A deep catalog of protein-coding variation in 985,830 individuals

Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.

Genotyping, sequencing and analysis of 140,000 adults from Mexico City

The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent.

Use of Whole-Genome Sequencing to Estimate the Contribution of Immune Evasion and Waning Immunity on Decreasing COVID-19 Vaccine Effectiveness

BACKGROUND

The impact variant-specific immune evasion and waning protection have on declining coronavirus disease 2019 (COVID-19) vaccine effectiveness (VE) remains unclear. Using whole-genome sequencing (WGS), we examined the contribution these factors had on the decline that followed the introduction of the Delta variant. Furthermore, we evaluated calendar-period-based classification as a WGS alternative.

METHODS

We conducted a test-negative case-control study among people tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between 1 April and 24 August 2021. Variants were classified using WGS and calendar period.

RESULTS

We included 2029 cases (positive, sequenced samples) and 343 727 controls (negative tests). VE 14-89 days after second dose was significantly higher against Alpha (84.4%; 95% confidence interval [CI], 75.6%-90.0%) than Delta infection (68.9%; 95% CI, 58.0%-77.1%). The odds of Delta infection were significantly higher 90-149 than 14-89 days after second dose (P value = .003). Calendar-period-classified VE estimates approximated WGS-classified estimates; however, calendar-period-based classification was subject to misclassification (35% Alpha, 4% Delta).

CONCLUSIONS

Both waning protection and variant-specific immune evasion contributed to the lower effectiveness. While calendar-period-classified VE estimates mirrored WGS-classified estimates, our analysis highlights the need for WGS when variants are cocirculating and misclassification is likely.

UGT1A1 genetic variants are associated with increases in bilirubin levels in rheumatoid arthritis patients treated with sarilumab

Sarilumab is a human monoclonal antibody against interleukin (IL)-6Rα that has been approved for the treatment of adult patients with moderately to severely active rheumatoid arthritis (RA) and an inadequate response or intolerance to one or more disease-modifying antirheumatic drugs (DMARDs). Mild liver function test abnormalities have been observed in patients treated with sarilumab. We describe a genome-wide association study of bilirubin elevations in RA patients treated with sarilumab. Array genotyping and exome sequencing were performed on DNA samples from 1075 patients. Variants in the UGT1A1 gene were strongly associated with maximum bilirubin elevations in sarilumab-treated patients (rs4148325; p = 2.88 × 10⁻⁴¹) but were not associated with aminotransferase elevations. No other independent loci showed evidence of association with bilirubin elevations after sarilumab treatment. These findings suggest that most bilirubin increases during sarilumab treatment are related to genetic variation in UGT1A1 rather than underlying liver injury.

ERAP1, ERAP2, and Two Copies of HLA-Aw19 Alleles Increase the Risk for Birdshot Chorioretinopathy in HLA-A29 Carriers

Purpose

Birdshot chorioretinopathy (BSCR) is strongly associated with HLA-A29. This study was designed to elucidate the genetic modifiers of BSCR in HLA-A29 carriers.

Methods

We sequenced the largest BSCR cohort to date, including 286 cases and 108 HLA-A29–positive controls to determine genome-wide common and rare variant associations. We further typed the HLA alleles of cases and 45,386 HLA-A29 controls of European ancestry to identify HLA alleles that associate with BSCR risk.

Results

Carrying a second allele that belongs to the HLA-Aw19 broad antigen family (including HLA-A29, -A30, -A31, and -A33) increases the risk for BSCR (odds ratio [OR] = 4.44; P = 2.2e-03). This result was validated by comparing allele frequencies to large HLA-A29-controlled cohorts (n = 45,386; OR > 2.5; P < 1.3e-06). We also confirm that ERAP1 and ERAP2 haplotypes modulate disease risk. A meta-analysis with an independent dataset confirmed that ERAP1 and ERAP2 haplotypes modulate the risk for disease at a genome-wide significant level: ERAP1-rs27432 (OR = 2.46; 95% confidence interval [CI], 1.85–3.26; P = 4.07e-10), an expression quantitative trait locus (eQTL) decreasing ERAP1 expression; and ERAP2-rs10044354 (OR = 1.95; 95% CI, 1.55–2.44; P = 6.2e-09), an eQTL increasing ERAP2 expression. Furthermore, ERAP2-rs2248374 that disrupts ERAP2 expression is protective (OR = 0.56; 95% CI, 0.45–0.70; P = 2.39e-07). BSCR risk is additively increased when combining ERAP1/ERAP2 risk genotypes with two copies of HLA-Aw19 alleles (OR = 13.53; 95% CI, 3.79–54.77; P = 1.17e-05).

Conclusions

The genetic factors increasing BSCR risk demonstrate a pattern of increased processing, as well as increased presentation of ERAP2-specific peptides. This suggests a mechanism in which exceeding a peptide presentation threshold activates the immune response in choroids of A29 carriers.

Heterozygosity for a Pathogenic Variant in SLC12A3 That Causes Autosomal Recessive Gitelman Syndrome Is Associated with Lower Serum Potassium

BACKGROUND

Potassium levels regulate multiple physiologic processes. The heritability of serum potassium level is moderate, with published estimates varying from 17% to 60%, suggesting genetic influences. However, the genetic determinants of potassium levels are not generally known.

