Single-cell analysis of the nervous system at small and large scales with instant partitions

Single-cell RNA sequencing is a new frontier across all biology, particularly in neuroscience. While powerful for answering numerous neuroscience questions, limitations in sample input size, and initial capital outlay can exclude some researchers from its application. Here, we tested a recently introduced method for scRNAseq across diverse scales and neuroscience experiments. We benchmarked against a major current scRNAseq technology and found that PIPseq performed similarly, in line with earlier benchmarking data. Across dozens of samples, PIPseq recovered many brain cell types at small and large scales (1,000-100,000 cells/sample) and was able to detect differentially expressed genes in an inflammation paradigm. Similarly, PIPseq could detect expected and new differentially expressed genes in a brain single cell suspension from a knockout mouse model; it could also detect rare, virally-la-belled cells following lentiviral targeting and gene knockdown. Finally, we used PIPseq to investigate gene expression in a nontraditional model species, the little skate (Leucoraja erinacea). In total, PIPSeq was able to detect single-cell gene expression changes across models and species, with an added benefit of large scale capture and sequencing of each sample.

Abstract 3134: Calling somatic variants from UG100 data using deep learning

UG100 is a novel next-generation sequencing platform that combines high throughput with significantly lower sequencing cost. Previous studies have demonstrated broad applicability of UG100 data for whole-genome germline variant calling, single cell transcriptomics and whole-genome methylation analysis, as well as for recalling cancer signatures from cfDNA at very low fraction of circulating tumor DNA.

Somatic variant calling is a natural application for this platform as it can benefit from lower sequencing cost to enable deeper sequencing coverage. Here, we describe the implementation and evaluation of a somatic calling pipeline from UG100 whole genome sequence data. Since deep-learning-based variant calling methods currently outperform statistical variant calling methods for germline variant calling on UG100 data, we cast somatic variant calling as a classification problem.

Specifically, we trained a classifier to distinguish if a candidate at a particular location is a somatic variant or a sequencing error. We used a version of DeepVariant optimized for UG100 data to train the deep-learning classifier in three scenarios: tumor only, tumor with an unmatched background sample and matched tumor-normal samples. The labeled truth set for training was generated by mixing whole genome sequenced samples from the genome-in-a-bottle project in a wide range of proportions (0-100% mixing ratio) to simulate various allele frequencies, with an average genome coverage of 100x. The tumor/normal model was the best-performing of the three models with a recall of >98% for SNPs and 90% for Indels at allele fraction > 10%. Notably, the model also showed high specificity as well with 16 false positive SNPs and 19 false positive indels at AF over 10% called on the chromosome that was not part of the training (chr20).

We then applied the model for calling from the WGS data on three well characterized pairs of matched tumor and normal cell lines: HCC1143, COLO829 and HCC1395. We evaluated the performance on the pre-defined UG-HCR (Ultima Genomics - High Confidence Region), which includes 95% of the human genome. DeepVariant models performed very well on calling SNPs (>92% recall at allele frequencies above 10%) and indels (>90% recall). The calls were also highly specific, with less than 1/Mb variants absent in the ground truth across the UG-HCR.

Lastly, we applied the models to 8 unpaired cell lines with known driver mutations and observed that we call 34/34 driver mutations of length <=20 bp that appear in COSMIC (100% recall).

We expect the UG100 sequencer to become an important tool for somatic genome analysis and to enable deep whole-genome sequencing to become a routine assay in clinical oncology.

Citation Format: Maya Levy, Doron Shem-Tov, Hila Benjamin, Sima Benjamin, Ilya Soifer, Shlomit Gilad, Danit Lebanony, Nika Iremadze, Eti Meiri, Doron Lipson, Omer Barad. Calling somatic variants from UG100 data using deep learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3134.

Abstract 5709: Whole genome error-corrected sequencing for sensitive circulating tumor DNA cancer monitoring

In many areas of oncology, we lack sensitive tumor-burden monitoring to guide critical decision making. While circulating tumor DNA (ctDNA) promises to enable disease monitoring, this approach is limited by the sparsity of ctDNA in the plasma. To overcome this challenge, error-corrected deep targeted sequencing has been proposed.

Nonetheless, this framework is limited by the low number of genomic equivalents (GEs, ~103/mL of plasma), imposing a ceiling on effective sequencing depth. We have previously shown that genome-wide mutational integration through plasma whole genome sequencing (WGS) can sever the dependency between available GEs and assay sensitivity (Zviran et al, 2020). In this approach, tumor-informed mutational profiles are applied to plasma WGS, allowing detection of tumor fractions as low as 10−5. However, the higher cost of WGS limits practical depth of coverage (20-30X) and may limit broad adoption. Lower costs may thus allow for enhanced ctDNA cancer monitoring via WGS. We therefore applied emerging lower-cost WGS (1USD/Gb, Almogy et al, 2022) to plasma from 7 patients with metastatic cancer at ~115x coverage depth. Read depth profiling and error rates were comparable between matched Ultima and standard platform datasets. Integration of deep learning architectures for signal to noise enrichment (Widman et al, biorxiv, 2022) with deeper WGS coverage enabled ctDNA detection at the parts per million range.

We reasoned that lower sequencing cost can be harnessed for duplex error-corrected WGS. Proof-of-concept experiments in mouse PDX samples showed ~1,500x decrease in errors. Applied to the plasma of stage IV melanoma patients (n=5), we obtained error rates ~10−7. We used this approach to tackle the challenging context of cancer monitoring in early-stage melanoma without matched tumor sequencing. While in uncorrected WGS, de novo mutation calling yielded limited ability to detect melanoma specific mutations, duplex-corrected WGS allowed us to harness melanoma mutational signatures for disease monitoring without matched tumor profiling. Analytic validation of our assay showed sensitive and specific cancer detection when the concentration of ctDNA was at 10−4 concentrations. Applied to a cohort of stage III melanoma patients with negative ctDNA detection using previously described methods, we detected ctDNA in all cases (n=4), demonstrating enhanced sensitivity using duplex WGS. These data demonstrate the exciting potential of low cost WGS for ultra-sensitive ctDNA cancer monitoring. In the tumor-informed setting, deeper sequencing increased sensitivity for mutational profile detection. Moreover, the application of duplex error-correction at genome scale allowed for sensitive cancer monitoring without matched tumor profiles. We envision that the era of low-cost sequencing will empower ultra-sensitive cancer monitoring via WGS, with transformative impact on cancer care.

Citation Format: Alexandre P. Cheng, Adam J. Widman, Anushri Arora, Itai Rusinek, William F. Hooper, Rebecca Murray, Daniel Halmos, Theophile Langanay, Giorgio Inghirami, Soren Germer, Melissa Marton, Adrienne Helland, Rob Furatero, Jaime McClintock, Lara Winterkorn, Zoe Steinsnyder, Yohyoh Wang, Srinivas Rajagopalan, Asrar I. Alimohamed, Murtaza S. Malbari, Ashish Saxena, Margaret K. Callahan, Dennie T. Frederick, Lavinia Spain, Ariel Jaimovich, Doron Lipson, Samra Turajlic, Michael C. Zody, Nasser K. Altorki, Jedd D. Wolchok, Michael A. Postow, Nicolas Robine, Genevieve Boland, Dan A. Landau. Whole genome error-corrected sequencing for sensitive circulating tumor DNA cancer monitoring. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5709.

A longitudinal circulating tumor DNA-based model associated with survival in metastatic non-small-cell lung cancer

One of the great challenges in therapeutic oncology is determining who might achieve survival benefits from a particular therapy. Studies on longitudinal circulating tumor DNA (ctDNA) dynamics for the prediction of survival have generally been small or nonrandomized. We assessed ctDNA across 5 time points in 466 non-small-cell lung cancer (NSCLC) patients from the randomized phase 3 IMpower150 study comparing chemotherapy-immune checkpoint inhibitor (chemo-ICI) combinations and used machine learning to jointly model multiple ctDNA metrics to predict overall survival (OS). ctDNA assessments through cycle 3 day 1 of treatment enabled risk stratification of patients with stable disease (hazard ratio (HR) = 3.2 (2.0-5.3), P < 0.001; median 7.1 versus 22.3 months for high- versus low-intermediate risk) and with partial response (HR = 3.3 (1.7-6.4), P < 0.001; median 8.8 versus 28.6 months). The model also identified high-risk patients in an external validation cohort from the randomized phase 3 OAK study of ICI versus chemo in NSCLC (OS HR = 3.73 (1.83-7.60), P = 0.00012). Simulations of clinical trial scenarios employing our ctDNA model suggested that early ctDNA testing outperforms early radiographic imaging for predicting trial outcomes. Overall, measuring ctDNA dynamics during treatment can improve patient risk stratification and may allow early differentiation between competing therapies during clinical trials.

Circulating Tumor DNA and Biomarker Analyses From the LOTUS Randomized Trial of First-Line Ipatasertib and Paclitaxel for Metastatic Triple-Negative Breast Cancer

PURPOSE

Combining the oral AKT inhibitor ipatasertib with paclitaxel as first-line therapy for metastatic triple-negative breast cancer significantly improved progression-free survival (PFS) in the placebo-controlled, randomized, phase II LOTUS trial, with a more pronounced effect in patients with PIK3CA/AKT1/PTEN-altered tumors. We report findings from the extensive translational research program.

