Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

Background

Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates.

Methods

We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel.

Results

21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Streptococcus pneumoniae (SPn, 29·0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9·6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load.

Conclusions

Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.

Diagnostic accuracy of an app-guided, self-administered test for influenza among individuals presenting to general practice with influenza-like illness: study protocol

INTRODUCTION

Diagnostic tests for influenza in Australia are currently only authorised for use in clinical settings. At-home diagnostic testing for influenza could reduce the need for patient contact with healthcare services, which potentially could contribute to symptomatic improvement and reduced spread of influenza. We aim to determine the accuracy of an app-guided nasal self-swab combined with a lateral flow immunoassay for influenza conducted by individuals with influenza-like illness (ILI).

METHODS AND ANALYSIS

Adults (≥18 years) presenting with ILI will be recruited by general practitioners (GP) participating in Australian Sentinel Practices Research Network. Eligible participants will have a nasal swab obtained by their GP for verification of influenza A/B status using reverse transcription polymerase chain reaction (RT-PCR) test at an accredited laboratory. Participants will receive an influenza test kit and will download an app that collects self-reported symptoms and influenza risk factors, then instructs them in obtaining a low-nasal self-swab, running a QuickVue influenza A+B lateral flow immunoassay (Quidel Corporation) and interpreting the results. Participants will also interpret an enhanced image of the test strip in the app. The primary outcome will be the accuracy of participants' test interpretation compared with the laboratory RT-PCR reference standard. Secondary analyses will include accuracy of the enhanced test strip image, accuracy of an automatic test strip reader algorithm and validation of prediction rules for influenza based on self-reported symptoms. A post-test survey will be used to obtain participant feedback on self-test procedures.

ETHICS AND DISSEMINATION

The study was approved by the Human Research and Ethic Committee (HREC) at the University of Adelaide (H-2019-116). Protocol details and any amendments will be reported to https://www.tga.gov.au/. Results will be published in the peer-reviewed literature, and shared with stakeholders in the primary care and diagnostics communities.

TRIAL REGISTRATION NUMBER

Australia New Zealand Clinical Trial Registry (U1111-1237-0688).

The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology

INTRODUCTION

Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterise, and potentially contain new and emerging influenza strains at both an individual and population level. The objective of this study is to use data gathered simultaneously from community and hospital sites to develop a model of how influenza enters and spreads in a population.

METHODS AND ANALYSIS

Starting in the 2018-2019 season, we have been enrolling individuals with acute respiratory illness from community sites throughout the Seattle metropolitan area, including clinics, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses and homeless shelters. At these sites, we collect clinical data and mid-nasal swabs from individuals with at least two acute respiratory symptoms. Additionally, we collect residual nasal swabs and data from individuals who seek care for respiratory symptoms at four regional hospitals. Samples are tested using a multiplex molecular assay, and influenza whole genome sequencing is performed for samples with influenza detected. Geospatial mapping and computational modelling platforms are in development to characterise the regional spread of influenza and other respiratory pathogens.

ETHICS AND DISSEMINATION

The study was approved by the University of Washington's Institutional Review Board (STUDY00006181). Results will be disseminated through talks at conferences, peer-reviewed publications and on the study website (www.seattleflu.org).

FRI0547 THE EFFECT OF CORRECTED INFLAMMATION, OXIDATIVE STRESS AND ENDOTHELIAL DYSFUNCTION ON FMD LEVELS IN PATIENTS WITH SELECTED CHRONIC DISEASES: A QUASI-EXPERIMENTAL STUDY

Background:

While the pathophysiology of chronic disorders varies there are three basic mechanisms - inflammation, oxidative stress and endothelial dysfunction – that are common in many chronic diseases. These mechanisms, which have a dynamic structure, are key to homeostasis. However, the failure of these mechanisms to work synchronously can lead to morbidity complicating the course of many chronic diseases.

Objectives:

To evaluate the effect of anti-atherosclerotic liquid (AAL), anti-inflammatory capsules (AIC) and anti-oxidant liquid (AOL) supplementation on the flow-mediated dilatation (FMD), inflammatory, oxidative stress and endothelial dysfunction markers in patients with selected chronic diseases

Methods:

We analyzed data of 178 patients from cohorts with selected chronic diseases (Rheumatoid arthritis, familial Mediterranean fever, DM type-2, Hypertension, Multiple sclerosis, Chronic obstructive pulmonary disease, Alzheimer disease and Cancer) in this quasi-experimental study. Endothelial dysfunction was determined by FMD and serum asymmetric dimethylarginine (ADMA) levels. Serum ADMA, high sensitive C-reactive protein (hs-CRP), serum PTX3, malondialdehyde (MDA), Cu/Zn-superoxide dismutase (Cu/Zn-SOD), glutathione peroxidase (GSH-Px) levels and FMD were studied in baseline and after 12 weeks of Morinda citrifolia (AAL, 3 ml once per day), omega-3 (AIC, 3 capsules once per day) and extract with Alaskan blueberry and 21 different red purple fruit vegetables (AOL, 30 ml once per day). Stepwise multivariate regression analysis evaluated the association of FMD with clinical and serologic parameters.

