A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats. Long-read ...sequencing technologies, such as Oxford Nanopore's MinION, enable direct measurement of complex loci without introducing many of the biases inherent to short-read methods, though they suffer from relatively lower throughput. This limitation has motivated recent efforts to develop amplification-free strategies to target and enrich loci of interest for subsequent sequencing with long reads. Here, we present CaBagE, a method for target enrichment that is efficient and useful for sequencing large, structurally complex targets. The CaBagE method leverages the stable binding of Cas9 to its DNA target to protect desired fragments from digestion with exonuclease. Enriched DNA fragments are then sequenced with Oxford Nanopore's MinION long-read sequencing technology. Enrichment with CaBagE resulted in a median of 116X coverage (range 39-416) of target loci when tested on five genomic targets ranging from 4-20kb in length using healthy donor DNA. Four cancer gene targets were enriched in a single reaction and multiplexed on a single MinION flow cell. We further demonstrate the utility of CaBagE in two ALS patients with C9orf72 short tandem repeat expansions to produce genotype estimates commensurate with genotypes derived from repeat-primed PCR for each individual. With CaBagE there is a physical enrichment of on-target DNA in a given sample prior to sequencing. This feature allows adaptability across sequencing platforms and potential use as an enrichment strategy for applications beyond sequencing. CaBagE is a rapid enrichment method that can illuminate regions of the 'hidden genome' underlying human disease.
Objectives Analyses of mechanical circulatory support (MCS) in pediatric heart surgery have primarily focused on single-center outcomes or narrow applications. We describe the patterns of use, ...patient characteristics, and MCS-associated outcomes across a large multicenter cohort. Methods Patients (aged <18 years) in the Society of Thoracic Surgeons (STS) Congenital Heart Surgery Database (2000-2010) were included. The characteristics and outcomes of those receiving postoperative MCS were described, and bayesian hierarchical models were used to examine variations in the adjusted MCS rates across institutions. Results Of 96,596 operations (80 centers), MCS was used in 2.4%. The MCS patients were younger (13 vs 195 days, P < .0001) and more often had STS-defined preoperative risk factors (57.2% vs 32.7%, P < .0001). The operations with the greatest MCS rates included the Norwood procedure (17%) and complex biventricular repairs (arterial switch, ventricular septal defect, and arch repair 14%). More than one half of the MCS patients did not survive to hospital discharge (53.2% vs 2.9% of non-MCS patients; P < .0001). MCS-associated mortality was greatest for truncus arteriosus and Ross-Konno operations (both 71%). The hospital-level MCS rates adjusted for patient characteristics and case mix varied by 15-fold across institutions, with both high- and low-volume hospitals having substantial variation in MCS rates. Conclusions Perioperative MCS use varied widely across centers. The MCS rates were greatest overall for the Norwood procedure and complex biventricular repairs. Although MCS can be a life-saving therapy, more than one half of MCS patients will not survive to hospital discharge, with mortality >70% for some operations. Future studies aimed at better understanding the appropriate indications, optimal timing, and management of MCS could help to reduce the variation in MCS use across hospitals and improve outcomes.
Obesity is a global public health challenge and strongly associated with type 2 diabetes (T2D), but its burden and effects are not well understood in people with type 1 diabetes (T1D). Particularly, ...the link between obesity and chronic kidney disease (CKD) in T1D is poorly characterized.
We included all T1D and, for comparison, T2D in the Geisinger Health System from 2004 to 2018. We evaluated trends in obesity (body mass index ≥ 30 kg/m2), low estimated glomerular filtration rate (eGFR) (≤60 mL/min/1.73m2), and albuminuria (urine albumin-to-creatinine ratio ≥ 30 mg/g). We used multivariable logistic regression to evaluate the independent association of obesity with CKD in 2018.
People with T1D were younger than T2D (median age 39 vs 62 years). Obesity increased in T1D over time (32.6% in 2004 to 36.8% in 2018), while obesity in T2D was stable at ~60%. The crude prevalence of low eGFR was higher in T2D than in T1D in all years (eg, 30.6% vs 16.1% in 2018), but after adjusting for age differences, prevalence was higher in T1D than T2D in all years (eg, 16.2% vs 9.3% in 2018). Obesity was associated with increased odds of low eGFR in T1D adjusted odds ratio (AOR) = 1.52, 95% CI 1.12-2.08 and T2D (AOR = 1.29, 95% CI 1.23-1.35).
Obesity is increasing in people with T1D and is associated with increased risk of CKD. After accounting for age, the burden of CKD in T1D exceeded the burden in T2D, suggesting the need for increased vigilance and assessment of kidney-protective medications in T1D.
Among patients with congenital heart disease (CHD), the coexistence of noncardiac congenital anatomic abnormalities (NC), genetic abnormalities (GA), and syndromes (S) may influence therapeutic ...strategies and outcomes. The appreciated prevalence of these abnormalities has risen because increased screening and improved diagnostic precision enable identification of these comorbidities in a larger fraction of neonates with CHD. We examined the contemporary prevalence and distribution of NC/GA/S across diagnostic groups among neonates undergoing cardiac operations using a large nationally representative clinical registry.
