Abstract PS11-13: Multidimensional molecular profiling of repeated metastatic TNBC biopsies in the intensive trial of omics <ITOMIC> safely guides treatment decisions

Background Metastatic triple negative breast cancer (mTNBC) is an inherently diverse disease and while molecular classification of mTNBC has assisted in treatment decisions, if based on only an initial biopsy, it does not take into account the evolution of metastatic cancer. Characterization of emerging metastases is needed to reveal both new resistance or sensitivity to available therapeutics. The goal of “Intensive Trial of OMics in Cancer (ITOMIC) - Intensive Longitudinal Monitoring in Subjects With Triple-Negative Breast Cancer” (NCT01957514) - was to determine the feasibility of longitudinal collection of patient biopsies that would be subjected to molecular analysis to provide actionable, relevant and timely information to guide treatment decisions.Methods Multiple biopsies were collected longitudinally, including pre- and post-treatment, from 29 mTNBC patients enrolled in the ITOMIC study and subjected to multi-dimensional molecular profiling including WES, WGS, cancer gene panel sequencing, RNA-seq, and proteomics and/or IHC for tumor biomarkers. This information was used to guide iterative, patient- and tumor- individualized treatment recommendations made by a multi-institutional ITOMIC Tumor Board (ITB) and conveyed to each subject’s oncologist.Results Longitudinal biopsy collection was found to be safe. Molecular profiling revealed that 2 of an original 31 enrolled subjects likely had lung cancer rather than mTNBC, supporting the merit of repeated tissue analysis. While the other 29 subjects had all been given a diagnosis of mTNBC before entering the trial, estrogen receptor, progesterone receptor, and/or HER2 were found to be over-expressed in at least one sample for 12 subjects; appearance of receptor positivity suggests targeted therapy may be effective. Tumor evolution in response to the first on-study treatment for most subjects (cisplatin) was revealed by copy number alterations, changes in single nucleotide variants, and insertions/deletions in pre-/post-treatment biopsies. Over the course of the study, the ITB convened 54 times and 39 of 182 recommended treatments were evaluated and accessed through either an existing clinical trial, a single patient IND, approved off label or label indication. While not all ITB treatment recommendations were followed, 24 subjects did receive at least one ITB-recommended drug, frequently as part of a clinical trial. Currently, for 27 subjects (2 withdrew) median survival is ~31 months. There are 4 surviving patients in treatment with a remarkable median survival of >51 months.Conclusion Collection and molecular analysis of multiple biopsies during the course of patient’s disease, shown here to be safe and feasible, provides information vital to appropriate treatment choice and reveals new targets for and resistance to therapy in metastatic TNBC.

Citation Format: Kimberly A Burton, Eric Q Konnick, Sibel Blau, Michael O Dorschner, Julie Gralow, Rahul Parulkar, Elisabeth Mahen, Patricia Spilman, Stephanie Parker, Francis M Senecal, Colin Pritchard, Christopher Szeto, Jing Zhu, Vijayakrishna K Gadi, Stephen C Benz, Shahrooz Rabizadeh, Patrick Soon-Shiong, Carl Anthony Blau. Multidimensional molecular profiling of repeated metastatic TNBC biopsies in the intensive trial of omics <ITOMIC> safely guides treatment decisions [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS11-13.

Association of Clonal Hematopoiesis in DNA Repair Genes With Prostate Cancer Plasma Cell-free DNA Testing Interference

Question

How often are cell-free DNA (cfDNA) studies in prostate cancer confounded by clonal hematopoiesis (CHIP) variants in genes used for poly(ADP) ribose polymerase inhibitor (PARPi) eligibility?

Findings

In this case series study of 69 men with advanced prostate cancer, 7 (10%) had CHIP variants in genes used for US Food and Drug Administration-approved indications of PARPi treatment, most frequently in ATM.

Meaning

Men with prostate cancer are at high risk of being misdiagnosed as being eligible for PARPi therapy using current cfDNA tests; assays should use a whole-blood control sample to distinguish CHIP variants from prostate cancer.

Importance

Cell-free DNA (cfDNA) testing is increasingly used in the treatment of patients with advanced prostate cancer. Clonal hematopoiesis of indeterminate potential (CHIP) can interfere with cfDNA testing and cause incorrect interpretation of results. There is an urgent need to better understand this problem following recent US Food and Drug Administration approval of poly(ADP) ribose polymerase inhibitors (PARPi) for metastatic prostate cancer based on variants in DNA repair genes that can be affected by CHIP.

