Oliver A. Zill

Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital SequencingTM is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient’s cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.

Impact of Chromatin Structures on DNA Processing for Genomic Analyses

Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP) experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome.

Interspecies variation reveals a conserved repressor of α-specific genes in Saccharomyces yeasts

The mating-type determination circuit in Saccharomyces yeast serves as a classic paradigm for the genetic control of cell type in all eukaryotes. Using comparative genetics, we discovered a central and conserved, yet previously undetected, component of this genetic circuit: active repression of alpha-specific genes in a cells. Upon inactivation of the SUM1 gene in Saccharomyces bayanus, a close relative of Saccharomyces cerevisiae, a cells acquired mating characteristics of alpha cells and displayed autocrine activation of their mating response pathway. Sum1 protein bound to the promoters of alpha-specific genes, repressing their transcription. In contrast to the standard model, alpha1 was important but not required for alpha-specific gene activation and mating of alpha cells in the absence of Sum1. Neither Sum1 protein expression, nor its association with target promoters was mating-type-regulated. Thus, the alpha1/Mcm1 coactivators did not overcome repression by occluding Sum1 binding to DNA. Surprisingly, the mating-type regulatory function of Sum1 was conserved in S. cerevisiae. We suggest that a comprehensive understanding of some genetic pathways may be best attained through the expanded phenotypic space provided by study of those pathways in multiple related organisms.

Abstract 172: Managing metastatic breast cancer via serial monitoring with circulating cell-free tumor DNA next generation sequencing testing: Table 1.

Background: Metastatic breast cancer (MBC) is an incurable disease with complex molecular features including somatic mutations that evolve in relation to genomic instability and selective treatment pressure. Patients with treatment-refractory MBC may benefit from tumor genomic evaluation using next generation sequencing (NGS). Furthermore, analysis of circulating tumor DNA (ctDNA) in patients with advanced disease offers the possibility of non-invasive molecular monitoring. Methods: A patient with MBC was tested at each progression with a ctDNA NGS panel (Guardant360™) that includes all NCCN-recommended somatic genomic variants for solid tumors and sequences complete exons of >50 genes to report single nucleotide variants (SNVs), fusions, amplifications, and indels with high sensitivity and ultra-high specificity (>99.9999%). The patient was diagnosed with invasive breast cancer at age 44 and treated with surgery and hormonal therapy. At age 61, she had axillary adenopathy and liver metastases. Treatment details are in Table 1. Results: ctDNA analysis was performed at the time of metastatic diagnosis and at 5 additional time points over the course of treatment. All samples revealed an ERBB2 exon 19 indel (p.Leu755_Glu757delinsSer), and multiple SNVs and gene amplifications. ERBB2 amplification was seen in 4 of 6 samples. Mutant allele fractions (Table 1) correlated with clinical response to treatment and progression. Conclusions: Analysis of ctDNA in this patient identified an ERBB2 exon 19 indel, which are present in 2-4% of non-small cell lung cancers but 1-2% in breast cancer. Treatment with anti-HER2 monoclonal antibody or dual anti-EGFR/ERBB2 tyrosine kinase inhibitor therapies may show clinical benefit. ctDNA analysis can detect emergence of actionable resistance mutations with the advantage of serial evaluation, allowing capture of inter- and intra-tumor heterogeneity and illustration of molecular progression and response. Citation Format: Laura Austin, Rebecca Nagy, Oliver Zill, Richard B. Lanman, AmirAli Talasaz, Massimo Cristofanilli. Managing metastatic breast cancer via serial monitoring with circulating cell-free tumor DNA next generation sequencing testing. [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 172.

Abstract P6-03-06: Circulating tumor DNA (ctDNA) for detection of molecular residual disease (MoRD) in breast cancer

