Next-generation Sequencing-based Genomic Profiling Research Articles

Diagnostic utility of DNA integrity number as an indicator of sufficient DNA quality in next-generation sequencing-based genomic profiling.

DNA integrity number (DIN) is a metric for assessing DNA degradation, calculated based on electrophoresis using the Agilent TapeStation System. The utility of DIN as a diagnostic indicator of sufficient DNA quality in clinical next-generation sequencing (NGS) has not been well described. We evaluated the DINs of 166 tumor formalin-fixed, paraffin-embedded (FFPE) tissue samples submitted for 124-gene panel sequencing. We also investigated a new metric on the electropherogram that could improve the predictive accuracy of the DIN. A DIN cutoff of 2.5 discriminated samples with successful analysis (n = 143) from samples with failed analysis (n = 23), with a sensitivity of 0.84 and a specificity of 0.78 (area under the curve [AUC] = 0.88). The DIN was positively correlated with the mean coverage (r = 0.72, P < .0001) but could not discriminate success from failure when the DIN was below 2.5 (negative predictive value, 0.44). We introduced a new metric, the peak/base ratio, that distinguished success from failure with higher accuracy than the DIN (cutoff = 1.6; sensitivity = 0.98, specificity = 0.83, and AUC =0.96). To predict successful NGS, the DNA quality of FFPE tissue can be easily and reliably assessed using the DIN and peak/base ratio.

Concordance Study of a 520-Gene Next-Generation Sequencing-Based Genomic Profiling Assay of Tissue and Plasma Samples.

Next-generation sequencing (NGS) enables simultaneous detection of actionable somatic variants and estimation of genomic signatures such as tumor mutational burden (TMB) or microsatellite instability (MSI) status, which empowers therapeutic decisions in clinical oncology. Our retrospective study investigated the clinical performance of somatic variant detection in paired tissue and blood samples using a large targeted gene panel, the OncoScreen Plus, which interrogates 520 cancer-related genes. We analyzed sequencing data derived from paired tissue and blood samples of 3005 patients spanning 20 solid tumor types, including lung (n = 1971), gastrointestinal (n = 625), breast (n = 120) and gynecological (n = 110), genitourinary (n = 38), and other cancers (n = 141). Across tumor types, the OncoScreen Plus panel achieved a high tissue detection rate, with an average of 97.9%. The average plasma detection rate was 72.2%, with an average tissue concordance rate of 36.6%. Considering all variant types, the plasma assay yielded an average sensitivity/true positive rate of 45.7%, with a positive predictive value of 64.7% relative to tissue assay. Pearson correlation analysis revealed a strong correlation in TMB estimated from blood and tissue samples (correlation coefficient 0.845, R2 = 0.756). MSI-high status was identified in five tumor types, including endometrial cancer (28.6%), colorectal cancer (2.5%), ovarian cancer (2.0%), gastric cancer (1.5%), and lung adenocarcinoma (0.2%). Paired tumor and blood samples from a large cohort of patients spanning 20 tumor types demonstrated that the OncoScreen Plus is a reliable pan-cancer panel for the accurate detection of somatic variants and genomic signatures that could guide individualized treatment strategies to improve the care of patients with advanced cancer.

Advantages and Limitations of Monitoring Circulating Tumor DNA Levels to Predict the Prognosis of Patients Diagnosed With Gastric Cancer.

Next-generation sequencing-based genomic profiling facilitates biomarker detection by cell-free DNA (cfDNA) liquid biopsy. However, the efficiency of mutation calling and the prognostic value of cfDNA biomarkers are disputed. We investigated 24 patients with gastric cancer in this study, using a 605-gene sequencing panel to sequence their plasma cfDNA and tumor tissue DNA. The mutation concordance between plasma cfDNA and tumor tissue DNA was 70.6% in stage IV gastric cancer and 30.2% in stage III gastric cancer, indicating insufficient mutation detection rates in stage III and early-stage cancer. When compared with total cfDNA load and blood tumor mutation burden (bTMB), the variant allele frequencies (VAF) of commonly mutated genes are highly accurate in representing disease burden. Further, VAF are a better prognostic indicator compared with serum biomarkers including carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9), cancer antigen 125 (CA125), and alpha-fetoprotein (AFP). The use of cfDNA in molecular profiling of patients allows prediction of patient survival and clinical response, as well as the development of personalized therapy regimens.

