Emerging Opportunities to Study Mobile Element Insertions and Their Source Elements in an Expanding Universe of Sequenced Human Genomes.

Three mobile element classes, namely Alu, LINE-1 (L1), and SVA elements, remain actively mobile in human genomes and continue to produce new mobile element insertions (MEIs). Historically, MEIs have been discovered and studied using several methods, including: (1) Southern blots, (2) PCR (including PCR display), and (3) the detection of MEI copies from young subfamilies. We are now entering a new phase of MEI discovery where these methods are being replaced by whole genome sequencing and bioinformatics analysis to discover novel MEIs. We expect that the universe of sequenced human genomes will continue to expand rapidly over the next several years, both with short-read and long-read technologies. These resources will provide unprecedented opportunities to discover MEIs and study their impact on human traits and diseases. They also will allow the MEI community to discover and study the source elements that produce these new MEIs, which will facilitate our ability to study source element regulation in various tissue contexts and disease states. This, in turn, will allow us to better understand MEI mutagenesis in humans and the impact of this mutagenesis on human biology.

Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants.

Complex structural variants (CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants. However, detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy. As a result, there has been limited progress for CSV discovery compared with simple structural variants. Here, we systematically analyzed the multi-breakpoint connection feature of CSVs, and proposed Mako, utilizing a bottom-up guided model-free strategy, to detect CSVs from paired-end short-read sequencing. Specifically, we implemented a graph-based pattern growth approach, where the graph depicts potential breakpoint connections, and pattern growth enables CSV detection without pre-defined models. Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms. Notably, validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%, where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp, respectively. Moreover, the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types, including two novel types of adjacent segment swap and tandem dispersed duplication. Further analysis of these CSVs also revealed the impact of sequence homology on the formation of CSVs. Mako is publicly available at https://github.com/xjtu-omics/Mako.

Mutagenesis of human genomes by endogenous mobile elements on a population scale.

Several large-scale Illumina whole-genome sequencing (WGS) and whole-exome sequencing (WES) projects have emerged recently that have provided exceptional opportunities to discover mobile element insertions (MEIs) and study the impact of these MEIs on human genomes. However, these projects also have presented major challenges with respect to the scalability and computational costs associated with performing MEI discovery on tens or even hundreds of thousands of samples. To meet these challenges, we have developed a more efficient and scalable version of our mobile element locator tool (MELT) called CloudMELT. We then used MELT and CloudMELT to perform MEI discovery in 57,919 human genomes and exomes, leading to the discovery of 104,350 nonredundant MEIs. We leveraged this collection (1) to examine potentially active L1 source elements that drive the mobilization of new Alu, L1, and SVA MEIs in humans; (2) to examine the population distributions and subfamilies of these MEIs; and (3) to examine the mutagenesis of GENCODE genes, ENCODE-annotated features, and disease genes by these MEIs. Our study provides new insights on the L1 source elements that drive MEI mutagenesis and brings forth a better understanding of how this mutagenesis impacts human genomes.

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies.

Virtually all genome sequencing efforts in national biobanks, complex and Mendelian disease programs, and medical genetic initiatives are reliant upon short-read whole-genome sequencing (srWGS), which presents challenges for the detection of structural variants (SVs) relative to emerging long-read WGS (lrWGS) technologies. Given this ubiquity of srWGS in large-scale genomics initiatives, we sought to establish expectations for routine SV detection from this data type by comparison with lrWGS assembly, as well as to quantify the genomic properties and added value of SVs uniquely accessible to each technology. Analyses from the Human Genome Structural Variation Consortium (HGSVC) of three families captured ~11,000 SVs per genome from srWGS and ~25,000 SVs per genome from lrWGS assembly. Detection power and precision for SV discovery varied dramatically by genomic context and variant class: 9.7% of the current GRCh38 reference is defined by segmental duplication (SD) and simple repeat (SR), yet 91.4% of deletions that were specifically discovered by lrWGS localized to these regions. Across the remaining 90.3% of reference sequence, we observed extremely high (93.8%) concordance between technologies for deletions in these datasets. In contrast, lrWGS was superior for detection of insertions across all genomic contexts. Given that non-SD/SR sequences encompass 95.9% of currently annotated disease-associated exons, improved sensitivity from lrWGS to discover novel pathogenic deletions in these currently interpretable genomic regions is likely to be incremental. However, these analyses highlight the considerable added value of assembly-based lrWGS to create new catalogs of insertions and transposable elements, as well as disease-associated repeat expansions in genomic sequences that were previously recalcitrant to routine assessment.

