Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma.

Mutational processes giving rise to lung adenocarcinomas (LADCs) in non-smokers remain elusive. We analyzed 138 LADC whole genomes, including 83 cases with minimal contribution of smoking-associated mutational signature. Genomic rearrangements were not correlated with smoking-associated mutations and frequently served as driver events of smoking-signature-low LADCs. Complex genomic rearrangements, including chromothripsis and chromoplexy, generated 74% of known fusion oncogenes, including EML4-ALK, CD74-ROS1, and KIF5B-RET. Unlike other collateral rearrangements, these fusion-oncogene-associated rearrangements were frequently copy-number-balanced, representing a genomic signature of early oncogenesis. Analysis of mutation timing revealed that fusions and point mutations of canonical oncogenes were often acquired in the early decades of life. During a long latency, cancer-related genes were disrupted or amplified by complex rearrangements. The genomic landscape was different between subgroups-EGFR-mutant LADCs had frequent whole-genome duplications with p53 mutations, whereas fusion-oncogene-driven LADCs had frequent SETD2 mutations. Our study highlights LADC oncogenesis driven by endogenous mutational processes.

ERα-associated translocations underlie oncogene amplifications in breast cancer.

Focal copy-number amplification is an oncogenic event. Although recent studies have revealed the complex structure1-3 and the evolutionary trajectories4 of oncogene amplicons, their origin remains poorly understood. Here we show that focal amplifications in breast cancer frequently derive from a mechanism-which we term translocation-bridge amplification-involving inter-chromosomal translocations that lead to dicentric chromosome bridge formation and breakage. In 780 breast cancer genomes, we observe that focal amplifications are frequently connected to each other by inter-chromosomal translocations at their boundaries. Subsequent analysis indicates the following model: the oncogene neighbourhood is translocated in G1 creating a dicentric chromosome, the dicentric chromosome is replicated, and as dicentric sister chromosomes segregate during mitosis, a chromosome bridge is formed and then broken, with fragments often being circularized in extrachromosomal DNAs. This model explains the amplifications of key oncogenes, including ERBB2 and CCND1. Recurrent amplification boundaries and rearrangement hotspots correlate with oestrogen receptor binding in breast cancer cells. Experimentally, oestrogen treatment induces DNA double-strand breaks in the oestrogen receptor target regions that are repaired by translocations, suggesting a role of oestrogen in generating the initial translocations. A pan-cancer analysis reveals tissue-specific biases in mechanisms initiating focal amplifications, with the breakage-fusion-bridge cycle prevalent in some and the translocation-bridge amplification in others, probably owing to the different timing of DNA break repair. Our results identify a common mode of oncogene amplification and propose oestrogen as its mechanistic origin in breast cancer.

Therapy-induced APOBEC3A drives evolution of persistent cancer cells.

Acquired drug resistance to anticancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified1-4, the underlying molecular mechanisms shaping tumour evolution during treatment are incompletely understood. Genomic profiling of patient tumours has implicated apolipoprotein B messenger RNA editing catalytic polypeptide-like (APOBEC) cytidine deaminases in tumour evolution; however, their role during therapy and the development of acquired drug resistance is undefined. Here we report that lung cancer targeted therapies commonly used in the clinic can induce cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Therapy-induced A3A promotes the formation of double-strand DNA breaks, increasing genomic instability in drug-tolerant persisters. Deletion of A3A reduces APOBEC mutations and structural variations in persister cells and delays the development of drug resistance. APOBEC mutational signatures are enriched in tumours from patients with lung cancer who progressed after extended responses to targeted therapies. This study shows that induction of A3A in response to targeted therapies drives evolution of drug-tolerant persister cells, suggesting that suppression of A3A expression or activity may represent a potential therapeutic strategy in the prevention or delay of acquired resistance to lung cancer targeted therapy.

Computational analysis of cancer genome sequencing data.

Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.

Orphan nuclear receptor COUP-TFII enhances myofibroblast glycolysis leading to kidney fibrosis.

