Comprehensive Next-generation Sequencing Assay Research Articles

Genomic Landscape of Advanced Solid Tumors in Middle East and North Africa Using Circulating Tumor DNA in Routine Clinical Practice

Introduction: Next-generation sequencing (NGS) of tumor DNA can detect actionable drivers and help guide therapy for patients with advanced-stage cancers. While tissue-based genotyping is considered a standard of care, blood-based genotyping is emerging as a valid alternative. Tumor genomic profiles may vary by region, and data from the Middle East and North Africa (MENA) are not widely available. This study elucidates the genomic landscape of advanced solid cancers in patients from the MENA region by retrospectively analyzing results from NGS circulating tumor DNA (ctDNA) testing. Methods: In routine clinical practice, 926 plasma samples from 767 patients with advanced cancers from the MENA region were profiled using a comprehensive NGS assay (Guardant360®). We conducted a pan-cancer analysis and sub-analyses focusing on lung, breast, and colorectal cancers. Results: In the pan-cancer group, TP53 (58.5%), EGFR (20.4%), and KRAS (18.9%) were the most frequently mutated genes. EGFR (10.2%), FGFR1 (4.9%), and PIK3CA (4.9%) showed the most amplifications, while fusions were observed in 2.7% of patients, including ALK, FGFR2, and RET. For lung adenocarcinoma, EGFR (30.5%), KRAS (19.3%), and ERBB2 (4.6%) were the most frequently identified alterations among the genes recommended for evaluation by the National Comprehensive Cancer Network (NCCN). In patients with breast cancer, PIK3CA (35.3%), ESR1 (21.7%), and BRCA1/2 (13.3%) had the most prevalent alterations among NCCN-recommended genes. In colorectal cancer, KRAS (39.0%), NRAS (8.0%), and BRAF (V600E, 4.0%) were the most observed mutations among genes recommended by the NCCN. Comparing this cohort to publicly available Western and Eastern datasets also indicated similarities (including PIK3CA in breast cancer) and variances (including EGFR in lung adenocarcinoma) in key genes of interest in the analyzed cancer types. Conclusion: Overall, our findings provide insight into the genomic landscape of individuals with advanced solid organ malignancies from the MENA region and support the role of ctDNA in guiding therapeutic decisions.

Abstract 317: Using the Biomek NGeniuS Next Generation Library Prep System to automate the Illumina TruSight Oncology 500 assay

Abstract Cancer researchers using next generation sequencing (NGS) need reliable sample preparation methodologies that generate high-quality, sequence-ready libraries from often-challenging samples. This process can be aided using automated liquid handling systems. The Biomek NGeniuS Next Generation Library Prep System from Beckman Coulter Life Sciences is a reliable, easy-to-use, purpose-built liquid handler for NGS library preparation ideal for laboratories requiring more flexibility and less hands-on time. The user-friendly software requires no programming skills, making it easy to set up and run. Biomek NGeniuS Next Generation Library Prep System’s hardware features include an on-deck thermal cycler, gripper, temperature-controlled reagent storage, and high-density tip storage which reduces user interventions and enables more walkaway time. An extensive and growing library of complimentary demonstrated NGS sample prep protocols allows the user to select from a variety of applications for NGS workflows. One such workflow is Illumina TruSight Oncology 500 assay, which represents a comprehensive NGS assay targeting the full coding regions of 523 genes implicated in the pathogenesis of solid tumors. Using enrichment-based library preparation techniques for use with formalin-fixed, paraffin-embedded (FFPE) samples, the Illumina TruSight Oncology 500 assay, when running the DNA Only workflow, can detect single nucleotide variants (SNVs), indels, amplifications, and multinucleotide variants (MNVs) in a single sequencing run. The Illumina TruSight Oncology 500 assay also detects immunotherapy biomarkers for tumor mutational burden (TMB) and microsatellite instability (MSI) in DNA samples. The Illumina TruSight Oncology 500 assay also offers a combined RNA/DNA workflow that also allows for the assessment of fusion events. In this poster, we show the utility of the Biomek NGeniuS Next Generation Library Prep System to perform the Illumina TruSight Oncology 500 assay, which saves researchers valuable hands-on time and offers a highly streamlined setup process for users new to liquid handling automation. Confidential - Company Proprietary Citation Format: Zach Smith. Using the Biomek NGeniuS Next Generation Library Prep System to automate the Illumina TruSight Oncology 500 assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 317.

