Differentiation of Asian population samples using the Illumina ForenSeq kit.

The Kidd set of ancestry informative SNPs are included in Illumina's ForenSeq DNA Signature Kit. We had previously reported on the capability of these SNPs together with some phenotypic SNPs with ancestry informative properties in differentiating individuals from the Chinese, Malay and Indian populations in Singapore. The Singapore population is primarily made up of Chinese, Malays and Indians, with individuals from other Asian countries making up the rest. In this study, we evaluated the ancestry prediction capabilities of the ForenSeq kit in 484 unrelated individuals of self-declared Bangladeshi, Burmese, Filipino, Indonesian and Vietnamese origin. 750 Chinese, Malay and Indian individuals previously reported were included in this study. 48 ancestry SNPs and 12 phenotypic SNPs with ancestry informative properties were selected for analyses. Ancestry modelling in STRUCTURE showed that the eight tested populations could be better classified as five. Principal component analysis also showed that the eight populations clustered in five groups based on general geographic location within Asia; with Chinese clustering with Vietnamese, Malays clustering with Indonesians, Indians clustering with Bangladeshi, and the Burmese and Filipino populations clustering in-between and overlapping with the Chinese and Malay populations. The 60 SNPs analysed could account for only 23 % of the variation between the populations. The lack of distinction between the populations resulted in poor (43 % correct self-classification) cross-validation using Snipper. While this was improved by merging the co-clustering populations into five groups (East, South-East, South Asian, Burmese & Filipino), successful self-classification was still relatively low (69 %). While the 60 tested ancestry informative markers were able to differentiate between individuals of East, South-East and South Asian origin, they are not sufficiently informative to effectively discriminate between Chinese, Malays and Indians, and Bangladeshi, Burmese, Filipino, Indonesian and Filipino populations in the country.

Patient outcomes after radiofrequency ablation stratified by Clinical, Etiology, Anatomy, and Pathophysiology classification.

OBJECTIVE: Venous insufficiency is a prevalent and potentially debilitating disease. Treatment guidelines and techniques such as radiofrequency ablation (RFA) developed in the United States and Europe have been shown to provide significant improvements in quality of life; however, these have not been clearly assessed in the populations of developing nations. This study examined quality of life outcomes after RFA of patients treated at a single Jamaican vein center. METHODS: In this study, 100 patients who underwent RFA from 2007 to 2012 were evaluated. Patients answered the Venous Insufficiency Epidemiological and Economic Study on Quality of Life/Symptoms (VEINES-QOL/Sym) questionnaire assessing quality of life before and after RFA. Improvements in specific categories, such as venous symptoms, work limitations, social limitations, and cosmetic concerns, were evaluated. Cumulative VEINES-Sym and VEINES-QOL scores were also assessed. RESULTS: Patients' quality of life responses were significantly improved in every individual VEINES question. Average cumulative VEINES-Sym t score improved 9.96 points (P < .01), and VEINES-QOL t score improved 11.15 points (P < .01). For patients with Clinical, Etiology, Anatomy, and Pathophysiology (CEAP) C5 and C6 disease, the only questions that did not show significant improvement were limitations to daily workplace activity and impact on clothing after RFA. However, in this subset, the average VEINES-Sym t score improved 11.83 points (P < .01), and the VEINES-QOL t score improved 11.96 points (P < .01) after RFA. CONCLUSIONS: Venous disease is often overlooked, and access to treatment can be limited in developing nations. This study demonstrated that venous treatment guidelines and RFA techniques developed in the United States and Europe could be successfully applied to a Jamaican population, resulting in significant improvements in quality of life.

Ancestry prediction in Singapore population samples using the Illumina ForenSeq kit.

The ability to predict bio-geographic ancestry can be valuable to generate investigative leads towards solving crimes. Ancestry informative marker (AIM) sets include large numbers of SNPs to predict an ancestral population. Massively parallel sequencing has enabled forensic laboratories to genotype a large number of such markers in a single assay. Illumina's ForenSeq DNA Signature Kit includes the ancestry informative SNPs reported by Kidd et al. In this study, the ancestry prediction capabilities of the ForenSeq kit through sequencing on the MiSeq FGx were evaluated in 1030 unrelated Singapore population samples of Chinese, Malay and Indian origin. A total of 59 ancestry SNPs and phenotypic SNPs with AIM properties were selected. The bio-geographic ancestry of the 1030 samples, as predicted by Illumina's ForenSeq Universal Analysis Software (UAS), was determined. 712 of the genotyped samples were used as a training sample set for the generation of an ancestry prediction model using STRUCTURE and Snipper. The performance of the prediction model was tested by both methods with the remaining 318 samples. Ancestry prediction in UAS was able to correctly classify the Singapore Chinese as part of the East Asian cluster, while Indians clustered with Ad-mixed Americans and Malays clustered in-between these two reference populations. Principal component analyses showed that the 59 SNPs were only able to account for 26% of the variation between the Singapore sub-populations. Their discriminatory potential was also found to be lower (GST=0.085) than that reported in ALFRED (FST=0.357). The Snipper algorithm was able to correctly predict bio-geographic ancestry in 91% of Chinese and Indian, and 88% of Malay individuals, while the success rates for the STRUCTURE algorithm were 94% in Chinese, 80% in Malay, and 91% in Indian individuals. Both these algorithms were able to provide admixture proportions when present. Ancestry prediction accuracy (in terms of likelihood ratio) was generally high in the absence of admixture. Misclassification occurred in admixed individuals, who were likely offspring of inter-ethnic marriages, and hence whose self-reported bio-geographic ancestries were dependent on that of their fathers, and in individuals of minority sub-populations with inter-ethnic beliefs. The ancestry prediction capabilities of the 59 SNPs on the ForenSeq kit were reasonably effective in differentiating the Singapore Chinese, Malay and Indian sub-populations, and will be of use for investigative purposes. However, there is potential for more accurate prediction through the evaluation of other AIM sets.

