Fragmentomic analysis of circulating tumor DNA-targeted cancer panels.

BACKGROUND: The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner. PATIENTS AND METHODS: We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets. RESULTS: In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99. CONCLUSIONS: To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.

Comparison of an Antioxidant Source and Antioxidant Plus BCAA on Athletic Performance and Post Exercise Recovery of Horses.

Antioxidant supplementation decreases postexercise oxidative stress but could also decrease muscle protein synthesis. This study compared the effects of three diets: low antioxidant (control, CON), high antioxidant (AO), and branched-chain amino acid high antioxidant (BCAO) supplementation on postexercise protein synthesis and oxidative stress. We hypothesized that supplementing antioxidants with branched-chain amino acids(BCAA) would reduce oxidative stress without hindering muscle protein synthesis. Eighteen mixed-breed polo horses (11 mares and 7 geldings, with age range between 5 and 18 years, were on CON diet for 30 days (from day -45 until day 0) and then were assigned to one of the treatments after the first lactate threshold test (day 0, LT). LT were also conducted on days 15 and 30 of supplemenation. Oxidative stress was assessed by measuring blood glutathione peroxidase, superoxide dismutase, and malondialdehyde concentrations before 2 and 4 hours after each LT. Muscle biopsies were taken before and 4 hours after each LT and analyzed for gene expression of protein synthesis by RTqPCR. Data were analyzed by ANOVA and compared by least-square means. A reduction in oxidative stress occurred over time (P < .05), from day 0 to day 30. An up-regulation in the abundance of muscle protein mRNA transcripts was found for CD36, CPT1, PDK4, MYF5, and MYOG (P < .05) after all lactate threshold tests, without a treatment effect. A treatment-by-exercise effect was observed for MYOD1 (P = .0041). Transcript abundance was upregulated in AO samples post exercise compared to other treatments. MYF6 exhibited a time-by-treatment effect (P = .045), where abundance increased more in AO samples from day 0 to day 15 and 30 compared to other treatments. Transcript abundance for metabolic and myogenic genes was upregulated in post exercise muscle samples with no advantage from supplementation of antioxidants with branched-chain amino acids compared to antioxidants alone.

The impact of service user's suicide on mental health professionals.

OBJECTIVES: Our principle objective was to examine the personal and professional impact of service user (SU) suicide on mental health professionals (MHPs). We also wished to explore putative demographic or clinical factors relating to SUs or MPHs that could influence the impact of SU suicide for MHPs and explore factors MHPs report as helpful in reducing distress following SU suicide. METHODS: A mixed-method questionnaire with quantitative and thematic analysis was utilised. RESULTS: Quantitative data indicated SU suicide was associated with personal and professional distress with sadness (79.5%), shock (74.5%) and surprise (68.7%) particularly evident with these phenomena lasting less than a year for more than 90% of MHPs. MHPs also reported guilt, reduced self-confidence and a fear of negative publicity. Thematic analysis indicated that some MHPs had greater expertise when addressing SU suicidal ideation and in supporting colleagues after experiencing a SU suicide. Only 17.7% of MHPs were offered formal support following SU suicide. CONCLUSION: SU suicide impacts MHPs personally and professionally in both a positive and negative fashion. A culture and clear pathway of formal support for MHPs to ascertain the most appropriate individualised support dependent on the distress they experience following SU suicide would be optimal.

Brain metastases: An update on the multi-disciplinary approach of clinical management.

IMPORTANCE: Brain metastasis (BM) is the most common malignant intracranial neoplasm in adults with over 100,000 new cases annually in the United States and outnumbering primary brain tumors 10:1. OBSERVATIONS: The incidence of BM in adult cancer patients ranges from 10-40%, and is increasing with improved surveillance, effective systemic therapy, and an aging population. The overall prognosis of cancer patients is largely dependent on the presence or absence of brain metastasis, and therefore, a timely and accurate diagnosis is crucial for improving long-term outcomes, especially in the current era of significantly improved systemic therapy for many common cancers. BM should be suspected in any cancer patient who develops new neurological deficits or behavioral abnormalities. Gadolinium enhanced MRI is the preferred imaging technique and BM must be distinguished from other pathologies. Large, symptomatic lesion(s) in patients with good functional status are best treated with surgery and stereotactic radiosurgery (SRS). Due to neurocognitive side effects and improved overall survival of cancer patients, whole brain radiotherapy (WBRT) is reserved as salvage therapy for patients with multiple lesions or as palliation. Newer approaches including multi-lesion stereotactic surgery, targeted therapy, and immunotherapy are also being investigated to improve outcomes while preserving quality of life. CONCLUSION: With the significant advancements in the systemic treatment for cancer patients, addressing BM effectively is critical for overall survival. In addition to patient's performance status, therapeutic approach should be based on the type of primary tumor and associated molecular profile as well as the size, number, and location of metastatic lesion(s).