A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections

BackgroundSexually transmitted infections (STIs) are prevalent throughout the world and impose a significant burden on individual health and public health systems. Missed diagnosis and late treatment of STIs can lead to serious complications such as infertility and cervical cancer. Although sexually transmitted co-infections are common, most commercial assays target one or a few STIs. The HPV-STI ChapterDx Next Generation Sequencing (NGS) assay detects and quantifies 29 HPVs and 14 other STIs in a single-tube and single-step PCR reaction and can be applied to tens to thousands of samples in a single sequencing run.MethodsA cohort of 274 samples, previously analyzed by conventional cytology/histology and Roche cobas HPV Test, were analyzed by ChapterDx HPV-STI NGS assay for detection of 43 HPV and STI. A set of 43 synthetic control DNA fragments for 43 HPV and STI were developed to evaluate the limit of detection, specificity, and sensitivity of ChapterDx HPV-STI NGS assay.ResultsThe assay was evaluated in this study, and the limit of detection was 100% at 50 copies for all targets, and 100%, 96%, 88% at 20 copies for 34, 8, and 1 target, respectively. The performance of this assay has been compared to Roche cobas HPV test, showing an overall agreement of 97.5% for hr-HPV, and 98.5% for both, HPV16 and HPV18. The assay also detected all HPV-infected CIN2/3 with 100% agreement with Roche cobas HPV results. Moreover, several co-infections with non-HPV STIs, such as C. trachomatis, T. vaginalis, M. genitalium, and HSV2 were identified.ConclusionsThe ChapterDx HPV-STI NGS assay is a user-friendly, easy to automate and cost-efficient assay, which provides accurate and comprehensive results for a wide spectrum of HPVs and STIs.

Genotyping Squamous Cell Lung Carcinoma in Colombia (Geno1.1-CLICaP).

BackgroundLung cancer is a public health problem, and squamous cell carcinoma (SCC) is the second most prevalent subtype of this neoplasm. Compared to other subtypes, including adenocarcinoma, SCC is less well understood in terms of molecular pathogenesis, limiting therapeutic options among targeted agents approved for other disease subgroups. In this study, we sought to characterize the SCC genomic profile using a validated Next Generation Sequencing (NGS) platform.MethodsThe comprehensive NGS assay (TruSight Tumor 170) was used in order to target the full coding regions of 170 cancer-related genes on SCC samples. PD-L1 expression in tumor cells (TCs) was assessed using clone 22C3 (Dako). Clinical outcomes were correlated with molecular profile, including progression free survival (PFS), overall response rate (ORR), and overall survival (OS).ResultsA total of 26 samples were included, median age was 67 years (r, 33–83) and 53.8% were men. Tobacco consumption was identified in all subjects (mean 34-year package). For first-line treatment 80.8% of patients received cisplatin or carboplatin plus gemcitabine. In terms of molecular profile, we identified a high prevalence of inactivating mutations in TP53 (61.5%), PIK3CA (34.6%), MLL2 (34.6%), KEAP1 (38.4%), and NOTCH1 (26.9%). PD-L1 expression ranged from negative, 1, 2–49, and ≥50% in 23.1, 38.5, 26.9, and 11.5%, respectively. Interestingly, the genetic alterations did not have an effect in PFS, OS or ORR in this study. However, PDL1 expression was higher among those who had mutations in TP53 (p = 0.037) and greater expression of PDL1 was related to PIK3CA alterations (p = 0.05).ConclusionsThe genomic profile of SCC encompasses important genes including TP53, PIK3CA and KEAP1. TP53 mutations could be associated with PDL1 expression, generating hypothesis regarding specific treatment options.

NGS-based molecular profiling (a multi-center collaborative, observation study in Japan) highlights pathogenic variants of DNA-repair genes in advanced or recurrent endometrial cancer.