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.

Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing1,2 with continuous long-read or high-fidelity3 sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.

Striking heterogeneity of somatic L1 retrotransposition in single normal and cancerous gastrointestinal cells.

Somatic LINE-1 (L1) retrotransposition has been detected in early embryos, adult brains, and the gastrointestinal (GI) tract, and many cancers, including epithelial GI tumors. We previously found numerous somatic L1 insertions in paired normal and GI cancerous tissues. Here, using a modified method of single-cell analysis for somatic L1 insertions, we studied adenocarcinomas of colon, pancreas, and stomach, and found a variable number of somatic L1 insertions in tumors of the same type from patient to patient. We detected no somatic L1 insertions in single cells of 5 of 10 tumors studied. In three tumors, aneuploid cells were detected by FACS. In one pancreatic tumor, there were many more L1 insertions in aneuploid than in euploid tumor cells. In one gastric cancer, both aneuploid and euploid cells contained large numbers of likely clonal insertions. However, in a second gastric cancer with aneuploid cells, no somatic L1 insertions were found. We suggest that when the cellular environment is favorable to retrotransposition, aneuploidy predisposes tumor cells to L1 insertions, and retrotransposition may occur at the transition from euploidy to aneuploidy. Seventeen percent of insertions were also present in normal cells, similar to findings in genomic DNA from normal tissues of GI tumor patients. We provide evidence that: 1) The number of L1 insertions in tumors of the same type is highly variable, 2) most somatic L1 insertions in GI cancer tissues are absent from normal tissues, and 3) under certain conditions, somatic L1 retrotransposition exhibits a propensity for occurring in aneuploid cells.

Incidence of insufficient intraoperative neuromuscular paralysis. A retrospective registry analysis.

STUDY OBJECTIVE: Muscular tone that inhibits anesthetic or surgical care characterizes insufficient neuromuscular block. The incidence of insufficient neuromuscular block is unknown, therefore we developed novel electronic search strategies to identify occurrences of insufficient neuromuscular block. Our primary goal was to determine the incidence of intraoperative insufficient neuromuscular block in abdominal and neurovascular surgery. Our secondary goal was to assess factors independently associated with insufficient block. DESIGN: Retrospective cohort. SETTING: Operating rooms in a tertiary care center. PATIENTS: Adults having abdominal, laparoscopic, and interventional neurovascular procedures under general anesthesia with endotracheal intubation between April 2005 and February 2013. MEASUREMENTS: An expert panel of anesthesiologists used a Delphi process to develop criteria to identify insufficient intraoperative neuromuscular block. 10 final criteria were agreed upon and used to determine the incidence of insufficient neuromuscular block. MAIN RESULTS: 48,315 surgeries met our inclusion requirements. Intraoperative insufficient neuromuscular block was identified in 13,538 cases, representing 28% (95% CI: 27.6%, 28.4%) of the operations. Younger age, male sex, type of surgery, longer duration of surgery, pre-existing conditions, and use of volatile anesthetics were independently associated with insufficient block after Bonferroni correction. CONCLUSION: Our results suggest that episodes of insufficient block occur in over a quarter of operations that are generally thought to require muscle relaxation. Without neuromuscular monitoring, it is difficult to separate inadequate anesthesia from inadequate neuromuscular block, and both presumably contributed in many cases.

Aberrantly High Levels of Somatic LINE-1 Expression and Retrotransposition in Human Neurological Disorders.