METHODS

A whole-exome sequencing association study of serum potassium levels in 5812 subjects of the Old Order Amish was performed. A dietary salt intervention in 533 Amish subjects estimated interaction between p.R642G and sodium intake.

RESULTS

A cluster of variants, spanning approximately 537 kb on chromosome 16q13, was significantly associated with serum potassium levels. Among the associated variants, a known pathogenic variant of autosomal recessive Gitelman syndrome (p.R642G SLC12A3) was most likely causal; there were no homozygotes in our sample. Heterozygosity for p.R642G was also associated with lower chloride levels, but not with sodium levels. Notably, p.R642G showed a novel association with lower serum BUN levels. Heterozygotes for p.R642G had a two-fold higher rate of self-reported bone fractures and had higher resting heart rates on a low-salt diet compared with noncarriers.

CONCLUSIONS

This study provides evidence that heterozygosity for a pathogenic variant in SLC12A3 causing Gitelman syndrome, a canonically recessive disorder, contributes to serum potassium concentration. The findings provide insights into SLC12A3 biology and the effects of heterozygosity on electrolyte homeostasis and related subclinical phenotypes that may have implications for personalized medicine and nutrition.

Limitations of Contemporary Guidelines for Managing Patients at High Genetic Risk of Coronary Artery Disease

BACKGROUND

Polygenic risk scores (PRS) for coronary artery disease (CAD) identify high-risk individuals more likely to benefit from primary prevention statin therapy. Whether polygenic CAD risk is captured by conventional paradigms for assessing clinical cardiovascular risk remains unclear.

OBJECTIVES

This study sought to intersect polygenic risk with guideline-based recommendations and management patterns for CAD primary prevention.

METHODS

A genome-wide CAD PRS was applied to 47,108 individuals across 3 U.S. health care systems. The authors then assessed whether primary prevention patients at high polygenic risk might be distinguished on the basis of greater guideline-recommended statin eligibility and higher rates of statin therapy.

RESULTS

Of 47,108 study participants, the mean age was 60 years, and 11,020 (23.4%) had CAD. The CAD PRS strongly associated with prevalent CAD (odds ratio: 1.4 per SD increase in PRS; p < 0.0001). High polygenic risk (top 20% of PRS) conferred 1.9-fold odds of developing CAD (p < 0.0001). However, among primary prevention patients (n = 33,251), high polygenic risk did not correspond with increased recommendations for statin therapy per the American College of Cardiology/American Heart Association (46.2% for those with high PRS vs. 46.8% for all others, p = 0.54) or U.S. Preventive Services Task Force (43.7% vs. 43.7%, p = 0.99) or higher rates of statin prescriptions (25.0% vs. 23.8%, p = 0.04). An additional 4.1% of primary prevention patients may be recommended for statin therapy if high CAD PRS were considered a guideline-based risk-enhancing factor.

CONCLUSIONS

Current paradigms for primary cardiovascular prevention incompletely capture a polygenic susceptibility to CAD. An opportunity may exist to improve CAD prevention efforts by integrating both genetic and clinical risk.

Association of the V122I Hereditary Transthyretin Amyloidosis Genetic Variant With Heart Failure Among Individuals of African or Hispanic/Latino Ancestry

Importance

Hereditary transthyretin (TTR) amyloid cardiomyopathy (hATTR-CM) due to the TTR V122I variant is an autosomal-dominant disorder that causes heart failure in elderly individuals of African ancestry. The clinical associations of carrying the variant, its effect in other African ancestry populations including Hispanic/Latino individuals, and the rates of achieving a clinical diagnosis in carriers are unknown.

Objective

To assess the association between the TTR V122I variant and heart failure and identify rates of hATTR-CM diagnosis among carriers with heart failure.

Design, Setting, and Participants

Cross-sectional analysis of carriers and noncarriers of TTR V122I of African ancestry aged 50 years or older enrolled in the Penn Medicine Biobank between 2008 and 2017 using electronic health record data from 1996 to 2017. Case-control study in participants of African and Hispanic/Latino ancestry with and without heart failure in the Mount Sinai BioMe Biobank enrolled between 2007 and 2015 using electronic health record data from 2007 to 2018.

Exposures

TTR V122I carrier status.

Main Outcomes and Measures

The primary outcome was prevalent heart failure. The rate of diagnosis with hATTR-CM among TTR V122I carriers with heart failure was measured.