e13510 Background: Although tumor molecular profiling has now become prevalent, next-generation sequencing (NGS)-based molecular profiling with adequate annotation is limited in recurrent endometrial cancers. We investigated the frequency of alterations in cancer-related genes in a Japanese cohort of incurable endometrial cancer patients. Methods: We enrolled 102 endometrial cancer patients, who had discontinued standard therapy, and extracted tumor DNA from their formalin-fixed paraffin-embedded specimens. Oncomine Comprehensive Assay v3 (ThermoFisher), which covers 161 cancer genes, was used as a comprehensive NGS assay. We only defined variants with the annotations “pathogenic” or “likely pathogenic.” Oncogenicity and actionability were defined with the Oncomine Knowledgebase and “Chrovis database” ( https://chrov.is/ ). The protocol was approved by the institutional ethics committee at each institute, and written informed consent was obtained from all patients before enrollment. Results: The ratios of pathogenic mutations in the PI3K-AKT pathway were 34.3%, 15.7%, and 3.9% for PIK3CA, PTEN, and AKT1, while those in the receptor tyrosine kinase-RAS-MAPK pathway were 3.9%, 2.0%, 3.9%, and 1.0% for FGFR2, KRAS, NF1, and BRAF, respectively. The pathogenic mutation ratios of TP53, ATM, CTNNB1, and FBXW7 were 21.6%, 3.9%, 10.8%, and 9.8%, respectively. In addition to 5.9% of MSH2 variants (five patients with 5-20% and one patient with 56% variant allele frequency (VAF)), pathogenic variants of BRCA1 and/or BRCA2 were identified in 7.8% (seven patients with 5-20% and one with 40% VAFs). Three fusion genes were identified in three patients ( TPR- NTRK1, ESR1- CCDC170, and TBL1XR1- PIK3CA). “Actionable” gene variants (applicable for clinical trials or approved drug available in Japan) were identified in 49.0% of patients. Candidate drugs for patients with actionable variants included ROS1/TRK, AKT, immune checkpoint, and PARP inhibitors. Conclusions: Molecular profiling in poor-prognostic endometrial cancer highlighted the significance of DNA-repair related genes ( TP53, ATM, BRCA1, and BRCA2) and Wnt-beta catenin signaling pathway, and the infrequent alterations in PTEN and KRAS genes, although PIK3CA was frequently mutated. Our data suggest that targeting DNA repair pathway (including PARP inhibitors), may be a treatment option in certain endometrial cancer patients. Clinical trial information: UMIN000027294.

Ultrasensitive multiplex detection of structural rearrangements in ALK, RET, ROS1 and PD-L1 using a comprehensive next-generation sequencing assay.

3572 Background: Oncogenic structural rearrangements (SR) in ALK, RET and ROS1 are well-described in lung cancer, and confer sensitivity to targeted therapy. SR disrupting the 3’UTR of PD-L1 gene have been reported in multiple cancer types and can potentially predict response to checkpoint immunotherapy. An amplicon-based next-generation sequencing (NGS) platform technology (AmpliMARK), previously optimized for detection of single nucleotide variations (SNVs), microsatellite instability and viral DNA, was extended to the multiplex detection of SR in ALK, RET, ROS1 and PD-L1 in cell-free DNA (cfDNA) and tumor tissue DNA. Methods: A hybrid primer-extension and adapter-ligation based method allowing detection of SR in a fusion-partner agnostic manner was utilized for multiplex target capture of genomic regions of ALK, RET, ROS1 and PD-L1 SR. Analytical validation was performed using admixtures of fragmented genomic DNA from an ALK SR-positive cell line, commercial standards containing RET and ROS1 SR, and synthetic PD-L1 SR gene constructs. Clinical performance was assessed in cfDNA samples from lung cancer patients and tumor tissue DNA samples from natural killer(NK)/T-cell lymphoma patients. Results: Detection of SR could be achieved to an allele frequency detection limit of 0.5% with sensitivity of 89.5% and specificity of 100% in admixture samples mimicking cfDNA. In an unselected series of 374 lung cancer cases, actionable SR for ALK, RET and ROS1 were detected in cfDNA of 9 samples, for an overall detection rate of 2.4%, and 1.8% (3 out of 168) when restricted to treatment-naive lung cancer cases only. In 29 NK/T-cell lymphoma tumor tissue samples, 9 samples were positive for PD-L1 SR, which were orthogonally confirmed by whole-genome sequencing, targeted sequencing or Sanger sequencing for a concordance rate of 100% across all samples. For 1 NK/T-cell lymphoma tumor tissue sample where matched plasma was available, the same PD-L1 SR was also detected in cfDNA. Conclusions: We have demonstrated and validated a comprehensive amplicon-based NGS assay for ultrasensitive multiplex detection of structural rearrangements in ALK, RET, ROS1 and PD-L1 across both cfDNA and tumor tissue DNA in analytical and clinical contexts. Ongoing studies will further evaluate the performance and utility of this assay across a larger number of clinical samples for the detection of these SR as well as additional cancer-associated SR involving NTRK1/2/3, FGFR2/3 and TMPRSS2.