Results:

Serum ADMA, MDA, PTX3, hsCRP and albumin levels, and proteinuria were significantly decreased and CuZn-SOD, GSH-Px and FMD levels were significantly increased following AAL, AIC and AOL therapies. FMD was negatively correlated with serum ADMA, MDA, PTX3, hsCRP levels, SBP and DBP and positively correlated to CuZn-SOD and eGFR levels both at baseline and after the 12-weeks treatment period. Multivariate regression analysis revealed that ADMA and PTX3 levels were independently related to FMD both before and after AAL, AIC and AOL therapies (Table 1, Figure 1).

Conclusion:

Our study shows that serum ADMA, MDA, PTX3 levels are associated with endothelial dysfunction in patients with selected chronic diseases. Short-term AAL, AIC and AOL therapies significantly improves FMD and normalizes ADMA, PTX3, hsCRP and MDA. This may have implications for adjunctive therapy in a number of chronic disorders.

References:

[1] Yilmaz MI, Saglam M, Caglar K, Cakir E, Sonmez A, Ozgurtas T et al. The determinants of endothelial dysfunction in CKD: oxidative stress and asymmetric dimethylarginine. Am J Kidney Dis. 2006;47(1):42-50. doi:10.1053/j.ajkd.2005.09.029.

Disclosure of Interests:

None declared

LB21. The Seattle Flu Study: A Community-Based Study of Influenza

Background

Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect and contain new and emerging flu strains at a population level. The objective of this study was to use data gathered simultaneously from community and hospital sites to develop a model of how flu enters and spreads in a population.

Methods

In the 2018–2019 season, we enrolled individuals with respiratory illness from community sites throughout the Seattle area, including homeless shelters, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses, clinics, and at home (Figure 1). We collected data and nasal swabs from individuals with at least two respiratory symptoms. Additionally, we collected residual nasal swabs and data from individuals who sought care at four regional hospitals. Home-based self-testing for influenza and prediction models for influenza were piloted. Swabs were tested with a multiplex molecular assay, and influenza whole-genome sequencing was performed. Geospatial mapping and computational modeling platforms were developed to characterize regional spread of respiratory pathogens.

Results

A total of 18,847 samples were collected in the 2018–2019 season. Of those tested to date, 291/3,653 (8%) community and 2,393/11,273 (21%) hospital samples have influenza detected. Of the community enrollments, 39% had influenza-like illness. Community enrollees were in age groups not well-represented from hospitals. Influenza A/H3N2 activity peaked on college campuses and homeless shelters 2 weeks before the peak in hospitals. We observed multiple independent introductions of influenza strains into the city and evidence of sustained transmission chains within the city (Figures 2 and 3).

Conclusion

Utilizing the city-wide infrastructure we developed, we observed the introduction of influenza A/H3N2 into the community before the hospital and evidence of transmissions of unique strains into and within the Seattle area. These data provide the blueprint for implementing city-wide, community-based surveillance systems for rapid detection, real-time assessment of transmission patterns, and interruption of spread of seasonal or pandemic strains.

Disclosures

Helen Y. Chu, MD MPH, Merck (Advisor or Review Panel member), Michael Boeckh, MD PhD, Ablynx (Consultant, Grant/Research Support), Ansun Biopharma (Consultant, Grant/Research Support), Bavarian Nordic (Consultant), Gilead (Consultant, Grant/Research Support), GlaxoSmithKline (Consultant), Vir Bio (Consultant, Grant/Research Support), Janet A. Englund, MD, Chimerix (Grant/Research Support), GlaxoSmithKline (Grant/Research Support), MedImmune/Astrazeneca (Grant/Research Support), Meissa Vaccines (Consultant), Merck (Grant/Research Support),Novavax (Grant/Research Support), Sanofi Pastuer (Consultant), Matthew Thompson, MD, Alere Inc. (Research Grant or Support), Roche Molecular Diagnostics (Consultant, Research Grant or Support, Speaker’s Bureau), . Other Authors: No reported disclosures.

1775. A Community-wide Study to Evaluate the Accuracy of Self-testing for Influenza: Works in Progress

Background

Seasonal influenza (flu) occurs annually, causing disease with substantial morbidity and mortality. Currently, flu is suspected from clinical features, but requires a laboratory test to confirm infection. No influenza tests in the United States are approved for use outside of clinical settings. We aimed to determine the accuracy of influenza self-testing using an at-home, app-guided, lateral flow assay compared with a molecular reference standard conducted at a laboratory among adults self-reporting influenza-like illness (ILI).