Objective

To determine the prevalence of clinically relevant CHIP interference in prostate cancer cfDNA testing.

Design, Setting, and Participants

We report a case series of 69 patients with advanced prostate cancer (metastatic disease or with rising PSA following localized therapy) who had cfDNA variant testing with a large panel cancer next generation sequencing assay (UW-OncoPlexCT). To determine the source of variants in plasma, we tested paired cfDNA and whole blood control samples. The study was carried out in an academic medical center system reference laboratory.

Main Outcomes and Measures

Prevalence and gene spectrum of CHIP interference in patients with prostate cancer undergoing cfDNA testing.

Results

We detected CHIP variants at 2% or more variant fraction in cfDNA from 13 of 69 men with prostate cancer (19%; 95% CI, 10%-30%). Seven men (10%; 95% CI, 4%-20%) had CHIP variants in DNA repair genes used to determine PARPi candidacy, including ATM (n = 5), BRCA2 (n = 1), and CHEK2 (n = 1). Overall, CHIP variants accounted for almost half of the somatic DNA repair gene variants detected. Participant CHIP variants were exponentially correlated with older age (R² = 0.82). CHIP interference variants could be distinguished from prostate cancer variants using a paired whole-blood control.

Conclusions and Relevance

In this case series, approximately 10% of men with advanced prostate cancer had CHIP interference in plasma cfDNA in DNA repair genes that are used for eligibility of PARPi therapy, most frequently in ATM. Clinical cfDNA testing should include a paired whole-blood control to exclude CHIP variants and avoid misdiagnosis.

Comparable specimen collection from both ends of at-home mid-turbinate swabs

Unsupervised upper respiratory specimen collection is a key factor in the ability to massively scale SARS-CoV-2 testing. But there is concern that unsupervised specimen collection may produce inferior samples. Across two studies that included unsupervised at-home mid-turbinate specimen collection, ~1% of participants used the wrong end of the swab. We found that molecular detection of respiratory pathogens and a human biomarker were comparable between specimens collected from the handle of the swab and those collected correctly. Older participants were more likely to use the swab backwards. Our results suggest that errors made during home-collection of nasal specimens do not preclude molecular detection of pathogens and specialized swabs may be an unnecessary luxury during a pandemic.

Complexities of Next-Generation Sequencing in Solid Tumors: Case Studies

With the promise and potential of clinical next-generation sequencing for tumor and germline testing to impact treatment and outcomes of patients with cancer, there are also risks of oversimplification, misinterpretation, and missed opportunities. These issues risk limiting clinical benefit and, at worst, perpetuating false conclusions that could lead to inappropriate treatment selection, avoidable toxicity, and harm to patients. This report presents 5 case studies illustrating challenges and opportunities in clinical next-generation sequencing interpretation and clinical application in solid tumor oncologic care. First is a case that dissects the origin of an ATM mutation as originating from a hematopoietic clone rather than the tumor. Second is a case illustrating the potential for tumor sequencing to suggest germline variants associated with a hereditary cancer syndrome. Third are 2 cases showing the potential for variant reclassification of a germline variant of uncertain significance when considered alongside family history and tumor sequencing results. Finally, we describe a case illustrating challenges with using microsatellite instability for predicting tumor response to immune checkpoint inhibitors. The common theme of the case studies is the importance of examining clinical context alongside expert review and interpretation, which together highlight an expanding role for contextual examination and multidisciplinary expert review through molecular tumor boards.

The regulatory landscape of precision oncology laboratory medicine in the United States - Perspective on the past 5 years and considerations for future regulation

The regulatory landscape for precision oncology in the United States is complicated, with multiple governmental regulatory agencies with different scopes of jurisdiction. Several regulatory proposals have been introduced since the Food and Drug Administration released a draft guidance to regulate laboratory-developed tests in 2014. Key aspects of the most recent proposals and discussion of central arguments related to the regulation of precision oncology laboratory tests provides insight to stakeholders for future discussions related to regulation of laboratory tests.

Validation and implementation of a modular targeted capture assay for the detection of clinically significant molecular oncology alterations

OBJECTIVES

The rapid discovery of clinically significant genetic variants has translated to next-generation sequencing assays becoming out-of-date by the time they are designed, validated, and implemented. UW-OncoPlex addresses this through the adoption of a modular panel capable of redesign as significant alterations are identified. We describe the validation of OncoPlex version 6 (OPXv6) for the detection of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), structural variants (SVs), microsatellite instability (MSI), and tumor mutational burden (TMB) in a panel of 340 genes.

