Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome.

BACKGROUND: Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark the performance of cancer CNV calling by six most recent and commonly used software tools on their detection accuracy, sensitivity, and reproducibility. In comparison to other orthogonal methods, such as microarray and Bionano, we also explore the consistency of CNV calling across different technologies on a challenging genome. RESULTS: While consistent results are observed for copy gain, loss, and loss of heterozygosity (LOH) calls across sequencing centers, CNV callers, and different technologies, variation of CNV calls are mostly affected by the determination of genome ploidy. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we establish a high confident CNV call set for the reference cancer cell line (HCC1395). CONCLUSIONS: NGS technologies and current bioinformatics tools can offer reliable results for detection of copy gain, loss, and LOH. However, when working with a hyper-diploid genome, some software tools can call excessive copy gain or loss due to inaccurate assessment of genome ploidy. With performance matrices on various experimental conditions, this study raises awareness within the cancer research community for the selection of sequencing platforms, sample preparation, sequencing coverage, and the choice of CNV detection tools.

Methodology for Good Machine Learning with Multi-Omics Data.

In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio-genomics-based prognostic and predictive factors for HR+/HER- metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi-omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as "maintaining effective communication" and "following good data science practices," followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.

Eligibility and Radiologic Assessment for Adjuvant Clinical Trials in Kidney Cancer.

PURPOSE: To harmonize the eligibility criteria and radiologic disease assessment definitions in clinical trials of adjuvant therapy for renal cell carcinoma (RCC). METHOD: On November 28, 2017, US-based experts in RCC clinical trials, including medical oncologists, urologic oncologists, regulators, biostatisticians, radiologists, and patient advocates, convened at a public workshop to discuss eligibility for trial entry and radiologic criteria for assessing disease recurrence in adjuvant trials in RCC. Multiple virtual meetings were conducted to address the issues identified at the workshop. RESULTS: The key workshop conclusions for adjuvant RCC therapy clinical trials were as follows. First, patients with non-clear cell RCC could be routinely included, preferably in an independent cohort. Second, patients with T3-4, N+M0, and microscopic R1 RCC tumors may gain the greatest advantages from adjuvant therapy. Third, trials of agents not excreted by the kidney should not exclude patients with severe renal insufficiency. Fourth, therapy can begin 4 to 16 weeks after the surgical procedure. Fifth, patients undergoing radical or partial nephrectomy should be equally eligible. Sixth, patients with microscopically positive soft tissue or vascular margins without gross residual or radiologic disease may be included in trials. Seventh, all suspicious regional lymph nodes should be fully resected. Eighth, computed tomography should be performed within 4 weeks before trial enrollment; for patients with renal insufficiency who cannot undergo computed tomography with contrast, noncontrast chest computed tomography and magnetic resonance imaging of the abdomen and pelvis with gadolinium should be performed. Ninth, when feasible, biopsy should be undertaken to identify any malignant disease. Tenth, when biopsy is not feasible, a uniform approach should be used to evaluate indeterminate radiologic findings to identify what constitutes no evidence of disease at trial entry and what constitutes radiologic evidence of disease. Eleventh, a uniform approach for establishing the date of recurrence should be included in any trial design. Twelfth, patient perspectives on the use of placebo, conditions for unblinding, and research biopsies should be considered carefully during the conduct of an adjuvant trial. CONCLUSIONS AND RELEVANCE: The discussions suggested that a uniform approach to eligibility criteria and radiologic disease assessment will lead to more consistently interpretable trial results in the adjuvant RCC therapy setting.

Eligibility and Radiologic Assessment in Adjuvant Clinical Trials in Bladder Cancer.

Objective: To harmonize eligibility criteria and radiographic disease assessments in clinical trials of adjuvant therapy for muscle-invasive bladder cancer (MIBC). Methods: National experts in bladder cancer clinical trial research, including medical and urologic oncologists, radiologists, biostatisticians, and patient advocates, convened at a public workshop on November 28, 2017, to discuss eligibility, radiographic entry criteria, and assessment of disease recurrence in adjuvant clinical trials in patients with MIBC. Results: The key workshop conclusions for adjuvant MIBC clinical trials included the following points: (1) patients with urothelial carcinoma with divergent histologic differentiation should be allowed to enroll; (2) neoadjuvant chemotherapy is defined as at least 3 cycles of neoadjuvant cisplatin-based combination chemotherapy; (3) patients with muscle-invasive, upper-tract urothelial carcinoma should be included in adjuvant trials of MIBC; (4) patients with severe renal insufficiency can enroll into trials using agents that are not renally excreted; (5) patients with microscopic surgical margins can be included; (6) patients should undergo a standard bilateral lymph node dissection prior to enrollment; (7) computed tomographic (CT) imaging should be performed within 4 weeks prior to enrollment. For patients with renal insufficiency who cannot undergo CT imaging with contrast, noncontrast chest CT and magnetic resonance imaging of the abdomen and pelvis with gadolinium should be done; (8) biopsy of indeterminate lesions to evaluate for malignant disease should be done when feasible; (9) a uniform approach to evaluate indeterminate radiographic lesions when biopsy is not feasible should be included in any trial design; (10) a uniform approach to determining the date of recurrence is important in interpreting adjuvant trial results; and (11) new high-grade, upper-tract primary tumors and new MIBC tumors should be considered recurrence events. Conclusions and Relevance: A uniform approach to eligibility criteria, definitions of no evidence of disease, and definitions of disease recurrence may lead to more consistent interpretations of adjuvant trial results in MIBC.