Recent studies demonstrate that metabolic disturbance, such as augmented glycolysis, contributes to fibrosis. The molecular regulation of this metabolic perturbation in fibrosis, however, has been elusive. COUP-TFII (also known as NR2F2) is an important regulator of glucose and lipid metabolism. Its contribution to organ fibrosis is undefined. Here, we found increased COUP-TFII expression in myofibroblasts in human fibrotic kidneys, lungs, kidney organoids, and mouse kidneys after injury. Genetic ablation of COUP-TFII in mice resulted in attenuation of injury-induced kidney fibrosis. A non-biased proteomic study revealed the suppression of fatty acid oxidation and the enhancement of glycolysis pathways in COUP-TFII overexpressing fibroblasts. Overexpression of COUP-TFII in fibroblasts also induced production of alpha-smooth muscle actin (αSMA) and collagen 1. Knockout of COUP-TFII decreased glycolysis and collagen 1 levels in fibroblasts. Chip-qPCR revealed the binding of COUP-TFII on the promoter of PGC1α. Overexpression of COUP-TFII reduced the cellular level of PGC1α. Targeting COUP-TFII serves as a novel treatment approach for mitigating fibrosis in chronic kidney disease and potentially fibrosis in other organs.

Chronic rhinosinusitis as a risk factor for intracranial and extracranial complications after endoscopic transsphenoidal surgery.

PURPOSE: To elucidate whether chronic rhinosinusitis (CRS), usually an inflammatory-mediated rather than infectious process, is a risk factor for extracranial and intracranial complications after elective endoscopic transsphenoidal surgery (ETSS). MATERIALS AND METHODS: A single-center retrospective cohort study of consecutive patients who underwent ETSS between January 2015 and July 2019 was performed, which included chart review and computed tomography assessment. CRS was defined by symptomatology and concurrent endoscopic or radiographic findings. RESULTS: Of 292 subjects, 11% (n = 33) met criteria for CRS. Median difference in Lund-Mackay scores between the CRS and non-CRS groups was 3.0 (95% CI 2.0-4.0). Complications included acute rhinosinusitis requiring antibiotics (23%, 68/292), epistaxis (10%, 28/292), meningitis (1%, 3/292), cerebrospinal fluid (CSF) leak (7%, 20/292), revision sinonasal procedures (10%, 28/292), and frequent in-office debridement (13%, 39/292). CRS was strongly associated with postoperative acute rhinosinusitis (aRR 1.85, 95% CI 1.18-2.90) and frequent debridement (aRR 1.96, 95% CI 1.00-3.83). Conversely, CRS was not associated with epistaxis (aRR 1.52, 95% CI 0.62-3.72), postoperative CSF leak (aRR 0.91, 95% CI 0.24-3.44), or additional sinonasal procedures (aRR 0.70, 95% CI 0.21-2.29). The rate of meningitis was not significantly higher in the CRS cohort (difference 2.2%, 95% CI -1.0% to 14.5%). CONCLUSIONS: CRS was a strong risk factor for acute rhinosinusitis and need for frequent in-office debridement after ETSS. It was not associated with other postoperative complications including epistaxis, CSF leak, or revision sinonasal procedures. CRS patients had a slightly higher rate of meningitis, which is likely not clinically meaningful.

Natural trajectory of recovery of COVID-19 associated olfactory loss.