Results

The cross-sectional cohort included 3724 individuals of African ancestry with a median age of 64 years (interquartile range, 57-71); 1755 (47%) were male, 2896 (78%) had a diagnosis of hypertension, and 753 (20%) had a history of myocardial infarction or coronary revascularization. There were 116 TTR V122I carriers (3.1%); 1121 participants (30%) had heart failure. The case-control study consisted of 2307 individuals of African ancestry and 3663 Hispanic/Latino individuals; the median age was 73 years (interquartile range, 68-80), 2271 (38%) were male, 4709 (79%) had a diagnosis of hypertension, and 1008 (17%) had a history of myocardial infarction or coronary revascularization. There were 1376 cases of heart failure. TTR V122I was associated with higher rates of heart failure (cross-sectional cohort: n = 51/116 TTR V122I carriers [44%], n = 1070/3608 noncarriers [30%], adjusted odds ratio, 1.7 [95% CI, 1.2-2.4], P = .006; case-control study: n = 36/1376 heart failure cases [2.6%], n = 82/4594 controls [1.8%], adjusted odds ratio, 1.8 [95% CI, 1.2-2.7], P = .008). Ten of 92 TTR V122I carriers with heart failure (11%) were diagnosed as having hATTR-CM; the median time from onset of symptoms to clinical diagnosis was 3 years.

Conclusions and Relevance

Among individuals of African or Hispanic/Latino ancestry enrolled in 2 academic medical center-based biobanks, the TTR V122I genetic variant was significantly associated with heart failure.

Author Correction: Genome-wide association study of alcohol consumption and use disorder in 274,424 individuals from multiple populations

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Author Correction: Genome-wide association study of alcohol consumption and use disorder in 274,424 individuals from multiple populations

The original version of this Article omitted the following from the Acknowledgements: 'Supported by the Mental Illness Research, Education and Clinical Center of the Veterans Integrated Service Network 4 of the Department of Veterans Affairs.' This has now been corrected in both the PDF and HTML versions of the Article.

Genome-wide association study of alcohol consumption and use disorder in 274,424 individuals from multiple populations

Alcohol consumption level and alcohol use disorder (AUD) diagnosis are moderately heritable traits. We conduct genome-wide association studies of these traits using longitudinal Alcohol Use Disorder Identification Test-Consumption (AUDIT-C) scores and AUD diagnoses in a multi-ancestry Million Veteran Program sample (N = 274,424). We identify 18 genome-wide significant loci: 5 associated with both traits, 8 associated with AUDIT-C only, and 5 associated with AUD diagnosis only. Polygenic Risk Scores (PRS) for both traits are associated with alcohol-related disorders in two independent samples. Although a significant genetic correlation reflects the overlap between the traits, genetic correlations for 188 non-alcohol-related traits differ significantly for the two traits, as do the phenotypes associated with the traits' PRS. Cell type group partitioning heritability enrichment analyses also differentiate the two traits. We conclude that, although heavy drinking is a key risk factor for AUD, it is not a sufficient cause of the disorder.

IDENTIFYING GENETIC ASSOCIATIONS WITH VARIABILITY IN METABOLIC HEALTH AND BLOOD COUNT LABORATORY VALUES: DIVING INTO THE QUANTITATIVE TRAITS BY LEVERAGING LONGITUDINAL DATA FROM AN EHR

A wide range of patient health data is recorded in Electronic Health Records (EHR). This data includes diagnosis, surgical procedures, clinical laboratory measurements, and medication information. Together this information reflects the patient's medical history. Many studies have efficiently used this data from the EHR to find associations that are clinically relevant, either by utilizing International Classification of Diseases, version 9 (ICD-9) codes or laboratory measurements, or by designing phenotype algorithms to extract case and control status with accuracy from the EHR. Here we developed a strategy to utilize longitudinal quantitative trait data from the EHR at Geisinger Health System focusing on outpatient metabolic and complete blood panel data as a starting point. Comprehensive Metabolic Panel (CMP) as well as Complete Blood Counts (CBC) are parts of routine care and provide a comprehensive picture from high level screening of patients' overall health and disease. We randomly split our data into two datasets to allow for discovery and replication. We first conducted a genome-wide association study (GWAS) with median values of 25 different clinical laboratory measurements to identify variants from Human Omni Express Exome beadchip data that are associated with these measurements. We identified 687 variants that associated and replicated with the tested clinical measurements at p<5×10-08. Since longitudinal data from the EHR provides a record of a patient's medical history, we utilized this information to further investigate the ICD-9 codes that might be associated with differences in variability of the measurements in the longitudinal dataset. We identified low and high variance patients by looking at changes within their individual longitudinal EHR laboratory results for each of the 25 clinical lab values (thus creating 50 groups - a high variance and a low variance for each lab variable). We then performed a PheWAS analysis with ICD-9 diagnosis codes, separately in the high variance group and the low variance group for each lab variable. We found 717 PheWAS associations that replicated at a p-value less than 0.001. Next, we evaluated the results of this study by comparing the association results between the high and low variance groups. For example, we found 39 SNPs (in multiple genes) associated with ICD-9 250.01 (Type-I diabetes) in patients with high variance of plasma glucose levels, but not in patients with low variance in plasma glucose levels. Another example is the association of 4 SNPs in UMOD with chronic kidney disease in patients with high variance for aspartate aminotransferase (discovery p-value: 8.71×10-09 and replication p-value: 2.03×10-06). In general, we see a pattern of many more statistically significant associations from patients with high variance in the quantitative lab variables, in comparison with the low variance group across all of the 25 laboratory measurements. This study is one of the first of its kind to utilize quantitative trait variance from longitudinal laboratory data to find associations among genetic variants and clinical phenotypes obtained from an EHR, integrating laboratory values and diagnosis codes to understand the genetic complexities of common diseases.