Retrotransposable elements (RTEs) have actively multiplied over the past 80 million years of primate evolution, and as a consequence, such elements collectively occupy ∼ 40% of the human genome. As RTE activity can have detrimental effects on the human genome and transcriptome, silencing mechanisms have evolved to restrict retrotransposition. The brain is the only known somatic tissue where RTEs are de-repressed throughout the life of a healthy human and each neuron in specific brain regions accumulates up to ∼13.7 new somatic L1 insertions (and perhaps more). However, even higher levels of somatic RTE expression and retrotransposition have been found in a number of human neurological disorders. This review is focused on how RTE expression and retrotransposition in neuronal tissues might contribute to the initiation and progression of these disorders. These disorders are discussed in three broad and sometimes overlapping categories: 1) disorders such as Rett syndrome, Aicardi-Goutières syndrome, and ataxia-telangiectasia, where expression/retrotransposition is increased due to mutations in genes that play a role in regulating RTEs in healthy cells, 2) disorders such as autism spectrum disorder, schizophrenia, and substance abuse disorders, which are thought to be caused by a combination of genetic and environmental stress factors, and 3) disorders associated with age, such as frontotemporal lobar degeneration (FTLD), amyotrophic lateral sclerosis (ALS), and normal aging, where there is a time-dependent accumulation of neurological degeneration, RTE copy number, and phenotypes. Research has revealed increased levels of RTE activity in many neurological disorders, but in most cases, a clear causal link between RTE activity and these disorders has not been well established. At the same time, even if increased RTE activity is a passenger and not a driver of disease, a detrimental effect is more likely than a beneficial one. Thus, a better understanding of the role of RTEs in neuronal tissues likely is an important part of understanding, preventing, and treating these disorders.

Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma.

Glioma is a unique neoplastic disease that develops exclusively in the central nervous system (CNS) and rarely metastasizes to other tissues. This feature strongly implicates the tumor-host CNS microenvironment in gliomagenesis and tumor progression. We investigated the differences and similarities in glioma biology as conveyed by transcriptomic patterns across four mammalian hosts: rats, mice, dogs, and humans. Given the inherent intra-tumoral molecular heterogeneity of human glioma, we focused this study on tumors with upregulation of the platelet-derived growth factor signaling axis, a common and early alteration in human gliomagenesis. The results reveal core neoplastic alterations in mammalian glioma, as well as unique contributions of the tumor host to neoplastic processes. Notable differences were observed in gene expression patterns as well as related biological pathways and cell populations known to mediate key elements of glioma biology, including angiogenesis, immune evasion, and brain invasion. These data provide new insights regarding mammalian models of human glioma, and how these insights and models relate to our current understanding of the human disease.

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology.

Mobile element insertions (MEIs) represent ∼25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases, and clinical genomics. Here, we describe the Mobile Element Locator Tool (MELT), which was developed as part of the 1000 Genomes Project to perform MEI discovery on a population scale. Using both Illumina WGS data and simulations, we demonstrate that MELT outperforms existing MEI discovery tools in terms of speed, scalability, specificity, and sensitivity, while also detecting a broader spectrum of MEI-associated features. Several run modes were developed to perform MEI discovery on local and cloud systems. In addition to using MELT to discover MEIs in modern humans as part of the 1000 Genomes Project, we also used it to discover MEIs in chimpanzees and ancient (Neanderthal and Denisovan) hominids. We detected diverse patterns of MEI stratification across these populations that likely were caused by (1) diverse rates of MEI production from source elements, (2) diverse patterns of MEI inheritance, and (3) the introgression of ancient MEIs into modern human genomes. Overall, our study provides the most comprehensive map of MEIs to date spanning chimpanzees, ancient hominids, and modern humans and reveals new aspects of MEI biology in these lineages. We also demonstrate that MELT is a robust platform for MEI discovery and analysis in a variety of experimental settings.

Postoperative Respiratory Complications in Patients at Risk for Obstructive Sleep Apnea: A Single-Institution Cohort Study.

BACKGROUND: Obstructive sleep apnea (OSA) is a prevalent condition that is associated with early postoperative respiratory complications (PRCs). As the majority of patients with OSA are undiagnosed, preoperative screening remains the most efficient method to identify suspected OSA. METHODS: This retrospective study was performed on patients undergoing anesthesia in a single academic medical center. We assigned OSA risk class retrospectively to all patients in the study by using the Perioperative Sleep Apnea Prediction (PSAP) score. We evaluated the relationship between PSAP categories and early postoperative invasive airway placement after adjusting for several preoperative and intraoperative factors (including surgical risk) previously associated with PRC occurrence. RESULTS: A total of 108,479 patients were included in the final analysis with an incidence of PRC was 0.3% (n = 280). High PSAP score was associated with postoperative intubation (adjusted odds ratio, 2.3; 95% confidence interval, 1.5-3.7). Several risk factors reflecting anesthetic agents, neuromuscular blocking agents, and opioids were also independently associated with early PRC. CONCLUSIONS: We report that suspected OSA based on the PSAP score is independently associated with increased risk of early PRC. Specific anesthetic agents are independently associated with early PRC, pointing to the potential for examining risk modification through these exposures in future studies.