PATIENTS AND METHODS

Pretreatment plasma and tumor samples were evaluated for genetic alterations using FoundationACT and FoundationOne (Foundation Medicine, Cambridge, MA) hybrid capture next-generation sequencing assays, respectively. Prevalences of the most common mutations and PIK3CA/AKT1 mutation status were determined using both assays, and concordance was assessed. In longitudinal analyses, circulating tumor DNA (ctDNA) mutations were quantified in baseline and on-treatment (cycle 3, day 1 [C3D1]) samples. The relationship between outcomes and ctDNA fraction (CTF; highest variant allele frequency) and CTF ratio (C3D1 CTF to baseline CTF) was explored.

RESULTS

Among 89 patients evaluable for ctDNA sequencing, 81 patients (91%) had 149 detectable mutations. There was high agreement between plasma- and tissue-based sequencing for known or likely short variant mutations but not amplifications. There was 100% concordance between ctDNA and tissue sequencing in patients with activating PIK3CA or AKT1 mutations. High baseline CTF was associated with shorter PFS in both treatment arms. Longitudinal analyses showed more favorable outcomes with lower absolute CTF at C3D1 and, to a lesser extent, greater CTF decreases.

CONCLUSION

These results suggest that plasma ctDNA sequencing may allow reliable and convenient assessment of prognosis and identification of genetic markers associated with increased benefit from ipatasertib. On-treatment CTF showed a meaningful association with objective response and PFS.

Homologous recombination in lung cancer, germline and somatic mutations, clinical and phenotype characterization

OBJECTIVES

Identifying new predictive biomarkers in lung cancer that will prolong survival for additional subgroups of patients is of utmost importance. We report response to treatment and survival among homologous recombination deficient (HRD) lung cancer patients mostly BRCA mutation carriers to better define the predictive value of HRD status among non-small cell lung cancer (NSCLC).

METHODS

We retrospectively evaluated our genetic and pathology database and identified 14 carriers of germline mutation in BRCA1 (n = 5), BRCA2 (n = 8), or PALB2 (n = 1) and a patient with a somatic BRCA2 mutation. Platinum compounds were part of the initial or follow-on treatment protocols in 9/11 with metastatic disease. Overall survival (OS) and response to platinum were analyzed in these patients.

RESULTS

Median OS for the 11 patients was 30 months. The 2- and 3-year survival rates in our cohort were 62.5% and 28.6%, respectively, and 7/10 patients with metastatic lung cancer survived for more than 1 year which compares favorably with the literature. Of eight patients who were treated with platinum compounds, seven responded; however, in two the response endured for <6 months. The Foundation Medicine LOH/HRD genomic score was calculated in three patients and the level was high in 2/3 (66%), including 1/2 tumors in germline BRCA mutation carriers and tumor in the patient with a somatic BRCA2 mutation. In both complete response to platinum was recorded.

CONCLUSION

Response rate to platinum compounds and survival in these patients do suggest that platinum-based therapies should still be incorporated in our treatment regimen for the patients with HRD lung cancer, and that BRCA and other HRR associated gene testing may be important in lung cancer patients.

MSI-H testing via hybrid capture based NGS sequencing of liquid biopsy samples

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Background: Microsatellite instability (MSI) testing has become critically important in clinical cancer care of patients with cancer given the recent pan-tumor FDA approval of pembrolizumab for use in patients with MSI-High (MSI-H) tumors. We previously demonstrated the robustness of a novel proprietary algorithm for determination of MSI status via NGS from solid tumor biopsy specimens (J Clin Oncol 34, 2016 (suppl; abstr 1523)). Traditional MSI tests such as PCR or IHC are impractical for pan-tumor adoption, as MSI-H prevalence outside of gastrointestinal and endometrial cancers is usually < 1%. NGS-based ctDNA profiling provides an opportunity for both MSI and actionable alteration testing in patients in whom tissue-based biopsy is not available. Methods: Genomic DNA (gDNA) from five previously characterized MSI-H cell lines: (DLD1, 22Rv1, LNCap, RL952, CL188), and one MSS cell line (SCC9) was enzymatically-fragmented to simulate ctDNA and titrated to various dilution levels with DNA from a healthy hapmap subject (NA12878). Samples were screened with a 70-gene panel, FoundationOne Liquid, that includes 180 mononucleotide repeat sequences (8-26bp long in the human reference genome). Length variability in the 180 repeat loci was utilized to generate an overall MSI score via principal components analysis. The NGS based MSI algorithm was applied to all the samples. Results: Assessment of these six cell lines, targeting five dilution levels confirmed by SNP mixing ratios, show that our NGS based MSI test for liquid biopsies has 96% sensitivity at > 2% tumor fraction with 100% PPV. The regression intercept of the MSI-H dilution samples with the pre-established MSI-H calling threshold shows our method has a LOD of 1.03% tumor fraction. MSI-H prevalence data from liquid biopsies of gastrointestinal tumors obtained during clinical care will also be presented. Conclusions: These data demonstrate the feasibility of using NGS-based liquid biopsy assays for MSI testing. This ctDNA-based approach will allow for increased access to checkpoint inhibitors in a pan-tumor setting, which would be especially relevant for cancers where routine MSI testing is impractical or when tissue is not available.

Abstract A41: Analytic validation and clinical feasibility of a next-generation sequencing assay to assess tumor mutational burden from blood (bTMB) as a biomarker for anti-PD-L1 response in NSCLC

Background: The need to identify biomarkers that predict benefit to checkpoint inhibitor therapies has led to the discovery and development of tumor mutational burden (TMB), a measure of potential tumor neoantigenicity derived from tissue biopsies that has shown clinical utility across a range of tumor types. A significant fraction of patients, however, are not candidates for tissue biopsies, presenting the need for blood-based methods to determine TMB. Here we describe the development of an assay to identify TMB from cell-free DNA derived from blood (bTMB). We present the analytic validation and clinical feasibility data that support the application of bTMB in a prospective clinical trial, BFAST (NCT03178552), evaluating the anti-PD-L1 agent atezolizumab in patients with non-small cell lung cancer (NSCLC).

Methods: The bTMB assay surveys somatic base substitutions down to 0.5% allele frequency across 394 genes from as little as 1% tumor content in a cell free DNA (cfDNA) sample derived from blood. Analytic validation was focused on establishing accuracy and precision of the bTMB measurement, as well as the minimum amount of cell-free and circulating tumor DNA required to make precise and reliable bTMB calls. The accuracy of two bTMB cutoffs was established against TMB derived from FoundationOne, an analytically validated TMB platform. Precision was evaluated by comparing the reproducibility of bTMB calls across replicate samples. We also retrospectively analyzed plasma samples from the OAK (NCT02008227) and POPLAR (NCT01903993) trials with the bTMB assay to determine the association of bTMB with atezolizumab clinical activity. The biomarker evaluable population (BEP) included 211 patients in POPLAR (intention-to-treat [ITT] =287) and 583 patients in OAK (excludes patients with known EGFR/ALK mutations; ITT=850), with blood samples available for targeted genomic sequencing. Assay positivity was defined as the presence of a number of somatic base substitutions greater than or equal to the bTMB cutoffs.

Results: The average positive percent agreement (PPA), negative percent agreement (NPA) and positive predictive value (PPV) across the bTMB cutoffs were 95%, 100% and 100%, respectively. The average precision was 96%, with a coefficient of variation of 7%. The assay limit of detection was defined as 1% tumor content in at least 20 ng of cfDNA. In POPLAR, improved progression-free survival (PFS) and overall survival (OS) hazard ratios (HRs) with atezolizumab vs docetaxel were observed for patients with bTMB at or above a range of bTMB thresholds compared with the ITT and BEP populations. In OAK, PFS benefit with atezolizumab vs docetaxel was observed at bTMB thresholds ≥10 (cut point ≥10: HR 0.73; n=251) compared with BEP (HR 0.87, 95% CI 0.73-1.04; n=585). bTMB did not correlate with PD-L1 expression as measured by VENTANA SP142 immunohistochemistry.

Conclusions: We have developed and analytically validated a blood-based assay to determine TMB with high accuracy and precision, using as little as 1% tumor content in a sample with 20 ng of cfDNA. Retrospective analyses from POPLAR and OAK data provide the first demonstrations that blood-based measurement of TMB may be associated with atezolizumab clinical efficacy in second-line NSCLC. Thus, the bTMB assay may provide a non-invasive biomarker to identify patients who derive clinical benefit from single agent PD-1/PD-L1 inhibition. Prospective studies using bTMB are currently ongoing in patients with first-line NSCLC, including BFAST and B-F1RST (NCT02848651).

Citation Format: Daniel S. Lieber, Emily White, Jacob Silterra, Shan Zhong, Tina Brennan, Michael Coyne, Mark Kennedy, David R. Gandara, Marcin Kowanetz, Sarah M. Paul, Erica Schleifman, Yan Li, Achim Rittmeyer, Louis Fehrenbacher, Lukas Amler, Todd Riehl, Craig Cummings, Priti S. Hegde, Wei Zou, Alan Sandler, Marcus Ballinger, Tony Mok, David S. Shames, Doron Lipson, Christine Malboeuf, David Fabrizio. Analytic validation and clinical feasibility of a next-generation sequencing assay to assess tumor mutational burden from blood (bTMB) as a biomarker for anti-PD-L1 response in NSCLC [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr A41.