DESIGN

One hundred twelve samples with diverse diagnoses were comprised of formalin-fixed-paraffin-embedded tissue, fresh-frozen tissue, plasma, peripheral blood, bone marrow, saliva, and cell-line DNA. Libraries were prepared from genomic and cell-free DNA, hybridized to a custom panel of xGen Lockdown probes, and sequenced on Illumina platforms. Sequences were processed through a custom bioinformatics pipeline, and variant calls were compared to prior orthogonal clinical results.

RESULTS

Accuracy was 99% for SNVs ≥5% allele frequency, 98% for indels, 97% for SVs, 99% for CNVs, 100% for MSI, and 100% for TMB (compared to previous OncoPlex versions). Library preparation turnaround time decreased by 40%, and sequencing quality improved with a 2.5-fold increase in average sequencing coverage and 4-fold increase in percent on-target.

CONCLUSIONS

OPXv6 demonstrates improvements over prior UW-OncoPlex versions including reduced capture cost, improved sequencing quality, and decreased time to results. The modular capture probe design also provides a nimble laboratory response in addressing the expansions necessary to meet the needs of the continuously evolving field of molecular oncology.

Increased Frequency of Heterozygous Alpha-1-Antitrypsin Deficiency in Liver Explants From Nonalcoholic Steatohepatitis Patients

Cirrhotic explanted livers occasionally have unexpected periodic acid-Schiff-diastase (PASD)-positive globules within the hepatocyte cytoplasm. It is often unclear whether this finding is a nonspecific consequence of cirrhosis or is indicative of an underlying alpha-1-antitrypsin deficiency (A1ATD) contributing to the cirrhosis. In this study, explanted livers were retrospectively evaluated for histopathology (including PASD status with confirmatory alpha-1-antitrypsin [A1AT] immunohistochemistry [IHC]), and chart review provided etiology of liver failure and general clinical parameters. Real-time polymerase chain reaction was used to detect A1AT genotype (SERPINA1 S and Z alleles) by melting curve analysis on liver explant tissue from selected cases. Of 196 explanted livers, 21 (11%) had PASD+ globules, which were significantly enriched in patients with a clinical diagnosis of nonalcoholic steatohepatitis (NASH; 47%) compared with other causes (P < 0.001). IHC confirmed all PASD+ globules were A1AT+, with 20 of 21 cases demonstrating diffuse A1AT staining. In an expanded NASH cohort, 42% (14/33) of explants had PASD+ globules, 92% of which were homozygous (n = 1) or heterozygous (n = 11) for the SERPINA1 Z allele, corresponding to nearly 40% of all NASH patients. Overall, the Z allele was present in 10% of all tested liver explants, with 85% of PASD+ cases genotyping homozygous (n = 2) or heterozygous (n = 20), which is far in excess of the estimated 2% in the general population. These results indicate PASD+ A1AT globules (with confirmatory genotyping showing at least 1 Z allele) are commonly observed in NASH, suggesting a synergistic relationship toward liver fibrosis. In addition, the high frequency of SERPINA1 Z alleles in liver transplantation patients supports the utility of pretransplant genotyping.

Malignant Intrarenal/Renal Pelvis Paraganglioma with Co-Occurring SDHB and ATRX Mutations

Paragangliomas are rare neuroendocrine tumors which originate from embryonic neural crest cells. These tumors may arise from parasympathetic or sympathetic paraganglia, may secrete catecholamines, and can occur in varied anatomic locations, with some locations being less common than others. Hereditary paraganglioma-pheochromocytoma (PGL/PCC) syndromes are characterized by paragangliomas and pheochromocytomas and have been associated with germline heterozygous mutations in MAX, SDHA, SDHAF2, SDHB, SDHC, SDHD, or TMEM127. Herein, we report a case of a middle-aged male who was diagnosed with an intrarenal/renal pelvis paraganglioma after presenting in hypertensive crisis with palpitations, headache, and diaphoresis. He was later found to have extensive metastatic disease, as well as genetic testing that showed biallelic inactivation of SDHB and a co-occurring somatic ATRX mutation. Respectively, these germline and somatic mutations have been associated with increased risk of metastatic spread and clinical aggressiveness. Despite multiple surgical resections and various treatment modalities, the patient eventually elected for palliative care measures and died of disease. Together, the findings seen in this patient are unique and serve as an appropriate catalyst for discussing the unusual locations, interesting genetic profiles, and metastatic risk factors that may be associated with paragangliomas.