IMPORTANCE: Prevalence of post-viral olfactory loss has increased dramatically due to the frequency and severity of olfactory dysfunction associated with infection by the SARS-CoV-2 virus. OBJECTIVE: To determine the trajectory of COVID-19 olfactory loss over a six-month period. A key secondary objective is to assess predictive factors associated with the recovery of olfaction. DESIGN: Longitudinal repeated-measures study that enrolled from May 5, 2020 to February 2, 2021, with the last date of data collection on June 15, 2021. SETTING: Barnes-Jewish HealthCare/Washington University School of Medicine facilities (Saint Louis, Missouri, USA). PARTICIPANTS: Individuals who tested positive for SARS-CoV-2 by real-time polymerase chain reaction on nasopharyngeal swab and indicated olfactory loss on COVID-19 screening questionnaire. Individuals were excluded if they had previously diagnosed history of olfactory loss, neurodegenerative disorders, <18 years of age, admitted to hospital service, unable to read, write, and understand English, or lacked computer or internet access. INTERVENTIONS/EXPOSURES: Watch and wait for spontaneous recovery. MAIN OUTCOME(S) AND MEASURE(S): Participants completed olfactory assessments every 30 days for six months. Each assessment consisted of the University of Pennsylvania Smell Identification Test (UPSIT), an objective "scratch-and-sniff" test, and Clinical Global Impressions (CGI), a subjective Likert rating scale. RESULTS: The mean age was 41 years old (SD = 16). 39 (80 %) were female and 42 (86 %) white. At baseline assessment of objective olfaction, 18 (36 %) participants had anosmia or severe hyposmia. Subjective, complete recovery at six months was 81 % (95 % CI 74 % to 88 %). Likelihood of recovery was associated with age <50 years (aHR = 8.1 (95 % CI 1.1 to 64.1)) and mild olfactory loss at baseline (UPSIT = 30-33 for males and 31-34 for females) (aHR 6.2 (95 % CI 1.2 to 33.0)). CONCLUSIONS AND RELEVANCE: The trajectory of olfactory recovery among adults with COVID-19 olfactory loss illustrated rapid recovery within 2-3 weeks of infection, and by six months 81 % had recovered based on self-report. Age <50 years old and mild severity of olfactory loss at baseline were associated with increased likelihood of recovery of olfaction. These findings can be used to inform shared decision-making with patients.

Smell Changes and Efficacy of Nasal Theophylline (SCENT) irrigation: A randomized controlled trial for treatment of post-viral olfactory dysfunction.

OBJECTIVE: To evaluate the efficacy and safety of intranasal theophylline saline irrigation on olfactory recovery in patients with post-viral olfactory dysfunction (PVOD). METHODS: Between May 2019 and April 2020, we conducted a double-blinded, placebo-controlled randomized clinical trial of adults with 6-36 months of PVOD. Patients were randomized to nasal theophylline saline irrigation or placebo saline irrigation twice a day for 6 weeks. The primary outcome was the Global Rating of Smell Change. Secondary outcomes were changes in the University of Pennsylvania Smell Identification Test (UPSIT) and Questionnaire of Olfactory Disorders-Negative Statements (QOD-NS). RESULTS: Twenty-two patients (n = 12, theophylline; n = 10, placebo) completed the study. Slightly more patients in the theophylline group (33%) reported improved smell compared to the placebo group (30%, difference 3.3%, 95% CI -35.6% to 42.3%). The median differences in pre- and post-treatment UPSIT and QOD-NS change between the two groups were 1 (95% CI -3 to 5) and -10 (95% CI -15 to -4), respectively in favor of theophylline. Three patients receiving theophylline and 2 receiving placebo had clinically meaningful improvements on the UPSIT (difference 5%, 95% CI -30% to 40%). There were no adverse events, and serum theophylline levels were undetectable in 10/10 patients. CONCLUSIONS: While safe, there were no clinically meaningful differences in olfactory change between the two groups except for olfaction-related quality of life, which was better with theophylline. The imprecise estimates suggest future trials will need substantially larger sample sizes or treatment modifications, such as increasing the theophylline dose, to observe larger treatment effects.

A fusion of CD63-BCAR4 identified in lung adenocarcinoma promotes tumorigenicity and metastasis.

BACKGROUND: Recently, fusion variants of the breast cancer anti-oestrogen-resistance 4 (BCAR4) gene were recurrently discovered in lung adenocarcinoma from the genome-wide studies. However, the functional characterisation of BCAR4 fusion has not been investigated. METHODS: Based on the analysis of RNA-sequencing data, we identified a fusion transcript of CD63-BCAR4 in a Korean patient with lung adenocarcinoma who did not harbour any known activating mutations in EGFR and KRAS genes. To investigate the oncogenic effect of CD63-BCAR4, in vitro and in vivo animal experiments were performed. RESULTS: In vitro experiments showed strongly enhanced cell migration and proliferation by the exogenous expression of CD63-BCAR4 protein in bronchial epithelial cells. Cell migration was notably reduced after knockdown of BCAR4 fusion by small-interfering RNA. The tumorigenic and metastatic capability of the CD63-BCAR4 fusion was confirmed by using the mouse xenograft model. Fusion-overexpressed cells result in metastasis to the liver and lung as well as the primary tumours after subcutaneous injection into mice. Cyclin D1, MMP1, Slug and mesenchymal markers were significantly increased after CD63-BCAR4 overexpression in the in vitro and in vivo experiments. CONCLUSIONS: Taken together, our results suggest a newly identified fusion gene, CD63-BCAR4 as a potential novel oncogene in lung adenocarcinoma.