Clinical utility of a liquid biopsy diagnostic approach in lung cancer using amplicon-based next-generation sequencing in parallel with allele-specific PCR.

e21516 Background: The utility of a liquid biopsy test for diagnosis and treatment is determined by its accuracy, molecular target coverage and timeliness to a clinically informative result. We describe our clinical experience of providing comprehensive next-generation sequencing (NGS) plasma testing for advanced lung cancer cases, including parallel testing with allele-specific PCR (AS-PCR) for rapid EGFR mutation detection. Methods: Plasma cell-free DNA (cfDNA) from advanced lung cancer patients (n = 374) underwent real-world testing with an amplicon-based NGS assay, in a CAP and ISO15189 accredited central laboratory. The assay covers 51 genes, including 8 guideline recommended biomarkers- EGFR, BRAF, MET, ALK, RET, ROS1, ERBB2 and KRAS. 168 cases (44.9%) were treatment-naïve (baseline) and 206 cases (55.1%) had received one or more lines of treatment. Parallel testing with AS-PCR for 10 specific EGFR mutations was done for 151 cases (90 baseline, 61 non-baseline). Concordance of EGFR mutation detection by the two methods, and the frequency of detection of clinically actionable (driver) mutations by NGS were assessed. Turnaround time (TAT) was calculated from sample receipt. Results: An overall concordance of 97.4% was observed for EGFR mutations between AS-PCR and NGS. When restricted to baseline cases, concordance was 100%. Among baseline cases which were concordant with AS-PCR for EGFR negativity (n = 63), driver mutations were identified in EGFR (n = 7 rarer mutations), KRAS, ERBB2, MET, NRAS, BRAF and ALK (n = 16 total) by NGS, providing an additional 37% diagnostic yield (23/63 cases). Among all baseline cases tested by NGS, a driver gene mutation was found in 64.28% of cases, including EGFR (36.9%) and KRAS mutations (11.9 %). Among non-baseline cases which were EGFR-negative by NGS and by AS-PCR, added diagnostic yield provided by NGS was 33.3% (10 of 30 cases), and included 16.7% rarer EGFR mutations. Overall, detection rate of ALK, RET, ROS1 fusions was 2.4% (n = 5, 3 and 1, respectively). Median TAT for EGFR results by AS-PCR was 1 day (range 1-2 days), while median TAT for NGS results was 10 days (range 4-13 days). Conclusions: We report excellent real-world performance of blood-based liquid biopsy testing for detecting recommended biomarkers in lung cancers, including an approach combining two orthogonal platforms for quick decision making. Clinically meaningful diagnostic yields can be obtained using a timely comprehensive NGS assay, either individually or in parallel with rapid AS-PCR testing.

Abstract B029: Comparison of a comprehensive NGS profiling assay and conventional molecular testing approaches for detection of clinically relevant alterations in NSCLC

Abstract Introduction: Genomic analysis using next-generation sequencing (NGS) enables simultaneous detection of targetable alterations and biomarkers with emerging clinical utility in non-small cell lung cancer (NSCLC) patients. Importantly, many of these alterations are mutually exclusive and tumor tissue for molecular testing is often limited. As such, we developed PGDx elioTM tissue complete (ETC) as a comprehensive NGS assay capable of detecting somatic single nucleotide variants (SNVs), insertions and deletions (indels), amplifications, and rearrangements, as well as microsatellite stability (MSI) and tumor mutational burden (TMB). Here, we present the performance of this assay in detecting key clinical variants in NSCLC. Methods: Studies comprising >300 NSCLC specimens (FFPE tissue and characterized cell lines) were analyzed using ETC, a 500+ gene assay (under development), across key clinically relevant variants in NSCLC, including tumor mutation burden (TMB). Accuracy of the results were compared to orthogonal methods (e.g. whole-exome sequencing (WES), IHC, FISH) and analyzed for the overall percent agreement (OPA). Additionally, archival FFPE samples from 46 NSCLC patients previously found to harbor ALK translocations, MET amplifications, MET exon 14 skipping mutations, EGFR mutations, and/or ROS1 translocations were also analyzed. The results were compared to orthogonal methods and the overall genomic landscape evaluated. Results: Clinical FFPE and characterized cell line specimens were evaluated for the following alterations: EGFR mutations (L858R, T790M, and Exon 19 deletions), BRAF V600E mutations, and ALK and ROS1 translocations. Compared to orthogonal methods, the NGS assay demonstrated >93% OPA across all variants. Comparison of TMB results to WES data demonstrated high accuracy and precision, across a range of DNA inputs (50-200 ng) and tumor purities (10-30%). In the 46 retrospective NSCLC cases, the NGS assay identified 15 ALK translocations, 6 MET amplifications, 1 MET exon 14 skipping mutation, and 5 EGFR mutations, with most being mutually exclusive. The majority of cases were confirmed by orthogonal assays, with the few apparent discordances likely due to tumor heterogeneity, assay distinctions, or analyte input. Higher TMB was found in cases without targetable alterations. Conclusions: ETC provides accurate and reproducible results for the detection of clinically relevant alterations in NSCLC. Further verification and validation studies of this gene panel are ongoing. Overall NGS showed excellent concordance with orthogonal variant detection methods. Importantly, ETC demonstrated added value in assessing all genomic alteration types in a single assay, as well as reporting composite genomic scores, suggesting that NGS may offer a comprehensive solution to molecular testing. Citation Format: Elizabeth Weingartner, Kelly M.R. Gerding, Gustavo Cerquiera, Christopher Gault, James Hernandez, Kenneth Valkenburg, Laurel Keefer, Eileen Sagini, Dorhyun Johng, Caitlin Gilley, Colby Ganey, Leila Ettehadieh, Diandra Denier, Christina Oliveras, Kartikeya Joshi, Eric Kong, Eniko Papp, Amy Greer, James R. White, Donna Nichol, John Simmons. Comparison of a comprehensive NGS profiling assay and conventional molecular testing approaches for detection of clinically relevant alterations in NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B029. doi:10.1158/1535-7163.TARG-19-B029