Femorofemoral Crossover Bypass Graft Has Excellent Patency When Performed with EVAR for AAA with UIOD.

OBJECTIVES: To compare the durability of the crossover femorofemoral bypass graft (CFFBG) in combination with aorto-uni-iliac stent graft (AUIS) for abdominal aortic aneurysm with the durability of CFFBG used in the treatment of unilateral iliac occlusive disease (UIOD). METHODS: We analyzed the clinical records of 69 patients who underwent CFFBG from 1992 until 2010. Group I consisted of 34 patients who received CFFBGs in combination with AUIS. Group II consisted of 35 patients treated with CFFBG for UIOD. The mean period of follow up was 2.7 years. Outcomes analyzed included primary graft patency, secondary graft patency, and postoperative morbidity and mortality. RESULTS: There was one death in each group. Wound infection complicated 11.4% of CFFBGs performed as a sole procedure for UIOD and 5.8% of cases in combination with AUIS (P = 0.673). Primary graft patency was 96.5% and 96.5% at 2 and 5 years in group I, compared with 76.6% and 53.7% in group II (P = 0.046, 0.009). Secondary graft patency at 5 years was 100% and 92.9% for groups I and II, respectively. No variables independently influenced primary graft patency. Patients in group I experienced complications that could be linked to the bypass graft in 20.5% of cases, after long-term follow-up. CONCLUSIONS: The CFFBG possesses superior long-term durability and patency when implemented in combination with aorto-uni-iliac stent grafts and does not seem to compromise the endpoint success of endovascular treatment.

Lung sounds: how doctors draw crackles and wheeze.

BACKGROUND: The content of medical records is a potential source of miscommunication between clinicians. Doctors' written entries have been criticised for their illegibility and ambiguity, but no studies have examined doctors' drawings that are commonly used for recording auscultation findings. OBJECTIVE: To compare doctors' drawings of auscultation findings, based on identical clinical information. METHODS: Doctors at the Royal London Hospital and a group of London based general practitioners (GPs) documented a respiratory examination with a drawing of the auscultation findings of bilateral mid and lower zone wheeze and right lower zone crackles. The graphical properties of each drawing were examined and the use of written captions and labels recorded. Drawings were classified into styles according to the use of symbols (defined as discrete characters or icons) and shading (cross-hatching, speckling or darkening) to depict the auscultation findings. The study was conducted between September and November 2011. RESULTS: Sixty-nine hospital doctors and 13 GPs participated. Ten drawing styles were identified from 78 completed drawings. Ten distinct symbols and a range of shading techniques were used. The most frequent style (21% of drawings) combined 'X' symbols representing crackles with musical notes for wheeze. There was inconsistency of representation across the drawings. Forty-seven (60%) drawings used an 'X' symbol exclusively to represent crackles, but six (8%) used 'X' only to represent wheeze, and 10 (13%) used 'X' to represent both findings. 91% of participants included captions or labels with their drawing. CONCLUSIONS: There was wide variation in doctors' drawings of identical auscultation findings, and inconsistency in the meaning of symbols both between and within drawings. Doctors risk incorrectly interpreting each other's drawings when they are not effectively labelled. We recommend doctors consider using a written description instead, or draw different findings with distinct symbols or shading, labelling all findings clearly.

Functional analyses of coronary artery disease associated variation on chromosome 9p21 in vascular smooth muscle cells.

Variation on chromosome 9p21 is associated with risk of coronary artery disease (CAD). This genomic region contains the CDKN2A and CDKN2B genes which encode the cell cycle regulators p16(INK4a), p14(ARF) and p15(INK4b) and the ANRIL gene which encodes a non-coding RNA. Vascular smooth muscle cell (VSMC) proliferation plays an important role in the pathogenesis of atherosclerosis which causes CAD. We ascertained whether 9p21 genotype had an influence on CDKN2A/CDKN2B/ANRIL expression levels in VSMCs, VSMC proliferation and VSMC content in atherosclerotic plaques. Immunohistochemical examination showed that VSMCs in atherosclerotic lesions expressed p16(INK4a), p14(ARF) and p15(INK4b). Analyses of primary cultures of VSMCs showed that the 9p21 risk genotype was associated with reduced expression of p16(INK4a), p15(INK4b) and ANRIL (P = 1.2 × 10(-5), 1.4 × 10(-2) and 3.1 × 10(-9)) and with increased VSMC proliferation (P = 1.6 × 10(-2)). Immunohistochemical analyses of atherosclerotic plaques revealed an association of the risk genotype with reduced p15(INK4b) levels in VSMCs (P = 3.7 × 10(-2)) and higher VSMC content (P = 5.6 × 10(-4)) in plaques. The results of this study indicate that the 9p21 variation has an impact on CDKN2A and CDKN2B expression in VSMCs and influences VMSC proliferation, which likely represents an important mechanism for the association between this genetic locus and susceptibility to CAD.

