Identifying Associations between Somatic Mutations and Clinicopathologic Findings in Lung Cancer Pathology Reports.

OBJECTIVE: We aim to build an informatics methodology capable of identifying statistically significant associations between the clinical findings of non-small cell lung cancer (NSCLC) recorded in patient pathology reports and the various clinically actionable genetic mutations identified from next-generation sequencing (NGS) of patient tumor samples. METHODS: We built an information extraction and analysis pipeline to identify the associations between clinical findings in the pathology reports of patients and corresponding genetic mutations. Our pipeline leverages natural language processing (NLP) techniques, large biomedical terminologies, semantic similarity measures, and clustering methods to extract clinical concepts in freetext from patient pathology reports and group them as salient findings. RESULTS: In this study, we developed and applied our methodology to lobectomy surgical pathology reports of 142 NSCLC patients who underwent NGS testing and who had mutations in 4 oncogenes with clinical ramifications for NSCLC treatment (EGFR, KRAS, BRAF, and PIK3CA). Our approach identified 732 distinct positive clinical concepts in these reports and highlighted multiple findings with strong associations (P-value ≤ 0.05) to mutations in specific genes. Our assessment showed that these associations are consistent with the published literature. CONCLUSIONS: This study provides an automatic pipeline to find statistically significant associations between clinical findings in unstructured text of patient pathology reports and genetic mutations. This approach is generalizable to other types of pathology and clinical reports in various disorders and can provide the first steps toward understanding the role of genetic mutations in the development and treatment of different types of cancer.

Is age an independent risk factor for medical complications following minimally invasive radical prostatectomy? An evaluation of contemporary American College of Surgeons National Surgical Quality Improvement (ACS-NSQIP) data.

While robotic-assisted laparoscopic radical prostatectomy (RALRP) is an effective treatment for localized prostate cancer, the risk of complications in older patients can be a deterrent to surgery. We evaluated the rate of medical complications following RALRP in a national dataset of safety events, and assessed whether age is an independent risk factor for these complications. Retrospective analysis of patients undergoing RALRP between 2009 and 2012 in the prospectively maintained American College of Surgeons National Surgical Quality Improvement (ACS-NSQIP) database was performed. Demographic and comorbid data were collated, medical complications occurring during the 30-day post-operative period were identified. We identified age-related comorbidities, and complications associated with these comorbidities. A binary logistic regression model with age and age-related comorbidities as predictors and specific complication as outcome, was used to evaluate whether age is an independent risk factor for these complications. 12,123 patients underwent RALRP between 2009 and 2012, with a mean age of 62 (22-92). Post-operative medical complications included urinary tract infection (UTI) (1.77 %), deep venous thrombosis (DVT) (0.67 %), pulmonary embolism (PE) (0.45 %), pneumonia (PNA) (0.27 %), myocardial infarction (MI) (0.12 %), and cerebrovascular accident (CVA) (0.01 %). Nine comorbidities were positively correlated with age (p < 0.05). Four medical complications were associated with these age-related comorbidities: MI, CVA, PNA, and UTI. On multivariate analysis, age was an independent risk factor for post-operative PNA (p < 0.05), but not for MI (p = 0.09), UTI (p = 0.3) or CVA (p = 0.2). Patient age was independently associated with post-operative pneumonia only. These data suggest that RALRP can be considered as a treatment option in selected older patients with minimal increased risk for post-operative complications.

Rationalising the treatment of anaemia in cardiac surgery: short and mid-term results from a local quality improvement initiative.