Reprogramming identifies functionally distinct stages of clonal evolution in myelodysplastic syndromes

Myeloid neoplasms, including myelodysplastic syndromes (MDS), are genetically heterogeneous disorders driven by clonal acquisition of somatic mutations in hematopoietic stem and progenitor cells (HPCs). The order of premalignant mutations and their impact on HPC self-renewal and differentiation remain poorly understood. We show that episomal reprogramming of MDS patient samples generates induced pluripotent stem cells from single premalignant cells with a partial complement of mutations, directly informing the temporal order of mutations in the individual patient. Reprogramming preferentially captured early subclones with fewer mutations, which were rare among single patient cells. To evaluate the functional impact of clonal evolution in individual patients, we differentiated isogenic MDS induced pluripotent stem cells harboring up to 4 successive clonal abnormalities recapitulating a progressive decrease in hematopoietic differentiation potential. SF3B1, in concert with epigenetic mutations, perturbed mitochondrial function leading to accumulation of damaged mitochondria during disease progression, resulting in apoptosis and ineffective erythropoiesis. Reprogramming also informed the order of premalignant mutations in patients with complex karyotype and identified 5q deletion as an early cytogenetic anomaly. The loss of chromosome 5q cooperated with TP53 mutations to perturb genome stability, promoting acquisition of structural and karyotypic abnormalities. Reprogramming thus enables molecular and functional interrogation of preleukemic clonal evolution, identifying mitochondrial function and chromosome stability as key pathways affected by acquisition of somatic mutations in MDS.

Clinical determinants for successful circulating tumor DNA analysis in prostate cancer

BACKGROUND

Plasma-based cell-free DNA is an attractive biospecimen for assessing somatic mutations due to minimally-invasive real-time sampling. However, next generation sequencing (NGS) of cell-free DNA (cfDNA) may not be appropriate for all patients with advanced prostate cancer (PC).

METHODS

Blood was obtained from advanced PC patients for plasma-based sequencing. UW-OncoPlex, a ∼2 Mb multi-gene NGS panel performed in the CLIA/CAP environment, was optimized for detecting cfDNA mutations. Tumor tissue and germline samples were sequenced for comparative analyses. Multivariate logistic regression was performed to determine the clinical characteristic associated with the successful detection of somatic cfDNA alterations (ie detection of at least one clearly somatic PC mutation).

RESULTS

Plasma for cfDNA sequencing was obtained from 93 PC patients along with tumor tissue (N = 67) and germline (N = 93) controls. We included data from 76 patients (72 prostate adenocarcinoma; 4 variant histology PC) in the analysis. Somatic DNA aberrations were detected in 34 cfDNA samples from patients with prostate adenocarcinoma. High PSA level, high tumor volume, and castration-resistance were significantly associated with successful detection of somatic cfDNA alterations. Among samples with somatic mutations detected, the cfDNA assay detected 93/102 (91%) alterations found in tumor tissue, yielding a clustering-corrected sensitivity of 92% (95% confidence interval 88-97%). All germline pathogenic variants present in lymphocyte DNA were also detected in cfDNA (N = 12). Somatic mutations from cfDNA were detected in 30/33 (93%) instances when PSA was >10 ng/mL.

CONCLUSIONS

Disease burden, including a PSA >10 ng/mL, is strongly associated with detecting somatic mutations from cfDNA specimens.

Genomic Characterization of Prostatic Ductal Adenocarcinoma Identifies a High Prevalence of DNA Repair Gene Mutations

PURPOSE

Ductal prostate cancer (dPC) is a rare variant of prostatic adenocarcinoma associated with poor outcomes. Although its histopathologic features are well characterized, the underlying molecular hallmarks of this aggressive subtype are not well described. We sought to provide a comprehensive overview of the spectrum of mutations associated with dPC.

METHODS

Three case series across multiple institutions were assembled. All patients had a diagnosis of dPC, and histopathologic classification was confirmed by an expert genitourinary pathologist. Case series 1 included men who were prospectively enrolled in a tumor sequencing study at the University of Washington (n = 22). Case series 2 and 3 included archival samples from men treated at Johns Hopkins Hospital (n = 21) and University of Calgary (n = 8), respectively. Tumor tissue was sequenced on a targeted next-generation sequencing assay, UW-OncoPlex, according to previously published methods. The frequency of pathogenic/likely pathogenic mutations are reported.

RESULTS

Overall, 25 patients (49%) had at least one DNA damage repair gene alteration, including seven (14%) with a mismatch repair gene mutation and 16 (31%) with a homologous repair mutation. Germline autosomal dominant mutations were confirmed or suspected in 10 patients (20%). Activating mutations in the PI3K pathway (n = 19; 37%), WNT pathway (n = 16; 31%), and MAPK pathway (n = 8; 16%) were common.