Conformational Landscapes of HER2 Exon 20 Insertions Explain Their Sensitivity to Kinase Inhibitors in Lung Adenocarcinoma.

HER2 exon 20 insertion (ex20ins) is one of the most intractable problems in lung cancer. Most ex20ins are resistant to available EGFR or pan-HER tyrosine kinase inhibitors (TKIs), with the exception of a few mutants. However, the mechanism for TKI response and resistance of HER2 ex20ins remains poorly understood. Next-generation sequencing-based genomic profiling data of 4139 patients with lung cancer were interrogated for HER2 ex20ins. Structural modeling and molecular dynamics simulations of common HER2 ex20ins were carried out to provide insights into the mechanism of activation and response heterogeneity of ex20ins. Molecular docking was performed to predict affinity to TKIs. Therapeutic decisions for patients were made on the basis of the results of genomic profiling. From 155 HER2-mutant lung cancer cases, Y772_A775dup and G778_P780dup were identified in 74 (47.7%) and 18 (11.6%) cases, respectively. Molecular dynamics simulations revealed that HER2 ex20ins led to ligand-independent kinase activation by changing the conformational landscape of HER2 kinase and restricting kinase conformation in the active state. G778_P780dup had a three-amino acid extension in the αC-β4 loop and retained the HER2-characteristic G776 and G778. Compared with Y772_A775dup, it had less restriction on kinase conformational sampling and higher affinity to afatinib, dacomitinib, pyrotinib, and poziotinib. Treating lung adenocarcinomas carrying G778_P780dup with these inhibitors led to sustained tumor responses in six of the 10 patients. The kinase conformational landscape dictated by the length of the αC-β4 loop and residues at HER2 776 and 778 position explains TKI sensitivity in ex20ins. This finding could guide therapeutic decisions with currently available therapies and future drug development strategies.

Next-generation sequencing-based genomic profiling analysis reveals novel mutations for clinical diagnosis in Chinese primary epithelial ovarian cancer patients

BackgroundOvarian cancer (OC) is one of the most malignant gynecological tumors, associated with excess death rate (50–60%) in ovarian cancer patients. Particularly, among newly occurred ovarian cancer patients, 70% of clinical cases are diagnosed at the advanced stage, which definitely delay the timely treatment and lead to high mortality rate within 5 years post diagnosis. Therefore, identification of sensitive gene markers, as well as development of reliable genetic diagnosis, are important for the early detection and precise therapy for OC patients. This study aims to identify novel genetic mutations and develop a feasible clinical approach for early OC diagnosis.MethodsThe OC tissue-derived DNA sample was acquired from 31 OC patients, and the somatic gene mutations will be identified after comparison with normal samples, using Genome-wide analysis and next-generation sequencing.ResultsA total of 463 somatic mutations, which were considered as potential pathogenic sites, were assigned to 473 genes. Among them, 15 genes (TP53, TTN, MUC16, OR4N2, BRCA1, CAD, CCDC129, INSR, NAV3, NELL2, NRAS, OBSCN, PGLYRP4, RBM15B and TRPC7) were mutated on at least two sites. These genes were mapped to RNA sequencing (RNAseq) data, and a total of 117 genes had an absolute fold- change ≥ 2 and p ≤ 0.01. Five genes were mutated in at least two OC patients. Gene ontology (GO) classification indicated that a majority of genes participated in biological processes. Kyoto Enrichment of Genes and Genomes (KEGG) enrichment pathway analysis revealed that the genes were mainly involved in the regulation of metabolic signaling pathways.ConclusionsTaken together, this study identified several novel genetic alterations pathway for early clinical diagnosis and provided abundant information for understanding molecular mechanisms of the OC occurrence and development.