BACKGROUND: Transfusion of red blood cells, while often used for treating blood loss or haemodilution, is also associated with higher infection rates and mortality. The authors implemented an initiative to reduce variation in the number of perioperative transfusions associated with cardiac surgery. METHODS: The authors examined patients undergoing non-emergent cardiac surgery at a single centre from the third quarter 2004 to the second quarter 2007. Phase I focused on understanding the current process of managing and treating perioperative anaemia. Phase II focused on (1) quality-improvement project dissemination to staff, (2) developing and implementing new protocols, and (3) assessing the effect of subsequent interventions. Data reports were updated monthly and posted in the clinical units. Phase III determined whether reductions in transfusion rates persisted. RESULTS: Indications for transfusions were investigated during Phase II. More than half (59%) of intraoperative transfusions were for low haematocrit (Hct), and 31% for predicted low Hct during cardiopulmonary bypass. 43% of postoperative transfusions were for low Hct, with an additional 16% for failure to diurese. The last Hct value prior to transfusion was noted (Hct 25-23, p=0.14), suggestive of a higher tolerance for a lower Hct by staff surgeons. Intraoperative transfusions diminished across phases: 33% in Phase I, 25.8% in Phase II and 23.4% in Phase III (p<0.001). Relative to Phase I, postoperative transfusions diminished significantly over Phase II and III. CONCLUSIONS: We report results from a focused quality-improvement initiative to rationalise treatment of perioperative anaemia. Transfusion rates declined significantly across each phase of the project.

Interval inset of TRAM flaps in immediate breast reconstruction: a technical refinement.

PURPOSE: Healthy, viable mastectomy skin is a critical factor in the outcome of immediate breast reconstruction. Unfortunately, mastectomy skin viability can be problematic and intraoperative assessment is unreliable. For this reason, we have modified our approach to immediate transverse rectus abdominus myocutaneous flap (TRAM) reconstruction. Instead of completing the reconstruction with a definitive inset at the time of the mastectomy, the TRAM flap is left intact and buried beneath the mastectomy skin for 3 to 5 days. This falls within the normal period of postoperative hospitalization, and at this point, the viability of the mastectomy skin is clear. Ischemic skin is debrided and replaced with healthy TRAM skin, and nipple reconstruction can be performed at the time of this interval inset. The purpose of this study was to review a large case series of patients who underwent an interval inset of their TRAM flap in the setting of immediate skin-sparing mastectomy. METHODS: Retrospective chart data were obtained for all TRAM patients who underwent immediate postmastectomy breast reconstruction by a single surgeon during a 5-year period. Data were collected on procedures, complications, margin status, and number of immediate versus delayed nipple reconstructions. RESULTS: There were 63 patients who underwent immediate TRAM reconstruction with interval inset of the flap. This included 25 bilateral cases, for a total of 89 flaps. Interval insets were performed an average of 3.9 days after the TRAM. Twenty-seven percent (17/63) required replacement of nonviable mastectomy skin with TRAM skin and had no nipple reconstruction; 4.8% (3/63) had additional skin taken because of residual tumor close to or at the mastectomy margins. Seventy-three percent of patients (46/63) had a nipple reconstruction with minimal or no mastectomy skin loss. CONCLUSION: We present the interval inset of TRAM flaps during the normal period of postoperative hospitalization as a technical refinement to optimize cosmetic outcomes. Mastectomy skin viability can be more easily assessed and necrotic or ischemic skin replaced with TRAM skin as needed. This avoids the need for prolonged dressing changes or a compromised aesthetic result from skin loss. When there is no major skin loss, the nipple reconstruction can be performed concurrently with the inset. These refinements optimize the appearance of the reconstructed breast and reduce the need for future surgeries. In addition, the surgical oncologist has the opportunity to excise close or positive margins as indicated by pathologic findings. Thus, the benefits of the interval inset of TRAM flaps are shared by the reconstructive surgeon, the surgical oncologist, and most importantly, the patient.

Transforming administrative data into real-time information in the Department of Surgery.