1887P - Development of a comprehensive next-generation targeted sequencing assay for detection of gene-fusions in solid tumors

BackgroundGene fusions caused by chromosomal rearrangements play an important role in oncogenesis, the progression of cancer and the selection of targeted therapies. Next-generation sequencing (NGS) using RNA enables sensitive, specific and precise detection of potentially clinically relevant gene fusions, especially when the fusion breakpoint is known. We have developed an NGS solution appropriate for FFPE tissues to detect fusion biomarkers in routine clinical research. MethodsFusion content was selected based on prioritization of actionability, verified fusion isoforms reported in the literature and collaborations, as well as prevalence of solid tumor fusion driver genes. The assay was designed to use Ion AmpliSeq multiplex PCR chemistry using manual or automated library preparation, automated templating on the Ion Chef, and sequencing on the Ion Torrent GeneStudioTM S5 sequencing platform. The analysis was supported by fully automated analysis software that performs sample QC, read-filtering, fusion calling and reporting. Streamlined access to decision support software was enabled by Oncomine™ Reporter. ResultsOver 1200 targeted isoforms from over 50 known fusion driver genes were incorporated into the assay that included prominent fusion drivers such as ALK, RET, ROS1, NTRK1/2/3 and FGFR1/2/3, and intragenic fusion events in MET, EGFR, BRAF and AR. The assay also reported non-targeted fusion events in relevant driver genes by using a novel statistically significant expression imbalance algorithm comparing 5’- and 3’- end gene expression. A preliminary development study was performed using commercially available total RNA for a Tri-Fusion control and Seraseq™ Fusion RNA Mix v3 where all of the expected fusions were detected with 100% sensitivity and specificity. Results were also concordant when characterized FFPE tumor samples with known fusion targets were tested using the assay. ConclusionsA comprehensive NGS assay was developed to support clinical research in oncology for detecting relevant RNA structural alterations from solid tumor FFPEs. An update on assay performance will be presented. Legal entity responsible for the studyThermo Fisher Scientific. FundingHas not received any funding. DisclosureV.K. Mittal: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. S.P. Myrand: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. D. Cyanam: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. P.D. Williams: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. G.G. Bee: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. A. Marcovitz: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. R. Gottimukkala: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. F. Hyland: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. C. Allen: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. E. Wong-Ho: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. S. Sadis: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. C. Van Loy: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. J. Kilzer: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. N. Khazanov: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific.