Methods

This is an observational study of individuals with self-reported ILI throughout the continental 48 United States recruited from the Flu Near You platform, online marketing, and clinics in the Seattle area. Recruitment took place from March 4 to April 26, 2019. Participants were directed to an iPhone App that determined eligibility, consent, and responses to symptom questions and risk factors. Individuals were mailed a commercially available CLIA-waived influenza lateral flow test to conduct at home, guided by the app, and returned the used test along with a second nasal swab collected in viral transport media to the research team. Influenza testing was performed by RT–PCR on the second nasal swab, as well as the residual fluid from the RDT. Accuracy of home test result (read by the participant), as well as image capture of the lateral flow test strip, were compared with the lab-based reference standard.

Results

To date, 1127 at-home flu tests were mailed to participants and 711 (63.1%) samples returned to the lab. There were 17 flu-positive results from the rapid diagnostic test for a flu positivity rate of 2.4%. Testing using the reference standard is currently in progress. We will share diagnostic accuracy results once testing of the reference standard is completed. Of the kits returned, 353 (49.7%)had an error recorded, which included errors in return packaging, reference standard, rapid test tube sample, or rapid test strip errors.

Conclusion

Overall, findings from this study will determine the accuracy of an at-home rapid diagnostic test, and inform more widely research design for evaluating smartphone-enhanced home tests for pathogens. Many samples returned to the lab had a recorded error, suggesting at-home testing requires additional feasibility testing and refinement of the current methods used.

Disclosures

All authors: No reported disclosures.

Diffusion-controlled crack propagation in alkali feldspar

The chemically driven propagation of interacting parallel cracks in monoclinic alkali feldspar was studied experimentally. Single crystals of potassium-rich gem-quality sanidine were shifted towards more sodium-rich compositions by cation exchange with a NaCl-KCl salt melt at a temperature of 850 ∘ C and close to ambient pressure. Initially, a zone with elevated sodium content formed at the crystal surfaces due to the simultaneous in-diffusion of sodium and out-diffusion of potassium, where the rate of cation exchange was controlled by sodium-potassium interdiffusion within the feldspar. A chemical shift of potassium-rich alkali feldspar towards more sodium-rich compositions produces highly anisotropic contraction of the crystal lattice. This induced a tensile stress state in the sodium-rich surface layer of the crystals, which triggered the formation of a system of nearly equi-spaced parallel cracks oriented approximately perpendicular to the direction of maximum shortening. Crack propagation following their nucleation was driven by cation exchange occurring along the crack flanks and was controlled by the intimate coupling of the diffusion-mediated build-up of a tensile stress state around the crack tips and stress release by successive crack propagation. The critical energy release rate of fracturing was determined as 1.8-2.2 J m - 2 from evaluation of the near-tip J-integral. The mechanism of diffusion-controlled crack propagation is discussed in the context of high-temperature feldspar alteration.

La(iii) biodistribution profiles from intravenous and oral dosing of two lanthanum complexes, La(dpp)3 and La(XT), and evaluation as treatments for bone resorption disorders

Trivalent lanthanum (La³⁺) has the potential to treat bone resorption disorders (such as osteoporosis) by eliciting a bone-building response in the cells which control skeletal remodelling. Because La³⁺ suffers from extremely poor intestinal absorption, specifically designed chelators are required in order that a biologically active form of lanthanum can be administered orally. Two such chelators, 1,2-dimethyl-3-hydroxy-4-pyridinone (Hdpp) and bis-{[bis(carboxymethyl)amino]methy}phosphinic acid (H₅XT), have previously been the subjects of extensive physical, in vitro, and in vivo testing as the tris- and mono-lanthanum(iii) complexes La(dpp)₃ and La(XT), respectively. In this manuscript, we expand upon those studies to include 4-week intravenous (IV) and oral La³⁺ biodistribution profiles, which show that the metal ion initially accumulates in the liver followed by preferential redistribution and retention by bone. Of the two compounds, La(XT) demonstrates the more favourable in vivo characteristics, therefore dose-dependent oral biodistribution studies were carried out with this complex. These show drug saturation above a dose of 100 mg kg^-1 day^-1, so liver histology was performed in order to assess any potential toxicity. Finally, we improve upon the physical characterization of La(dpp)₃ to include a single crystal X-ray structure, which exhibits an 8-coorindate La³⁺ centre with two bound water molecules, and a disordered exoclathrate-type hydrogen bonded network.

Flow cytometry as an improved method for the titration of Chlamydiaceae and other intracellular bacteria

Chlamydiaceae is a family of intracellular bacteria causing a range of diverse pathological outcomes. The most devastating human diseases are ocular infections with C. trachomatis leading to blindness and genital infections causing pelvic inflammatory disease with long-term sequelae including infertility and chronic pelvic pain. In order to enable the comparison of experiments between laboratories investigating host-chlamydia interactions, the infectious titer has to be determined. Titer determination of chlamydia is most commonly performed via microscopy of host cells infected with a serial dilution of chlamydia. However, other methods including fluorescent ELISpot (Fluorospot) and DNA Chip Scanning Technology have also been proposed to enumerate chlamydia-infected cells. For viruses, flow cytometry has been suggested as a superior alternative to standard titration methods. In this study we compared the use of flow cytometry with microscopy and Fluorospot for the titration of C. suis as a representative of other intracellular bacteria. Titer determination via Fluorospot was unreliable, while titration via microscopy led to a linear read-out range of 16 - 64 dilutions and moderate reproducibility with acceptable standard deviations within and between investigators. In contrast, flow cytometry had a vast linear read-out range of 1,024 dilutions and the lowest standard deviations given a basic training in these methods. In addition, flow cytometry was faster and material costs were lower compared to microscopy. Flow cytometry offers a fast, cheap, precise, and reproducible alternative for the titration of intracellular bacteria like C. suis. © 2016 International Society for Advancement of Cytometry.