Abstract 4544: A validated diagnostic assay for identifying ovarian cancer patients with deleterious BRCA mutations and high genomic loss of heterozygosity (LOH)

Introduction: In patients with advanced-stage ovarian cancer, FDA has recently granted approval of treatment with PARP inhibitors (PARPi) in patients harboring deleterious BRCA mutations (~25% of population). However, there is clear evidence of “BRCA-like” patients who respond to PARPi without BRCA mutations. To identify such patients, it has been shown that deficiency in homologous recombination repair leads to a common phenotype of genome-wide loss of heterozygosity (LOH). Depending on the cutoff employed, genomic LOH could identify more than twice the number of ovarian cancer patients who could benefit from PARPi than measuring BRCA alone. We present here an NGS-based platform developed and performed in compliance with FDA 21 CFR part 820. The assay provides a tumor measurement of BRCA1/2 (FDA-approved as FoundationFocus CDx BRCA) as well as genomic LOH, and is on the same platform as the comprehensive FoundationOne CDx, which interrogates 324 genes. Methods: DNA extracted from FFPE tumor tissue underwent whole-genome shotgun library construction and hybridization-based capture, followed by sequencing using Illumina HiSeq 4000. Sequence data were processed using a proprietary analysis pipeline designed to detect base substitutions, indels, copy number alterations (CNA), genomic rearrangements, microsatellite instability (MSI), and tumor mutational burden (TMB). A genome-wide LOH profile based on SNPs is measured as part of the CNA pipeline, and is summarized as the percentage of the tumor genome displaying LOH (scored from 0-100%), with ≥16% being considered LOH high based on clinical data derived from ARIEL2 Part 1, a phase II study of the PARPi rucaparib for the treatment of platinum-sensitive ovarian cancer (ARIEL2; NCT01891344) Results: For analytical validity, BRCA limit of detection (LoD) was at allele frequency 5.9% for substitutions and non-repetitive indels, and 30% tumor content for LOH. Overall percent agreement with comparator NGS assay was 97.3% for BRCA. No orthogonal platform concordance was established for LOH as no validated test exists. Within-assay reproducibility was measured with overall concordance of 100% for BRCA, and 98% for LOH. Conclusion: We developed a novel diagnostic assay (in compliance with FDA 21 CFR part 820) that can measure BRCA and genomic LOH simultaneously, and established robust analytical validation data.

Citation Format: James X. Sun, Kevin Lin, Yali Li, Kyle Gowen, Yuting He, Coren Milbury, Christine Burns, Jun Luo, Steve Roels, Murtaza Mehdi, John Truesdell, Pei Ma, Lakshman Ramamurthy, Christine Vietz, Jeri Beltman, Thomas Harding, Doron Lipson, Jeffrey Ross, Vincent Miller, Philip Stephens, Michael Doherty, Julia Elvin. A validated diagnostic assay for identifying ovarian cancer patients with deleterious BRCA mutations and high genomic loss of heterozygosity (LOH) [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 4544.

Abstract 1607: An ERBB2 follow-on companion diagnostic for clinical care of patients with breast cancer

Introduction: Patients with HER2-positive breast cancer may benefit from targeted therapies including trastuzumab and pertuzumab. While FDA has approved companion diagnostics (CDx) using FISH or IHC for identifying ERBB2 amplifications, molecular diagnostic testing in breast cancer is rapidly evolving towards comprehensive genomic profiling (CGP) due to an increasing number of biomarkers. However, clinical validity of ERBB2 testing in CGP has not yet been demonstrated in an FDA-approved manner. We present the first ERBB2 test using NGS as a follow-on CDx, which is part of FoundationOne CDx (F1CDx). Methods: Clinical validity was established against the FDA-approved HER2 FISH test, using retrospective breast cancer patient samples. For each sample, two tests using the FISH assay were performed, and clinical validity was established such that the F1CDx result is statistically non-inferior to the performance between two runs of FISH. Concordance was calculated on samples that agree between the two FISH tests. Results: Results are shown in Table 1. An exploratory analysis including low-level ERBB2 amplifications (CN=4; ploidy+2) detected by F1CDx demonstrated an improved PPA of 93.8%. A non-inferiority test demonstrated a margin of 8.0%. Further analysis showed that the discordance is most significant among samples with a low FISH ratio. In samples that are FISH-positive but F1CDx-negative, a second test of FISH only yields a FISH-FISH concordance of only 55%, suggesting significantly decreased FISH-FISH reproducibility. Conclusion: We presented a follow-on CDx for ERBB2. The F1CDx platform provides a single assay that identifies cancer patients who may be eligible to receive FDA-approved targeted therapeutics, conserves tissue by avoiding serial testing and can serve as clinical trial assay for studies requiring a molecular biomarker for eligibility. The data demonstrating clinical and analytical validity of ERBB2 may accelerate the use of CGP for routine clinical use.

Table 1. The ERBB2 companion diagnostic in FoundationOne CDxCompanion diagnosticERBB2 amplificationIndicated useTrastuzumab, ado-trastuzumab-emtansine, or pertuzumab in breast cancerApproved CDx comparatorHER2 FISH PharmDx® Kit (Dako Denmark A/S)Positive percent agreement (PPA)89.4% (101/113)Negative percent agreement (NPA)98.4% (180/183)Median unique sequence coverage&gt;500XPrecision100%Limit of Detection19.7% tumor content

Citation Format: Wai-ki Yip, Joel Skoletsky, Pei Ma, Jun Luo, Coren Milbury, Christine Burns, John Truesdell, Julia Elvin, Geoff Otto, Doron Lipson, Jeffrey Ross, Vincent Miller, Philip Stephens, Michael Doherty, Christine Vietz, James X. Sun, Yali Li. An ERBB2 follow-on companion diagnostic for clinical care of patients with breast cancer [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 1607.

Abstract 2964: On-treatment changes in circulating tumor DNA (ctDNA) level as an early predictor of clinical outcome in the LOTUS randomized phase 2 trial of 1st-line ipatasertib (IPAT) + paclitaxel (PAC) for metastatic triple-negative breast cancer (mTNBC)

Purpose: There is high interest in longitudinal analysis of plasma ctDNA as an early predictor of response and long-term outcomes. We report a retrospective longitudinal analysis of ctDNA in the double-blind placebo (PBO)-controlled randomized phase 2 LOTUS (NCT02162719) trial of the oral Akt inhibitor IPAT + PAC for mTNBC.

Methods: Pre-treatment plasma samples were analyzed to identify and quantify genomic alterations in ctDNA using a hybrid-capture-based NGS assay that interrogates 62 genes (FoundationACT). A narrow ctDNA panel quantified the same mutations in on-treatment samples collected at 8 wks (d1, cycle 3). The ctDNA fraction (CTF) was defined as the highest mutant allele frequency in each sample. The ratio of CTF in on-treatment vs pre-treatment samples was compared with objective response (RECIST v1.1) and progression-free survival (PFS) in the experimental (IPAT + PAC) and control (PBO + PAC) arms.

Results: Paired on-treatment samples were evaluable from 66 of 88 patients with evaluable pre-treatment samples. The most common reason for no on-treatment sample was disease progression (PD) before cycle 3. In 81 baseline samples, 149 mutations were identified. Calculated CTF ratios ranged from 0% (not detected in on-treatment sample) to 648% (increase in on-treatment sample). In both arms and the pooled population, a greater CTF decrease was associated with objective response and longer PFS (Table).

Conclusions: On-treatment change in CTF shows a meaningful association with objective response and PFS in LOTUS. This effect was seen in the experimental and control arms, suggesting independence from the specific mechanism of therapy. Evaluation of samples from the time of PD is ongoing. Inclusion of additional timepoints will likely improve the predictive ability of CTF, possibly allowing its use as an early surrogate trial endpoint.

IPAT + PAC (n=32)PBO + PAC (n=34)Pooled arms (n=66)Median CTF ratio, % (IQR)Confirmed complete/partial response(n=14)(n=14)(n=28)0.4 (0-14.3)0.2 (0-46.9)0.3 (0-17.8)Stable/progressive disease(n=18)(n=20)(n=38)8.2 (4.4-45.9)26.9 (8.4-91.4)20.7 (4.9-67.9)Median PFS, months (95% CI)CTF ratio ≤5%(n=15)(n=14)(n=29)7.2 (3.7-NE)6.3 (3.6-NE)7.2 (5.1-12.9)CTF ratio &gt;5%(n=17)(n=20)(n=37)3.7 (3.5-5.3)3.7 (2.8-5.4)3.7 (3.6-5.0)PFS hazard ratio (95% CI)0.46 (0.19-1.09)0.43 (0.17-0.97)0.43 (0.23-0.78)CI = confidence interval; IQR = interquartile range; NE = not estimable.

Citation Format: Matthew J. Wongchenko, Doron Lipson, Travis Clark, Mark Kennedy, Mandy Greene, Virginia Breese, Alyssa Tsiros, Sung-Bae Kim, Cristina Saura, Mafalda Oliveira, Jose Baselga, Amy V. Kapp, Wai Y. Chan, Stina M. Singel, Steven Gendreau, Rebecca Dent. On-treatment changes in circulating tumor DNA (ctDNA) level as an early predictor of clinical outcome in the LOTUS randomized phase 2 trial of 1st-line ipatasertib (IPAT) + paclitaxel (PAC) for metastatic triple-negative breast cancer (mTNBC) [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 2964.

Hybrid Capture-Based Comprehensive Genomic Profiling Identifies Lung Cancer Patients with Well-Characterized Sensitizing Epidermal Growth Factor Receptor Point Mutations That Were Not Detected by Standard of Care Testing

BACKGROUND

In our recent study, of cases positive for epidermal growth factor receptor (EGFR) exon 19 deletions using comprehensive genomic profiling (CGP), 17/77 (22%) patients with prior standard of care (SOC) EGFR testing results available were previously negative for exon 19 deletion. Our aim was to compare the detection rates of CGP versus SOC testing for well-characterized sensitizing EGFR point mutations (pm) in our 6,832-patient cohort.