The Resistance Landscape of Abivertinib, a Third-Generation EGFR Tyrosine Kinase Inhibitor, and Clinical Strategy to Overcome Resistance in EGFR T790M-Positive Non-Small Cell Lung Cancer

Background: Resistance to third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) presents a major clinical challenge in advanced non-small cell lung cancer (NSCLC). Here, we report resistance mechanisms to abivertinib, a novel third-generation EGFR TKI, from a phase I dose-escalation/expansion study (NCT02330367), and describe clinical strategies to overcome EGFR amplification-mediated resistance. Methods: Patients with EGFR T790M-positive advanced NSCLC and progression on prior EGFR TKIs received abivertinib in dose escalation (50-350 mg twice daily [BID]) or expansion (300 mg BID) cohorts. Patients enrolled at Guangdong Lung Cancer Institute who underwent next-generation sequencing-based genomic profiling upon abivertinib progression (prior to October 30, 2018) were enrolled in this exploratory analysis. Findings: Thirty-two of 73 patients enrolled were eligible for resistance analysis. A heterogeneous landscape of resistance mechanisms to abivertinib was observed with 14% (4/28) experiencing EGFR T790M loss and 13% (4/32) developing EGFR tertiary mutations including C797S. EGFR amplification was observed in 11 patients (34%), and considered a putative resistance mechanism in seven (22%) patients. Other EGFR-independent resistance mechanisms involved CDKN2A, MET, PIK3CA, HER2, TP53, Rb1 and small-cell lung cancer transformation. We demonstrated that abivertinib plus nimotuzumab or afatinib is effective and tolerable in overcoming EGFR amplification-mediated resistance to abivertinib. Interpretation: Our findings reveal a heterogenous pattern of resistance mechanisms to abivertinib which is distinct from that previously reported with osimertinib. EGFR amplification was the most common resistance mechanism in this cohort and may be overcome by combining abivertinib with an EGFR monoclonal antibody or afatinib. Funding: This work was supported by The National Key R&D Program of China (Grant No. 2016YFC1303800, to Q Zhou), Key Lab System Project of Guangdong Science and Technology Department – Guangdong Provincial Key Lab of Translational 447 Medicine in Lung Cancer (Grant No. 2012A061400006/2017B030314120, to YL WU). Medical writing support was provided by Siân Marshall PhD, SIANTIFIX Inc., Cambridge, UK, funded by ACEA Therapeutics Inc. Declaration of Interest: QZ declares grants from National Key R&D Program of China, speaker fees from AstraZeneca and Roche. Y-LW declares grants from Key Lab System Project of Guangdong Science and Technology Department, speaker fees from AstraZeneca, Eli Lilly, Pfizer, Roche, and Sanofi. XX is the CEO and stock owner of ACEA Therapeutics Inc. WT, FRL are employees of ACEA Therapeutics Inc. S-KC, J-YY, H-ZH, ZZ are employees of Burning Rock Biotech. Other authors declare no competing interests. Ethical Approval: This study was approved by the ethics committee at Guangdong General Hospital, and all patients provided written, informed consent. The study adhered to the principles of Declaration of Helsinki and the Good Clinical Practice guidelines.

Next-Generation Sequencing-based genomic profiling of brain metastases of primary ovarian cancer identifies high number of BRCA-mutations

Ovarian cancer represents the most common gynaecological malignancy and has the highest mortality of all female reproductive cancers. It has a rare predilection to develop brain metastases (BM). In this study, we evaluated the mutational profile of ovarian cancer metastases through Next-Generation Sequencing (NGS) with the aim of identifying potential clinically actionable genetic alterations with options for small molecule targeted therapy. Library preparation was conducted using Illumina TruSight Rapid Capture Kit in combination with a cancer specific enrichment kit covering 94 genes. BRCA-mutations were confirmed by using TruSeq Custom Amplicon Low Input Kit in combination with a custom-designed BRCA gene panel. In our cohort all eight sequenced BM samples exhibited a multitude of variant alterations, each with unique molecular profiles. The 37 identified variants were distributed over 22 cancer-related genes (23.4%). The number of mutated genes per sample ranged from 3 to 7 with a median of 4.5. The most commonly altered genes were BRCA1/2, TP53, and ATM. In total, 7 out of 8 samples revealed either a BRCA1 or a BRCA2 pathogenic mutation. Furthermore, all eight BM samples showed mutations in at least one DNA repair gene. Our NGS study of BM of ovarian carcinoma revealed a significant number of BRCA-mutations beside TP53, ATM and CHEK2 mutations. These findings strongly suggest the implication of BRCA and DNA repair malfunction in ovarian cancer metastasizing to the brain. Based on these findings, pharmacological PARP inhibition could be one potential targeted therapeutic for brain metastatic ovarian cancer patients.

Next-generation Sequencing-based genomic profiling: Fostering innovation in cancer care?