The Role of Somatic L1 Retrotransposition in Human Cancers.

The human LINE-1 (or L1) element is a non-LTR retrotransposon that is mobilized through an RNA intermediate by an L1-encoded reverse transcriptase and other L1-encoded proteins. L1 elements remain actively mobile today and continue to mutagenize human genomes. Importantly, when new insertions disrupt gene function, they can cause diseases. Historically, L1s were thought to be active in the germline but silenced in adult somatic tissues. However, recent studies now show that L1 is active in at least some somatic tissues, including epithelial cancers. In this review, we provide an overview of these recent developments, and examine evidence that somatic L1 retrotransposition can initiate and drive tumorigenesis in humans. Recent studies have: (i) cataloged somatic L1 activity in many epithelial tumor types; (ii) identified specific full-length L1 source elements that give rise to somatic L1 insertions; and (iii) determined that L1 promoter hypomethylation likely plays an early role in the derepression of L1s in somatic tissues. A central challenge moving forward is to determine the extent to which L1 driver mutations can promote tumor initiation, evolution, and metastasis in humans.

Development and validation of a Score for Preoperative Prediction of Obstructive Sleep Apnea (SPOSA) and its perioperative outcomes.

BACKGROUND: Postoperative respiratory complications (PRCs) are associated with significant morbidity, mortality, and hospital costs. Obstructive sleep apnea (OSA), often undiagnosed in the surgical population, may be a contributing factor. Thus, we aimed to develop and validate a score for preoperative prediction of OSA (SPOSA) based on data available in electronic medical records preoperatively. METHODS: OSA was defined as the occurrence of an OSA diagnostic code preceded by a polysomnography procedure. A priori defined variables were analyzed by multivariable logistic regression analysis to develop our score. Score validity was assessed by investigating the score's ability to predict non-invasive ventilation. We then assessed the effect of high OSA risk, as defined by SPOSA, on PRCs within seven postoperative days and in-hospital mortality. RESULTS: A total of 108,781 surgical patients at Partners HealthCare hospitals (2007-2014) were studied. Predictors of OSA included BMI >25 kg*m-2 and comorbidities, including pulmonary hypertension, hypertension, and diabetes. The score yielded an area under the curve of 0.82. Non-invasive ventilation was significantly associated with high OSA risk (OR 1.44, 95% CI 1.22-1.69). Using a dichotomized endpoint, 26,968 (24.8%) patients were identified as high risk for OSA and 7.9% of these patients experienced PRCs. OSA risk was significantly associated with PRCs (OR 1.30, 95% CI 1.19-1.43). CONCLUSION: SPOSA identifies patients at high risk for OSA using electronic medical record-derived data. High risk of OSA is associated with the occurrence of PRCs.

Retrospective observational evaluation of postoperative oxygen saturation levels and associated postoperative respiratory complications and hospital resource utilization.

INTRODUCTION: The clinical importance of postoperative episodic hypoxemia is still unclear, and therefore largely under-studied. As a result, there is limited understanding of its relationship with early postoperative respiratory complications (PRC, defined as intubation within three days of surgery) and hospital resource utilization. MATERIALS AND METHODS: This single center study was performed using a retrospective observational design. We described population based definitions of desaturation from continuous SpO2 monitoring data captured in the post anesthesia care unit (PACU), namely median SpO2 in PACU, duration of desaturation below median, nadir desaturation, and length of oxygen therapy relative to PACU duration. These measures were evaluated against the occurrence of early PRC in logistic regression models. Measures that were independently associated with early PRC were accepted as the primary study exposures. Stratified logistic regression models were planned if significant interaction occurred with high risk surgical procedures. Models were adjusted by including several patient conditions, procedural, and anesthesia risk factors. Propensity matching on desaturation occurrence was planned to evaluate the relationship with postoperative resource utilization. RESULTS: Among 125,740 patients included in the univariate analyses, 351 patients (0.3%) developed early PRC. Nadir desaturation <89% [14.3% of patients; adjusted odds ratio 2.02; 95% CI 1.52, 2.68; p<0.001] and PACU oxygen therapy requirements greater than 60 min [adjusted odds ratio 1.92 (>60 min) to 3.04 (>90 min); p<0.001] were identified as independent predictors of early PRC occurrence. A modest interaction was observed between desaturation and higher surgical risk. Propensity matching for postoperative oxygen requirement was performed in 37,354 matched patients. Matched analysis demonstrated significant increase in day of surgery charges, respiratory charges, total charges, hospital length of stay, reintubation and use of invasive or non-invasive ventilatory support. CONCLUSIONS: In summary, we report that prolonged PACU oxygen therapy and nadir desaturation <89% in PACU as captured in a retrospective database are independently associated with early PRC. This study describes resource implications of PACU desaturation in a large academic medical center in North America.