The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) was queried to identify neonates (≤30 days) who underwent index cardiac operations from 2010 to 2013. The fundamental cardiac diagnosis was used to identify 10 diagnostic groups. The prevalence of NC/GA/S was reported across each group.
The cohort included 15,376 index neonatal operations from 112 centers. Overall, 18.8% (2,894 of 15,376) of operations were performed in neonates with NC/GA/S. Patients with atrioventricular septal defect (212 of 357 59.4%), interrupted aortic arch (248 of 567 43.7%), truncus arteriosus (204 of 554 36.8%), and tetralogy of Fallot (417 of 1,383 30.2%) had the highest prevalence of NC/GA/S abnormalities, whereas those with transposition of the great arteries (111 of 2,778 4.0%) had the lowest prevalence. The most commonly identified NC/GA/S included heterotaxy (597 of 15,376 3.9%), DiGeorge syndrome or 22q11 deletion (550 of 15,376 3.6%), Down syndrome or trisomy 21 (318 of 15, 376 2.1%), intestinal malrotation (220 of 15,376 1.4%), and Turner syndrome or 45XO (189 of 15,376 1.2%).
The prevalence of NC/GA/S varies widely across CHD diagnostic groups. This information may be useful for patient counseling, recommendations for screening for anomalies and genetic disorders, and perioperative management.
A high frequency of single nucleotide somatic mutations in the placenta has been recently described, but its relationship to placental dysfunction is unknown.
We performed a pilot case-control study ...using paired fetal, maternal, and placental samples collected from healthy live birth controls (n = 10), live births with fetal growth restriction (FGR) due to placental insufficiency (n = 7), and stillbirths with FGR and placental insufficiency (n = 11). We quantified single nucleotide and structural somatic variants using bulk whole genome sequencing (30-60X coverage) in four biopsies from each placenta. We also assessed their association with clinical and histological evidence of placental dysfunction.
Seventeen pregnancies had sufficiently high-quality placental, fetal, and maternal DNA for analysis. Each placenta had a median of 473 variants (range 111–870), with 95 % arising in just one biopsy within each placenta. In controls, live births with FGR, and stillbirths, the median variant counts per placenta were 514 (IQR 381–779), 582 (450–735), and 338 (245–441), respectively. After adjusting for depth of sequencing coverage and gestational age at birth, the somatic mutation burden was similar between groups (FGR live births vs. controls, adjusted diff. 59, 95 % CI -218 to +336; stillbirths vs controls, adjusted diff. −34, −351 to +419), and with no association with placental dysfunction (p = 0.7).
We confirmed the high prevalence of somatic mutation in the human placenta and conclude that the placenta is highly clonal. We were not able to identify any relationship between somatic mutation burden and clinical or histologic placental insufficiency.
•Somatic mutation is highly prevalent in the human placenta.•95 % of comatic variants were present in just one of four biopsies in each placenta.•Somatic mutation estimates were driven by sequencing depth and gestational age.•Two variant calling algorithms yield very different somatic variation estimates.•We found no association between somatic variant burden and clinical outcome.
More than 90% of coronary artery bypass grafting (CABG) is performed with a single-arterial bypass graft (SABG), based on the left internal thoracic artery (ITA) with supplemental vein grafts. This ...practice, often justified by safety concerns with multiple-arterial grafting (MABG), defies evidence of improved late survival achieved with bilateral ITA (BITA-MABG) or left ITA plus radial artery (RA-MABG). We hypothesized that MABG and SABG are equally safe.
We analyzed The Society of Thoracic Surgeons National Database (2004 to 2015) to assess the operative safety of BITA-MABG (n = 73,054) and RA-MABG (n = 97,623) vs SABG (n = 1,334,511). Primary end points were operative (30-day or same hospitalization) mortality (OM) and deep sternal wound infections (DSWI). Risk-adjusted odds ratios (AOR) and 95% confidence intervals (CIs) were derived from by logistic regression with sensitivity analyses in multiple subcohorts including MABG use rate.
SABG (73.8% men; median age, 66 years), BITA-MABG (85.1% men; median age, 59 years), and RA-MABG (82.5% men; median age, 61 years) showed distinctly different patient characteristics. Compared with SABG (1.91% OM; 0.73% DSWI), observed OM was lower for BITA-MABG (1.19%, p < 0.001) and RA-MABG (1.19%, p < 0.001). DSWI was higher among BITA-MABG (1.08%, p < 0.001) and similar for RA-MABG (0.71%, p = 0.55). BITA-MABG showed marginally increased, likely not clinically significant, OM (AOR, 1.14; 95% CI, 1.00 to 1.30; p = 0.05) and doubled DSWI (AOR, 2.09; 95% CI, 1.80 to 2.43; p < 0.001). RA-MABG had similar OM (AOR, 1.01; 95% CI, 0.89 to 1.15; p = 0.85) and DSWI (AOR, 0.97; 95% CI, 0.83 to 1.13; p = 0.70). Results were consistent across multiple subcohorts. A U-shaped OM vs BITA use relation was documented, with worse OM at hospitals with low (<5%: AOR, 1.38; 95% CI, 1.18 to 1.61; p < 0.001) and high (≥40%: AOR, 1.31; 95% CI, 1.00 to 1.70; p = 0.049) BITA use.