Human Ontogeny of Drug Transporters: Review and Recommendations of the Pediatric Transporter Working Group

The critical importance of membrane-bound transporters in pharmacotherapy is widely recognized, but little is known about drug transporter activity in children. In this white paper, the Pediatric Transporter Working Group presents a systematic review of the ontogeny of clinically relevant membrane transporters (e.g., SLC, ABC superfamilies) in intestine, liver, and kidney. Different developmental patterns for individual transporters emerge, but much remains unknown. Recommendations to increase our understanding of membrane transporters in pediatric pharmacotherapy are presented.

High-throughput pairing of T cell receptor alpha and beta sequences (TECH2P.930)

Conventional high-throughput immunosequencing methods profile TCR alpha (TRA) and/or TCR beta (TRB) repertoires, but do not enable pairing of the cognate subunits comprising functional TCRs. We developed a method called pairSEQ that can pair hundreds of thousands of TRA and TRB sequences in a single experiment. Our approach works by allocating random samples of T cells to a micro-titer plate, sequencing amplified cDNA from TRA and TRB genes, and DNA bar-coding the wells. Most TCR sequences uniquely identify clonal cell populations, so pairs can be assigned based on TRA and TRB sequences that occupy the same wells. To validate our method we identified cognate pairs from a sample of cells mixed from two people. The cross-sample pairs directly measure false pairing rates, which closely matched predictions from our statistical model. To show our method can be targeted to any clonal frequency range of interest, we designed a 3-plate experiment to capture pairs with repertoire frequencies from 0.5% to less than 1 in 10 million. These experiments yielded over 300,000 confident TCR pairs with one 96-well plate alone providing over 200,000 pairs. This technology is not restricted by material; in a single experiment we used this method to identify 6,349 TCR pairs from tumor infiltrating lymphocytes in 9 tumor samples. Our TCR pairing method is highly scalable, and should be broadly applicable to all somatically rearranged immune receptor loci, including immunoglobulins.

De novo detection and HLA-association of public T cell responses to Cytomegalovirus using high-throughput immune repertoire sequencing (VIR1P.1134)

We investigated the public T cell response to cytomegalovirus by sequencing rearranged T cell receptors (TCRs) in 640 subjects (287 with & 353 without CMV). We performed an experiment similar to a GWAS study, assessing the concordance of millions of unique TCRs with CMV serostatus, looking for significant associations. With CMV serostatus and TCR sequencing data, we identify 142 public T cell responses to CMV (each with p ≤ 1.0 x 10-4; FDR ≈ 0.20). Using this method to identify public clones, we predict CMV serostatus in a leave-one-out cross-validation experiment with a diagnostic odds ratio of 66. Using HLA typing, we then estimate the HLA-association of each public CMV clone by assessing the over-representation of particular HLA types in associated subjects. Of 142 CMV public clones, 26 were HLA-associated at p &lt; 10-6; no clones were significantly associated with multiple HLA alleles. When comparing our results to the literature, we find substantial concordance; most previously-reported public CMV clones are seen in our data, though only 2 are significantly associated with CMV serostatus in this cohort; both were significantly HLA-associated and in both cases the associated allele confirms previous findings. We demonstrate the validity of association studies using immunosequencing for detection and HLA-association of public T cell responses to infection, and report that assessing the presence of public T cell responses can serve as a powerful diagnostic classifier.

Abstract 1895: Identifying clonal T-cell receptor sequences and monitoring recurrent/persistent disease by T-cell receptor repertoire profiling in patients with mature T-cell neoplasms

This study demonstrates the broad potential of high-throughput sequencing of T-cell receptors to contribute to the post-therapeutic monitoring of T cell neoplasia in mature T-cell neoplasms. Identification of recurrent or persistent disease in T-cell neoplasms is important for individualized patient care. While patients with T-cell lineage lymphomas and leukemias are a small subset of all lymphoma and leukemia patients, the incidence of refractory disease in these patients can be higher than patients with B-cell lineage neoplasms. We recently developed a method to sequence the diversity of the TCR CDR3 rearrangements (Blood. 2009; 114(19): 4099-107) that exploits the capacity of high-throughput sequencing (HTS) to document the diverse repertoire of TCRB CDR3 chains simultaneously. These assays can describe both the breadth of the T-cell repertoire and quantify individual clones. This technology thus provides a potential opportunity to identify and then track the presence and frequency of clones in the context of an evolving, adaptive immune system, during the course of ongoing therapy.