Trends in use of the only Food and Drug Administration-approved commercially available fenestrated endovascular aneurysm repair device in the United States.

BACKGROUND: Fenestrated endografts are customized, patient-specific, endovascular devices with potential to significantly reduce morbidity and mortality of short-neck infrarenal and juxtarenal abdominal aortic aneurysm repair. The Zenith fenestrated endovascular graft (ZFEN) for abdominal aortic aneurysms (Cook Medical, Bloomington, Ind), Food and Drug Administration-approved in 2012, remains the only fenestrated device available in the United States. This technology is among the most technically complex catheter-based procedures and, therefore, inherently associated with serious risk for device-related complications. We sought to define patterns of physician and hospital adoption of ZFEN. METHODS: Deidentified datasets containing numbers of physicians trained, orders by physicians and hospitals, and designs (fenestration/scallop configuration) was provided for U.S. ZFEN devices ordered (April 2012-August 2015). We evaluated the number of physicians trained, the number of devices ordered, hospital characteristics, and fenestration/scallop design configurations. Cook Medical assembled the datasets but played no role in study design, analysis, or interpretation of data. RESULTS: Between April 2012 and August 2015, 553 physicians attended formal ZFEN training sessions, 388 (70%) of whom ordered a total of 2669 devices. An increase in orders per month (nine in June 2012 and 91 in August 2015, 911% growth; P < .001) and in number of physicians ordering per month (eight in June 2012 and 62 in August 2015, 675% growth; P < .001) was observed. Teaching hospitals, representing all U.S. regions (Midwest 927, 35%; South 799, 30%; Northeast 547, 20%; West 396, 15%), accounted for 1703 (64%) ZFEN orders. Of 553 trained physicians, 165 (30%) ordered no devices, 116 (21%) ordered 1 device, 144 (26%) ordered 2-5 devices, 61 (11%) ordered 6-10 devices, 39 (7%) ordered 11-20, and 28 (5%) ordered >20 devices. For physicians contributing >6 months of data (n = 336), the average number of devices ordered per year was three (standard deviation, 4); 272 (81%) ordered ≤ 5 devices/year, 15 (4.5%) ordered 11-20 devices/year, and 3 (0.9%) ordered >20 devices/year. Of devices with design details available (2618 of 2669; 98%), most common designs were 2 small fenestrations/1 scallop (1443; 55%), 2 small fenestrations/1 large fenestration (568; 22%), 1 small fenestration/1 scallop (173, 6.6%), and 2 small fenestrations (169; 6.5%). The average number of target vessels incorporated in each design was 2.7/device; 2071 (79%) incorporated three, 398 (15%) incorporated two. CONCLUSIONS: Since 2012, ZFEN has demonstrated a ninefold increase in monthly orders, with 553 physicians trained. Unlike the experience of rapid dissemination seen with infrarenal endografts, only 28 (5%) physicians have ordered >20, whereas 165 (30%) have ordered none, and 272 (81%) ordered ≤ 5 devices/year. Assuming that volume, in general, correlates with outcomes, this adoption pattern raises questions whether fenestrated technology should be regionalized to high-volume centers.

The increased use of computed tomography angiography and magnetic resonance angiography as the sole imaging modalities prior to infrainguinal bypass has had no effect on outcomes.