Making electronic prescribing alerts more effective: scenario-based experimental study in junior doctors.

OBJECTIVE: Expert authorities recommend clinical decision support systems to reduce prescribing error rates, yet large numbers of insignificant on-screen alerts presented in modal dialog boxes persistently interrupt clinicians, limiting the effectiveness of these systems. This study compared the impact of modal and non-modal electronic (e-) prescribing alerts on prescribing error rates, to help inform the design of clinical decision support systems. DESIGN: A randomized study of 24 junior doctors each performing 30 simulated prescribing tasks in random order with a prototype e-prescribing system. Using a within-participant design, doctors were randomized to be shown one of three types of e-prescribing alert (modal, non-modal, no alert) during each prescribing task. MEASUREMENTS: The main outcome measure was prescribing error rate. Structured interviews were performed to elicit participants' preferences for the prescribing alerts and their views on clinical decision support systems. RESULTS: Participants exposed to modal alerts were 11.6 times less likely to make a prescribing error than those not shown an alert (OR 11.56, 95% CI 6.00 to 22.26). Those shown a non-modal alert were 3.2 times less likely to make a prescribing error (OR 3.18, 95% CI 1.91 to 5.30) than those not shown an alert. The error rate with non-modal alerts was 3.6 times higher than with modal alerts (95% CI 1.88 to 7.04). CONCLUSIONS: Both kinds of e-prescribing alerts significantly reduced prescribing error rates, but modal alerts were over three times more effective than non-modal alerts. This study provides new evidence about the relative effects of modal and non-modal alerts on prescribing outcomes.

The incidence of peripheral arterial embolism in association with a patent foramen ovale (right-to-left shunt).

OBJECTIVES: The aim of this study was to examine a cohort of patients who had suffered an arterial embolism to see whether a patent foramen ovale (PFO) was an identifiable cause. DESIGN: This study was conducted in two parts; a retrospective limb involving an audit of patient records over a period of 10 years, and a prospective limb including selected patients from that audit to search for a PFO using an agitated saline test with transcranial Doppler ultrasound monitoring of the anterior cerebral artery. Data on patients with peripheral vascular disease were collected using a structured questionnaire. SETTING: A clinical vascular department. All patients were seen in the vascular outpatients clinic. PARTICIPANTS: Patients who had been identified from a retrospective search based on the headline diagnosis of arterial embolus. Collected data on the 71 patients revealed that 75% had predisposing factors for DVT, 70% were male smokers, and 84.4% had a significant past history of vascular symptoms. MAIN OUTCOME MEASURES: Whether or not patients identified as having a possible PFO actually had one on objective testing with transcranial Doppler assessment of the cerebral circulation with an agitated saline solution. RESULTS: Fifteen patients who were suspected of having a PFO were selected from these 71 patients; 12 of these were found to have no PFO on testing, and three had already undergone a percutaneous PFO closure. CONCLUSION: The incidence of a PFO in this small study group is no higher than that found in the general population (3/15, 20%). There was high prevalence of male smokers with associated predisposing factors leading to a DVT.

Presenting patient data in the electronic care record: the role of timelines.

OBJECTIVE: To establish the current level of awareness and investigate the use of timelines within clinical computing systems as an organized display of the electronic patient record (EPR). DESIGN: Multicentre survey conducted using questionnaires and interview. SETTING: Seven UK hospitals and several general practice surgeries. PARTICIPANTS: A total of 120 healthcare professionals completed a questionnaire which directed structured interviews. Participants fell into two cohorts according to whether or not they had used clinical timelines, which gave 60 'timeline users' and 60 'prospective timeline users'. MAIN OUTCOME MEASURES: To investigate the awareness of timelines, and the potential benefits of timelines within clinical computing systems. RESULTS: Fifty-eight percent of participants had not heard of the specific term 'timelines' despite 75% of users utilizing a form of timeline on a daily basis. The potential benefits of future timelines were clinical audit (95%CI 77.6-91.6), increased time efficiency (95%CI 77.7-91.6%), reduced clinical error (95%CI 71.0-86.7) and improved patient safety (95%CI 70.0-85.9). One continuous timeline view between primary and secondary care was considered to be of great potential benefit in allowing communication via a unified patient record. CONCLUSIONS: The concept of timelines has enjoyed proven success in healthcare in the USA and in other sectors worldwide. Clinicians are supportive of timelines in healthcare. Formal input from clinicians should be sought when designing and implementing computer systems in healthcare. Timelines in healthcare support clinicians' cognitive processes by improving the amount of data available and improving the way in which data are presented.