We amplified the TCR repertoire of 98 index samples to identify high-frequency TCRB or TCRG rearrangements. Clones were classified as neoplastic if occurring at a proportion greater than 7 standard deviations above the mean frequency of the most abundant rearranged TCRB in control samples of blood, bone marrow, or lymphoid tissues. Eight-four percent of index samples, based on these criteria, had a tractable TCR rearrangement. Samples that lacked a detectable TCRB clone were excluded. For 35 patients, at least one subsequent follow-up sample was available. For these 59 samples, we sequenced the TCRB repertoire to screen for the corresponding index clone. We find that for most samples, high-throughput sequencing concurs with currently available, routine clinical measures of disease, such as clinical flow cytometry or PCR-based evaluation of TCRG rearrangement. High-throughput sequencing of TCRB was concordant in 46 samples with identification of the index clones and in 7 additional samples without the identification of the index clones. However, 5 of 59 samples were only positive for recurrent disease based on HTS only, and 1 of the 59 samples was only positive for recurrent disease based on current diagnostic technology but not HTS.

We find that for most disease diagnoses - high-throughput sequencing identifies a tractable clone. In addition, we find that for most samples, high-throughput sequencing concurs with currently available, routine clinical measures of disease, such as clinical flow cytometry or PCR-based evaluation of TCRG rearrangement and T-cell repertoire analysis may be useful for clinical laboratory evaluation of patients with T-cell neoplasms.

Citation Format: Anna M. Sherwood, Harlan Robins, Jonathan R. Fromm, Harvey A. Greisman, Daniel E. Sabath, Ryan O. Emerson, Mark Rieder, Brent Wood, David Wu. Identifying clonal T-cell receptor sequences and monitoring recurrent/persistent disease by T-cell receptor repertoire profiling in patients with mature T-cell neoplasms. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1895. doi:10.1158/1538-7445.AM2014-1895

Detection of minimal residual disease in B lymphoblastic leukemia by high-throughput sequencing of IGH

PURPOSE

High-throughput sequencing (HTS) of immunoglobulin heavy-chain genes (IGH) in unselected clinical samples for minimal residual disease (MRD) in B lymphoblastic leukemia (B-ALL) has not been tested. As current MRD-detecting methods such as flow cytometry or patient-specific qPCR are complex or difficult to standardize in the clinical laboratory, sequencing may enhance clinical prognostication.

EXPERIMENTAL DESIGN

We sequenced IGH in paired pretreatment and day 29 post-treatment samples using residual material from consecutive, unselected samples from the Children's Oncology Group AALL0932 trial to measure MRD as compared with flow cytometry. We assessed the impact of ongoing recombination at IGH on MRD detection in post-treatment samples. Finally, we evaluated a subset of cases with discordant MRD results between flow cytometry and sequencing.

RESULTS

We found clonal IGH rearrangements in 92 of 98 pretreatment patient samples. Furthermore, while ongoing recombination of IGH was evident, index clones typically prevailed in MRD-positive post-treatment samples, suggesting that clonal evolution at IGH does not contribute substantively to tumor fitness. MRD was detected by sequencing in all flow cytometry-positive cases with no false-negative results. In addition, in a subset of patients, MRD was detected by sequencing, but not by flow cytometry, including a fraction with MRD levels within the sensitivity of flow cytometry. We provide data that suggest that this discordance in some patients may be due to the phenotypic maturation of the transformed cell.

CONCLUSION

Our results provide strong support for HTS of IGH to enhance clinical prognostication in B-ALL.

A next-gen pipeline for generation, error correction and annotation of high-throughput immunosequencing data (TECH1P.842)

Immunosequencing is emerging as a new technology with substantial scientific and clinical relevance in immunology, hematology and oncology. Thanks to the highly-randomized somatic rearrangement of antigen receptor genes in lymphocytes, each clonal population of lymphocytes bears a receptor rearrangement that is essentially unique. Thus, sequencing of rearranged antigen receptors in B and T cells can provide a thorough characterization of the diversity and clonal structure of the adaptive immune system. Despite the significant promise of immunosequencing, accurate and consistent methods for data generation and cleaning have proven elusive in practice. Outstanding issues include biased amplification of rearranged antigen receptor genes; computational correction of PCR and sequencing errors in raw sequencing data; alignment of receptor sequences to germline gene receptor loci for accurate reconstruction of rearrangement events; and methods for extrapolation from sequencing reads attributed to each unique rearrangement to absolute input cell numbers. Using a set of robust experiments in which carefully-controlled conditions and synthetic molecules are utilized to precisely determine correct output, we have developed an experimental paradigm and data analysis pipeline that address these concerns and set a new standard for accuracy and data quality in the field of immunosequencing.