Abstract 2557: Germline mutations in renal cancer predisposing genes: Analysis of the Geisinger MyCode population

Renal cell cancer (RCC) is not a single disease but is made up of a number of cancers, each with a unique histology, biology, clinical course and response to therapy. Alterations in at least 16 hereditary genes have been attributed to the risk of developing RCC. In this study, we describe the prevalence and spectrum of germline variants among these genes and highlight correlations between germline genotype with tumor phenotype. Using the Geisinger MyCode cohort, we sequenced the whole exomes of 42,933 subjects. Subjects were divided into those with a renal cancer diagnosis, other cancer diagnosis and no cancer diagnosis. We analyzed the DNA sequences of 16 hereditary renal cancer genes from each of these groups. The damaging mutations was determined by following ACMG guidelines. Among the 42,933 subjects in the Geisinger MyCode cohort, 168 were diagnosed with RCC. None of these subjects had a family history of RCC. Clear cell RCC (ccRCC) was the most predominant histology (77%), followed by Type 1 papillary RCC (7%), chromophobe RCC (6%), and Type 2 papillary RCC (5%). Mutations in all the predisposing genes were identified in all the renal cancer subtypes but only a subset were deemed damaging. The top 2 ccRCC predisposing genes with damaging or likely damaging mutations were TSC2 (8%) and SDHD (4%). While TSC2 damaging variants were also found in the other histologies, novel TSC2 variants were differentially associated with high grade and metastatic disease in ccRCC as compared to those with low grade or non-metastatic disease. The genes harboring damaging or likely damaging variants in Type 1 and Type 2 papillary RCC were MET and FH respectively. Predisposing RCC germline mutations were found in a significant number of subjects with sporadic RCC. Family history was unhelpful in predicting the affected subjects. Knowledge of these mutations would be beneficial in counseling patients and their families as well as improving our understanding of the disease to direct patient care.

Citation Format: Heinric Williams, Raghu Metpally, Mahmoud Mohamed, Sarath Krishnamurthy, Sertac Kip, David J. Carey, Aris Baras, John Overton. Germline mutations in renal cancer predisposing genes: Analysis of the Geisinger MyCode population. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2557.

Mutation of NLRC4 causes a syndrome of enterocolitis and autoinflammation

Upon detection of pathogen-associated molecular patterns, innate immune receptors initiate inflammatory responses. These receptors include cytoplasmic NOD-like receptors (NLRs), whose stimulation recruits and proteolytically activates caspase-1 within the inflammasome, a multi-protein complex. Caspase-1 mediates the production of interleukin-1 family cytokines (IL1FCs), leading to fever, and inflammatory cell death (pyroptosis)^1,2. Mutations that constitutively activate these pathways underlie several autoinflammatory diseases with diverse clinical features³. We describe a family with a previously unreported syndrome featuring neonatal-onset enterocolitis, periodic fever, and fatal/near-fatal episodes of autoinflammation caused by a de novo gain-of-function mutation (p.V341A) in the HD1 domain of NLRC4 that co-segregates with disease. Mutant NLRC4 causes constitutive Interleukin-1 family cytokine production and macrophage cell death. Infected patient macrophages are polarized toward pyroptosis and exhibit abnormal staining for inflammasome components. These findings describe and reveal the cause of a life-threatening but treatable autoinflammatory disease that underscores the divergent roles of the NLRC4 inflammasome.

Pattern recognition in long‐term Sooty Shearwater data: applying machine learning to create a harvest index

Rakiura Māori (New Zealand's southernmost group of indigenous peoples) have harvested the chicks of burrow-nesting Sooty Shearwaters (Tītī; Puffinus griseus) for generations. As part of the harvest process, some families have maintained annual harvest diaries, some dating back to the 1950s. We used generalized boosted regression models, a machine-learning algorithm, to calculate a harvest index that takes into account factors that could impact the numbers of birds taken on any given hunt. For predicted vs. observed values, r2 was between 0.59 and 0.90 for the nanao (first half of the season, when chicks are harvested from burrows during the day) and 0.67 and 0.88 for the rama (second half of the season, during which chicks are harvested from the surface at night). Exploration of the controlling factors of the models revealed that “day of season” plays an important role in predicting daily harvest during the second half of the season (the rama). The nightly tally in the rama peaked approximately halfway through (10–15 days in), which is probably related to the timing of birds emerging from burrows to fledge. The models also suggested that data from the rama (when chicks are 100–120 days old) may be the most suitable for long-term monitoring of populations of Sooty Shearwaters due to consistencies in calculated harvest indices between diaries. Nanao harvest indices, although less consistent, showed patterns similar to those of the rama. When comparing these data to the harvest indices calculated by general linear models by Clucas and colleagues, we found that the agreement between both indices was r2 = 0.31 and r2 = 0.59 for the nanao and rama, respectively. The use of machine learning to correct for extraneous factors (e.g., hunting effort, skill level, or weather) and to create standardized measures could be applied to other systems such as fisheries or terrestrial resource management.