OBJECTIVES:With the development of next-generation sequencing (NGS) technologies, DNA sequencing has been increasingly utilized in clinical practice. Our goal was to investigate the impact of genomic evaluation on treatment decisions for heavily pretreated patients with metastatic cancer.METHODS:We analyzed metastatic cancer patients from a single institution whose cancers had progressed after all available standard-of-care therapies and whose tumors underwent next-generation sequencing analysis. We determined the percentage of patients who received any therapy directed by the test, and its efficacy.RESULTS:From July 2013 to December 2015, 185 consecutive patients were tested using a commercially available next-generation sequencing-based test, and 157 patients were eligible. Sixty-six patients (42.0%) were female, and 91 (58.0%) were male. The mean age at diagnosis was 52.2 years, and the mean number of pre-test lines of systemic treatment was 2.7. One hundred and seventy-seven patients (95.6%) had at least one identified gene alteration. Twenty-four patients (15.2%) underwent systemic treatment directed by the test result. Of these, one patient had a complete response, four (16.7%) had partial responses, two (8.3%) had stable disease, and 17 (70.8%) had disease progression as the best result. The median progression-free survival time with matched therapy was 1.6 months, and the median overall survival was 10 months.CONCLUSION:We identified a high prevalence of gene alterations using an next-generation sequencing test. Although some benefit was associated with the matched therapy, most of the patients had disease progression as the best response, indicating the limited biological potential and unclear clinical relevance of this practice.

Abstract A23: Comprehensive next-generation sequencing-based genomic profiling identifies actionable genomic alterations in diverse pediatric tumor types: The Foundation Medicine (FMI) experience

Abstract Background: Solid tumor oncology is amidst a paradigm shift with the advent and increasingly successful utilization of targeted therapies that inhibit specific genomic alterations driving an individual patient's disease. Unfortunately, many pediatric tumors lack approved targeted therapies, and routine genomic profiling of pediatric tumors has yet to be applied in a widespread manner. More comprehensive testing platforms are required to determine the landscape of genomic alterations in pediatric solid tumors and thereby broaden targeted treatment options. We have developed a solid tumor next-generation sequencing (NGS)-based diagnostic test, optimized for routine clinical FFPE specimens including needle biopsies and malignant effusions, and report here on 193 pediatric patients' tumors analyzed to date in our CLIA-certified and CAP-accredited laboratory. Methods: Hybridization capture of 3,320 exons from 182 cancer-related genes and 37 introns of 14 genes commonly rearranged in cancer (previous version of the test) or 3,769 exons from 236 cancer-related genes and 47 introns of 19 genes commonly rearranged in cancer (current version of the test) was applied to ≥ 50ng of DNA extracted from over 190 pediatric FFPE tumor specimens and sequenced to high, uniform coverage. Genomic alterations (base substitutions, small indels, rearrangements, copy number alterations) were determined and then reported for these patient samples. Results: Successful profiles were generated from 193 pediatric patient specimens from individuals ≤21 years old at the time of biopsy. A total of 361 genomic alterations were identified, with 145/193 (75%, 95% CI 68%-81%) of cases harboring at least one genomic alteration, for an average of 2.5 genomic alterations per case (range 0-14). The number of genomic alterations varied widely depending on tumor type (average alterations per sample): 4 colon cancer samples (9.0), 11 bone sarcoma samples (3.7), 13 leukemia samples (3.1), 23 brain cancer samples (2.4), 27 soft tissue sarcoma samples (2.2), 6 liver samples (2.0), 26 neuroblastoma samples (1.7), 6 lung cancer samples (1.2), 5 kidney cancer samples (1.2), and 24 other tumor types. These alterations included 146 base substitutions, 54 indels, 133 copy number alterations, and 28 rearrangements. This corresponded to alterations within 102 genes with recurrent alterations observed in 61 genes. We identified 249 actionable alterations with 109/193 (56%) of these pediatric patients found to have at least one actionable alteration. Seventy one percent (176/249) of the actionable genomic alterations would not be detected by available tumor type specific tests or hotspot panels. This approach has led to novel insights into pediatric cancers including: novel potentially druggable kinase gene fusions (e.g. ALK, RET) and non-fusion alterations in known drug targets (e.g. EGFR, BRAF, ALK, MET, PTCH1, PIK3CA, KIT, PDGFRA, FGFR1). Conclusions: Comprehensive NGS-based genomic profiling identified alterations in 75% of 193 unselected pediatric cancer clinical cases; and 56% of these patients (N=109) were found to have at least one therapeutically actionable alteration. Widespread deployment of this approach may provide treatment options for pediatric cancer patients. Citation Format: Matthew J. Hawryluk, Kai Wang, Juliann Chmielecki, Siraj M. Ali, Gary Palmer, Lazaro Garcia, Emily White, Roman Yelensky, Philip J. Stephens, Jeffrey S. Ross, Vincent A. Miller. Comprehensive next-generation sequencing-based genomic profiling identifies actionable genomic alterations in diverse pediatric tumor types: The Foundation Medicine (FMI) experience. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A23.