Using public T cell responses to predict cytomegalovirus infection status in silico (VIR1P.1004)

The ability of a host’s adaptive immune system to address an incipient infection relies on the previous existence of T cells which have randomly generated an appropriate antigen-specific T cell receptor (TCR). The nature of V(D)J recombination ensures that despite the enormous space of potential TCRs, there are many TCR specificities that are common in the naïve T cell repertoires across individuals. Hence, many pathogenic antigens are known to induce a “public” T cell response, in which the same functional TCR is found to be immunodominant in multiple individuals. Despite historical limitations on sequencing depth and the limited size of investigational cohorts, previous work on public T cell responses has identified many individual examples of public T cell responses to diseases including CMV, EBV, influenza and others. Using high-throughput TCRβ sequencing, we performed deep characterization of the TCR repertoires of 650 healthy subjects (356 CMV- and 294 CMV+) to enable massively parallel discovery of public T cell responses to CMV. We have identified in one experiment hundreds of CMV-associated public T cell responses. Using cross-validation, we demonstrate that taken collectively public T cell responses to CMV contain enough information to predict CMV status in new subjects using TCR sequencing alone, showing for the first time that assaying the host adaptive immune system could be a valid diagnostic strategy in the context of infectious disease.

Annotation of pseudogenous gene segments by high-throughput sequencing of rearranged lymphocyte receptor loci (TECH1P.844)

The adaptive immune system generates a huge breadth of antigen-specific T (TCRs) and B cell receptors (BCRs) by combinatoric shuffling of gene segments. Lymphocytes undergo somatic recombination of variable (V), diversity (D), and joining (J) region gene segments, with deletions and non-templated insertions at the junctions, collectively encoding the CDR3 region. Many of the gene segments are annotated as non-functional; however, full annotation of genes as functional, pseudogene or ORF has proven elusive. We used high-throughput sequencing to identify 100K’s of rearranged TCRB and IGH receptors from a large cohort of healthy adults. We then annotated V and J gene segments as functional or pseudogenes based on selection. Random chance predicts that less than one-third of somatic rearrangements will lead to in-frame transcripts, but only lymphocytes with a productive receptor are selected. Non-functional rearrangements (out-of-frame or pseudogene) persist only as a second allele in mature T and B cells. Based on these data we annotated the functional status of each gene segment based on the realized ratio of productive to non-productive rearrangements. Some gene segments are currently mis-annotated: in TCRB 2 presumed-functional gene segments are pseudogenes, in IgH 3 presumed-functional genes are pseudogenes and 1 annotated pseudogene is functional. Additionally, in both loci we identified cases of gene segment functional/pseudogene status segregating among healthy subjects.

Defining accuracy and sensitivity of T-cell receptor repertoire profiling for monitoring recurrent/persistent disease in patients with mature T-cell neoplasms (TECH1P.857)

Accurate and sensitive identification of recurrent or persistent disease in T-cell neoplasms is important for proper patient care. We developed a method that amplifies rearranged TCR CDR3 sequences and uses high-throughput sequencing (HTS) to sequence tens of thousands of chains simultaneously. Because the technology utilizes gDNA the frequency of sequenced CDR3 chains is representative of the relative frequency of each CDR3 sequence in the sample population of T cells. Thus these assays can describe both the breadth of the T-cell receptor repertoire and quantify individual clones; enabling tracking the presence and frequency of neoplastic clones. To demonstrate the potential of this technology, we first test the assay’s sensitivity and accuracy (1 lymphocyte in 1M total cells). Then, to show utility, we apply the technology to monitor persistent/recurrent disease in a set of mature T-cell lymphoma samples. To identify the neoplasm’s CDR3 chain, we sequence the TRB and TRG repertoire of 35 index samples. Then, to diagnose persistent disease, we sequence the TCR repertoire of follow-up samples and search for the neoplastic sequence. We then define persistent disease based on the sensitivity and accuracy of the assay. Concurrently, as part of standard clinical practice, a number of other methods were used to identify persistent disease. We compare these two methods to demonstrate that HTS technology is a viable alternative to traditional methods to detect and monitor lymphoma.

Identifying lymphoma antigen receptor sequences by immune repertoire profiling (TUM2P.915)

Neoplastic T and B cells rapidly expand, leading to T and B-cell receptor (TCR and BCR) repertoires dominated by one rearrangement. However clones reacting to an antigen also expand. Differentiating high-frequency reactive clones from lymphomas is important for both diagnosing and monitoring lymphomas. To document the diverse repertoire of TRB and IGH CDR3 chains, we developed a method to deeply sequence the CDR3 rearrangements using high-throughput sequencing (HTS). This technology provides a potential opportunity to identify and monitor neoplastic clones during the course of therapy. To demonstrate the potential of HTS of T and B-cell receptors to contribute to diagnosing and monitoring neoplasia in mature lymphomas; we amplify the TCR repertoire of 98 and the BCR repertoire of 60 index samples to identify high-frequency TRB or IGH rearrangements. Concurrently, we sequence the TRB and IGH repertoire in control blood, bone marrow, and reactive lymph tissue. Clones are classified as neoplastic if occurring at a proportion greater than 7 standard deviations above the mean frequency of the most abundant rearranged TRB or IGH in control samples. Using these criteria, Eighty-four percent of index samples have a tractable rearrangement. We find that for most disease diagnoses, high-throughput sequencing identifies a tractable clone and T-cell and B-cell receptor repertoire analysis may be useful for clinical laboratory evaluation of patients with T and B-cell neoplasms.

