reserved for late stage disease. As a result, (as noted in our previous publication[8]), the solid tumor cohort was significantly enriched for metastatic disease and markers of poor prognosis - triple negative subtype, late presentation, and therapy resistance.…”

“…The general patient characteristics are shown in Table 1 and more detailed patient information is shown in Supplemental Table 1. We utilized 46 of the 48 breast cancer cases previously described in a report by Gurda et al [8]. All of these cases underwent AmpliSeq Cancer Hotspot Panel v2 NGS testing between January 1, 2013 and March 31, 2015 within the UPMC health system.…”

“…The original 46 gene AmpliSeq Cancer Hotspot Panel (Thermo Fisher Scientific) was shown to have a diagnostic suitability in primary lung, colon, and pancreatic cancers [7], however, our previous report that surveyed the clinical usefulness of the 50 gene AmpliSeq Cancer Hotspot Panel V2 in breast cancer found that the panel lacks numerous key known drivers of advanced breast cancer [8]. For example, the panel does not include any amplicons in ESR1 , which harbor mutations which are known to contribute to hormone therapy resistance (for review see [9]), and lacks coverage of the majority of known driver mutations in ERBB2 [10].…”

Whole genome amplification of cell-free DNA enables detection of circulating tumor DNA mutations from fingerstick capillary blood

“…However, for one patient (CF31), blood was obtained ~1.5 months prior to the results of metastatic tumor biopsy but an insufficient plasma volume was banked that yielded less than the required ~20 ng of input cfDNA for MammaSeq analysis. Collection of tumor specimens was described previously 23 , 45 . CA 27–29 tumor marker levels were obtained from the clinical registry in a de-identified manner.…”

Do Histopathological Features and Microcalcification Affect the Elasticity of Breast Cancer?

“…Breast cancer is a heterogeneous disease with different histopathological features, responses to therapy, and prognoses. Histopathological characteristics of tumors are used to plan the treatment of breast cancer and predict prognosis . Radiological imaging has a major role in the diagnosis, staging, and treatment of breast cancer, and it may also be useful to estimate molecular subtypes and histological grades of patients with breast cancer for guiding therapy …”