Intraperitoneal drains during open appendicectomy for gangrenous and perforated appendicitis

Intra-abdominal drains are still routinely used in the surgical management of gangrenous and perforated appendicitis. A systematic review was performed with the aim of establishing their influence on postoperative complications in such cases. A literature search was conducted using the search engines PubMed and Cochrance Central Register of Controlled Trials. Included were retrospective case-controlled and prospective randomized controlled trials on the use of drain for open appendicectomy in gangrenous and perforated appendicitis. Twelve articles were found that met the inclusion criteria. Intrabdominal abscesses, postoperative ileus, surgical site infections, fecal fistulas and burst abdomen had significant higher incidences in the drain vs non drain group (10.3%, 20.3%, 32.5%, 3.4% and 5.7% vs 4.7%, 8.5%, 16.2%, 0% and 0%, respectively). In most cases the risk was more than doubled in the drain group compared to the non-drain one. There were no significant differences among groups in terms of mortality while the results were underpowered to effectively evaluate wound dehiscence and adhesions. The use of intra-abdominal drains in the management of gangrenous and perforated appendicitis by open appendicectomy is associated with an increased rate of common postoperative complications.

Cytokine response of electrolytic ablation in an ex vivo perfused liver model

BACKGROUND

The inflammatory response following hepatic ablation depends on different factors including the method used, the duration and intensity of the treatment and the presence or absence of ischemia. Debate continues about the use of different modalities and whether some aspects of the response may be advantageous by releasing immunological active substances. Little data have been published concerning the cytokine response elicited by hepatic electrolytic ablation (EA). Study of an ex vivo liver model could allow for the evaluation of this response without the influence of confounding systemic factors.

METHODS

Livers explanted from 11 pigs were perfused extracorporeally with normothermic autologous blood. Four of them underwent EA after 1 h of reperfusion. Serum samples were obtained up to 6 h after the reperfusion and assayed for IL-1 beta, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IFN-gamma, TNF-alpha.

RESULTS

Significant changes in the control group were observed for IL-6 after the second hour and IL-8 after the first hour compared with baseline levels (P < 0.001). In the EA group, IL-6 and IL-12 were raised after the second hour and IL-8 and IL-10 after the first hour (P < 0.001). The comparison between groups showed significant differences for IL-2, IL-4 (decreased in the EA group compared with controls), IL-10 and TNF-alpha (EA group increased compared with controls; P < 0.001).

CONCLUSIONS

The ex vivo perfused liver model demonstrated changes in levels of IL-2, IL-4, IL-10 and TNF-alpha following hepatic EA.

INTERCELLULAR CONNECTIONS IN THE OUTGROWING STOLON OF CORDYLOPHORA

Outgrowth of the stolon in the hydroid Cordylophora has been studied at the cellular level. Staining experiments and histological examination indicate that the generative region of the stolon is at its base where interstitial cells are prominent. Cells in the ectoderm at the stolon tip appear to be actively synthesizing new perisarc as the tip advances over the substrate, rather than involved in proliferation. The fine structure of cellular relationships in these regions has been considered and an attempt has been made to correlate the structure and distribution of intercellular attachments with these various functional zones along the outgrowing stolon. Intercellular attachments are similar to those previously described in Hydra, but favorable cases provide a more complete description. The series of intercellular septa each consist of two electron-opaque bodies lying close together midway between the two plasma membranes and separated from the membranes by a region of lesser density. The plasma membranes contain electron-opaque and transparent regions which alternate with the septa. These regions extend over about 70 A. The position of intercellular connections relative to the outer surface of the cenosarc varies in different parts of the stolon.

STUDIES ON THE ORGANIZATION OF THE BRUSH BORDER IN INTESTINAL EPITHELIAL CELLS : II. Fine Structure of Fractions of Tris-Disrupted Hamster Brush Borders

Two of the fractions obtained by density gradient centrifugation of Tris-disrupted brush borders from hamster intestinal mucosa have been identified as the microvillus cores and their surrounding membranous coats, respectively. This identification has the following morphological basis. In shadowed preparations one fraction (cores) appears as rounded, compact rods, and the other fraction (coats) appears as flattened sheets. Both rods and sheets have dimensions appropriate to the identities assigned to them. In addition, negative staining shows that the rods are composed of aligned particles of roughly 60 A, consistent with the appearance of the core in tissue section, where 60-A fibrils are characteristic. The sheets are covered by non-aligned particles of approximately the same size. Sectioned preparations show that the core fraction contains predominantly fibrous material with some membranous contamination and that the coat fraction is apparently composed exclusively of elongated sacs with a unit membrane structure. Some details of the structure of the core are evident in cases where the compact rod appears to be loosened, revealing a doubled strand. The strand is approximately 350 A wide; the compact rod is roughly twice this width. With negative staining the strand shows a dense central region. The morphological identification presented here is consistent with the distribution of enzymic activity among the density gradient fractions described in the preceding paper.

Ferguson hemorrhoidectomy with radiofrequency versus classic diathermy

BACKGROUND

This randomized study compared results obtained with the Ferguson's technique for the treatment of hemorrhoids performed with a radiofrequency (RF) scalpel and traditional diathermy.