Background Metastatic breast cancer (BC) is an incurable condition and treated with palliative intent. Standard diagnostic imaging and serum markers have limited sensitivity and are not recommended in clinical practice. Micrometastatic disease in the bone marrow (DTC) and peripheral blood (CTCs) is a recognized prognostic marker but with limited clinical utility. The detection of asymptomatic disease using a sensitive, reproducible and robust blood-based molecular test, or molecular residual disease (MoRD) could potentially represents a tool with the capability to design early therapeutic interventions and improve outcome. Circulating tumor DNA (ctDNA) has the potential to reflect residual tumor burden with higher diagnostic accuracy. We performed a pilot study in patients with high-risk primary BC. Methods This is a prospective study of 30 patients with either locally advanced BC who had completed primary therapy (21 patients) and had no evidence of disease (NED), or were metastatic but treated with curative intent and currently NED or stable (9 patients). Plasma was analyzed for ctDNA either after completing neo-adjuvant therapy (NAT), for recurrence monitoring after surgery, or when there was a clinical suspicion of recurrence. Guardant360™(Guardant Health) is a ctDNA next generation sequencing panel which produces a quantitative measurement of the mutant allele fraction for single nucleotide variants in 54 genes and copy number variants in 3 genes (panel was expanded to 68 genes in Feb 915) using digital sequencing technology. Results Baseline ctDNA analysis was done for 30 patients and 25 (83%) had serial draws for a total of 76 samples. All patients were stage 3-4 except for two stage 2 patients. ctDNA or MoRD was detected in 17 (57%) of patients and in 39 (51%) of the samples. Of the 18 patients treated with NAT, 11 achieved pCR or had minimal residual disease. Of these 11, six had no ctDNA detected after surgery, 3 had mixed results of no ctDNA and low volume ctDNA alterations on different draws, and 2 had persistent mutations on 2 draws. Ten of these 11 patients remain NED with median follow up of 24 months, while the one patient who recurred had persistent low volume missense ctDNA alterations on serial draws, first detected 6 months before clinically evident recurrence. Of the 7 patients with significant residual disease (less than PR) after NAT, 6 had post-surgical ctDNA detected and 5 have recurred at a median of 13 months after surgery. Four of those patients had ctDNA tested prior to recurrence and all had alterations detected in the blood prior to clinical recurrence. Lastly, one HER2+ metastatic patient treated with curative intent with a subsequent negative PET scan and no ctDNA detected after HER2-targeted therapy progressed on CT 2 months later and repeat ctDNA revealed EGFR mutant allele fraction of 51% and ERBB2 amplification. Conclusions The evaluation of ctDNA in high-risk BC patients can identify MoRD and predict for clinical recurrence. Patients with no or low volume ctDNA after primary treatment remained NED longer than those with multiple or high volume alterations. Future studies will validate these early observations and aid in selecting patients for additional systemic therapy with the hope of improving outcome. Citation Format: Austin L, Jaslow R, Fortina P, Nagy R, Zill O, Talasaz A, Cristofanilli M. Circulating tumor DNA (ctDNA) for detection of molecular residual disease (MoRD) in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-06.

Abstract 4343: Comparison of over 10,000 clinical NGS circulating tumor DNA profiles to tissue-derived genomic compendia

Analysis of cell-free circulating tumor DNA (ctDNA) enables non-invasive and serially repeatable genomic profiling of advanced cancer patients, providing options when tissue biopsy is contra-indicated or of insufficient quantity (20-25% of solid tumor patients). Liquid biopsy studies to-date have been limited to modest-sized cohorts and case studies. Here we present genomic profiling results from liquid biopsies of >10,000 advanced cancer patients in whom Guardant360TM (G360) was ordered for clinical care. G360 provides deep-coverage (15,000x average) and highly accurate sequencing of ctDNA across a 70-gene target-capture panel. It detects single nucleotide variants, indels, gene amplifications, and fusions across all NCCN-recommended solid tumor genomic alterations with analytic specificity >99.9999% and analytic sensitivity Of the >10,000 patients (>50 solid cancer types), 80% of patients had at least one somatic alteration detected in ctDNA (median = 3; mean = 4.3 alterations). The most common cancers were lung (32%), gastrointestinal (23%), and breast (14%). Mutational spectra across the 70 analyzed genes were similar to TCGA results with the notable exception of increased prevalence of resistance mutations in the liquid biopsy cohort, likely owing to ongoing/prior therapy. Canonical drivers in NSCLC patients were generally mutually exclusive, although activating EGFR or RAS mutations were observed in 12.5% of patients with fusions (5/40). Colorectal cancers showed both mutual exclusivity among KRAS, NRAS, and BRAF drivers, and convergent evolution toward downstream pathway activation under anti-EGFR therapy, with some samples showing multiple resistance mechanisms. Mutation patterns for the most frequently mutated genes were generally well correlated between ctDNA and published tissue data, including for commonly altered tumor suppressor genes (for TP53: Pearson r = 0.94, Spearman ρ = 0.80). G360 is ordered prior to initial treatment when biopsy tissue is exhausted, unobtainable or under-genotyped, but more often is ordered upon progression to identify evolving resistance mechanisms that may be targetable. Thus, relative frequencies of genomic alterations were expected to differ from published frequencies established in unselected, early-stage, treatment-naive cohorts. Nonetheless, the specific patterns of alterations in ctDNA from this unprecedented liquid biopsy cohort largely recapitulated patterns observed in published tissue sequencing studies. Moreover, ctDNA sequencing clearly and robustly identified convergent evolution of drug resistance occurring under therapy. Citation Format: Oliver A. Zill, Kimberly C. Banks, Coyt Jackson, Stefanie Mortimer, Arthur Baca, Becky Nagy, Richard B. Lanman, Helmy Eltoukhy, AmirAli Talasaz. Comparison of over 10,000 clinical NGS circulating tumor DNA profiles to tissue-derived genomic compendia. [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 4343.