CONCLUSION

This study strongly suggests that dPCs are enriched for actionable mutations, with approximately 50% of patients demonstrating DNA damage repair pathway alteration(s). Patients with dPC should be offered next-generation sequencing to guide standard-of-care treatment (eg, immune checkpoint inhibitors) or triaged toward an appropriate clinical trial (eg, poly [ADP-ribose] polymerase inhibitors).

The mutational landscape of recurrent versus nonrecurrent human papillomavirus-related oropharyngeal cancer

BACKGROUND

Human papillomavirus-related (HPV-related) oropharyngeal squamous cell carcinomas (OPSCCs) have an excellent response rate to platinum-based chemoradiotherapy. Genomic differences between primary HPV-related OPSCCs that do or do not recur are unknown. Furthermore, it is unclear if HPV-related OPSCCs that recur share a genomic landscape with HPV-negative head and neck cancers (HNCs).

METHODS

We utilized whole exome sequencing to analyze somatic nucleotide (SNVs) and copy number variants (CNVs) among a unique set of 51 primary HPV-related OPSCCs, including 35 that did not recur and 16 that recurred. We evaluated 12 metachronous recurrent OPSCCs (7 with paired primary OPSCCs) and 33 primary HPV-unrelated oral cavity and OPSCCs.

RESULTS

KMT2D was the most frequently mutated gene among primary HPV-related OPSCCs (n = 51; 14%) and among metachronous recurrent OPSCCs (n = 12; 42%). Primary HPV-related OPSCCs that recurred shared a genomic landscape with primary HPV-related OPSCCs that did not recur. However, TSC2, BRIP1, NBN, and NFE2L2 mutations occurred in primary OPSCCs that recurred but not in those that did not recur. Moreover, primary HPV-related OPSCCs that recur harbor features of HPV-unrelated HNCs, notably including MAPK, JAK/STAT, and differentiation signaling pathway aberrations. Metachronous recurrent OPSCCs shared a genomic landscape with HPV-unrelated HNCs, including a high frequency of TP53, CASP8, FAT1, HLA-A, AJUBA, and NSD1 genomic alterations.

CONCLUSION

Overall, primary HPV-related OPSCCs that recur share a genomic landscape with nonrecurrent OPSCCs. Metachronous recurrent OPSCCs share genomic features with HPV-negative HNCs. These data aim to guide future deescalation endeavors and functional experiments.

FUNDING

This study is supported by the American Cancer Society (RSG TBG-123653), funding support for RAH (T32DC00018, Research Training in Otolaryngology, University of Washington), funds to EM from Seattle Translational Tumor Research (Fred Hutchinson Cancer Research Center), and center funds from the Fred Hutchinson Cancer Research Center to EM. UD is supported by the Department of Veterans Affairs, Biomedical Laboratory Research and Development (BLR&D), grant IO1-oo23456, and funds from the Pittsburgh Foundation and PNC Foundation.

Using Somatic Mutations from Tumors to Classify Variants in Mismatch Repair Genes

Present guidelines for classification of constitutional variants do not incorporate inferences from mutations seen in tumors, even when these are associated with a specific molecular phenotype. When somatic mutations and constitutional mutations lead to the same molecular phenotype, as for the mismatch repair genes, information from somatic mutations may enable interpretation of previously unclassified variants. To test this idea, we first estimated likelihoods that somatic variants in MLH1, MSH2, MSH6, and PMS2 drive microsatellite instability and characteristic IHC staining patterns by calculating likelihoods of high versus low normalized variant read fractions of 153 mutations known to be pathogenic versus those of 760 intronic passenger mutations from 174 paired tumor-normal samples. Mutations that explained the tumor mismatch repair phenotype had likelihood ratio for high variant read fraction of 1.56 (95% CI 1.42-1.71) at sites with no loss of heterozygosity and of 26.5 (95% CI 13.2-53.0) at sites with loss of heterozygosity. Next, we applied these ratios to 165 missense, synonymous, and splice variants observed in tumors, combining in a Bayesian analysis the likelihood ratio corresponding with the adjusted variant read fraction with pretest probabilities derived from published analyses and public databases. We suggest classifications for 86 of 165 variants: 7 benign, 31 likely benign, 22 likely pathogenic, and 26 pathogenic. These results illustrate that for mismatch repair genes, characterization of tumor mutations permits tumor mutation data to inform constitutional variant classification. We suggest modifications to incorporate molecular phenotype in future variant classification guidelines.