METHODS

28 patients affected by grade IV hemorrhoids were randomized to receive either the Ferguson operation with the RF scalpel (group A) or traditional diathermy (group B). The operating time, intra- and postoperative bleeding, postoperative pain, and overall patient satisfaction were all recorded.

RESULTS

Six patients (three for each group) did not attend follow-up controls. Group A showed a significant reduction of the surgical time (23 vs. 33 min; p < .01), pain at first postoperative day (Visual Analog Scale [VAS] score 3.4 vs. 4.8; p < .05), and at the first evacuation (3.4 vs. 5.0; p < .05). No significant differences were observed for the pain score at the seventh postoperative day, or overall satisfaction scores at the 7th postoperative day, and six months postoperatively (p = NS). No severe complications were recorded. Two patients in group A (18.2%) and four patients in group B (36.4%) reported transitory gas incontinence that spontaneously resolved within one month (p = NS). Three patients in group A (27.3%) and four patients in group B (36.4%) required postoperative catheterization due to urinary retention (p = NS).

CONCLUSIONS

RF scalpel shortens the operating time of the Ferguson operation and is less painful in the early postoperative period.

Reshaping development aid: implications for political and economic relationships

New Zealand's relationship with its Pacific Island neighbours stretches back centuries, being characterised by movements of people, ideas, commodities, services and finance. It has been a reciprocal and dynamic relationship. Aid from New Zealand to Pacific Island states has been but one of its elements and one that has existed by that name only in the last 50 years or so. Yet it has proved to be one of the most volatile in terms of changing policies and priorities and it is presently under another phase of review.

The influence of BMI, smoking, and age on vaginal erosions after synthetic mesh repair of pelvic organ prolapses. A multicenter study

OBJECTIVE

To study the influence of body mass index (BMI), smoking, and age on the risk of vaginal erosions after mesh repair of pelvic prolapses.

DESIGN

Retrospective study.

SETTING

Three university and community hospitals.

POPULATION AND SAMPLE

Patients that underwent mesh correction of prolapses between 2002 and 2007. Excluded were those with stress urinary incontinence, ongoing clinical infections, with a complete antibiotic course in the last six months and with systemic diseases affecting tissue oxygenation.

METHODS

Revision of medical notes.

MAIN OUTCOME MEASURES

Risk contributions for age, smoking, and BMI on the occurrence of vaginal erosions.

RESULTS

Data were collected from 460 patients. Postoperative erosions were present in 7%. BMI greater than 30 conferred a 10.1-fold increase in the risk of developing erosions, smoking a 3.7-fold increase, and age greater than 60 years a 2.2-fold increase. A cut-off value of seven pack years was determined for smoking where the risk associated with light smokers was similar to that of non-smokers.

CONCLUSIONS

BMI, smoking, and age are important risk factors for pelvic organ prolapse surgery. Our data could be used to stratify patients according to their risk so that preventative measures can be taken in high-risk patients.

In silico mutagenesis: a case study of the melanocortin 4 receptor

The melanocortin 4 receptor (MC4R) is a G-protein-coupled receptor (GPCR) and a key molecule in the regulation of energy homeostasis. At least 159 substitutions in the coding region of human MC4R (hMC4R) have been described experimentally; over 80 of those occur naturally, and many have been implicated in obesity. However, assessment of the presumably functionally essential residues remains incomplete. Here we have performed a complete in silico mutagenesis analysis to assess the functional essentiality of all possible nonnative point mutants in the entire hMC4R protein (332 residues). We applied SNAP, which is a method for quantifying functional consequences of single amino acid (AA) substitutions, to calculate the effects of all possible substitutions at each position in the hMC4R AA sequence. We compiled a mutability score that reflects the degree to which a particular residue is likely to be functionally important. We performed the same experiment for a paralogue human melanocortin receptor (hMC1R) and a mouse orthologue (mMC4R) in order to compare computational evaluations of highly related sequences. Three results are most salient: 1) our predictions largely agree with the available experimental annotations; 2) this analysis identified several AAs that are likely to be functionally critical, but have not yet been studied experimentally; and 3) the differential analysis of the receptors implicates a number of residues as specifically important to MC4Rs vs. other GPCRs, such as hMC1R.—Bromberg, Y., Overton, J., Vaisse, C., Leibel, R. L., Rost, B. In silico mutagenesis: a case study of the melanocortin 4 receptor.

Primary carcinoids of the liver: a review of symptoms, diagnosis and treatments

INTRODUCTION

To elucidate the clinical presentation, diagnosis and management of primary hepatic carcinoid tumours, a literature search was conducted and summarized.

MATERIALS AND METHODS

Published primary hepatic carcinoid tumour case reports and series were searched and selected in the Medline, EMBASE and Cochrane Library databases.

RESULTS

Sixty-nine cases meeting the inclusion criteria were identified. Twenty-eight patients were male (28/69 = 40.6%). The median age at diagnosis was 50 years (range 8-83 years). The most common presentation described was abdominal pain (23/69 = 33.3%), or no symptoms at all (16/69 = 23.2%). Symptoms of carcinoid syndrome were described in 18.9% of cases (13/69). The most frequently secreted hormones were gastrin (7/69 = 10.1%) and chromogranin A. In 31.9% of patients (22/69), surgical treatment was not adopted. Of those treated surgically, 63.8% underwent a hepatic resection (44/69) and 4.3% a liver transplantation (3/69). After a median follow-up of 31 months (range 0-180 months), 39.1% of patients (27/69) died and 52.2% (36/69) survived.