Free vascularized parascapular fat flap for parotidectomy reconstruction.

OBJECTIVE: The contour defect resulting after parotidectomy can be cosmetically unappealing. Multiple reconstructive efforts have been reported to mitigate this problem. We describe a novel technique of vascularized parascapular fat reconstruction based on the circumflex scapular vessels and evaluate its outcomes. METHODS: Consecutive patients who underwent parotidectomy with or without additional resections and vascularized parascapular fat flap reconstruction in 2020 were included. Demographic, morphologic, intraoperative, and postoperative data were assessed. RESULTS: Eight patients (3 female) were included. Median cut-to-close time was 247 (range 209-298) minutes, including tumor ablation. None of the patients had any wound complications, and all except one was discharged on postoperative day 1. Flap monitoring was not performed. None reported any significant donor site morbidity except scar formation. At last follow up, all patients reported satisfactory facial contour. CONCLUSION: Vascularized parascapular fat flap reconstruction of parotidectomy contour defects has satisfactory cosmetic outcomes with minimal morbidity and short hospitalization courses.

The rise of oncology biosimilars: from process to promise.

Biosimilars are biologic products that are highly similar to, and have no clinically meaningful differences from, the approved originator molecule. They are poised to play an increasingly central role in cancer treatment, helping to improve access by driving down costs. Regulatory bodies have set out robust mechanisms for the approval of biosimilars, based on comprehensive and rigorous analytical and nonclinical comparisons with the originator. Product attributes (e.g., post-translational modifications) that are important to the function of the molecule must be similar between biosimilar and originator. This should be followed by a robust clinical development program, assessing pharmacokinetics, pharmacodynamics, efficacy, safety and immunogenicity. Equivalence in one indication might allow extrapolation across all the indications of the originator biologic. The recent approval of several trastuzumab biosimilars provides an example of how this process can work in practice for the benefit of patients, clinicians and payers.

Mirror Image Based Three-Dimensional Virtual Surgical Planning and Three-Dimensional Printing Guide System for the Reconstruction of Wide Maxilla Defect Using the Deep Circumflex Iliac Artery Free Flap.

A patient was diagnosed with squamous cell carcinoma of the maxillary sinus and consequently underwent a unilateral total maxillectomy and reconstruction using an anterolateral thigh (ALT) free flap. Soft tissue transplantation without a bone graft at the large maxillary defect site caused a midfacial collapse, which worsened, especially after radiotherapy. The 3-dimensional positioning of the composite flap for wide maxillary reconstruction is aesthetically important. To achieve ideal symmetry and aesthetics, a mirror image was created using the normal contralateral side. Through computer simulation, the function and symmetry of the virtually reconstructed maxilla was evaluated, and the surgical guide was made using a 3D printing system. Based on the prepared surgical guide, a deep circumflex iliac artery (DCIA) free flap was harvested, and its implementation in the reconstruction ultimately led to satisfactory results. Utilization of mirror image based virtual surgical planning and a 3D printing guide is a significantly effective method for maxilla reconstruction with DCIA flaps.

Endoscopic Flexor Hallucis Longus Tendon Transfer for Reconstruction of the Achilles Tendon Rupture in High-Risk Patients: A Case Series.

The neglected Achilles tendon rupture requires surgical reconstruction for the best functional outcome. According to the current literature, there are many reconstructive options available that demonstrate acceptable functional results in most cases. These procedures require large incisions, leading to potential wound-healing complications. Therefore, these procedures may not be suitable for patients who are at high risk for wound-healing problems. A minimally invasive approach is desirable in this situation to decrease the risk of this potential complication. Endoscopic transfer of the flexor hallucis longus tendon is described in this series as an alternative to reconstruct the Achilles tendon in 2 such high-risk individuals. Both patients had a successful outcome with no wound-healing problems and regained acceptable functional status.