Assessing B lymphocyte clonal diversity and expansion by high-throughput sequencing of rearranged IgH loci from naïve and memory repertoires (IRM8P.708)

Diversity in B cell antigen specificity arises from structural diversity of the B cell receptor generated by somatic rearrangement of the immunoglobulin heavy (IgH) and light chain loci during B cell development. Antigen-experienced (memory) B cells are stimulated to proliferate upon successful binding of antigen, whereas the extent to which antigen-inexperienced (naïve) cells proliferate, and therefore the total diversity of circulating naïve B cells, is unclear. High-throughput sequencing of rearranged IgH CDR3 regions was performed for sorted memory and naïve B cell samples from each of 3 adults. For each sample, approximately 5 million B cells were split among 188 libraries for multiplex PCR amplification of IgH CDR3 segments, allowing us to estimate clone abundances using the number of libraries occupied by each distinct CDR3 segment. Modeling sample clone abundances as a superposition of homogeneous Poisson processes, memory repertoire clone abundance was characterized. Data from naïve samples suggest extreme diversity with more than 98% of clones occupying only one library (i.e., almost surely present in only one cell in the sample). A measure-theoretic upper bound on mean clone abundance in the naive repertoire was computed based on Monte Carlo simulation, indicating that naïve B cells typically undergo little, if any, expansion. We estimate the diversity of circulating naive B cells to be on the order of 100 million in healthy adults.

Functional IGH V polymorphism is frequent in humans: implications for immunity and vaccination (HUM8P.349)

Antibody heavy chain variable region genes (VH) are important for antigen binding, as evidenced by the dominant usage of particular VHs, such as the VH3b subfamily, in the immune responses to the capsular polysaccharide of H. influenza b. The presence or absence of particular VH alleles may be important for immunity. To screen for polymorphic VH alleles in humans, we sequenced functionally rearranged VH from 500K circulating B cells in each of 100 healthy young adults. We focused on the naïve repertoire (0-1 mutations compared to the closest known germline allele), and analyzed the proportion of rearrangements that were in-frame without stop codons (IF). In mice, low IF VHs have not undergone robust selection and are often pseudogenes. We confirmed several polymorphically functional VH genes with variable IF fractions, including V3-20, V5-a, V3-f, V1-8, and V3-9. We also identified homozygous individuals carrying novel, non-functional alleles at V7-4-1, V6-1, V3-66 and V2-70. Comparison of VH usage patterns between individuals revealed significant variation in the number of functional VH contributing to the naïve repertoire, with between 36 and 43 functional VH segments observed in each individual. These data demonstrate a significant level of functional allelic diversity and VH copy number variation between individuals, which could contribute to differential disease susceptibility, as well as influence vaccine efficacy.

Minimizing PCR bias in high-throughput adaptive immune repertoire sequencing assays (P3389)

The human adaptive immune system is a primary defense against the vast world of potential pathogens. To counter this, B and T cells rearrange a diverse repertoire of surface receptors. This system functions in part by clonal expansion, so measuring changes in the abundance of both unique and total clones is necessary to understand the immune response. We developed immune profiling assays to amplify and sequence rearranged receptors. To efficiently capture receptor diversity we use a multiplex PCR approach. However, small variations in annealing kinetics can have large impacts on amplification efficiency causing PCR amplification bias (PAB). To address this issue, we developed a method to quantify and correct PAB introduced by multiplex PCR. We demonstrate this method using our T cell receptor γ (TCRG) assay. Our method uses a quantitated, synthetic immune repertoire standard consisting of every possible Variable(V) and Joining(J) gene combination. Following multiplex TCRG PCR amplification, we assessed the difference between the synthetic VJ composition before and after amplification and quantified PAB. We adjusted primer concentrations and redesigned primers to generate an unbiased multiplex PCR assay. Using this method we reduced PAB for the TCRG assay from a 340-fold to a 4.5-fold dynamic range. Now the abundance of receptor sequences is representative of the frequency of each receptor chain in the input sample, allowing for accurate quantification of the TCRG repertoire.

Autosomal dominant familial dyskinesia and facial myokymia: single exome sequencing identifies a mutation in adenylyl cyclase 5

BACKGROUND

Familial dyskinesia with facial myokymia (FDFM) is an autosomal dominant disorder that is exacerbated by anxiety. In a 5-generation family of German ancestry, we previously mapped FDFM to chromosome band 3p21-3q21. The 72.5-Mb linkage region was too large for traditional positional mutation identification.