Comprehensive Sequencing Identifies High Frequency of Copy Number Changes in Korean Patients with Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is a genetically complex and heterogeneous disease with a wide range of genetic variations thus identified. As genomic profiling and sequencing studies have revealed genetic basis of ALL, a number of genetic variations are gaining clinical significance in connection with risk stratification and targeted therapy. With the need for comprehensive high-throughput analysis, next-generation sequencing (NGS) has become a good candidate for clinical testing. We have designed a comprehensive NGS assay to detect somatic mutations, translocations, and copy number changes and have evaluated its clinical utility in patients with ALL. The panel reliably detected single nucleotide variations (SNV) and copy number analysis was exceptionally helpful in identifying geneic and chromosomal deletions and duplications.A total of 101 samples of 96 patients were tested. Those patients consist of 40 adults (median age 38, range 21-76) and 56 children (median age 6.5, range 0-17), and diagnoses include 76 B-ALLs and 20 T-ALLs. The most-frequently mutated gene was TP53 (7/96, 7.3%). Ras pathway were also frequently observed (21/96, 29%) in B-ALL and were associated with hyperdiploidy (P< 0.001). Mutations in PHF6, PTEN, FBXW7, JAK3 and WT1 were detected in patients with T-ALL, and all the variants were SNVs. PHF6 mutations were most common among T-ALL patients (7/20, 35%), followed by mutations in FBXW7 (5/20, 25%). Deletions outnumbered duplications, and the most frequently deleted was CDKN2A, followed by transcription factor genes including, IKZF1, PAX5, EBF1, and ETV6. IKZF1 deletion was more frequent in adults (P<0.005), and associated with BCR-ABL1 translocation (P<0.001). PAX5 deletion was also associated with BCR-ABL1 (P<0.001) and also observed in translocations representing Philadelphia-like ALL.Fifty patients were with chromosomal abnormality detected by NGS, and some of them showed normal cytogenetics with a conventional method. Hyperdiploidy and interstitial deletion or duplication can be more easily detected; 11 cases were reclassified as B-ALL with hyperdiploidy, and numerical abnormalities and other copy number changes were identified in seven and 20 patients, respectively. Among 31 gene fusions identified by RT-PCR or NGS RNA fusion panel, only 17 (54.8%) were detected by DNA-based NGS testing.Our NGS gene panel and bioinformatics tools showed excellent performance confirming the clinical utility in identification of important variants in patients with ALL. SNVs and CNVs could be identified simultaneously in a single assay, which could be an alternative or supplement for several conventional tests and simplify the testing processes. We found unexpectedly high proportion of CNVs in ALL, suggesting the need for intensive bioinformatics analysis for CNVs and careful interpretation. DisclosuresNo relevant conflicts of interest to declare.

Abstract 936: Analysis of cell-free DNA from 32,991 advanced cancers reveals novel co-occurring activating RET alterations and oncogenic signaling pathway aberrations

Abstract Background The receptor tyrosine kinase (RTK), RET, is an emerging oncogenic target. Inhibitors targeting activating RET alterations (alts), including on-target resistance alts, are being studied in solid tumors. We present a large cohort of patients (pts) with metastatic solid tumors and somatic RET alts detected by next generation sequencing (NGS) of cell-free DNA (cfDNA). cfDNA provides a global description of RET and other genomic alts in advanced disease, typically exposed to one or more lines of systemic therapy, complementing previous descriptions of RET alts in tissue which is often obtained from early stage/untreated tumors (e.g. TCGA). Methods Somatic activating RET alts (fusions/missense alts predicted to be oncogenic) were identified from 32,991 consecutive pts tested with a 68-73 gene cfDNA assay (Guardant Health, CA) between 02/2015-07/2017. This comprehensive NGS assay evaluates single nucleotide variants, and select indels, fusions, and copy number gains. Variants of uncertain significance and synonymous alts were excluded. Results 175 somatic activating RET alts were detected in 170 pts with non-small cell lung (NSCLC, n=123), colorectal (n=15), breast (n=8), thyroid (n=8), or other cancers (n=13). 141 pts had 142 RET fusions involving 7 different partners, most commonly KIF5B (n=77). Nineteen unique activating RET missense alts were detected in 29 pts, the most common being M918T (n=8). Two pts had multiple activating RET missense alts. Advanced cancers with activating RET alts commonly harbored additional alts in oncogenic signaling pathway genes: other RTKs (n=57 pts), cell cycle (n=48), MAPK (n=46), PI3K (n=27). The frequency and distribution of alts in these co-occurring pathway genes varied by specific RET alt. Missense RET alts had a lower proportion of co-occurring TP53 alts and a higher proportion of PIK3CA alts compared to RET fusions. Non-KIF5B-RET fusions were enriched for co-occurring alts in MAPK and other RTK genes relative to tumors with KIF5B-RET fusions. In pts with NSCLC, KIF5B-RET fusions were rarely observed with other bona fide oncogenic drivers whereas known EGFR driver alts were identified in pts with CCDC6-RET (10/31), NCOA4-RET (4/14), and TRIM24-RET (1/2) fusions. 12/15 had EGFR T790M and 3/12 had C797S mutations. Prior treatment with anti-EGFR therapy was confirmed in 5 pts. The RET fusion arose without (n=1), concurrent with (n=2), and subsequent to (n=2) emergence of T790M. Conclusions In the largest cohort of pts with advanced cancers harboring RET activating alts, we describe novel co-occurrences of oncogenic signaling pathway aberrations. Additionally, our findings suggest that CCDC6- and NCOA4-RET fusions may contribute to anti-EGFR therapy resistance in NSCLC. Understanding the clinical significance of co-occurring alts is essential to evaluating the efficacy of RET-directed therapies. Citation Format: Karen L. Reckamp, Thereasa A. Rich, Young Kwang Chae, Robert C. Doebele, Wade T. Iams, Michael Oh, Victoria M. Raymond, Richard B. Lanman, Thomas E. Stinchcombe, Vivek Subbiah, David R. Trevarthen, Oliver P. Gautschi. Analysis of cell-free DNA from 32,991 advanced cancers reveals novel co-occurring activating RET alterations and oncogenic signaling pathway aberrations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 936.