CONCLUSIONS

Primary hepatic carcinoids are an important entity in which the exclusion of different primary locations is necessary. When feasible, hepatic resection is the treatment of choice. Liver transplantation has been described in a small number of unresectable cases.

Pseudomonas aeruginosa necrotizing infection of the abdominal flap in a post-bariatric patient undergoing body contouring surgery

Pseudomonas aeruginosa infections may involve any organ or body district and may give serious clinical sequelae. We report the case of an infection of the abdominoplasty flap that compromised wound closure and jeopardized the aesthetic outcome. To the best of our knowledge, this is the first such case reported in the literature for this group of patients. We have presented this case in order to alert plastic and general surgeons who may encounter this complication in future, such that they may be aware of the need to adopt an aggressive approach to manage these patients. This consisted of the accurate monitoring of the patient's clinical condition, prescribing appropriate antibiotics, and performing serial debridement of necrotic tissue.

Recommended guidelines for reporting on emergency medical dispatch when conducting research in emergency medicine: the Utstein style

OBJECTIVES

To establish a uniform framework describing the system and organisation of emergency medical response centres and the process of emergency medical dispatching (EMD) when reporting results from studies in emergency medicine and prehospital care.

DESIGN AND RESULTS

In September 2005 a task force of 22 experts from 12 countries met in Stavanger; Norway at the Utstein Abbey to review data and establish a common terminology for medical dispatch centres including core and optional data to be used for health monitoring, benchmarking and future research.

Urinary tract reconstruction using the controlateral native ureter and a combined open-retroperitoneoscopic approach after renal transplantation

An alternative technique for urinary tract (UT) reconstruction is described in a renal transplant recipient who developed a severe stenosis of the graft ureter. This approach entails the retroperitoneoscopic preparation of the native ureter contralateral to the graft, followed by an open reconstruction of the UT. The ureter was dissected along its entire length to the level of the iliac vessels, with its associated mesentery still attached in order to preserve the vascular supply. The corresponding native kidney contralateral to the graft was endoscopically removed. A longitudinal sub-umbilical incision allowed the excision of the stenotic tract and the reconstruction of the UT by means of a manual end-to-end anastomosis between the new ureter and the graft pelvis. No post-operative complications occurred and renal function immediately resumed. The approach described represents an alternative solution for the surgical management of severe ureteric graft stenosis. We believe that the magnification of the anatomy granted by the endoscope during the dissection of the ureter and neighboring structures provides the gentle handling of the tissues and the remote dissection away from the ureter with the highest precision.

Positional cloning of "Lisch-Like", a candidate modifier of susceptibility to type 2 diabetes in mice

In 404 Lep^ob/ob F2 progeny of a C57BL/6J (B6) x DBA/2J (DBA) intercross, we mapped a DBA-related quantitative trait locus (QTL) to distal Chr1 at 169.6 Mb, centered about D1Mit110, for diabetes-related phenotypes that included blood glucose, HbA1c, and pancreatic islet histology. The interval was refined to 1.8 Mb in a series of B6.DBA congenic/subcongenic lines also segregating for Lep^ob. The phenotypes of B6.DBA congenic mice include reduced β-cell replication rates accompanied by reduced β-cell mass, reduced insulin/glucose ratio in blood, reduced glucose tolerance, and persistent mild hypoinsulinemic hyperglycemia. Nucleotide sequence and expression analysis of 14 genes in this interval identified a predicted gene that we have designated “Lisch-like” (Ll) as the most likely candidate. The gene spans 62.7 kb on Chr1qH2.3, encoding a 10-exon, 646–amino acid polypeptide, homologous to Lsr on Chr7qB1 and to Ildr1 on Chr16qB3. The largest isoform of Ll is predicted to be a transmembrane molecule with an immunoglobulin-like extracellular domain and a serine/threonine-rich intracellular domain that contains a 14-3-3 binding domain. Morpholino knockdown of the zebrafish paralog of Ll resulted in a generalized delay in endodermal development in the gut region and dispersion of insulin-positive cells. Mice segregating for an ENU-induced null allele of Ll have phenotypes comparable to the B.D congenic lines. The human ortholog, C1orf32, is in the middle of a 30-Mb region of Chr1q23-25 that has been repeatedly associated with type 2 diabetes.