Real-Time PCR to Detect α-1 Antitrypsin S and Z Alleles in Formalin-Fixed Paraffin-Embedded Tissue

BACKGROUND

α-1 Antitrypsin (A1AT) deficiency is an autosomal recessive genetic disease with incomplete penetrance that can cause pulmonary and liver disease. Multiple methods are available to determine A1AT genotype using peripheral blood specimens, but none are validated to detect A1AT alleles in formalin-fixed paraffin-embedded (FFPE) tissue.

METHODS

A real-time PCR assay was validated to detect the SERPINA1 S and Z alleles (NM_000295.4: c.863A>T, p.E288V and c.1096G>A, p.E366K, respectively) in FFPE liver tissue using allele-specific dual hybridization probes and melting curve analysis. Validation experiments were performed on genomic DNA samples (n = 11) with A1AT genotypes previously determined by orthogonal methods.

RESULTS

The S and Z allele assays accurately genotyped all FFPE validation specimens that had a threshold cycle <32. Validation samples produced mean melting temperatures of 55.4 °C (SD = 0.30) for mutant S alleles, 48.6 °C (SD = 0.28) for non-S alleles, 61.2 °C (SD = 0.34) for mutant Z alleles, and 54.7 °C (SD = 0.19) for non-Z alleles. Samples failing to meet quality control parameters were infrequent.

CONCLUSIONS

Poor PCR amplification because of low nucleic acid concentration in small biopsy specimens and time-dependent degradation in specimens stored for extended periods were the most common reasons for assay failure. The ability to determine A1AT genotype from archived surgical pathology specimens can facilitate research on the role of A1AT globules in liver disease.

Microsatellite instability in prostate cancer by PCR or next-generation sequencing

BACKGROUND

Microsatellite instability (MSI) is now being used as a sole biomarker to guide immunotherapy treatment for men with advanced prostate cancer. Yet current molecular diagnostic tests for MSI have not been evaluated for use in prostate cancer.

METHODS

We evaluated two next-generation sequencing (NGS) MSI-detection methods, MSIplus (18 markers) and MSI by Large Panel NGS (> 60 markers), and compared the performance of each NGS method to the most widely used 5-marker MSI-PCR detection system. All methods were evaluated by comparison to targeted whole gene sequencing of DNA mismatch-repair genes, and immunohistochemistry for mismatch repair genes, where available.

RESULTS

In a set of 91 prostate tumors with known mismatch repair status (29-deficient and 62-intact mismatch-repair) MSIplus had a sensitivity of 96.6% (28/29) and a specificity of 100% (62/62), MSI by Large Panel NGS had a sensitivity of 93.1% (27/29) and a specificity of 98.4% (61/62), and MSI-PCR had a sensitivity of 72.4% (21/29) and a specificity of 100% (62/62).

CONCLUSIONS

We found that the widely used 5-marker MSI-PCR panel has inferior sensitivity when applied to prostate cancer and that NGS testing with an expanded panel of markers performs well. In addition, NGS methods offer advantages over MSI-PCR, including no requirement for matched non-tumor tissue and an automated analysis pipeline with quantitative interpretation of MSI-status.

Accurate Pan-Cancer Molecular Diagnosis of Microsatellite Instability by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing

BACKGROUND

Microsatellite instability (MSI) is an emerging actionable phenotype in oncology that informs tumor response to immune checkpoint pathway immunotherapy. However, there remains a need for MSI diagnostics that are low cost, highly accurate, and generalizable across cancer types. We developed a method for targeted high-throughput sequencing of numerous microsatellite loci with pan-cancer informativity for MSI using single-molecule molecular inversion probes (smMIPs).

METHODS

We designed a smMIP panel targeting 111 loci highly informative for MSI across cancers. We developed an analytical framework taking advantage of smMIP-mediated error correction to specifically and sensitively detect instability events without the need for typing matched normal material.

RESULTS

Using synthetic DNA mixtures, smMIPs were sensitive to at least 1% MSI-positive cells and were highly consistent across replicates. The fraction of identified unstable microsatellites discriminated tumors exhibiting MSI from those lacking MSI with high accuracy across colorectal (100% diagnostic sensitivity and specificity), prostate (100% diagnostic sensitivity and specificity), and endometrial cancers (95.8% diagnostic sensitivity and 100% specificity). MSI-PCR, the current standard-of-care molecular diagnostic for MSI, proved equally robust for colorectal tumors but evidenced multiple false-negative results in prostate (81.8% diagnostic sensitivity and 100% specificity) and endometrial (75.0% diagnostic sensitivity and 100% specificity) tumors.