BACKGROUND: Angiography remains the gold standard imaging modality before infrainguinal bypass. Computed tomography angiography (CTA) and magnetic resonance angiography (MRA) have emerged as noninvasive alternatives for preoperative imaging. We sought to examine contemporary trends in the utilization of CTA and MRA as isolated imaging modalities before infrainguinal bypass and to compare outcomes following infrainguinal bypass in patients who underwent CTA or MRA versus those who underwent conventional arteriography. METHODS: Patients undergoing infrainguinal bypass within the Vascular Study Group of New England were identified (2003-2012). Patients were stratified by preoperative imaging modality: CTA/MRA alone or conventional angiography. Trends in utilization of these modalities were examined and demographics of these groups were compared. Primary end points included primary patency, secondary patency, and major adverse limb events (MALE) at 1 year as determined by Kaplan-Meier analysis. Multivariable Cox proportional hazards models were constructed to evaluate the effect of imaging modality on primary patency, secondary patency, and MALE after adjusting for confounders. RESULTS: In 3123 infrainguinal bypasses, CTA/MRA alone was used in 462 cases (15%) and angiography was used in 2661 cases (85%). Use of CTA/MRA alone increased over time, with 52 (11%) bypasses performed between 2003 and 2005, 189 (41%) bypasses performed between 2006 and 2009, and 221 (48%) bypasses performed between 2010 and 2012 (P < 0.001). Patients with CTA/MRA alone, compared with patients with angiography, more frequently underwent bypass for claudication (33% vs. 26%, P = 0.001) or acute limb ischemia (13% vs. 5%, P < 0.0001), more frequently had prosthetic conduits (39% vs. 30%, P = 0.001), and less frequently had tibial/pedal targets (32% vs. 40%, P = 0.002). After adjusting for these and other confounders, multivariable analysis demonstrated that the use of CTA/MRA alone was not associated with a significant difference in 1 year primary patency (hazard ratio [HR] 0.95, 95% confidence interval [CI] 0.78-1.16), secondary patency (HR 1.30, 95% CI 0.99-1.72), or MALE (HR 1.08, 95% CI 0.89-1.32). CONCLUSIONS: CTA and MRA are being increasingly used as the sole preoperative imaging modality before infrainguinal bypass. This shift in practice patterns appears to have no measurable effect on outcomes at 1 year.

Outcomes reported by the Vascular Quality Initiative and the National Surgical Quality Improvement Program are not comparable.

OBJECTIVE: The Vascular Quality Initiative (VQI) and National Surgical Quality Improvement Program (NSQIP) have emerged as the primary vascular surgery quality measurement tools with the purpose of evaluating perioperative outcomes and assessing hospital and physician quality. VQI uses self-reporting to capture all index vascular procedures during the inpatient period. NSQIP employs nurse abstractors to capture a sample of procedures and covers 30-day events. We hypothesize that patients undergoing lower extremity bypass (LEB) will exhibit high concordance for preoperative variables and low concordance for postoperative variables between these data sets. METHODS: All patients undergoing LEB for peripheral arterial disease at the University of Massachusetts captured in both VQI and NSQIP databases were reviewed (2007-2012). Concordance between categorical variables was assessed by κ correlation coefficient. All postoperative variables were compared during equivalent inpatient stay. Events between discharge and 30 days postoperatively were tabulated with use of the NSQIP data set. RESULTS: We identified 240 patients undergoing LEB captured in both VQI and NSQIP. Comparison of this identical patient cohort between VQI and NSQIP revealed a moderate to strong agreement for most preoperative variables except for congestive heart failure (κ = 0.14) and hypertension (κ = 0.35), which showed poor agreement. Concordance for inpatient postoperative variables was high for mortality (κ = 1.0) and myocardial infarction (κ = 0.86) but moderate for pulmonary complications (κ = 0.57) and poor for unplanned return to the operating room (κ = 0.41), wound infection (κ = -0.01), and change in renal function (κ = -0.01). A majority of postoperative events (71%) occurred between discharge and 30 days postoperatively, with a significantly higher incidence of wound infections in the outpatient setting (4.2% vs 95.8%; P < .0001). CONCLUSIONS: VQI and NSQIP demonstrate substantial concordance for most preoperative variables and poor concordance for most postoperative variables, even at identical collection periods. This discordance is a result of differences in data collection methods and variable definitions. On the basis of these findings, VQI and NSQIP data sets cannot be used to directly compare risk-adjusted patient outcomes between institutions.

The effects of Mozart's music on the performance of glaucoma patients on automated perimetry.

PURPOSE: The purpose of this study was to examine the impact of the Mozart effect on the reliability of the Humphrey visual field (HVF; Carl Zeiss Meditec, Dublin, CA) test in subjects with glaucoma. A previous study showed improved reliability in normal subjects undergoing HVF testing. METHODS: One hundred sixty subjects with glaucoma were randomized to three groups: control, headphones, or music for 10 minutes before HVF testing. The headphone group was provided noise-cancellation headphones but no music. The music group listened to Mozart's Sonata for Two Pianos in D Major. After treatment, subjects took an HVF test in both eyes. The reliability of the test was then compared between the groups and also to prior HVF results with regard to fixation losses, false positives, and false negatives. RESULTS: The rate of fixation losses did not differ significantly between the three groups (P = 0.30 right eye, P = 0.24 left eye). There were also no significant differences in the rate of false positives (P = 0.82 right eye, P = 0.18 left eye) or false negatives (P = 0.91 right eye, P = 0.97 left eye). The reliability of the subject's HVF result was also compared with past field results. No improvements were seen in fixation losses (P = 0.94 right eye, P = 0.17 left eye), false positives (P = 0.85 right eye, P = 0.38 left eye), and false negatives (P = 0.13 right eye, P = 0.50 left eye). CONCLUSIONS: The rate of fixation losses, false positives, and false negatives did not improve in subjects with glaucoma after they listened to Mozart's music. The Mozart effect did not enhance the reliability of the visual field test to a statistically significant degree (ClinicalTrials.gov number, NCT01027039).