Type 2 diabetes (T2D) accounts for over 90% of instances of diabetes and is a leading cause of medical morbidity and mortality. Twin studies indicate a strong polygenic contribution to susceptibility within the context of obesity. Although approximately ten genes making important contributions to individual risk have been identified, it is clear that others remain to be identified. In this study, we intercrossed obese, diabetes-resistant and diabetes-prone mouse strains to implicate a genetic interval on mouse Chr1 associated with reduced β-cell numbers and elevated blood glucose. We narrowed the region using molecular genetics and computational approaches to identify a novel gene we designated “Lisch-like” (Ll). The orthologous human genetic interval has been repeatedly implicated in T2D. Mice with an induced mutation that reduces Ll expression are impaired in both β-cell development and glucose metabolism, and reduced expression of the homologous gene in zebrafish disrupts islet development. Ll is expressed in organs implicated in the pathophysiology of T2D (hypothalamus, islets, liver, and skeletal muscle) and is predicted to encode a transmembrane protein that could mediate cholesterol transport and/or convey signals related to cell division. Either mechanism could mediate effects on β-cell mass that would predispose to T2D.

Cardiac arrest management

Approximately 1,000 people in the United States suffer cardiac arrest each day, most often as a complication of acute myocardial infarction (AMI) with accompanying ventricular fibrillation or unstable ventricular tachycardia. Increasing the number of patients who survive cardiac arrest and minimizing the clinical sequelae associated with cardiac arrest in those who do survive are the objectives of emergency medical personnel. In 1990, the American Heart Association (AHA) suggested the chain of survival concept, with four links--early access, cardiopulmonary resuscitation (CPR), defibrillation, and advanced care--as the way to approach cardiac arrest. The recently published International Resuscitation Guidelines 2000 of the AHA have addressed advances in our understanding of the chain of survival. While the chain of survival concept has withstood a decade of scrutiny, there are only a few scientifically rigorous research studies that support changes in prehospital patient care. Additional research efforts carried out in the prehospital setting are needed to support the concepts included in the chain of survival for cardiac arrest patients. Participants at the second Turtle Creek Conference, a meeting of experts in the field of emergency medicine held in Dallas, Texas, on March 29-31, 2000, discussed these and other issues associated with prehospital emergency care in the cardiac arrest patient. This paper addresses a number of the issues associated with each of the links of the chain of survival, the evidence that exists, and what should be done to achieve the clinical evidence needed for true clinical significance. Also included in this paper are the consensus statements developed from small discussion groups held after the main presentation. These comments provide another perspective to the problems and to possible approaches to deal with them.

Optimal prehospital cardiovascular care

Optimal prehospital cardiovascular care may improve the morbidity and mortality associated with acute myocardial infarctions (AMIs) that begin in the community. Reducing the time delays from AMI symptom onset to intervention begins with maximizing effective patient education to reduce patient delay in recognizing symptoms and seeking assistance. Transportation delays can be minimized by appropriate use of 911 systems and improving technological 911 support. Patient triage to heart centers from the prehospital setting requires strict and comprehensive definition of the criteria for these centers by competent, unbiased clinical societies or governmental agencies. Prehospital 12-lead electrocardiograms and initiation of thrombolytic therapy can provide acute diagnosis and early treatment, thus facilitating faster processing and more directed in-hospital intervention. They also minimize over- and undertriage of patients to cardiac centers. Although evidence from investigational trials suggests that many of these procedures are effective, more research is required to ensure correct implementation and quality assurance at all emergency service levels.

Measurement of urinary retinol binding protein by immunonephelometry

A method is described for the determination of retinol binding protein (RBP) by immunonephelometry. The assay is sensitive to 5 microg/l and has acceptable imprecision. The method correlates with an established ELISA assay. A provisional normal range is proposed for daytime random urine samples. The increased excretion of RBP in adult subject with type 1 diabetes mellitus is demonstrated.

Synchronization of timepieces to the atomic clock in an urban emergency medical services system

STUDY OBJECTIVE

Erroneous time documentation of emergency treatment caused by the variation in the accuracy of timepieces has profound medical, medicolegal, and research consequences. The purpose of this study was to confirm the variation of critical timepiece settings in an urban emergency care system noted in previous studies and to implement and monitor the results of a prospective program to improve time synchronization.

METHODS

Timepieces (n = 393) used by firefighters, paramedics, and emergency physicians and nurses were randomly sampled immediately before and at two time intervals (1 and 4 months) after attempted synchronization to the US atomic clock standard. The setting on each timepiece was compared with the atomic clock. From the data, a mathematical simulation estimated the number of time-related documentation errors that would occur in 2,500 simulated cardiac arrest cases using timepieces with accuracy similar to those found in the EMS system before and after attempted synchronization.

RESULTS

Before attempted synchronization, the timepieces had a mean error of 2.0 (95% confidence interval 1.8 to 2.3) minutes. One month after attempted synchronization, the mean error decreased significantly to .9(.8 to 1.1) minute. However, it increased to 1.7 (1.5 to 1.9) minutes within 4 months. Mathematical simulation before attempted synchronization predicted that 93% of cardiac arrest cases would contain a documentation error of 2 minutes or more and that 41% of cases would contain a documentation error of 5 minutes or more. Attempted synchronization cut the 2-minute documentation error rate in half and reduced the 5-minute documentation error rate by three fourths. However, the error rates were predicted to return to baseline 4 months after attempted synchronization.

CONCLUSION

Emergency medical timepieces are often inaccurate, making it difficult to reconstruct events for medical, medicolegal, or research purposes. Community synchronization of timepieces to the atomic clock can reduce the problem significantly, but the effects of a one-time attempted synchronization event are short-lived.