BACKGROUND: Cardiothoracic surgical programmes face increasingly more complex procedures performed on evermore challenging patients. Public and private stakeholders are demanding these programmes report process-level and clinical outcomes as a mechanism for enabling quality assurance and informed clinical decision-making. Increasingly these measures are being tied to reimbursement and institutional accreditation. The authors developed a system for linking administrative and clinical registries, in real-time, to track performance in satisfying the needs of the patients and stakeholders, as well as helping to drive continuous quality improvement. METHODS: A relational surgical database was developed to link prospectively collected clinical data to administrative data sources at Dartmouth-Hitchcock Medical Center. Institutional performance was displayed over time using process control charts, and compared with both internal and regional benchmarks. RESULTS: Quarterly reports have been generated and automated for five surgical cohorts. Data are displayed externally on our dedicated website, and internally in the cardiothoracic surgical office suites, operating room theatre and nursing units. Monthly discussions are held with the clinical staff and have resulted in the development of quality-improvement projects. CONCLUSIONS: The delivery of clinical care in isolation of data and information is no longer prudent or acceptable. The present study suggests that an automated and real-time computer system may provide rich sources of data that may be used to drive improvements in the quality of care. Current and future work will be focused on identifying opportunities to integrate these data into the fabric of the delivery of care to drive process improvement.

Screening for recurrences in patients treated with breast-conserving surgery: is there a role for MRI?

BACKGROUND: Although it has been shown that magnetic resonance imaging (MRI) is more sensitive than mammography in the detection of breast cancer in high-risk populations, there is little data on the use of MRI as a screening tool to detect recurrence after breast-conserving surgery. Our objective was to determine the potential role of MRI in the screening of breast cancer patients treated with breast-conserving surgery. METHODS: Retrospective chart review of all patients undergoing margin-negative lumpectomy and adjuvant radiation therapy for infiltrating breast carcinoma between 1(st) January 1993 and 1(st) January 2004. Patients were followed for recurrence in the ipsilateral or contralateral breast by physical exam and mammography. RESULTS: Four hundred and seventy-six primary tumor excisions were performed. Patients were followed for a median of 5.4 years. Ipsilateral breast recurrences developed in eight patients (1.7%) with a mean diameter of 1.6 cm. All of these women are alive and free of metastases. Contralateral cancers developed in 11 patients (2.3%) with a mean diameter of 1.5 cm. Ten of these 11 women are alive and free of disease. CONCLUSIONS: In a contemporary patient population the risk of local recurrence after lumpectomy and radiation therapy is very low. If screening MRI had been a part of annual follow-up, a total of 2570 MRIs would have been performed. Given the small tumor size at detection and the excellent survival of those who recurred, annual screening MRI would have incurred significant cost and would have been unlikely to improve overall survival.

How many patients are needed to provide reliable evaluations of individual clinicians?

PURPOSE: The purpose of this study was to determine how many patients are needed to provide reliable patient ratings of care at the individual clinician level. SETTING AND SOURCES OF DATA: The study was conducted in an academic medical center and was based on analysis of 34,985 patients who completed a 50-item survey rating the care received during a recent outpatient visit to a physician or midlevel provider. STUDY DESIGN: Analyses of patient satisfaction surveys was done to: 1) confirm the dimensions of satisfaction with outpatient care in an existing measure, and 2) determine the number of patients required to provide reliable estimates of clinician care for single items and an 11-item composite scale. PRINCIPAL FINDINGS: Factor analysis showed that the survey measured 2 dimensions of satisfaction: 1) clinician care, and 2) features of visiting the office. The 11-item clinician care scale had high reliability (Cronbach's alpha=0.97). The number of patients needed to achieve reliability of 0.80 at the clinician level was 66 for the 11-item scale and ranged from 52 to 91 for individual items. For primary care physicians only, the comparable number of patients per clinician was 77 for the 11-item scale and ranged from 50 to 147 across items. CONCLUSIONS: For the survey items that we analyzed, the answer to the question "How many patients are needed to obtain useful and reliable feedback?" is at least 50, but varies by item type (global vs. specific) and by number of items (composite scale or single-item rating) and by the conditions of use (for self-assessment and learning or reward and punishment).