Next-generation sequencing in patients with advanced cancer: are we ready for widespread clinical use? A single institute's experience.

The next-generation sequencing (NGS) assay targeting cancer-relevant genes has been adopted widely for use in patients with advanced cancer. The primary aim of this study was to assess the clinical utility of commercially available NGS. We retrospectively collected demographic and clinicopathologic data, recommended therapy, and clinical outcomes of 30 patients with a variety of advanced solid tumors referred to Foundation Medicine NGS. The initial pathologic examination was performed at the pathology department of the referring hospital. The comprehensive clinical NSG assay was performed on paraffin-embedded tumor samples using the Clinical Laboratory Improvement Amendments-certified FoundationOne platform. The median number of genomic alterations was 3 (0-19). The median number of therapies with potential benefit was 2 (0-8). In 12 cases, a comprehensive clinical NGS assay did not indicate any therapy with potential benefit according to the genomic profile. Ten of the 30 patients received treatments recommended by genomic profile results. In six of the 10 cases, disease progressed within 2 months and four patients died within 3 months of treatment initiation. Three of the 30 patients benefited from a comprehensive clinical NGS assay and the subsequent recommended therapy. The median PFS was 12 weeks (95% confidence interval 10-57) in patients treated with molecularly targeted agents chosen on the basis of tumor genomic profiling versus 48 weeks (95% confidence interval 8-38) in the control group treated with physician choice therapy (P=0.12). Our study suggests that NGS can detect additional treatment targets in individual patients, but prospective medical research and appropriate clinical guidelines for proper clinical use are vital.

Abstract 4261: Prospective next generation sequencing (NGS) of rare or poor prognosis cancers

Abstract Background. Genomic screening for somatic alterations in individual tumors is informative for understanding tumor biology and identifying novel treatment approaches and research opportunities. We initiated a research study where patients with rare or poor prognosis cancers were enrolled and underwent targeted sequencing using a CLIA certified assay. Sequencing results were reviewed at a molecular tumor board and therapeutic strategies were suggested if appropriate. Preliminary results of this study are now presented. Experimental procedures. We analyzed the genomic profiles of formalin-fixed paraffin embedded tumor specimens from 72 patients using the FoundationOne™ (Foundation Medicine, Cambridge, MA) platform for targeted sequencing of the entire coding sequence of 236 genes and 47 introns of 19 genes involved in fusions in a CLIA-certified CAP accredited laboratory. A range of evaluated tumor subtypes of epithelial and mesenchymal origin were evaluated (20). The majority of cases were from rare or uncommon histologic classes, though recurrent/refractory cases of colon cancer and triple negative breast cancers were also enrolled. Both clinical history and sequencing data were presented at a multidisciplinary molecular tumor board for development of therapeutic recommendations. Results. At least one genomic alteration was found in 68 cases (95%) and none in four cases (6%). Serial specimens were obtained in six patients. Five had a gain of at least one mutation in serial specimens. The average number of mutations identified was 3.6 (range 0-10). The most common genomic alterations detected were in p53 (40%), KRAS (17%), PI3K (15%) and PTEN (10%). Alterations in the FGF pathway were surprisingly common (16%). A number of mutations occurred at low frequency but included an additional large set of potentially actionable genes: ALK, ERBB2, BRCA2, MET. The majority of cases had mutations for which our molecular tumor board had recommended action: either potential enrollment in clinical trial or off label use of approved therapy. NGS sequencing results led to implemented clinical action in ∼15% of cases. Conclusion. Use of a comprehensive clinical NGS assay in a diverse set of cancers identifies a number of actionable genomic changes associated with targeted therapies. An institutional molecular tumor board is an effective venue to systematically review sequencing data and generate clinical recommendations. Knowledge of genomic alterations has led to referral to clinical trials, off label use of targeted therapy, and planned trials of agents targeting identified pathways. Challenges to effectively implementing clinical recommendations included lack of practical access to clinical trials and limited availability of targeted agents. Expanding clinical trial portfolios, and increasing access to targeted agents is critical for successfully implementing genomic-guided precision cancer therapy. Citation Format: Kim M. Hirshfield, Siraj M. Ali, Vincent A. Miller, Philip J. Stephens, Vassiliki Karantza, Robert S. DiPaola, Lorna Rodriguez-Rodriguez, Shridar Ganesan. Prospective next generation sequencing (NGS) of rare or poor prognosis cancers. [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 4261. doi:10.1158/1538-7445.AM2014-4261