Abstract 4268: An unbiased survey of cancer-related rearrangements in 5,917 solid tumors identifies therapeutically actionable fusions across multiple disease subtypes

Abstract The growing trend to make cancer treatment more precise depends on the accurate identification of clinically actionable genomic alterations within a patient's tumor. Fusion proteins that result from genomic rearrangements are attractive therapeutic targets because they are tumor-specific and cancer cells depend on their expression for survival. The goal of this study was to investigate the breadth of genomic rearrangements in 19 genes shown to be fused in at least one solid cancer across a collection of 5,917 tumors from a diverse variety of subtypes. All tumor samples were submitted to a CLIA-certified CAP-accredited laboratory (Foundation Medicine, Cambridge MA) for next-generation sequencing-based genomic profiling of 3,769 exons from 236 cancer related genes and 47 introns of 19 genes frequently rearranged in cancer. We observed 350 genomic rearrangements in 338 samples from 82 different solid tumor pathologies. Rearrangements involving kinases were observed in 176 samples (3% of total samples). We identified potentially druggable rearrangements of BRAF (n=13 unique partners; 9 pathologies), ALK (n=11 unique partners; 11 pathologies), FGFR2 (n=9 unique partners; 6 pathologies), ROS1 (n=7 unique partners ; 3 pathologies), RET (n=7 unique partners; 5 pathologies), FGFR3 (n=5 unique partners; 6 pathologies), NTRK1 (n=3 unique partners; 3 pathologies), ERBB2 (n=2 unique partners; 2 pathologies), and ERBB3 (n=2 unique partners; 2 pathologies). ALK, ROS1, RET, and NTRK1 fusions in lung cancer have all shown sensitivity to targeted agents in patients. The largest number of genomic rearrangements (n=87) was found in lung adenocarcinoma (12% of cases). Interestingly, we identified a KIAA1549-BRAF fusion in a triple negative breast cancer sample, a FIP1L1-PDGFRA fusion in glioblastoma, a KIF5B-RET fusion in ovarian cancer, and an NCOA4-RET fusion in colon adenocarcinoma. These fusions have been identified previously in pilocytic astrocytoma, myeloid malignancies, lung cancer and thyroid cancer, respectively, but have rarely been reported outside of these diseases; importantly, hypereosinophilic syndromes harboring FIP1L1-PDGFRA are sensitive to imatinib, and lung cancers with KIF5B-RET are sensitive to cabozantinib. Collectively, these data demonstrate that gene fusions exist across a multitude of tumor types and that known fusions are not always confined to the disease in which they appear most often. These rearrangements include clinically actionable fusions which may identify tumors that are sensitive to selective FDA-approved targeted agents. Citation Format: Juliann Chmielecki, Garrett Frampton, Doron Lipson, Jie He, Geoff Otto, Siraj Ali, Jeffrey S. Ross, Vincent A. Miller, Roman Yelensky, Philip J. Stephens. An unbiased survey of cancer-related rearrangements in 5,917 solid tumors identifies therapeutically actionable fusions across multiple disease subtypes. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4268. doi:10.1158/1538-7445.AM2014-4268

High Frequency of Therapeutically Relevant Genomic Alterations in Advanced Small Cell Lung Cancer Detected By Targeted Next-Generation Sequencing from Small Biopsy Samples