Diagnosing Tongue Base Obstruction in Pierre Robin Sequence Infants: Sleep vs Awake Endoscopy.

OBJECTIVE: To investigate whether awake endoscopy can diagnose base-of-tongue obstruction as reliably as sleep endoscopy in infants with Pierre Robin sequence (PRS). DESIGN: The study was retrospective with the clinicians blinded to patient identity. Endoscopy findings were assessed and measured by the performing pediatric otolaryngologist. SETTING: Tertiary care children's hospital. PATIENTS: All infants with PRS managed between January 2005 and July 2015 were included. There were 141 patients, of which 35 underwent both awake endoscopy (AE) and drug-induced sleep endoscopy (DISE). INTERVENTIONS: Bedside AE and DISE in the operating room. MAIN OUTCOME MEASURES: Presence of moderate or severe base-of-tongue collapse was assessed. Sensitivity, specificity, and positive likelihood ratio of AE findings as well as intertest differences between AE and DISE were calculated. RESULTS: AE had 50.0% sensitivity (95% confidence interval [CI] 27.2%-72.8%) and 86.7% specificity (95% CI 59.5%-98.3%) for detecting base-of-tongue obstruction compared to DISE; false negative rate was 50.0% (n = 10). Positive likelihood ratio was 3.75 (CI 0.96-14.65). Compared to AE, DISE demonstrated significantly more cases of base-of-tongue obstruction ( P = .039). CONCLUSIONS: Bedside AE has low sensitivity for detecting base-of-tongue collapse in infants with PRS. Because of the substantial false negative rate, AE may not be a reliable diagnostic modality for ruling out base-of-tongue obstruction in this susceptible population. DISE may be indicated in high-risk patients to avoid underdiagnosing upper airway obstruction.

Vascular applications of contrast-enhanced ultrasound imaging.

OBJECTIVE: Contrast-enhanced ultrasound (CEUS) imaging is a powerful noninvasive modality offering numerous potential diagnostic and therapeutic applications in vascular medicine. CEUS imaging uses microbubble contrast agents composed of an encapsulating shell surrounding a gaseous core. These microbubbles act as nearly perfect intravascular reflectors of ultrasound energy and may be used to enhance the overall contrast and quality of ultrasound images. The purpose of this narrative review is to survey the current literature regarding CEUS imaging and discuss its diagnostic and therapeutic roles in current vascular and selected nonvascular applications. METHODS: The PubMed, MEDLINE, and Embase databases were searched until July 2016 using the PubMed and Ovid Web-based search engines. The search terms used included contrast-enhanced, microbubble, ultrasound, carotid, aneurysm, and arterial. RESULTS: The diagnostic and therapeutic utility of CEUS imaging has grown exponentially, particularly in the realms of extracranial carotid arterial disease, aortic disease, and peripheral arterial disease. Studies have demonstrated that CEUS imaging is diagnostically superior to conventional ultrasound imaging in identifying vessel irregularities and measuring neovascularization to assess plaque vulnerability and end-muscle perfusion. Groups have begun to use microbubbles as agents in therapeutic applications for targeted drug and gene therapy delivery as well as for the enhancement of sonothrombolysis. CONCLUSIONS: The emerging technology of microbubbles and CEUS imaging holds considerable promise for cardiovascular medicine and cancer therapy given its diagnostic and therapeutic utility. Overall, with proper training and credentialing of technicians, the clinical implications are innumerable as microbubble technology is rapidly bursting onto the scene of cardiovascular medicine.

Role of computational modeling in thoracic aortic pathology: a review.

Thoracic aortic diseases are life-threatening conditions causing significant mortality and morbidity despite advances in diagnostic and surgical treatments. Computational methods combined with imaging techniques provide quantitative information of disease progression, which may improve clinical treatments and therapeutic strategies for clinical practice. Since hemodynamic and wall mechanics play important roles in the natural history and progression of aortic diseases, we reviewed the potential application of computational modeling of the thoracic aorta. We placed emphasis on the clinical relevance of these techniques for the assessment of aortic dissection, thoracic aortic aneurysm, and aortic coarctation. Current clinical guidelines and treatment are also described.

Airway protection and outcomes after staged versus concurrent bilateral neck dissections with transoral base of tongue cancer resection.