MATERIALS AND METHODS

DNA was extracted from 40 microns of formalin-fixed paraffin-embedded sections from 6,832 consecutive cases of non-small cell lung cancer (NSCLC) of various histologies (2012-2015). CGP was performed using a hybrid capture, adaptor ligation-based next-generation sequencing assay to a mean coverage depth of 576×. Genomic alterations (pm, small indels, copy number changes and rearrangements) involving EGFR were recorded for each case and compared with prior testing results if available.

RESULTS

Overall, there were 482 instances of EGFR exon 21 L858R (359) and L861Q (20), exon 18 G719X (73) and exon 20 S768I (30) pm, of which 103 unique cases had prior EGFR testing results that were available for review. Of these 103 cases, CGP identified 22 patients (21%) with sensitizing EGFR pm that were not detected by SOC testing, including 9/75 (12%) patients with L858R, 4/7 (57%) patients with L861Q, 8/20 (40%) patients with G719X, and 4/7 (57%) patients with S768I pm (some patients had multiple EGFR pm). In cases with available clinical data, benefit from small molecule inhibitor therapy was observed.

CONCLUSION

CGP, even when applied to low tumor purity clinical-grade specimens, can detect well-known EGFR pm in NSCLC patients that would otherwise not be detected by SOC testing. Taken together with EGFR exon 19 deletions, over 20% of patients who are positive for EGFR-activating mutations using CGP are previously negative by SOC EGFR mutation testing, suggesting that thousands of such patients per year in the U.S. alone could experience improved clinical outcomes when hybrid capture-based CGP is used to inform therapeutic decisions.

IMPLICATIONS FOR PRACTICE

This study points out that genomic profiling, as based on hybrid capture next-generation sequencing, can identify lung cancer patients with point mutation in epidermal growth factor receptor (EGFR) missed by standard molecular testing who can likely benefit from anti-EGFR targeted therapy. Beyond the specific findings regarding false-negative point mutation testing for EGFR, this study highlights the need for oncologists and pathologists to be cognizant of the performance characteristics of testing deployed and the importance of clinical intuition in questioning the results of laboratory testing.

Abstract 2582: A novel PI3K/Akt-pathway activation biomarker using comprehensive genomic profiling (CGP) for clinical trial assay

Introduction Patients with PI3K/Akt-pathway activation may be sensitive to selective Akt-inhibitors that are currently under development. We have developed a novel next-generation sequencing (NGS)-based composite biomarker assay that identifies patients with PI3K/Akt-pathway activated tumors by identifying activating PIK3CA and AKT1 alterations, and inactivating alterations in PTEN. This assay was analytically validated, and applied to triple-negative breast cancer (TNBC) patients in the LOTUS trial (NCT02162719), a placebo-controlled phase II clinical trial to assess the safety and efficacy of adding ipatasertib to paclitaxel treatment in patients with metastatic TNBC (Kim et al., 2017).

Methods DNA extracted from FFPE tumor tissue underwent whole-genome shotgun library construction and hybridization-based capture, followed by sequencing using Illumina HiSeq 4000. Sequence data were processed using a proprietary analysis pipeline designed to detect base substitutions, indels, copy number alterations, genomic rearrangements, microsatellite instability, and tumor mutational burden. The assay further evaluated the PI3K/Akt-pathway activation biomarker status that consists of six features: 1-2) AKT1 and PIK3CA activating mutations, 3) PTEN homozygous deletion, 4) PTEN heterozygous deletion (HE), 5) PTEN dominant negative mutations, and 6) bi-allelically inactivated (BI) PTEN mutations defined as mutation plus loss of heterozygosity (LOH). We evaluated the limit of detection (LoD) and the precision of the biomarker for two novel genomic features: HE and BI, with the other four features previously validated.

Results Analytical validation of novel biomarker features: The LoD of detecting PTEN HE and BI was determined to be 30%, the lowest tumor content at which the features can be detected at 90% probability. In the precision study, 100% (81/81) agreement was achieved across different replicates within the same sequencer run and across different sequencer runs for biomarker positive samples, demonstrating high reproducibility in calling PTEN HE and BI.

Conclusions We developed and analytically validated an NGS-based assay that identifies complex and novel genomic alterations (heterozygous deletion and bi-allelic inactivation) in PTEN that is part of a composite PI3K/Akt-pathway activation biomarker. This assay identified patients that appeared to derive greater benefit in the Phase II LOTUS study as compared to using PTEN IHC to only identify patients with PTEN protein loss (Kim et al., 2017). This assay could be generalized to identify other biomarkers with similar types of genetic alterations. It also demonstrates that NGS-based CGP can broaden the intent to treat population to be more specifically related to the mechanism of action of a drug, while also being more selective to patients with potential to respond.

Citation Format: Yuting He, Matthew Wongchenko, Joel Skoletsky, Christine Burns, Yali Li, Paula Maness, Doris Kim, Doron Lipson, Philip Stephens, Vincent Miller, Jeffrey Ross, Steven Gendreau, James Sun. A novel PI3K/Akt-pathway activation biomarker using comprehensive genomic profiling (CGP) for clinical trial assay [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 2582.

Abstract 4757: A clinically validated comprehensive companion diagnostic platform for care of patients with advanced cancer

Introduction: Increase in targeted therapies has resulted in the need for a single assay capable of detecting diverse biomarkers indicated for these agents. Comprehensive genomic profiling (CGP) provides such a solution, but due to the complexity and number of assays available today, standardization of validation has become critically important. We present FoundationOne CDx, the first NGS-based comprehensive companion diagnostics (CDx) platform developed and performed in compliance with FDA 21 CFR part 820. The assay interrogates 324 genes, and has CDx indications in five tumor types associated with 17 targeted therapies (Table 1). The versatile assay design will facilitate streamlined development of future CDx indications.

Methods: DNA extracted from FFPE tumor tissue underwent whole-genome shotgun library construction and hybridization-based capture, followed by sequencing using Illumina HiSeq 4000. Sequence data were processed using a proprietary analysis pipeline designed to detect base substitutions, indels, copy number alterations, rearrangements, microsatellite instability (MSI), and tumor mutational burden (TMB).

Results: Clinical validity was established such that the concordance between CGP and approved CDx were statistically non-inferior to that of two runs of approved CDx. For analytical validity, limit of detection (LoD) was at allele frequency 4% for known substitutions and indels. LoD was 16% tumor content for copy number amplifications, 30% for homozygous deletions, 11% for rearrangements, 12% for MSI, and 20% for TMB. Concordance with an orthogonal NGS platform was 94.6% for substitutions and indels. Within-assay reproducibility had PPA 99.4%.

Conclusion: Rapid expansion of targeted therapies and CDx has necessitated a new approach and urgency to defining performance standards. We developed a comprehensive CDx assay and demonstrated clinical and analytical validity to support and accelerate using CGP for routine clinical care.

Table 1. Companion Diagnostic IndicationsIndicationBiomarkerTherapyNon-small cell lung cancer (NSCLC)EGFR exon 19 deletions and EGFR exon 21 L858R alterationsafatinib, gefitinib, or erlotinibEGFR exon 20 T790M alterationsosimertinibALK rearrangementsalectinib, crizotinib, or ceritinibBRAF V600Edabrafenib in combination with trametinibMelanomaBRAF V600Edabrafenib, vemurafenibBRAF V600E and V600Ktrametinib, cobimetinib, in combination with vemurafenibBreast cancerERBB2 (HER2) amplificationtrastuzumab, ado-trastuzumab-emtansine, or pertuzumabColorectal cancerKRAS wild-type (absence of mutations in codons 12 and 13)cetuximabKRAS and NRAS wild-type (absence of mutations in exons 2, 3, and 4)panitumumabOvarian cancerBRCA1/2 alterationsrucaparib

Citation Format: James X. Sun, Yali Li, Coren Milbury, Joel Skoletsky, Christine Burns, Wai-ki Yip, Jun Luo, Ninad Dewal, Adrienne Johnson, Kyle Gowen, Jing Tong, Yuting He, Jie He, Pei Ma, Jared White, Steve Roels, John Truesdell, Eric Peters, Houston Gilbert, Charlie Wu, Erica Schleifman, Johannes Noe, Carl Barrett, Kenneth Thress, Suzanne Jenkins, Julia Elvin, Geoff Otto, Doron Lipson, Jeffrey Ross, Vincent Miller, Philip Stephens, Michael Doherty, Christine Vietz. A clinically validated comprehensive companion diagnostic platform for care of patients with advanced cancer [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 4757.

Analytical Validation of a Hybrid Capture-Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA

Genomic profiling of circulating tumor DNA derived from cell-free DNA (cfDNA) in blood can provide a noninvasive method for detecting genomic biomarkers to guide clinical decision making for cancer patients. We developed a hybrid capture–based next-generation sequencing assay for genomic profiling of circulating tumor DNA from blood (FoundationACT). High-sequencing coverage and molecular barcode–based error detection enabled accurate detection of genomic alterations, including short variants (base substitutions, short insertions/deletions) and genomic re-arrangements at low allele frequencies (AFs), and copy number amplifications. Analytical validation was performed on 2666 reference alterations. The assay achieved >99% overall sensitivity (95% CI, 99.1%–99.4%) for short variants at AF >0.5%, >95% sensitivity (95% CI, 94.2%–95.7%) for AF 0.25% to 0.5%, and 70% sensitivity (95% CI, 68.2%–71.5%) for AF 0.125% to 0.25%. No false positives were detected in 62 samples from healthy volunteers. Genomic alterations detected by FoundationACT demonstrated high concordance with orthogonal assays run on the same clinical cfDNA samples. In 860 routine clinical FoundationACT cases, genomic alterations were detected in cfDNA at comparable frequencies to tissue; for the subset of cases with temporally matched tissue and blood samples, 75% of genomic alterations and 83% of short variant mutations detected in tissue were also detected in cfDNA. On the basis of analytical validation results, FoundationACT has been approved for use in our Clinical Laboratory Improvement Amendments–certified/College of American Pathologists–accredited/New York State–approved laboratory.