Implicit development of gaze strategies support motor improvements during action encoding training of prosthesis use.

BACKGROUND: Action observation training has been suggested to facilitate motor improvements in the lives of persons with neural injury. Previous studies have shown that for persons with upper limb amputation, matched limb training, where prosthesis users emulate each other, has shown promise above mismatched training where a prosthesis user emulates actions of a person with sound limbs (most commonly that of a therapist). OBJECTIVE: The mechanism underlying the matched limb training benefit is unclear. Gaze strategies may reveal unique patterns between matched and mismatched training which could explain improvements in motor function in matched limb training. METHODS: Twenty persons with sound limbs were trained on how to use a prosthesis simulator using matched or mismatched limb training in a single session. Eye movements were recorded during the training phase. Kinematics were recorded as persons performed the task. RESULTS: Gaze patterns showed differences between the training groups. The mismatched group demonstrated a higher probability of gaze on the path between the start and end of the action, while the matched group demonstrated a significantly higher probability of focusing on the elements of the path of the action and a trend of focusing on the shoulders. Kinematics also revealed overall improvements in motor control for the matched group. CONCLUSIONS: This study proposes a putative mechanism that may explain improvements in matched limb training through shifting gaze strategies. Further work is needed to understand whether implicit visual strategies seen during matched limb training might encourage motor learning during functional training with prostheses.

The Chinese Children and Families Cohort Study: The Nutrition, Physical Activity, and Ultraviolet Radiation Data Collection.

This article reports the study design, methodological issues and early results of a pilot study testing methods for collecting nutrition, physical activity, and ultraviolet (UV) radiation exposure data in a groundbreaking study in China. Epidemiological studies suggest that exposures across the entire life course, including in utero, early childhood, and adolescence, may be important in the etiology of adult cancers and other chronic diseases. The Chinese Children and Families Cohort Study intends to follow-up subjects from the 1993 to 1995 Community Intervention Program of folic acid supplementation for the prevention of neural tube defects. This cohort is unique in that only folic acid exposure during pregnancy varies between groups as other supplements were not available, and there were nutrient deficiencies in the populations. Prior to launching a large-scale follow-up effort, a pilot study was conducted to assess the feasibility of recontacting original study participants to collect extensive diet, physical activity, and UV radiation exposure data in this population. The pilot study included 92 mothers and 184 adolescent children aged 14 to 17 years from 1 urban and 1 rural Community Intervention Program site. Subjects completed a Food Frequency Questionnaire, a 3-day food record, a physical activity questionnaire, a 3-day sun exposure diary together with 3 days of personal UV dosimetry, and 7 days of pedometry measurements and provided blood, saliva, and toenail samples. Grip strength and body composition measurements were taken, and ambient solar UV radiation was monitored in both study sites. While most of the assessments were successful, future studies would likely require different dietary intake instruments. The purpose of this report is to describe the study design and methodological issues emerging from this pilot work relevant for the follow-up of this large birth cohort.

Comparison of Cardiovascular Outcomes Between Statin Monotherapy and Fish Oil and Statin Combination Therapy in a Veteran Population.

A study that compared the use of statin therapies with and without fish oil in a veteran population found an insignificant difference between the 2 arms.

Novel behavioral indicator of explicit awareness reveals temporal course of frontoparietal neural network facilitation during motor learning.

Deficits in sequential motor learning have been observed in many patient populations. Having an understanding of the individual neural progression associated with sequential learning in healthy individuals may provide valuable insights for effective interventions with these patients. Due to individual variability in motor skill acquisition, the temporal course of such learning will be vary, suggesting a need for a more individualized approach. Knowing when a subject becomes aware of movement patterns may provide a marker with which to identify each individual's learning time course. To avoid interfering with the incidental nature of discovery during learning, such an indicator requires an indirect, behaviorally-based approach. In Part I, our study aimed to identify a reliable behavioral indicator predictive of the presence of incidental explicit awareness in a sequential motor learning task. Part II, utilized the predictive indicator and EEG to provide neural validation of perceptual processing changes temporally correlated with the indicator. Results of Part I provide a reliable predictive indicator for the timing of explicit awareness development. Results from Part II demonstrates strong classification reliability, as well as a significant neural correlation with behavior for subjects developing awareness (EXP), not observed with subjects without awareness (NOEXP). Additionally, a temporal correlation of peak activation between neural regions was noted over frontoparietal regions, suggesting that the incidental discovery of motor patterns may involve a facilitative network during awareness development. The proposed indicator provides a tool in which to further examine potential impacts of awareness associated with incidental, or exploratory, motor learning, while the individual nature of the indicator provides a tool for monitoring progress in rehabilitative, exploratory motor learning paradigms.