MABG in the United States is associated with OM comparable to SABG and increased DSWI risk with BITA-MABG. Our findings highlight the importance of surgeon and institutional experience and careful patient selection for BITA-MABG. Our short-term results should not in any way dissuade the use of MABG, given its well-established long-term survival advantage.
As less invasive alternatives to surgical pulmonary valve replacement (PVR) are being refined and evaluated, there is a need for benchmark data concerning outcomes from surgical PVR.
We examined ...in-hospital outcomes from surgical PVR in The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) and Adult Cardiac Surgery Database (STS-ACSD) between 2007 and 2013, with a focus on patients likely to be eligible for transcatheter PVR (ie, ≥ 5 years age and ≥ 30 kg). Patient characteristics, morbidity, and mortality were described.
The STS-CHSD included 6,431 eligible patients with a median age of 17 years (interquartile range IQR, 14-25 years). Preoperative comorbidities were uncommon: arrhythmia (1.7%), renal failure (0.1%), endocarditis (0.3%), neurologic deficit (0.8%), and diabetes (0.5%). In-hospital mortality was 0.9%. A major complication occurred in 2.2%. The STS-ACSD included 3,352 eligible patients; the median age was 41 years (IQR, 30-55 years). Preoperative comorbidities were more common: arrhythmia (24.3%), renal failure (3.8%), endocarditis (12.2%), cerebrovascular disease (7.9%), and diabetes (10.9%). In-hospital mortality was 4.1%. A major complication occurred in 20.9%.
Contemporary outcomes from surgical PVR include a low risk of in-hospital death or major complications. Patients in the STS-ACSD are older and have an increased prevalence of preoperative factors, which may contribute to higher morbidity and mortality.
Robotic technology is one of the most recent technological changes in coronary artery bypass graft (CABG) operations. The current analysis was conducted to identify trends in the use and outcomes of ...robotic-assisted CABG (RA-CABG).
A retrospective analysis was performed using data from The Society of Thoracic Surgeons Adult Cardiac Surgery Database between 2006 and 2012. Patient and site-level characteristics were compared between traditional CABG and RA-CABG. Operative death, postoperative length of stay, and postoperative complications were compared between the two groups.
The number of sites using RA-CABG remained relatively constant during the study period (from 148 in 2006 to 151 in 2012). The volume of RA-CABG as a percentage of the total CABG procedures increased slightly from 0.59% (872 RA-CABG of 127,717 total CABG) in 2006 to 0.97% (1,260 RA-CABG of 97,249 total CABG) in 2012. The RA-CABG patients were significantly younger (64 vs 65 years, p < 0.0001), had fewer comorbidities, and had lower rates of cardiopulmonary bypass use (22.4% vs 80.4%, p < 0.0001). RA-CABG patients had significantly lower unadjusted major complication rates (10.2% vs 13.5%, p < 0.0001), including postoperative renal failure (2.2% vs 2.9%, p < 0.0001), and shorter length of stay (4 vs 5 days, p < 0.0001). The difference in operative death was not significant (odds ratio, 1.10; 95% confidence interval, 0.92 to 1.30, p = 0.29).
RA-CABG use remained relatively stagnant during the analysis period despite lower rates of major perioperative complications and no difference in operative deaths. Additional analysis is needed to fully understand the role that robotic technology will play in CABG operations in the future.
In this paper, we define the Association of Standardized Patient Educators (ASPE) Standards of Best Practice (SOBP) for those working with human role players who interact with learners in a wide ...range of experiential learning and assessment contexts. These human role players are variously described by such terms as standardized/simulated patients or simulated participants (SP or SPs). ASPE is a global organization whose mission is to share advances in SP-based pedagogy, assessment, research, and scholarship as well as support the professional development of its members. The SOBP are intended to be used in conjunction with the International Nursing Association for Clinical Simulation and Learning (INACSL) Standards of Best Practice: Simulation
, which address broader simulation practices. We begin by providing a rationale for the creation of the ASPE SOBP, noting that with the increasing use of simulation in healthcare training, it is incumbent on ASPE to establish SOBP that ensure the growth, integrity, and safe application of SP-based educational endeavors. We then describe the three and a half year process through which these standards were developed by a consensus of international experts in the field. Key terms used throughout the document are defined. Five underlying
inform the SOBP: safety, quality, professionalism, accountability, and collaboration. Finally, we describe five
of best practice: safe work environment; case development; SP training for role portrayal, feedback, and completion of assessment instruments; program management; and professional development. Each domain is divided into
with accompanying key
that provide clear and practical guidelines for achieving desired outcomes and creating simulations that are safe for all stakeholders. Failure to follow the ASPE SOBP could compromise the safety of participants and the effectiveness of a simulation session. Care has been taken to make these guidelines precise yet flexible enough to address the diversity of varying contexts of SP practice. As a living document, these SOBP will be reviewed and modified periodically under the direction of the ASPE Standards of Practice Committee as SP methodology grows and adapts to evolving simulation practices.
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