Distinct age-associated molecular profiles in acute myeloid leukemia defined by comprehensive clinical genomic profiling

Large scale comprehensive genomic profiling (CGP) has led to an improved understanding of oncogenic mutations in acute myeloid leukemia (AML), as well as identification of alterations that can serve as targets for potential therapeutic intervention. We sought to gain insight into age-associated variants in AML through comparison of extensive DNA and RNA-based GP results from pediatric and adult AML. Sequencing of 932 AML specimens (179 pediatric (age 0-18), 753 adult (age ≥ 19)) from diagnostic, relapsed, and refractory times points was performed. Comprehensive DNA (405 genes) and RNA (265) sequencing to identify a variety of structural and short variants was performed. We found that structural variants were highly prevalent in the pediatric cohort compared to the adult cohort (57% vs. 30%; p < 0.001), with certain structural variants detected only in the pediatric cohort. Fusions were the most common structural variant and were highly prevalent in AML in very young children occurring in 68% of children < 2 years of age. We observed an inverse trend in the prevalence of fusions compared to the average number of mutations per patient. In contrast to pediatric AML, adult AML was marked by short variants and multiple mutations per patient. Mutations that were common in adult AML were much less common in the adolescent and young adult cohort and were rare or absent in the pediatric cohort. Clinical CGP demonstrates the biologic differences in pediatric vs. adult AML that have significant therapeutic impacts on prognosis, therapeutic allocation, disease monitoring, and the use of more targeted therapies.

A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal

A key constraint in genomic testing in oncology is that matched normal specimens are not commonly obtained in clinical practice. Thus, while well-characterized genomic alterations do not require normal tissue for interpretation, a significant number of alterations will be unknown in whether they are germline or somatic, in the absence of a matched normal control. We introduce SGZ (somatic-germline-zygosity), a computational method for predicting somatic vs. germline origin and homozygous vs. heterozygous or sub-clonal state of variants identified from deep massively parallel sequencing (MPS) of cancer specimens. The method does not require a patient matched normal control, enabling broad application in clinical research. SGZ predicts the somatic vs. germline status of each alteration identified by modeling the alteration’s allele frequency (AF), taking into account the tumor content, tumor ploidy, and the local copy number. Accuracy of the prediction depends on the depth of sequencing and copy number model fit, which are achieved in our clinical assay by sequencing to high depth (>500x) using MPS, covering 394 cancer-related genes and over 3,500 genome-wide single nucleotide polymorphisms (SNPs). Calls are made using a statistic based on read depth and local variability of SNP AF. To validate the method, we first evaluated performance on samples from 30 lung and colon cancer patients, where we sequenced tumors and matched normal tissue. We examined predictions for 17 somatic hotspot mutations and 20 common germline SNPs in 20,182 clinical cancer specimens. To assess the impact of stromal admixture, we examined three cell lines, which were titrated with their matched normal to six levels (10–75%). Overall, predictions were made in 85% of cases, with 95–99% of variants predicted correctly, a significantly superior performance compared to a basic approach based on AF alone. We then applied the SGZ method to the COSMIC database of known somatic variants in cancer and found >50 that are in fact more likely to be germline.

We introduce SGZ, a computational method for predicting somatic vs. germline origin and homozygous vs. heterozygous or sub-clonal state of variants identified from deep massively parallel sequencing of clinical formalin-fixed, paraffin embedded (FFPE) cancer specimens. The method does not require fresh tissue or a patient matched normal control, enabling broad application in clinical research. It supports functional prioritization and interpretation of alterations discovered on routine testing and may inform clinical decision making and ultimately expand treatment choices for cancer patients.

Comprehensive genomic profiling of ctDNA in patients with colon cancer and its fidelity to the genomics of the tumor biopsy

569

Background: The liquid biopsy offers the ability to non-invasively analyze the genome of a tumor through circulating tumor (ct) DNA to identify targetable and prognostic genomic alterations. Few studies have rigorously analyzed ctDNA results and determined the fidelity with which they recapitulate the genomics of the tumor. The clinical utility study (CUS) for FoundationACT (Foundation Medicine, Cambridge, MA; NCT02620527) is a large multi-center prospective clinical study to validate this ctDNA assay for multiple solid tumor types. In this subset of the CUS study, paired specimens from 98 patients with colon cancer were analyzed with comprehensive genomic profiling of the tumor (FoundationOne) and a blood sample (FoundationACT). Methods: Maximum somatic allele fraction (MSAF) was used to estimate the fraction of ctDNA in the sample. The set of genes and targeted regions common to both FoundationOne and FoundationACT were compared for each subject. Results: 60% were male; 73 had stage IV, 17 had stage III, and 8 had stage II disease. 16% of cases had an MSAF value of 0, indicating that no ctDNA were in these samples. For the cases with MSAF > 0, 153 insertion/deletions (indels)/substitutions were identified in the tumor, and 73% of these identical alterations were also identified in the ctDNA samples. As robust analytical performance for FoundationACT has been demonstrated at MSAF > 0.5% for indel/subs, further analysis was conducted using this threshold. 83% of the alterations identified with FoundationOne were identified with FoundationACT. Further, 90% of NRAS/KRAS and 75% BRAF alterations (NCCN guideline genes) were concordant between the two assays. Lastly, there were 11 patients with tumor biopsy and blood draw taken within 30 days of each other, and in these there was 100% concordant. Association of the genomics results with other clinical variables will be presented for the available subset of patients. Conclusions: In cases where tumor profiling is not possible, these results provide compelling evidence that comprehensive molecular profiling of ctDNA in colon cancer can be used to identify most clinically relevant alterations and has fidelity to the genomics of the tumor. Clinical trial information: NCT02620527.

Genomic alterations (GA) predicted to confer lack of benefit from trastuzumab in advanced esophagogastric cancers (EGC): Analysis of 527 HER2-amplified (HER2amp) cases

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Background: The addition of trastuzumab to chemotherapy improves survival in first line treatment of advanced HER2 overexpressing EGC. However, the response rate is under 50% in this molecularly heterogeneous group of cancers. Genomic alterations (GA) associated with lack of benefit from trastuzumab are understudied. Methods: We prospectively analyzed clinical samples from patients with EGC using hybrid-capture based comprehensive genomic profiling (CGP). Pre-specified literature review was used to determine GA associated with de-novo trastuzumab resistance. Results: From 2,245 gastroesophageal junction (GEJ) adenocarcinomas and 1,883 gastric adenocarcinomas (GC) we identified 395 HER 2-amplified GEJ (18%) and 132 HER 2-amplified (HER2amp) GC (7.0%) cases. Median HER 2 copy number was 19 in GEJ and 16 in GC samples. PIK3CA GA and METamp were observed in ~9% and ~5% of both HER 2amp and non- HER2amp EGC cases; however, co-amplification of cell-cycle mediators CDK6 and CCCNE1 were each significantly enriched in HER 2amp cases (Table). MYCamp and deleterious SMAD4 GA were also significantly enriched in cases with Her2amp. CDKN2A GA were common regardless of HER 2amp, particularly in GEJ . In cases with >100 estimated HER 2 copies, only PIK3CA GA were significantly less frequent than in those with 6-99 copies (2.3% vs. 9.8%, P =0.04). All HER 2amp cases were microsatellite stable. A clinically annotated HER 2amp cohort will be presented. Conclusions: GA predicted to decrease trastuzumab sensitivity exist in a significant portion of HER 2amp EGC, although not all are enriched relative to non- HER 2amp cases. CGP may provide additive information to traditional HER2 testing and identify patients less likely to benefit from therapy. Larger clinical datasets are needed to validate our observations. [Table: see text]

Abstract 2367: Identification of ALK alternative transcription initiation in BRAF-negative metastatic melanoma patients

Background:

Genomic alterations in the ALK tyrosine kinase, such as copy number gains, point mutations, and ALK gene fusions, have been described in a broad spectrum of malignancies. Recently a novel mechanism of ALK activation in melanoma was discovered in which ALK transcription was initiated from a de novo alternative transcription initiation (ATI) site in ALK intron 19 (ALK-ATI) [1]. In this study, we used whole transcriptome sequencing (WTS) to interrogate a cohort of clinical melanoma specimens in order to identify those that express ALK-ATI.

Method:

RNA-seq libraries of 33 BRAF-negative clinical metastatic melanoma specimens were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase with 200ng RNA as input and sequenced on Illumina HiSeq 4000 at 2x75bp. The specimens were sequenced to an average of 69.4m total read pairs with 11.3m on-target distinct read pairs. Sequencing reads were mapped to the human genome and transcriptome, gene- and exon-level expressions were quantified. An algorithm to identify the ALK-ATI was developed based on assessing 1) transcription of intron 19 putative ATI region, 2) ALK relative RNA expression and 3) ALK 5’ to 3’ differential expression. In addition, immunohistochemistry (IHC) staining for ALK (using D5F3 antibody) was done on 10 of the 33 samples with adequate tumor material.

