Abstract P1-15-21: The molecular characterisation of early and advanced breast cancer in a Middle-Eastern breast cancer cohort treated with neo/adjuvant anthracycline+/-taxane-based chemotherapy

Neoadjuvant therapy for breast cancer enables improved conservative operative approaches for breast cancer with similar survival. In addition, it may be used to define clinical as well as molecular systemic therapy sensitivity, aid molecular subtyping analysis of residual disease as well as incorporating potential mechanisms of resistance. Breast cancer in women in the Middle East is characterized by younger median age, more advanced stage at presentation and a higher proportion of patients with triple-negative disease. Recently, Symmans et al. published the results of neoadjuvant anthracycline+/-taxane-based chemotherapy demonstrating a strong association between residual cancer burden (RCB) and overall survival. In this and other cohorts e.g. TCGA, ICGC molecular data of pts from the Middle-East is under-represented.

Aim:

The aim of this project was to define the above parameters in a cohort of women treated with systemic therapy from June 2016 to October 2017 in a Middle Eastern breast cancer referral centre treated in the neo/adjuvant setting. In the neoadjuvant setting we are examining the association between primary biopsy and pathological response tissue (RCB criteria) integrating molecular pathology using massive parallel sequencing (MPS) analyses.

Methodology:

We designed a custom 1000 gene panel using Illumina IDT capture-based assay design and sequenced tumour samples to greater than 500X coverage. Sequencing analysis and variant calling were performed using Broad GAKT best practice; BWA, Mutect2, Oncotator pipeline.

Results:

We present a cohort of 57 pts with median age of 45(26-66), presenting with clinical stage I 2(4%), stageII 30(53%), stage III 25(44%) breast cancer for neoadjuvant (20) or adjuvant (37) anthracycline +/- taxane-based chemotherapy. Standard immunohistochemical (IHC) analysis revealed ER-pos PR-pos HER2-neg 38(67%) ER-pos PR-neg HER2-neg 2(4%) ER-neg PR-neg HER2-pos 3(5%), ER-pos PR-pos HER2-pos 5(9%), TNBC 9(16%). In the neoadjuvant cohort (20) pts, 7 were clinical stage II and 12 stage 3 at presentation. Anthracycline+/-taxane-based chemotherapy achieved pCR/RCB 0 7(35%), RCB I 3(15%), RBC II 4(20%), RCB III 6(30%). All Her2 positive patients received concurrent taxane-trastuzumab.

Implications:

Predictive molecular expression algorithms for response to systemic chemotherapy in the neoadjuvant setting have been published (Hatzis JAMA 2011; Masuda Clin Ca Res 2013).Molecular characterisation of RCB after neoadjuvant chemotherapy has looked at DNA mutations (Jiang PLOS Med 2016) and RNA expression (Lehmann J PLOS One 2016; Echavarria Clin Ca Res 2018). Integration of both provides insight into mechanisms of sensitivity and relapse using pathway analysis. We present genomic data on 20 of the neoadjuvant samples with sufficient quality DNA analysed using a custom designed 1000 gene panel using Illumina IDT capture-based assay design to greater than 500X coverage. The most commonly aberrant genes TP53, PIK3CA, GATA3, KMT2Dwere observed, with notable differences in PAX3, BRCA2, CHD2, FGFR4. Using integrated comprehensive tumour molecular comparisons pre- and post-treatment in the neoadjuvant patients and circulating tumour DNA analyses of the whole cohort will be presented.

Citation Format: Dawood S, Korbie D, Pheasant M, Kazim H, Al Hamadi A, Lloyd C, Dent R, Mainwaring PN. The molecular characterisation of early and advanced breast cancer in a Middle-Eastern breast cancer cohort treated with neo/adjuvant anthracycline+/-taxane-based chemotherapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-15-21.

Abstract P4-05-16: Quality metric study of real-time targeted massive parallel sequencing (MPS) (ampliseq comprehensive cancer panel (CCP)) and bioinformatics in early breast cancer (EBC) using life technologies ion proton system

We undertook a prospective quality assurance and metric study in 26 women with early breast cancer (EBC) in order to identify issues that may interfere with real-time integration of massive parallel sequencing (MPS) with clinical and pathology parameters for clinical decision making.

Pre-operatively, patients underwent formal informed consent process with the aid of bespoke multimedia (iPad) technology to educate patients on a) the logistical aims of the trial b) somatic and hereditary genomics c) privacy and off target (non-cancer) issues.

On Day 1, seven patients (27%) underwent WLE & SNB, 17 (65%) WLE & AXLND, 2 (7%) Mastectomy & SNB.

Samples (tumour and normal) were collected fresh into Qiagen PaxGene Tissue Container preserving both morphology and biomolecules of the sample with lysis of tissues overnight.

Day 2&3; DNA extraction was performed using the Qiagen DSP kit over 1 hour.

DNA MPS CCP was performed on Life technologies Proton P1 chip using in-house modification of manufacturers protocol. The average time taken to run CCP includes 2 days library preparation; 4 hour sequencing run, 8 hours primary analysis for generating read alignments and sequencing files. The Ampliseq protocol required modifications with respect to template input amount and cycling parameters in order to increase the fidelity of library preparation. Limitations in sequencing depth and read qualities with the current technologies lend themselves to approximately 5-6 samples/sequencing run/day if 500x read depth per amplicon is desired.

Days 4-6 manually curated bioinformatics against publicly available mutation databases (e.g. COSMIC, ENSEMBL etc.)

Day 7 communication of results

Molecular Pathology results

The median age was 57, (32-84), 18 (72%) were postmenopausal. Histopathology invasive ductal 22 (84%), invasive lobular 2 (8%) metaplastic 2 (8%).

TNM Staging: T1b 5 (19%), T1c 9 (35%) T2 12 (46%); N0 23 (88%), N1mi 1 (4%), N1a 1 (4%), N2a 1 (4%).

Hormone receptors antibodies: ER (Roche SP1) Strong 20 (77%), Moderate 1 (4%), Weak 1 (4%), Negative 4 (15%); PR (Roche 1E2) Strong 11 (42%), Moderate 10 (38%), Weak 0 (0%), Negative 5 (19%); HER2 IHC (Ventana 4B5) Strong 1 (4%), Moderate 6 (23%), Weak 6 (23%), Negative 13 (50%); HER2 SISH (Ventana inform single probe); 1 SISH positive (mean copy number 29.6); 4 patients (15%) triple negative.

Molecular aberrations identified included oncogenes TP53 2 (8%), PIK3CA 12 (46%) HRAS 2 (8%), AKT1 1 (4%); tumour suppressor genes MLL3 2 (8%), MSH6 1 (4%), ARID1A 1 (4%), and in the germline in tumour suppressor genes EPHB6 1 (4%) and LTK 1 (4%).

Significant technical and bioinformatic challenges were encountered during the development of this metric study including Ampliseq protocol modification and parameter tuning for variant calling algorithm.

In summary, many challenges face the clinical laboratory developing high throughput MPS using desktop MPS. To date this is the first publication of the new Ion Proton P1 chips in development for real-time clinical decision making. Copy-number variation (CNV), RNA-Seq, Methyl-Seq data will be available for presentation at San Antonio.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-16.

The UCSC Genome Browser Database: update 2009

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.