CONCLUSIONS

smMIP capture provides an accurate, diagnostically sensitive, and economical means to diagnose MSI across cancer types without reliance on patient-matched normal material. The assay is readily scalable to large numbers of clinical samples, enables automated and quantitative analysis of microsatellite instability, and is readily standardized across clinical laboratories.

A Phase I Clinical Trial of AZD1775 in Combination with Neoadjuvant Weekly Docetaxel and Cisplatin before Definitive Therapy in Head and Neck Squamous Cell Carcinoma

Purpose: The WEE1 tyrosine kinase regulates G₂-M transition and maintains genomic stability, particularly in p53-deficient tumors which require DNA repair after genotoxic therapy. Thus, a need arises to exploit the role of WEE1 inhibition in head and neck squamous cell carcinoma (HNSCC) mostly driven by tumor-suppressor loss. This completed phase I clinical trial represents the first published clinical experience using the WEE1 inhibitor, AZD1775, with cisplatin and docetaxel.Patients and Methods: We implemented an open-label phase I clinical trial using a 3+3 dose-escalation design for patients with stage III/IVB HNSCC with borderline-resectable or -unresectable disease, but who were candidates for definitive chemoradiation. Escalating AZD1775 was administered orally twice a day over 2.5 days on the first week, then in combination with fixed cisplatin (25 mg/m²) and docetaxel (35 mg/m²) for 3 additional weeks. The primary outcome measure was adverse events to establish MTD. Secondary measures included response rates, pharmacokinetics (PK), pharmacodynamics, and genomic data.Results: The MTD for AZD1775 was established at 150 mg orally twice per day for 2.5 days. RECISTv1.1 responses were seen in 5 of 10 patients; histologic adjustment revealed three additional responders. The only drug-limiting toxicity was grade 3 diarrhea. The PK C8hr target of 240 nmol/L was achieved on day 4 at all three doses tested. Pharmacodynamic analysis revealed a reduction in pY15-Cdk, and increases in γH2AX, CC3, and RPA32/RPA2 were noted in responders versus nonresponders.Conclusions: The triplet combination of AZD1775, cisplatin, and docetaxel is safe and tolerable. Preliminary results show promising antitumor efficacy in advanced HNSCC, meriting further investigation at the recommended phase II dose. Clin Cancer Res; 24(12); 2740-8. ©2018 AACR.

Abstract 2713: The mutational landscape of recurrent and nonrecurrent human papillomavirus-associated head and neck squamous cell carcinoma

Background: Despite the better prognosis for human papillomavirus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) compared to HPV-negative HNSCC, 10% to 25% of HPV-associated cases recur within 3 years of completing therapy. We sought to compare the mutational profiles of primary tumors among recurrent and non-recurrent HPV-associated HNSCC. We hypothesized that the mutational profile of primary tumors from recurrent cases resembles that of HPV-negative HNSCC.

Methods: Sequencing was performed on DNA extracted from the primary tumors of p16-positive recurrent and non-recurrent HNSCC cases utilizing a high-coverage (&gt;500X), CLIA-certified, 262 multiplexed gene sequencing panel (i.e., UW OncoPlex). Primary tumors from 11 recurrent and 13 non-recurrent cases were included in our sample. Mutational differences between the primary tumors of recurrent and non-recurrent tumors were evaluated.

Results: 88% of patients were male with a mean (standard deviation; SD) age of 60.3 (11) years. Among the recurrent cases, 100% arose from the oropharynx. Among the non-recurrent cases, 77% arose from the oropharynx with the remainder originating from the oral cavity, nasal cavity, and larynx. 83% of patients presented with stage III or higher disease, and the median survival time was 21 months and 19 months among the recurrent and non-recurrent cases, respectively. The mean (SD) number of somatic nucleotide variants per tumor among the recurrent cases was 16.4 (12.2) compared to 4.3 (1.5) among non-recurrent cases (p &lt; 0.05). The ratio of nonsynonymous to synonymous variants among primary tumors of recurrent cases was 2 vs 5 among the non-recurrent cases (p = 0.224). Among primary tumors of recurrent cases, 17% of variants included indels, splice site, and nonsense mutations vs 14% of variants among the non-recurrent cases. The mean (SD) number of tumor suppressor mutations per tumor was 1.2 (1.3) among recurrent cases vs 1.0 (1.0) among non-recurrent cases (p = 0.81). Interestingly, the mean (SD) number of mutations in DNA damage response (DDR) genes among the primary tumors of recurrent cases was 2.7 (2.4) compared to 0.7 (1.2) mutations per tumor among non-recurrent cases (p = 0.07).