Results:

High coverage (median 30x) of intron 19 ATI region and high ALK relative expression (log ratio &gt; 2) were observed in 4 of the 33 specimens tested, in which the ATI site is consistent with what had been reported in [1]. Among the 4 potential ALK-ATI positive cases, 3 have shown significant 3’ to 5’ overexpression of ALK. IHC staining were performed on the 4 putative ALK-ATI positive cases and 6 putative negative cases, and has confirmed ALK-ATI calls detected by WTS assay. Two of the ALK IHC positive cases harbor the highest ALK expression, and the other two ALK-ATI likely cases are ALK IHC weak positive. ALK-ATI occurred in cutaneous, mucosal, and unknown primary melanoma, and co-occurred with other driver mutations (NRAS, NF1, KIT). None of the above specimens had ALK rearrangements detected from DNAseq (by FoundationOne) or WTS.

Conclusions:

Our findings confirmed previously reported ALK activation through ALK-ATI in an independent melanoma cohort, and provided direct evidence that such events can be detected using whole transcriptome sequencing and align with IHC results in clinical FFPE tumor specimens. This confirmation together with future functional validation and clinical evidence may provide new therapeutic opportunities for BRAF-negative metastatic melanoma patients.

1. Wiesner, T. et al. Alternative transcription initiation leads to expression of a novel ALK isoform in cancer. Nature 526, 453-457 (2015).

Citation Format: Shan Zhong, Christine Lovly, Christine Malboeuf, Kristina Brennan, Douglas Johnson, Kelsie Riemenschneider, Catherine Meador, Emily White, Geoff A. Otto, Doron Lipson, Philip Stephens, Vincent Miller, Jeffrey Ross, Jie He. Identification of ALK alternative transcription initiation in BRAF-negative metastatic melanoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2367. doi:10.1158/1538-7445.AM2017-2367

High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis

Genomic profiling is widely predicted to become a standard of care in clinical oncology, but more effective data sharing to accelerate progress in precision medicine will be required. Here, we describe cancer-associated genomic profiles from 18,004 unique adult cancers. The dataset was composed of 162 tumor subtypes including multiple rare and uncommon tumors. Comparison of alteration frequencies to The Cancer Genome Atlas identified some differences and suggested an enrichment of treatment-refractory samples in breast and lung cancer cohorts. To illustrate novelty within the dataset, we surveyed the genomic landscape of rare diseases and identified an increased frequency of NOTCH1 alterations in adenoid cystic carcinomas compared with previous studies. Analysis of tumor suppressor gene patterns revealed disease specificity for certain genes but broad inactivation of others. We identified multiple potentially druggable, novel and known kinase fusions in diseases beyond those in which they are currently recognized. Analysis of variants of unknown significance identified an enrichment of SMAD4 alterations in colon cancer and other rare alterations predicted to have functional impact. Analysis of established, clinically relevant alterations highlighted the spectrum of molecular changes for which testing is currently recommended, as well as opportunities for expansion of indications for use of approved targeted therapies. Overall, this dataset presents a new resource with which to investigate rare alterations and diseases, validate clinical relevance, and identify novel therapeutic targets. Cancer Res; 77(9); 2464-75. ©2017 AACR.

Abstract P6-07-08: The complete spectrum of ESR1 mutations from 7590 breast cancer tumor samples

Background: Approximately 70% of newly diagnosed breast cancers express estrogen receptor alpha (ERα), and are treated with agents that block ER signaling. Acquired mutations in ESR1, the gene that encodes ERα, have been associated with resistance to aromatase inhibitor therapy in patients with ER positive metastatic breast cancer (ER+ mBC). The most frequently occurring ESR1 mutations are clustered between amino acids 536 to 538 within the ligand binding domain (LBD), although limited data exists characterizing the full mutation profile in a large number of breast cancer samples.

Methods: We surveyed the Foundation Medicine dataset of 7590 primary and metastatic breast cancer tumor samples for ESR1 short variants and copy number alterations. Hormone receptor status was unavailable, therefore two assumptions were made to provide an estimate of prevalence in the ER+ HER2- population: 70% of the tumor samples are from ER+ HER2- patients, and all ESR1 mutations from non-HER2 amplified metastatic sites are from ER+ HER2- patients. In a separate cohort of 48 ER+ mBC patients, circulating tumor DNA (ctDNA) was analyzed for ESR1 mutations using the BEAMing method by Sysmex and with Foundation Medicine's sequencing assay, FoundationACT (Assay for Circulating Tumor DNA).

Results: The prevalence of mutations in ER+ HER2- breast cancer was estimated to be 22% in samples from metastatic sites but less than 3% in samples from primary sites. ESR1 amplification was rare in samples from both primary and metastatic disease sites at 1.3% and 2.0% respectively. A total of 153 unique short variants of known and unknown status were identified. In addition to hotspot mutations at 537 and 538, previously undescribed rare mutations were identified throughout the entire length of the LBD, although 10 alterations at amino acids 380, 463, 536, 537, and 538 account for 86% of all ESR1 mutations in the ER+ HER2- metastatic sites. We also characterized the overlap of ESR1 alterations with commonly altered and clinically relevant genes in breast cancer, including PIK3CA mutations and HER2 amplification, and we report here a landscape of co-occurring alterations. In the cohort of patient samples where ctDNA was analyzed, BEAMing and FoundationAct assays both detected ESR1 mutations in 19 out of 48 samples, and overall concordance of mutation status (wild-type vs mutant) was 100%. A total of 51 individual mutations were detected with the BEAMing assay, 42 of which were detected with the FoundationACT assay. Seven mutations that were undetected by FoundationACT had mutant allele frequencies less than 0.1%. Ten ESR1 mutations were detected only by FoundationACT, 9 of which are not covered with the BEAMing assay. Alterations in PIK3CA, CDH1, TP53, ERBB2, and other breast cancer relevant genes were also detected with FoundationACT.

Conclusions: Understanding the mutational landscape of ESR1 and co-occurring alterations is important for diagnostic development in conjunction with the clinical development of novel anti-endocrine therapies. Our data demonstrate a large spectrum of mutations in the LBD in addition to known hotspot mutations. In addition, the FoundationACT assay offers a robust NGS-based method to screen for mutations in ctDNA that is highly concordant with digital PCR methods.

Citation Format: Spoerke JM, Schleifman E, Clark TA, Young G, Nahas M, Kennedy M, Young L, Chmielecki J, Otto GA, Lipson D, Wilson TR, Gendreau S, Lackner MR. The complete spectrum of ESR1 mutations from 7590 breast cancer tumor samples [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-07-08.

Comprehensive genomic profiling (CGP) of esophageal and tubular GI tumors to identify frequencies of ErbB family member amplification with therapeutic implications

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Background: As described in the MyPathway study, amplification and other mutations in ErbB-family proteins are actionable events across solid tumors. Targeting ERBB2 amplifications (amp) in tubular GI cancers (TGC) improves patient outcomes. ErbB family comparisons across anatomic sites is lacking and here we describe the largest known series in TGC. Methods: DNA was extracted from 12,685 FFPE clinical TGC specimens, including 1,720 esophageal CA*. CGP was performed on hybrid-capture, adaptor ligation based libraries to a mean coverage depth of 720X for up to 315 genes plus 47 introns from 19 genes frequently rearranged in cancer. Results: Across all TGC cases, amp was the most frequent genomic alteration among ErbB members at 8.7%. ERBB2 amp was 2.3x as common as EGFR amp across TGC. Across TGC sites, EGFR amp was most frequent in esophageal SCC (13.7%) and ERBB2 amp was most common in gastroesophageal junction adenoCA (21%) compared with overall frequencies of 2.7% and 5.5% respectively. ERBB3 and ERBB4 amp were rare, and most common in gastroesophageal adenoCA relative to other TGC. Clinical support with outcomes for patients treated with anti-ErbB targeted therapy across TGC will be presented, including profiling from cases of acquired resistance to anti-ErbB targeted therapy. Conclusions: Among TGC, esophageal CA harbored the most ErbB family member amp with variation by histology. Profiling across ErbB proteins in TGC suggests biologic differences and may affect response to treatment. CGP can expand the population who may benefit from anti-ErbB directed therapies and refine treatment choices. Further research is warranted. [Table: see text]

Individualized Molecular Analyses Guide Efforts (IMAGE): A Prospective Study of Molecular Profiling of Tissue and Blood in Metastatic Triple-Negative Breast Cancer

PURPOSE

The clinical utility of next-generation sequencing (NGS) in breast cancer has not been demonstrated. We hypothesized that we could perform NGS of a new biopsy from patients with metastatic triple-negative breast cancer (TNBC) in a clinically actionable timeframe.

EXPERIMENTAL DESIGN

We planned to enroll 40 patients onto a prospective study, Individualized Molecular Analyses Guide Efforts (IMAGE), to evaluate the feasibility of obtaining a new biopsy of a metastatic site, perform NGS (FoundationOne), and convene a molecular tumor board to formulate treatment recommendations within 28 days. We collected blood at baseline and at time of restaging to assess cell-free circulating plasma tumor DNA (ptDNA).