Frequency of inadequate neuromuscular blockade during general anesthesia.

STUDY OBJECTIVE: We used electronic health record data to define frequency of inadequate intraoperative neuromuscular blockade (NMB). DESIGN: Retrospective observational study using electronic health record data. SETTING: Operating room in a tertiary care academic hospital. PATIENTS: A total of 129,209 adult patients with American Society of Anesthesiologists physical status 1 to 5 undergoing general anesthesia in an outpatient or inpatient setting who received nondepolarizing NMB. We excluded patients intubated before arrival to the operating room, patients undergoing a liver transplant or cardiac surgery, and patients who remained intubated at the end of the operation. INTERVENTIONS: None. MEASUREMENTS: The primary outcomes were inadequate NMB defined by (1) documentation of patient movement and (2) documentation of surgical request for additional NMB, followed by NMB agent administration. MAIN RESULTS: A total of 1261 patients (1.0%) demonstrated either intraoperative movement (369 or 0.29%) or prompted surgical request for additional NMB agent (921 or 0.71%). Trend analysis showed a variation in the annual rate of inadequate NMB, with an increase from 2004 to 2013 for criteria 1 and 2. CONCLUSIONS: Nearly 1% of all general anesthetic procedures involving NMB exhibit inadequate relaxation resulting in procedural interruption. These data suggest that current use of neuromuscular blocking drugs and NMB monitoring expose patients to inadequate blockade. The risk of this phenomenon warrants further study.

Observational study on patterns of neuromuscular blockade reversal.

BACKGROUND: Using electronic health record data, we hypothesized that larger reversal doses are used for patients with deeper levels of neuromuscular blockade (NMB) as evidenced by the last recorded TOF measurement. We also examined if dosing regimens reflect current practice guidelines of using ideal body weight (IBW) for NMB agents and total body weight (TBW) for neostigmine. METHODS: This is a retrospective observational study of adult, ASA 1-4 patients who underwent general anaesthesia and received non-depolarizing NMB agents between 01/01/2004 and 12/31/2013. For the primary outcome, percentages of cases receiving neostigmine and median doses administered for each subjective train-of-four (TOF) category were calculated. Secondary analyses evaluated associations between NMB dosing and neostigmine administration based on Body Mass Index (BMI) categories. RESULTS: A total of 135,633 cases met inclusion criteria for the study. There was no clinically significant difference in median neostigmine dosing based on last TOF count prior to reversal administration: 37.5 mcg/kg for TOF of 4/4 vs. 37.9 mcg/kg for TOF of 0/4 for the total neostigmine dose. Significantly higher number of patients with lower TOF counts received additional neostigmine administration: 5.7 % for 0/4 vs. 1.5 % for 4/4 TOF counts. The median times to extubation following neostigmine administration were clinically similar across TOF count categories. The median doses for neostigmine based on TBW decreased with higher BMI categories and were significantly different between the lowest and highest categories: 42.8 mcg/kg vs 30.8 mcg/kg for total doses (p < .0001) respectively. The percentages of cases requiring reversal in addition to the initial dose increased with increasing BMI categories and were 2.1 % for BMI < 18 vs. 3.3 % for BMI ≥ 40. The total median dose of NMB agents in ED95 equivalents per IBW increased from 2.9 in the Underweight category to 4.2 in the Class III Obese category. The majority of patients in the pancuronium subgroup received very low ED95 equivalent dose of 0.1 and did not require reversal. Patients receiving cisatracurium were given significantly higher median ED95 equivalent dose of 5.6 vs 2.8-3.9 compared to other intermediate acting NMB agents, while receiving clinically similar doses of neostigmine. CONCLUSIONS: Neither neostigmine dosing nor times to extubation were affected by the depth of the neuromuscular blockade prior to reversal. The need for additional reversal, or rescue, correlated strongly with the depth of NMB. There was significant variability in neostigmine dosing across the BMI categories. Underweight patients received relatively lower NMB doses while simultaneously receiving relatively higher reversal doses, and the opposite was true for patients with BMI >40.