Treatment time, ease of use and cost associated with use of Equashield™, PhaSeal® , or no closed system transfer device for administration of cancer chemotherapy to a dog model.

This prospective experimental simulation study evaluated the efficiency, ease of use (EOU) and cost of administering chemotherapy with two closed system transfer devices (CSTD, Equashield™ and PhaSeal® ) and no CSTD. Forty-six veterinary technicians (VT) working in oncology specialty practices were timed during chemotherapy administration simulated with water and a model canine limb 10 times with each system and with no CSTD. EOU and likelihood of recommending each system were rated by VT using visual analog scales. Costs were obtained from veterinary distributors. Administration was fastest with Equashield™ (P = 0.0003), but the difference was not enough to affect case flow. Equashield™ was easier to use than PhaSeal® or no CSTD (P = 0.002), however VT recommended both CSTD more strongly than no CSTD (P < 0.0001). Equashield™ cost less than PhaSeal® but was sold only in bulk quantities. CSTD did not decrease efficiency in administering chemotherapy and were readily accepted by VT.

Febrile neutropenia in cats treated with chemotherapy.

The purpose of this study was to describe the clinical presentation, potential causative agents, treatment and outcome of febrile neutropenia (FN) in chemotherapy-treated cats. Medical records from eight institutions were retrospectively reviewed. A total of 22 FN events in 20 cats were evaluated. Lymphoma was the most common cancer diagnosis; lomustine and vinca alkaloids were the most frequently implicated causative agents. Presenting clinical signs included decreased appetite, lethargy, vomiting and diarrhoea. Median body temperature and absolute neutrophil count at presentation were 104.1 °F; 40 °C (range: 103.1-105.1 °F; 39.5-40.6 °C) and 246 mL-1 (range: 0-1600 mL-1 ), respectively. Median number of days between chemotherapy administration and FN onset was 5 (range: 4-25 days). All but one cat were treated with intravenous fluids and broad spectrum antibiotics. Fevers resolved in all cases and absolute neutrophil counts returned to normal in 19 cats. Clinical presentation of cats with FN appears similar to that of dogs.

Retrospective evaluation of toceranib phosphate (Palladia®) toxicity in cats.

The purpose of this study was to describe the toxicity profile of toceranib phosphate in tumour bearing cats. Medical records were reviewed from seven institutions. Patients with incomplete medical records and those receiving concurrent chemotherapy or NSAIDs (non-steroidal anti-inflammatory) were excluded. Fifty-five cats met the inclusion criteria. Carcinoma was diagnosed in 55% of cases. Median oral toceranib dose was 2.7 mg kg-1 and was most commonly administered on Monday, Wednesday and Friday. Thrombocytopenia (16.3%) and neutropenia (9.1%) were the most common haematologic toxicities. Azotemia (14.5%) and alanine aminotransferase (ALT) elevations (7.2%) were the most frequently encountered biochemical alterations. Gastrointestinal (GI) toxicity was seen in 21.8% of cats, and was lower than previously reported in dogs. The results of this study showed that treatment of cats with toceranib is well-tolerated and toxicity is uncommon. Additional studies to define a more structured dosing schedule and to evaluate the efficacy of toceranib in the treatment of feline cancers are needed.

Prospective evaluation of the safety of compounded bulk material L-asparaginase in dogs with lymphoma.