RESULTS

We enrolled 26 women with metastatic TNBC who had received ≥1 line of prior chemotherapy, and 20 (77%) underwent NGS of a metastatic site biopsy. Twelve (60%) evaluable patients received treatment recommendations within 28 days of consent. The study closed after 20 patients underwent NGS, based on protocol-specified interim futility analysis. Three patients went on to receive genomically directed therapies. Twenty-four of 26 patients had genetic alterations successfully detected in ptDNA. Among 5 patients, 4 mutations found in tumor tissues were not identified in blood, and 4 mutations found in blood were not found in corresponding tumors. In 9 patients, NGS of follow-up blood samples showed 100% concordance with baseline blood samples.

CONCLUSIONS

This study demonstrates challenges of performing NGS on prospective tissue biopsies in patients with metastatic TNBC within 28 days, while also highlighting the potential use of blood as a more time-efficient and less invasive method of mutational assessment. Clin Cancer Res; 23(2); 379-86. ©2016 AACR.

Genomic Profiling of a Large Set of Diverse Pediatric Cancers Identifies Known and Novel Mutations across Tumor Spectra

Pediatric cancers are generally characterized by low mutational burden and few recurrently mutated genes. Recent studies suggest that genomic alterations may help guide treatment decisions and clinical trial selection. Here, we describe genomic profiles from 1,215 pediatric tumors representing sarcomas, extracranial embryonal tumors, brain tumors, hematologic malignancies, carcinomas, and gonadal tumors. Comparable published datasets identified similar frequencies of clinically relevant alterations, validating this dataset as biologically relevant. We identified novel ALK fusions in a neuroblastoma (BEND5-ALK) and an astrocytoma (PPP1CB-ALK), novel BRAF fusions in an astrocytoma (BCAS1-BRAF) and a ganglioglioma (TMEM106B-BRAF), and a novel PAX3-GLI2 fusion in a rhabdomyosarcoma. Previously characterized ALK, NTRK1, and PAX3 fusions were observed in unexpected malignancies, challenging the "disease-specific" alterations paradigm. Finally, we identified recurrent variants of unknown significance in MLL3 and PRSS1 predicted to have functional impact. Data from these 1,215 tumors are publicly available for discovery and validation. Cancer Res; 77(2); 509-19. ©2017 AACR.

RET Fusion Lung Carcinoma: Response to Therapy and Clinical Features in a Case Series of 14 Patients

BACKGROUND

RET (rearranged during transfection) fusions have been reported in 1% to 2% of lung adenocarcinoma (LADC) cases. In contrast, KIF5B-RET and CCDC6-RET fusion genes have been identified in 70% to 90% and 10% to 25% of tumors, respectively. The natural history and management of RET-rearranged LADC are still being delineated.

MATERIALS AND METHODS

We present a series of 14 patients with RET-rearranged LADC. The response to therapy was assessed by the clinical response and an avatar model in 2 cases. Patients underwent chemotherapy, targeted therapy, and immunotherapy.

RESULTS

A total of 14 patients (8 women; 10 never smokers; 4 light smokers; mean age, 57 years) were included. KIF5B-RET and CCDC6-RET variants were diagnosed in 10 and 4 cases, respectively. Eight patients had an early disseminated manifestation, seven with KIF5B-RET rearranged tumor. The features of this subset included bilateral miliary lung metastases, bone metastases, and unusual early visceral abdominal involvement. One such patient demonstrated an early and durable complete response to cabozantinib for 7 months. Another 2 patients treated with cabozantinib experienced a partial response, with rapid significant clinical improvement. Four patients with tumors harboring CCDC6-RET and KIF5B-RET fusions showed pronounced and durable responses to platinum-based chemotherapy that lasted for 8 to 15 months. Two patients' tumors showed programmed cell death ligand 1-positive staining but did not respond to pembrolizumab. The median overall survival was 22.8 months.

CONCLUSION

RET-rearranged LADC in our series tended to occur as bilateral disease with early visceral involvement, especially with KIF5B fusion. Treatment with cabozantinib achieved responses, including 1 complete response. However, further studies are required in this group of patients.

Abstract 3965: Rigorous validation of a clinical circulating tumor DNA assay for cancer molecular profiling

Background:

Profiling cell-free circulating tumor DNA (ctDNA) for genomic alterations which drive oncogenesis in patients with cancer promises to provide information important for understanding cancer biology, informing therapy selection when conventional FFPE biopsies are unobtainable and potentially monitoring response to therapy. To allow routine use of blood-based ctDNA molecular profiling with clinical samples we developed and performed analytic validation of an accurate, targeted NGS-based assay. The analytic validation included over 400 samples demonstrating ≥99% sensitivity and ≥99% positive predictive value for base substitutions, indels and rearrangements with limit-of-detection below 1%.

Methods:

To ensure robust performance, the ctDNA assay was developed as part of an integrated workflow including sample collection, storage and transport, and ctDNA purification, followed by optimized construction of adaptor-ligated sequencing libraries and enrichment by solution hybridization and then sequencing to high depth (Illumina HiSeq). Computational methodologies were developed to enable sensitive and specific detection of base substitutions, indels, genomic rearrangements and high-level amplifications from ctDNA. Accuracy and reproducibility were analytically validated in a CLIA-certified laboratory using reference samples with known alterations (117 cell-line mixtures and synthetic constructs) and 268 clinical ctDNA samples. Many alterations found in clinical ctDNA samples were validated with orthogonal reference methods including a CLIA-validated NGS assay, droplet digital PCR and break-point PCR.

Results:

The ctDNA assay validation demonstrated ≥99% sensitivity and ≥99% positive predictive value for base substitutions, indels and rearrangements with a limit-of-detection below 1% and robust detection of high-level, focal amplifications when present at adequate tumor fraction. In addition, the assay accurately reports the allele frequency of alterations in the sample. In 48 clinical ctDNA samples, 95 alterations of all classes were 100% confirmed by orthogonal testing. As part of our extensive clinical utility study, we report results comparing alterations from patient-matched ctDNA and FFPE biopsies across more than 200 lung, breast and other cancer samples.

Conclusions:

Accurate clinical profiling of ctDNA enables detection of genomic alterations in patient plasma samples to provide rationale targeted therapeutic options. Our rigorous analytic validation study demonstrates high-sensitivity detection of alterations present in blood at low frequency with a very low rate of false positives, realizing the potential of ctDNA-based molecular profiling for the management of patients with cancer. This validated assay allows us to embark upon a rigorous investigation of clinical best-practices based on tumor-type specific assessment of matched ctDNA and solid biopsy specimens.

Citation Format: Travis A. Clark, Mark Kennedy, Jie He, Geneva Young, Mandy Zhao, Mike Coyne, Virginia Breese, Lauren Young, Shan Zhong, Mark Bailey, Bernard Fendler, Erica Schleifman, Eric Peters, Phil J. Stephens, Geoff A. Otto, Doron Lipson. Rigorous validation of a clinical circulating tumor DNA assay for cancer molecular profiling. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3965.

Abstract LB-178: Genomic profiling of 1239 diverse pediatric cancers identifies novel discoveries across tumors

Pediatric cancers are rare and diverse entities characterized by low mutational burden. Multiple studies investigating the genomic events driving oncogenesis have identified characteristic diagnostic lesions as well as targets suitable for therapeutic exploitation in common tumor subtypes. Here, we present genomic profiles from 1239 pediatric tumors (ages 0-18) from 51 disease subtypes representing sarcomas (26.6%), other blastomas (22.4%), brain tumors (20.4%), hematological malignancies (19.5%), carcinomas (9.8%), and gonadal tumors (1.4%). This collection represents real-world tumor specimens in which select cancer-associated genes were analyzed for all classes of alterations as part of routine clinical care. Samples were sequenced to a median unique depth of &gt;500x to allow for optimal detection of oncogenic events in low purity specimens. Additionally, 635 samples (51%) were analyzed by targeted RNA-seq for fusions in 265 genes. Alterations with proven clinical actionability in pediatric cancers (BRAF V600E and ALK, NTRK1, and ABL1 fusions) were found in 3.9% of samples from brain, sarcoma, and heme cases. Three novel ALK fusions were identified in a neuroblastoma (BEND5-ALK), a soft tissue sarcoma (IGFBP5-ALK), and an astrocytoma (PPP1CB-ALK). Two novel BRAF fusions were also found in an astrocytoma (BCAS1-BRAF) and a ganglioglioma (TMEM106B-BRAF). In rhabdomyosarcoma, we identified a novel PAX3-GLI2 fusion and confirmed a second occurrence of the rare PAX3-NCOA1 fusion. This large data set also challenged the paradigm of “disease-specific” alterations as previously characterized fusions involving ALK, NTRK1, and PAX3 were observed in novel diseases from which they were originally reported. We investigated variants of unknown significance for potentially novel cancer mutations, and identified four recurrent and likely somatic variants in KMT2C, PRSS1, and CTNNB1 predicted to have functional impact by in silico analyses. Compared to other large published data sets in neuroblastoma, ALL, AML, rhabdomyosarcoma, and medulloblastoma, similar frequencies of clinically significant alterations were observed, thereby validating this dataset as biologically relevant. While many common and diagnostic alterations have been described in pediatric cancers, researchers are becoming increasingly aware of other rarer, yet equally important, clinically relevant genomic alterations. As demonstrated by the identification of novel fusions and mutations, this data set is ripe with discovery potential, and can be used to generate hypotheses, validate rare findings, and investigate the genomic landscape of rare tumors for which only small studies exist. Data from these 1239 tumors will be publicly available to the research community for exploration and incorporation into future experiments that will ultimately improve the treatment and prognosis for children with cancer.