Conclusion: We observed a greater mutational burden among the primary tumors of recurrent HPV-associated HNSCC compared to non-recurrent HNSCC. Moreover, among the primary tumors of recurrent cases, there were more mutations in DNA damage response genes coupled and relatively fewer deleterious mutations compared to non-recurrent cases. Dysregulation of DDR genes may select for advantageous mutations via genomic instability. Alternatively, gain of function of DDR genes may promote treatment resistance. Future work aims to further characterize mutational differences between the primary tumors of HPV-associated recurrent and non-recurrent HNSCC and evaluate mechanisms promoting treatment resistance.

Citation Format: Richard A. Harbison, Mark Kubik, Eric Q. Konnick, Seok-Geun Lee, Michael Kao, Michael Mason, Thomas Yu, Chang Xu, Daniel Faden, Colin C. Pritchard, Cristina P. Rodriguez, Chu Chen, Justin Guinney, Umamaheswar Duvvuri, Eduardo Mendez. The mutational landscape of recurrent and nonrecurrent human papillomavirus-associated head and neck squamous cell carcinoma [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 2713. doi:10.1158/1538-7445.AM2017-2713

Mismatch repair deficiency may be common in ductal adenocarcinoma of the prostate

Precision oncology entails making treatment decisions based on a tumor's molecular characteristics. For prostate cancer, identifying clinically relevant molecular subgroups is challenging, as molecular profiling is not routine outside of academic centers. Since histologic variants of other cancers correlates with specific genomic alterations, we sought to determine if ductal adenocarcinoma of the prostate (dPC) - a rare and aggressive histopathologic variant - was associated with any recurrent actionable mutations. Tumors from 10 consecutive patients with known dPC were sequenced on a targeted next-generation DNA sequencing panel. The median age at diagnosis was 59 years (range, 40-73). Four (40%) patients had metastases upon presentation. Archival tissue from formalin-fixed paraffin-embedded prostate tissue samples from nine patients and a biopsy of a metastasis from one patient with castration-resistant prostate cancer were available for analysis. Nine of 10 samples had sufficient material for tumor sequencing. Four (40%) patients' tumors had a mismatch repair (MMR) gene alteration (N = 2, MSH2; N = 1, MSH6; and N = 1, MLH1), of which 3 (75%) had evidence of hypermutation. Sections of the primary carcinomas of three additional patients with known MMR gene alterations/hypermutation were histologically evaluated; two of these tumors had dPC. MMR mutations associated with hypermutation were common in our cohort of dPC patients. Since hypermutation may predict for response to immune checkpoint blockade, the presence of dPC may be a rapid means to enrich populations for further screening. Given our small sample size, these findings require replication.

Germline, hematopoietic, mosaic, and somatic variation: interplay between inherited and acquired genetic alterations in disease assessment

Advances in genetic analysis have revealed new complexities in the interpretation of genetic variants. Correct assessment of a genetic variant relies on the clinical context and knowledge of the underlying biology. We outline four scenarios encountered in genetic testing where careful consideration of the origin of genetic variation is required for variant interpretation.

Preventing Genetic Testing Order Errors With a Laboratory Utilization Management Program

OBJECTIVES

To characterize error rates for genetic test orders between medical specialties and in different settings by examining detailed order information.

METHODS

We performed a retrospective analysis of a detailed utilization management case database, comprising 2.5 years of data and almost 1,400 genetic test orders. After review by multiple reviewers, we categorized order modifications and cancellations, quantified rates of positive results and order errors, and compared genetics with nongenetics providers and inpatient with outpatient orders.

RESULTS

High cost or problems with preauthorization were the most common reasons for modification and cancellation, respectively. The cancellation rate for nongenetics providers was three times the rate for geneticists, but abnormal result rates were similar between the two groups. The approval rate for inpatient orders was not significantly lower than outpatient orders, and abnormal result rates were similar for these two groups as well. Order error rates were approximately 8% among tests recommended by genetics providers in the inpatient setting, and tests ordered or recommended by nongeneticists had error rates near 5% in both inpatient and outpatient settings.

CONCLUSIONS

Clinicians without specialty training in genetics make genetic test order errors at a significantly higher rate than geneticists. A laboratory utilization management program prevents these order errors from becoming diagnostic errors and reaching the patient.