A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer.

Although human LINE-1 (L1) elements are actively mobilized in many cancers, a role for somatic L1 retrotransposition in tumor initiation has not been conclusively demonstrated. Here, we identify a novel somatic L1 insertion in the APC tumor suppressor gene that provided us with a unique opportunity to determine whether such insertions can actually initiate colorectal cancer (CRC), and if so, how this might occur. Our data support a model whereby a hot L1 source element on Chromosome 17 of the patient's genome evaded somatic repression in normal colon tissues and thereby initiated CRC by mutating the APC gene. This insertion worked together with a point mutation in the second APC allele to initiate tumorigenesis through the classic two-hit CRC pathway. We also show that L1 source profiles vary considerably depending on the ancestry of an individual, and that population-specific hot L1 elements represent a novel form of cancer risk.

Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study.

INTRODUCTION: Obstructive sleep apnoea (OSA), the most common type of sleep-disordered breathing, is associated with significant immediate and long-term morbidity, including fragmented sleep and impaired daytime functioning, as well as more severe consequences, such as hypertension, impaired cognitive function and reduced quality of life. Perioperatively, OSA occurs frequently as a consequence of pre-existing vulnerability, surgery and drug effects. The impact of OSA on postoperative respiratory complications (PRCs) needs to be better characterised. As OSA is associated with significant comorbidities, such as obesity, pulmonary hypertension, myocardial infarction and stroke, it is unclear whether OSA or its comorbidities are the mechanism of PRCs. This project aims to (1) develop a novel prediction score identifying surgical patients at high risk of OSA, (2) evaluate the association of OSA risk on PRCs and (3) evaluate if pharmacological agents used during surgery modify this association. METHODS: Retrospective cohort study using hospital-based electronic patient data and perioperative data on medications administered and vital signs. We will use data from Partners Healthcare clinical databases, Boston, Massachusetts. First, a prediction model for OSA will be developed using OSA diagnostic codes and polysomnography procedural codes as the reference standard, and will be validated by medical record review. Results of the prediction model will be used to classify patients in the database as high, medium or low risk of OSA, and we will investigate the effect of OSA on risk of PRCs. Finally, we will test whether the effect of OSA on PRCs is modified by the use of intraoperative pharmacological agents known to increase upper airway instability, including neuromuscular blockade, neostigmine, opioids, anaesthetics and sedatives. ETHICS AND DISSEMINATION: The Partners Human Research Committee approved this study (protocol number: 2014P000218). Study results will be made available in the form of manuscripts for publication and presentations at national and international meetings.

Pulmonary Nontuberculous Mycobacterial Infection. A Multisystem, Multigenic Disease.

RATIONALE: The clinical features of patients infected with pulmonary nontuberculous mycobacteria (PNTM) are well described, but the genetic components of infection susceptibility are not. OBJECTIVES: To examine genetic variants in patients with PNTM, their unaffected family members, and a control group. METHODS: Whole-exome sequencing was done on 69 white patients with PNTM and 18 of their white unaffected family members. We performed a candidate gene analysis using immune, cystic fibrosis transmembrance conductance regulator (CFTR), cilia, and connective tissue gene sets. The numbers of patients, family members, and control subjects with variants in each category were compared, as was the average number of variants per person. MEASUREMENTS AND MAIN RESULTS: A significantly higher number of patients with PNTM than the other subjects had low-frequency, protein-affecting variants in immune, CFTR, cilia, and connective tissue categories (35, 26, 90, and 90%, respectively). Patients with PNTM also had significantly more cilia and connective tissue variants per person than did control subjects (2.47 and 2.55 compared with 1.38 and 1.40, respectively; P = 1.4 × 10(-6) and P = 2.7 × 10(-8), respectively). Patients with PNTM had an average of 5.26 variants across all categories (1.98 in control subjects; P = 2.8 × 10(-17)), and they were more likely than control subjects to have variants in multiple categories. We observed similar results for family members without PNTM infection, with the exception of the immune category. CONCLUSIONS: Patients with PNTM have more low-frequency, protein-affecting variants in immune, CFTR, cilia, and connective tissue genes than their unaffected family members and control subjects. We propose that PNTM infection is a multigenic disease in which combinations of variants across gene categories, plus environmental exposures, increase susceptibility to the infection.