Citation Format: Juliann Chmielecki, Mark Bailey, Jie He, Julia Elvin, Jo-Anne Vergilio, Shakti Ramkissoon, James Suh, Garrett M. Frampton, Siraj Ali, Jeffrey Ross, Vincent A. Miller, Philip J. Stephens, Doron Lipson. Genomic profiling of 1239 diverse pediatric cancers identifies novel discoveries across tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-178.

Patient-derived xenotransplants can recapitulate the genetic driver landscape of acute leukemias

Genomic studies have identified recurrent somatic mutations in acute leukemias. However, current murine models do not sufficiently encompass the genomic complexity of human leukemias. To develop pre-clinical models, we transplanted 160 samples from patients with acute leukemia (AML, MLL, B-ALL and T-ALL) into immunodeficient mice. Of these, 119 engrafted with expected immunophenotype. Targeted sequencing of 374 genes and 265 frequently rearranged RNAs detected recurrent and novel genetic lesions in 48 paired primary tumor (PT) and patient-derived xenotransplant (PDX) samples. Overall, the frequencies of 274 somatic variant alleles correlated between PT and PDX samples, although the data were highly variable for variant alleles present at 0-10%. 17% of variant alleles were detected in either PT or PDX samples only. Based on variant allele frequency changes, 24 PT-PDX pairs were classified as concordant while the other 24 pairs showed various degree of clonal discordance. There was no correlation of clonal concordance with clinical parameters of diseases. Significantly more bone marrow samples than peripheral blood samples engrafted discordantly. These data demonstrate the utility of developing PDX banks for modeling human leukemia, and emphasize the importance of genomic profiling of PDX and patient samples to ensure concordance before performing mechanistic or therapeutic studies.

Nonamplification ERBB2 genomic alterations in 5605 cases of recurrent and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies

BACKGROUND

Activating, nonamplification ERBB2 mutations (ERBB2mut) are not detected by immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH), but are detected by DNA sequencing and may predict clinical responses to human epidermal growth factor receptor (HER2)-targeted therapy. The authors queried 5605 advanced/metastatic breast cancers (mBC) to uncover the frequency of ERBB2mut genomic alterations. Clinical responses to anti-HER2 therapeutics were identified.

METHODS

DNA was extracted from 40 µm of formalin-fixed paraffin-embedded (FFPE) sections. Comprehensive genomic profiling (CGP) was used to evaluate up to 315 genes (592× mean coverage depth). Results were analyzed for base substitutions, short indels, copy number changes, and selected rearrangements.

RESULTS

Of 5605 cases, 698 (12.5%) featured ERBB2 alterations, including 596 (10.6%) ERBB2 amplifications (ERBB2amp) and 138 (2.4%) ERBB2mut; 38 cases (0.7%) had co-occurring ERBB2amp and ERBB2mut. ERBB2mut predominantly affected the kinase (124 cases; 90%) or extracellular (15 cases; 11%) domains. Both primary BC (52 cases; 38%) and metastatic site biopsies (86 cases; 62%) were found to harbor ERBB2mut, which were distributed across carcinoma not otherwise specified (NOS) (69 cases; 50%), invasive ductal carcinoma (IDC) (40 cases; 29%), invasive lobular carcinoma (ILC) (27 cases; 20%), and mucinous mBC (2 cases; 1%). Genes commonly coaltered with ERBB2 were tumor protein 53 (TP53) (49%); phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) (42%); cadherin 1, type 1 (CDH1) (37%); MYC (17%); and cyclin D1 protein (CCND1) (16%). CDH1 mutations were enriched in ERBB2mut mBC (P<0.0006) and associated with recurrent mBC. Selected patients with ERBB2mut, without ERBB2amp, who responded to anti-HER2 targeted therapies are presented herein.

CONCLUSIONS

Within this large series, 1.8% of cases harbored ERBB2mut, which are undetectable by standard-of-care IHC or FISH tests. Metastatic BC driven by ERBB2mut respond to anti-HER2 targeted therapies, and expanding clinical trials designed to detect ERBB2mut by CGP and optimize targeted treatments are warranted. Cancer 2016. © 2016 American Cancer Society. Cancer 2016;122:2654-2662. © 2016 American Cancer Society.

Comprehensive Genomic Profiling Identifies a Subset of Crizotinib-Responsive ALK-Rearranged Non-Small Cell Lung Cancer Not Detected by Fluorescence In Situ Hybridization

INTRODUCTION

For patients with non-small cell lung cancer (NSCLC) to benefit from ALK inhibitors, sensitive and specific detection of ALK genomic rearrangements is needed. ALK break-apart fluorescence in situ hybridization (FISH) is the U.S. Food and Drug Administration approved and standard-of-care diagnostic assay, but identification of ALK rearrangements by other methods reported in NSCLC cases that tested negative for ALK rearrangements by FISH suggests a significant false-negative rate. We report here a large series of NSCLC cases assayed by hybrid-capture-based comprehensive genomic profiling (CGP) in the course of clinical care.

MATERIALS AND METHODS

Hybrid-capture-based CGP using next-generation sequencing was performed in the course of clinical care of 1,070 patients with advanced lung cancer. Each tumor sample was evaluated for all classes of genomic alterations, including base-pair substitutions, insertions/deletions, copy number alterations and rearrangements, as well as fusions/rearrangements.

RESULTS

A total of 47 patients (4.4%) were found to harbor ALK rearrangements, of whom 41 had an EML4-ALK fusion, and 6 had other fusion partners, including 3 previously unreported rearrangement events: EIF2AK-ALK, PPM1B-ALK, and PRKAR1A-ALK. Of 41 patients harboring ALK rearrangements, 31 had prior FISH testing results available. Of these, 20 were ALK FISH positive, and 11 (35%) were ALK FISH negative. Of the latter 11 patients, 9 received crizotinib based on the CGP results, and 7 achieved a response with median duration of 17 months.

CONCLUSION

Comprehensive genomic profiling detected canonical ALK rearrangements and ALK rearrangements with noncanonical fusion partners in a subset of patients with NSCLC with previously negative ALK FISH results. In this series, such patients had durable responses to ALK inhibitors, comparable to historical response rates for ALK FISH-positive cases.

IMPLICATIONS FOR PRACTICE

Comprehensive genomic profiling (CGP) that includes hybrid capture and specific baiting of intron 19 of ALK is a highly sensitive, alternative method for identification of drug-sensitive ALK fusions in patients with non-small cell lung cancer (NSCLC) who had previously tested negative using standard ALK fluorescence in situ hybridization (FISH) diagnostic assays. Given the proven benefit of treatment with crizotinib and second-generation ALK inhibitors in patients with ALK fusions, CGP should be considered in patients with NSCLC, including those who have tested negative for other alterations, including negative results using ALK FISH testing.

Comprehensive Genomic Profiling of Clinically Advanced Medullary Thyroid Carcinoma

OBJECTIVE

The aim of this study was to determine the genomic alterations of cancer-related genes in advanced medullary thyroid carcinoma during the course of clinical care.

METHODS

Hybrid-capture-based comprehensive genomic profiling was performed on 34 consecutive medullary thyroid carcinoma cases to identify all four classes of genomic alterations, and outcome for an index patient was collected.

RESULTS

RET was mutated in 88% (30/34) of cases, with RET M918T being responsible for 70% (21/30) of the RET alterations. The other RET alterations were RET E632_L633del, C634R, C620R, C618G/R/S, V804M, and RET amplification. Two of the four RET wild-type patients harbored mutations in KRAS or HRAS (1/34 each). The next most frequent genomic alterations were amplifications of CCND1, FGF3, and FGF19 and alterations in CDKN2A (3/34 each). One case with a RET M918T mutation developed acquired resistance to progressively dose-escalated vandetanib. When the mTOR inhibitor everolimus was added to continued vandetanib treatment, the patient achieved a second 25% reduction of tumor volume (RECIST 1.1) for 8 months.

CONCLUSIONS

Comprehensive genomic profiling identified the full breadth of RET alterations in metastatic medullary thyroid carcinoma and possible cooperating oncogenic driver alterations. This approach may refine the use of targeted therapy for these patients.

Comprehensive genomic profiling of anal squamous cell carcinoma reveals distinct genomically defined classes

BACKGROUND

Squamous cell cancers of the anal canal (ASCC) are increasing in frequency and lack effective therapies for advanced disease. Although an association with human papillomavirus (HPV) has been established, little is known about the molecular characterization of ASCC. A comprehensive genomic analysis of ASCC was undertaken to identify novel genomic alterations (GAs) that will inform therapeutic choices for patients with advanced disease.

PATIENTS AND METHODS

Hybrid-capture-based next-generation sequencing of exons from 236 cancer-related genes and intronic regions from 19 genes commonly rearranged in cancer was performed on 70 patients with ASCC. HPV status was assessed by aligning tumor sequencing reads to HPV viral genomes. GAs were identified using an established algorithm and correlated with HPV status.

RESULTS

Sixty-one samples (87%) were HPV-positive. A mean of 3.5 GAs per sample was identified. Recurrent alterations in phosphoinositol-3-kinase pathway (PI3K/AKT/mTOR) genes including amplifications and homozygous deletions were present in 63% of cases. Clinically relevant GAs in genes involved in DNA repair, chromatin remodeling, or receptor tyrosine kinase signaling were observed in 30% of cases. Loss-of-function mutations in TP53 and CDKN2A were significantly enhanced in HPV-negative cases (P < 0.0001).

CONCLUSIONS

This is the first comprehensive genomic analysis of ASCC, and the results suggest new therapeutic approaches. Differing genomic profiles between HPV-associated and HPV-negative ASCC warrants further investigation and may require novel therapeutic and preventive strategies.