Next-generation sequencing (NGS) in metastatic colorectal cancer (CRC) patients (pts) in Israel.

e14548 Background: Many metastatic CRC pts progress after exhausting all approved standard therapies but maintain a good performance status and could be candidates for further therapy. We hypothesized that a comprehensive NGS assay (FoundationOne) could identify novel therapy targets not routinely considered for CRC pts. Methods: Hybridization capture of 3,769 exons from 236 cancer-related genes and 47 introns of 19 genes commonly rearranged in cancer was applied to ≥ 50 ng of DNA extracted from CRC FFPE specimens and sequenced to high, uniform coverage. Genomic alterations (GA) including base substitutions, small indels, copy number alterations, and select gene fusions, were characterized and reported for each pt sample. Actionable GAs were defined as those identifying anti-cancer targeted therapies on the market or in registered clinical trials. Results: Thirty three CRC pts were included in the analysis(mean age, 54.2 years; range, 28-81; 52% male). Clinical samples used for NGS originated from colon (...

Next-generation sequencing (NGS) to identify actionable genomic changes in common and rare solid tumors: The FMI experience with the initial 50 consecutive patients.

10590 Background: Solid tumor (ST) oncology has been transformed by the linkage of genomic changes with targeted therapeutics. Unfortunately, most STs still have no alteration detected with currently available assays. Thus, more informative testing platforms are needed to analyze genomic changes in FFPE biopsy samples often limited by tumor size, heterogeneity and ploidy. Methods: We reviewed the genomic profiles of the first 50 clinical specimens received by our CLIA lab (Foundation Medicine) and analyzed by our NGS assay (Ross J. ASCO 2011). 182 genes known altered in STs and 14 genes known rearranged in STs were included. Genomic alterations were categorized as “actionable” if linked to an approved therapy in the ST under study or another ST (e.g. ALK rearrangement in lung or breast cancer, respectively), a known or suspected contraindication to a given therapy (e.g. KRAS G12D in colorectal cancer) or a clinical trial linked to the alteration (e.g. mTOR inhibition in a tumor with STK11 loss). Results: Fifty tumor specimens were received from 50 patients (median age 54, F/M=30/20) representing 35 sites. Two samples failed analysis and 6 had no detectable genomic alteration. Among 16 primary tumor types, lung (n=15), colorectal (n=7), sarcoma (n=5), breast and esophageal/gastric (n=4 each) were most common. We reported 135 genomic alterations (mean 2.8, range 0-6) unequivocally involved in oncogenesis and 69 actionable alterations. At most, 29 of these (42%) would have been detected by current assays (138% increase with NGS). Thirty seven patients had one or more actionable alterations (range 1-4) detected by NGS (74%, 95% CI 60-85%) versus only 21 (42%, 95% CI 28-57%) in whom changes would have been detected by current assays. Conclusions: Use of a broad, comprehensive NGS assay identifies an unprecedented number of actionable genomic alterations across a variety of STs from routine FFPE samples. This assay can serve as a paradigm for improving access to approved therapies in STs, minimizing use of ineffective therapies and enhancing enrollment in rationally chosen trials. Ongoing and planned trials will study the impact on several efficacy endpoints.