Abstract C80: Development of EGFR C797S mutation in serial liquid biopsy assessments in the clinical practice setting

Introduction: EGFR T790M has emerged as an important biomarker to predict response to 3rd-generation tyrosine kinase inhibitors (TKI). Therapies such as AZD 9291 and Rociletinib demonstrated impressive results in the clinical setting in patients with non-small cell lung cancer (NSCLC). However just as this resistance biomarker (T790M) has developed as a result of treatment with prior EGFR TKIs, EGFR C797S mutation is an acquired resistance mechanism to EGFR T790M inhibitors. This mutation was recently reported for the first time in clinical practice utilizing tissue-biopsy based next generation sequencing (NGS) and in the clinical trial setting in cell-free circulating DNA (cfDNA). Here we report the first case of a patient with NSCLC and emergence of C797S mutation utilizing a cfDNA biopsy-free NGS panel in serial assessments in the clinical setting. Methods: Patients with NSCLC were seen at Levine Cancer Institute and had serial blood draws to assess molecular aberrations in cfDNA over time for comparison with radiographic reviews. Blood samples were sent to Guardant360 for assessment by NGS with a targeted cfDNA NGS panel for 68 genes with complete exon sequencing for all 28 exons in EGFR, and other genes in the panel. Mutant allele fractions (MAF) are reported as% of mutant DNA molecules divided by total molecules (mostly leukocyte DNA-derived) overlapping the same mutated nucleotide base position. Results: A 50 year old African-American female never-smoker with lung adenocarcinoma developed a tissue-biopsy confirmed EGFR T790M mutation after 12 months on erlotinib for EGFR exon 19 deletion. She had significant clinical and radiographic responses to a 3rd generation TKI started May 2014. cfDNA NGS tests in March and April 2015 showed no genomic alterations detectable. In late May 2015, she developed clinical symptoms of cough, dyspnea and fatigue but no definitive radiographic evidence of progression on scans June 2015. She received steroids and antibiotics and continued treatment with the 3rd generation TKI. However, corresponding cfDNA NGS testing revealed emergence of multiple low level mutations and the original deletion in EGFR (EGFR L747_P753 DelInsS, T790M, C797S, and A755G variant of uncertain significance) and TP53 (all Discussion: Complete exon sequencing of cfDNA upon clinical progression uncovered the simultaneous re-emergence of the original driver EGFR exon 19 del and resistance driver mutation EGFR T790M as well as the emergence of the next resistance driver mutation EGFR C797S. The latter mutation interferes with covalent binding of a 3rd generation TKI and under treatment pressure, the tumor appears to have simultaneously evolved two different EGFR C797S clones at low MAFs. cfDNA can be a dynamic measure of tumor response, easily obtained from a patient on any visit with potential for detection before macroscopic/radiographic evidence of progression, as demonstrated in this case with tumor evolution of the EGFR T790M and C797S alterations. Citation Format: Kathryn F. Mileham, Qing Zhang, Carol J. Farhangfar, Daniel E. Haggstrom, Stephen Fairclough, Oliver A. Zill, Daniel R. Carrizosa, Richard B. Lanman, Edward S. Kim. Development of EGFR C797S mutation in serial liquid biopsy assessments in the clinical practice setting. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C80.