ABSTRACT Aim: The information regarding therapeutically relevant genomic alterations in advanced small cell lung cancer (SCLC) is not well developed due to the lack of suitable tumor specimens for integrative genomic analysis. We assessed the potentially actionable genomic alterations in advanced SCLC using a next-generation sequencing-based genomic profiling assay from biopsy samples. Methods: Genomic DNA extracted from biopsy samples were subjected to the 1.499 Mb custom target capturing panel including all exons of 244 cancer-related genes. Targeted sequence enrichment was performed using the Agilent SureSelect Target Enrichment Kit (Agilent Technologies). Ninety SCLC samples were applied to the target sequencing. Results: The demographics of the 90 patients were as follows: median age 67 years (range: 37-85); male 71 (79%); history of smoking 88 (98%) and clinical stage II/III/IV=1/26/63. We repeatedly confirmed the high prevalence of inactivating mutations in TP53 (81%) and RB1 (44%). Additionally, genetic alterations in the PI3K/AKT/mTOR pathway were detected in 28 (31%) of the tumors: PIK3CA 3%, PTEN 7%, AKT2 1%, AKT3 1%, TSC1 2%, TSC2 11%, RPTOR 3%, RICTOR 3% and mTOR 3%. Alterations in targetable receptor tyrosine kinase (RTK) genes were also identified in the present study: EGFR 4%, ERBB2 3%, KIT 6%, PDGFRA 9%, ALK 11%, ROS1 12%, and RET 6%. Many of them were potentially targetable with currently available drugs. Conclusions: Sequencing based molecular profiling of SCLC is feasible from clinically available small biopsy samples. Advanced SCLC harbored frequent genomic alterations in PI3K/AKT/mTOR pathway and in targetable RTK genes. We are planning clinical trials targeting for these alterations. Disclosure: All authors have declared no conflicts of interest.

Clinical application of comprehensive next-generation sequencing-based genomic profiling for identification of actionable genomic alterations in pediatric solid tumors and hematolymphoid malignancies: The Foundation Medicine pediatric experience.

10035 Background: Oncology is undergoing a paradigm shift with the advent and increasingly successful utilization of targeted therapies. Unfortunately, many pediatric tumors lack approved targeted ...

A Targeted Next-Generation Sequencing Assay Detects a High Frequency of Therapeutically Targetable Alterations in Primary and Metastatic Breast Cancers: Implications for Clinical Practice

The aim of this study was to assess the frequency of potentially actionable genomic alterations in breast cancer that could be targeted with approved agents or investigational drugs in clinical trials using a next-generation sequencing-based genomic profiling assay performed in a Clinical Laboratory Improvement Amendments-certified and College of American Pathologists-accredited commercial laboratory. Methods. Fifty-one breast cancers were analyzed, including primary tumor biopsies of 33 stage I-II and 18 stage IV cancers (13 soft tissue, 3 liver, and 2 bone metastases). We assessed 3,230 exons in 182 cancer-related genes and 37 introns in 14 genes often rearranged in cancer for base substitutions, indels, copy number alterations, and gene fusions. The average median sequencing depth was 1,154×. Results. We observed 158 genomic alterations in 55 genes in 48 of 51 (94%) tumors (mean 3.1, range 0-9). The average number of potentially therapeutically relevant alterations was similar in primary (1.6, range 0-4) and in heavily pretreated metastatic cancers (2.0, range 0-4) (p = .24). The most common actionable alterations were in PIK3CA (n = 9, phosphatidylinositol 3-kinase [PI3K]/mammalian target of rapamycin [mTOR] inhibitors), NF1 (n = 7, PI3K/mTOR/mitogen-activated protein kinase inhibitors), v-akt murine thymoma viral oncogene homolog 1-3 (n = 7, PI3K/mTOR/AKT inhibitors), BRCA1/2 (n = 6, poly[ADP-ribose] polymerase inhibitors), and CCND1,2 and CCNE (n = 8)/cycline dependent kinase (CDK)6 (n = 1) (CDK4/6 inhibitors), KIT (n = 1, imatinib/sunitinib), ALK (n = 1, crizotinib), FGFR1,2 (n = 5, fibroblast growth factor receptor inhibitors), and EGFR (n = 2, epidermal growth factor receptor inhibitors). Our sequencing assay also correctly identified all six cases with HER2 (ERBB2) amplification by fluorescence in situ hybridization when tumor content was adequate. In addition, two known activating HER2 mutations were identified, both in unamplified cases. Conclusion. Overall, 84% of cancers harbored at least one genomic alteration linked to potential treatment options. Systematic evaluation of the predictive value of these genomic alterations is critically important for further progress in this field.