Use of compounded L-asparaginase became routine in veterinary oncology when manufacturing of Elspar® was discontinued in 2012. The objective of this study was to evaluate the safety of compounded L-asparaginase (CLASP, KRS Global Biotechnology, Boca Raton, FL, USA) in comparison with Elspar® (Lundbeck LLC, Deerfield, IL, USA). In addition, we documented the response to CLASP in combination with a corticosteroid in this population of dogs with lymphoma. Dogs were prospectively treated with 10 000 IU/m2 CLASP or Elspar® subcutaneously. Corticosteroids were administered concurrently. Adverse events (AE) were assessed according to the Veterinary Cooperative Oncology Group Common Terminology Criteria for Adverse Events v1.1 (VCOG-CTCAE). Response was recorded. Seventy-three dogs received 75 treatments (CLASP, n = 47; Elspar® , n = 28). No AE were attributed to CLASP. Grade I and II AE probably or possibly related to treatment were observed following two Elspar® treatments. The overall response rate to the combination of CLASP and a corticosteroid was 80% (24% CR and 56% PR). In combination with a steroid, the compounded L-asparaginase evaluated in this study is safe and demonstrates activity against canine lymphoma. In the face of the discontinuation of Elspar® , veterinarians should seek compounded LASP products that have been tested for activity, purity, and sterility.

A prospective evaluation of the impact of second-opinion histopathology on diagnostic testing, cost and treatment in dogs and cats with cancer.

Second-opinion histopathology is a common practice in human medicine to avoid unnecessary procedures, costs and to optimize therapy. Histopathology review has been recommended in veterinary oncology as well. In this prospective evaluation of 52 tumours over a 1-year period, there was diagnostic agreement between first and second opinions in 52% of cases. Twenty-nine percent of cases had partial diagnostic disagreement, most often a change in grade, tumour subtype or margin status. Nineteen percent had complete diagnostic disagreement, including a change in cell of origin or a change from benign to malignant. Minor disagreements, which would not affect treatment or prognosis, were present in 21% of cases. Major disagreements, which would affect either treatment or prognosis, were present in 37% of cases. Costs of ideal staging and treatment recommendations were considerably different between first and second opinions.

Hemin uptake and release by neurons and glia.

Hemin accumulates in intracerebral hematomas and may contribute to cell injury in adjacent tissue. Despite its relevance to hemorrhagic CNS insults, very little is known about hemin trafficking by neural cells. In the present study, hemin uptake and release were quantified in primary murine cortical cultures, and the effect of the hemin-binding compound deferoxamine (DFO) was assessed. Net uptake of (55)Fe-hemin was similar in mixed neuron-glia, neuron, and glia cultures, but was 2.6-3.6-fold greater in microglia cultures. After washout, 40-60% of the isotope signal was released by mixed neuron-glia cultures into albumin-containing medium within 24 h. Inhibiting hemin breakdown with tin protoporphyrin IX (SnPPIX) had minimal effect, while release of the fluorescent hemin analog zinc mesoporphyrin was quantitatively similar to that of (55)Fe-hemin. Isotope was released most rapidly by neurons (52.2 ± 7.2% at 2 h), compared with glia (15.6 ± 1.3%) and microglia (17.6 ± 0.54%). DFO did not alter (55)Fe-hemin uptake, but significantly increased its release. Mixed cultures treated with 10 µM hemin for 24 h sustained widespread neuronal loss that was attenuated by DFO. Concomitant treatment with SnPPIX had no effect on either enhancement of isotope release by DFO or neuroprotection. These results suggest that in the presence of a physiologic albumin concentration, hemin uptake by neural cells is followed by considerable extracellular release. Enhancement of this release by DFO may contribute to its protective effect against hemin toxicity.

Diagnostic evaluation and treatment recommendations for dogs with substage-a high-grade multicentric lymphoma: results of a survey of veterinarians.

The goal of this study was to survey veterinarians regarding their current initial diagnostic and treatment recommendations for dogs with substage-a high-grade multicentric lymphoma. A written survey was conducted at the 2009 Veterinary Cancer Society conference asking veterinarians to provide demographic information, initial staging diagnostics and treatment recommendations for canine lymphoma. The most commonly recommended staging diagnostics were complete blood count (100%), chemistry panel (100%), urinalysis (85%), lymph node cytology (88%), thoracic radiographs (84%), immunophenotyping (76%) and abdominal ultrasound (75%). The most commonly used first-line B-cell protocols combined the drugs L-asparaginase, cyclophosphamide, doxorubicin, vincristine and prednisone (L-CHOP, 51%). CHOP (30%) and other CHOP-based protocols (12%) were used as well. Thirty-one percent of responders treated B- and T-cell lymphomas differently. Protocol lengths varied from ≤ 16 weeks to >2 years. Current staging and treatment recommendations for canine lymphoma are varied. Efforts to standardize recommendations should be considered.

Comparison of first-opinion and second-opinion histopathology from dogs and cats with cancer: 430 cases (2001-2008).