OBJECTIVES: To assess airway, safety, and resource utilization outcomes between transoral base of tongue (BOT) surgery with staged versus concurrent bilateral neck dissections (BND). METHODS: A retrospective cohort study of patients with human papilloma virus (HPV)-related BOT cancer who underwent transoral surgery and BND from January 2015 through June 2022 was conducted. Free flap patients were excluded. RESULTS: Of 126 patients (46 [37%] staged and 80 [63%] concurrent BND), there were no significant differences in rates of postoperative intubation, tracheostomy, intensive care admission, operative takebacks, gastrostomy, and 30-day readmission. Total operative time (median difference 1.4 [95% CI 0.9-1.8] hours), length of stay (1.0 [1.0-1.0] day), and time between primary surgery and adjuvant therapy initiation (4.0 [0.0-8.0] days) were lower in the concurrent BND cohort. CONCLUSION: Concurrent BND alongside transoral BOT resection is safe with similar airway outcomes and lower total operative time, length of stay, and time to adjuvant therapy initiation compared to staged BND.

Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns.

Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.

Predicting response to immune checkpoint blockade therapy among mismatch repair-deficient patients using mutational signatures.

Despite the overall efficacy of immune checkpoint blockade (ICB) for mismatch repair deficiency (MMRD) across tumor types, a sizable fraction of patients with MMRD still do not respond to ICB. We performed mutational signature analysis of panel sequencing data (n = 95) from MMRD cases treated with ICB. We discover that T>C-rich single base substitution (SBS) signatures-SBS26 and SBS54 from the COSMIC Mutational Signatures catalog-identify MMRD patients with significantly shorter overall survival. Tumors with a high burden of SBS26 show over-expression and enriched mutations of genes involved in double-strand break repair and other DNA repair pathways. They also display chromosomal instability (CIN), likely related to replication fork instability, leading to copy number losses that trigger immune evasion. SBS54 is associated with transcriptional activity and not with CIN, defining a distinct subtype. Consistently, cancer cell lines with a high burden of SBS26 and SBS54 are sensitive to treatments targeting pathways related to their proposed etiology. Together, our analysis offers an explanation for the heterogeneous responses to ICB among MMRD patients and supports an SBS signature-based predictor as a prognostic biomarker for differential ICB response.

Tracking clonal evolution of drug resistance in ovarian cancer patients by exploiting structural variants in cfDNA.

Drug resistance is the major cause of therapeutic failure in high-grade serous ovarian cancer (HGSOC). Yet, the mechanisms by which tumors evolve to drug resistant states remains largely unknown. To address this, we aimed to exploit clone-specific genomic structural variations by combining scaled single-cell whole genome sequencing with longitudinally collected cell-free DNA (cfDNA), enabling clonal tracking before, during and after treatment. We developed a cfDNA hybrid capture, deep sequencing approach based on leveraging clone-specific structural variants as endogenous barcodes, with orders of magnitude lower error rates than single nucleotide variants in ctDNA (circulating tumor DNA) detection, demonstrated on 19 patients at baseline. We then applied this to monitor and model clonal evolution over several years in ten HGSOC patients treated with systemic therapy from diagnosis through recurrence. We found drug resistance to be polyclonal in most cases, but frequently dominated by a single high-fitness and expanding clone, reducing clonal diversity in the relapsed disease state in most patients. Drug-resistant clones frequently displayed notable genomic features, including high-level amplifications of oncogenes such as CCNE1, RAB25, NOTCH3, and ERBB2. Using a population genetics Wright-Fisher model, we found evolutionary trajectories of these features were consistent with drug-induced positive selection. In select cases, these alterations impacted selection of secondary lines of therapy with positive patient outcomes. For cases with matched single-cell RNA sequencing data, pre-existing and genomically encoded phenotypic states such as upregulation of EMT and VEGF were linked to drug resistance. Together, our findings indicate that drug resistant states in HGSOC pre-exist at diagnosis and lead to dramatic clonal expansions that alter clonal composition at the time of relapse. We suggest that combining tumor single cell sequencing with cfDNA enables clonal tracking in patients and harbors potential for evolution-informed adaptive treatment decisions.