Second-opinion histopathology is intended to detect clinically significant discrepancies that have a direct impact on patient care. We sought to determine if this practice at our institution affected patient management and prognosis. First- and second-opinion histopathology reports from cases were retrospectively reviewed. Reports were considered to be in diagnostic agreement, partial diagnostic disagreement or complete diagnostic disagreement. Four hundred and thirty cases were studied. In 70% of cases there was a diagnostic agreement. In 20% of cases, there was partial diagnostic disagreement, where diagnoses were the same but information such as grade or lymphatic and/or vascular invasion was changed. In 10% of cases, complete diagnostic disagreement resulted from a change in degree of malignancy (malignant to benign, or converse; 7%) or a change in cell type (3%). In 17% of the cases evaluated, the histopathology review prompted a change in treatment or prognosis. These findings support the use of second-opinion histopathology as an important part of patient care.

Human epidermal growth factor receptor-2 and estrogen receptor expression, a demonstration project using the residual tissue repository of the Surveillance, Epidemiology, and End Results (SEER) program.

BACKGROUND: In 2001, the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) program established Residual Tissue Repositories (RTR) in the Hawaii, Iowa, and Los Angeles Tumor Registries to collect discarded tissue blocks from pathologic laboratories within their catchment areas. To validate the utility of the RTR for supplementing SEER's central database, we assessed human epidermal growth factor receptor-2 (HER2) and estrogen receptor expression (ER) in a demonstration project. MATERIALS: Using a prepared set of tissue microarrays (TMAs) residing in the Hawaii Tumor Registry (HTR), we performed standard immunohistochemistry. Breast cancers in the TMA were diagnosed in 1995, followed through 2006, and linked to SEER's main database. RESULTS: The TMA included 354 cases, representing 51% of 687 breast cancers in the HTR (1995). The HTR and TMA cases were similar with respect to patient demographics and tumor characteristics. Seventy-six percent (76%, 268 of 354) of TMA cases were HER2+ and/or ER+, i.e., 28 HER2+ER-, 12 HER2+ER+, and 228 HER2-ER+. There were 67 HER2-ER- cases and 19 were unclassified. Age distributions at diagnosis were bimodal with dominant early-onset modes for HER2+ER- tumors and dominant late-onset modes for HER2-ER+ breast cancers. Epidemiologic patterns for concordant HER2+ER+ (double-positive) and HER2-ER- (double-negative) were intermediate to discordant HER2+ER- and HER2-ER+. CONCLUSION: Results showed contrasting incidence patterns for HER2+ (HER2+ER-) and ER+ (HER2-ER+) breast cancers, diagnosed in 1995. Though sample sizes were small, this demonstration project validates the potential utility of the RTR for supplementing the SEER program.

Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant.

BACKGROUND: Genomic disorders are often caused by non-allelic homologous recombination between segmental duplications. Chromosome 16 is especially rich in a chromosome-specific low copy repeat, termed LCR16. METHODS AND RESULTS: A bacterial artificial chromosome (BAC) array comparative genome hybridisation (CGH) screen of 1027 patients with mental retardation and/or multiple congenital anomalies (MR/MCA) was performed. The BAC array CGH screen identified five patients with deletions and five with apparently reciprocal duplications of 16p13 covering 1.65 Mb, including 15 RefSeq genes. In addition, three atypical rearrangements overlapping or flanking this region were found. Fine mapping by high-resolution oligonucleotide arrays suggests that these deletions and duplications result from non-allelic homologous recombination (NAHR) between distinct LCR16 subunits with >99% sequence identity. Deletions and duplications were either de novo or inherited from unaffected parents. To determine whether these imbalances are associated with the MR/MCA phenotype or whether they might be benign variants, a population of 2014 normal controls was screened. The absence of deletions in the control population showed that 16p13.11 deletions are significantly associated with MR/MCA (p = 0.0048). Despite phenotypic variability, common features were identified: three patients with deletions presented with MR, microcephaly and epilepsy (two of these had also short stature), and two other deletion carriers ascertained prenatally presented with cleft lip and midline defects. In contrast to its previous association with autism, the duplication seems to be a common variant in the population (5/1682, 0.29%). CONCLUSION: These findings indicate that deletions inherited from clinically normal parents are likely to be causal for the patients' phenotype whereas the role of duplications (de novo or inherited) in the phenotype remains uncertain. This difference in knowledge regarding the clinical relevance of the deletion and the duplication causes a paradigm shift in (cyto)genetic counselling.