OBJECTIVE

To identify the gene responsible for FDFM by exome resequencing of a single affected individual.

PARTICIPANTS

We performed whole exome sequencing in 1 affected individual and used a series of bioinformatic filters, including functional significance and presence in dbSNP or the 1000 Genomes Project, to reduce the number of candidate variants. Co-segregation analysis was performed in 15 additional individuals in 3 generations.

MAIN OUTCOME MEASURES

Unique DNA variants in the linkage region that co-segregate with FDFM.

RESULTS

The exome contained 23 428 single-nucleotide variants, of which 9391 were missense, nonsense, or splice site alterations. The critical region contained 323 variants, 5 of which were not present in 1 of the sequence databases. Adenylyl cyclase 5 (ADCY5) was the only gene in which the variant (c.2176G>A) was co-transmitted perfectly with disease status and was not present in 3510 control white exomes. This residue is highly conserved, and the change is nonconservative and predicted to be damaging.

CONCLUSIONS

ADCY5 is highly expressed in striatum. Mice deficient in Adcy5 develop a movement disorder that is worsened by stress. We conclude that FDFM likely results from a missense mutation in ADCY5. This study demonstrates the power of a single exome sequence combined with linkage information to identify causative genes for rare autosomal dominant mendelian diseases.

Biological, clinical and population relevance of 95 loci for blood lipids

Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.

Hair analysis provides a historical record of cortisol levels in Cushing's syndrome

The severity of Cushing's Syndrome (CS) depends on the duration and extent of the exposure to excess glucocorticoids. Current measurements of cortisol in serum, saliva and urine reflect systemic cortisol levels at the time of sample collection, but cannot assess past cortisol levels. Hair cortisol levels may be increased in patients with CS, and, as hair grows about 1 cm/month, measurement of hair cortisol may provide historical information on the development of hypercortisolism. We attempted to measure cortisol in hair in relation to clinical course in six female patients with CS and in 32 healthy volunteers in 1 cm hair sections. Hair cortisol content was measured using a commercially available salivary cortisol immune assay with a protocol modified for use with hair. Hair cortisol levels were higher in patients with CS than in controls, the medians (ranges) were 679 (279-2500) and 116 (26-204) ng/g respectively (P<0.001). Segmental hair analysis provided information for up to 18 months before time of sampling. Hair cortisol concentrations appeared to vary in accordance with the clinical course. Based on these data, we suggest that hair cortisol measurement is a novel method for assessing dynamic systemic cortisol exposure and provides unique historical information on variation in cortisol, and that more research is required to fully understand the utility and limits of this technique.

An assessment of cortisol analysis in hair and its clinical applications

Hair analyses for exogenous compounds, specifically drugs of abuse, have been a useful tool in detecting long-term drug exposure. More recently, studies have delved into the exposure of endogenous compounds in hair. Cortisol is synthesized in the adrenal cortex in response to stress-induced activation of the hypothalamic-pituitary-adrenal (HPA) axis. While catecholamines generally indicate acute stress, cortisol can be used as an indicator for sub-acute and chronic stress. Studies on the effects of chronic stress are most often subjective in nature, relying on questionnaires asking the participant to recall on past stressors. This can lead to the issue of recall and reporting bias. A new objective measure of chronic stress is needed for a more accurate understanding of the effects of chronic stress on the body. This review uses emerging evidence to describe the usefulness of hair analysis for cortisol and discusses the current methods used.

High-temperature growth of anatase on kaolinite substrate

When a fine fraction of kaolinite (less than 2 μm) is mixed with titanyl sulphate (weight ratio approx. 1:7), hydrolysed, washed, dried and heated to temperatures between 750 and 900 ° C, it transforms into metakaolin, and titania crystallizes as anatase with a small particle size (approx. 20–30 nm). In parallel experiments with plain titania (without kaolinite), rutile is the sole product phase at 850 and 900 ° C and the dominant phase in a mixture with anatase at 750 ° C. The particle sizes are much larger (approx. 400–1100 nm). It appears that kaolinite is instrumental in preserving titania in the anatase form and with a small particle size even at fairly high temperatures and hindering its transformation to rutile. However, this anatase exhibits poor photocatalytic activity.

Impaired endothelial function in Hodgkin lymphoma survivors receiving mediastinal radiation

e19526

Background: Mediastinal radiation (RT) is a cause of premature coronary artery disease (CAD) in Hodgkin lymphoma survivors (HLS). Early detection of atherosclerosis may allow for improved health outcomes. Peripheral arterial tonometry (PAT) is a non-invasive technique that measures endothelial function (EF), as a surrogate marker of sub-clinical atherosclerosis. The objective of our study was to evaluate EF in HLS and age-matched controls using PAT and to determine the association of mediastinal RT. Methods: Cross sectional evaluation of 26 HLS age 12–30 years and within a minimum of two years from the completion of therapy and matched controls. Evaluation for CAD risk factors included measurement of body mass index and blood pressure, fasting lipoproteins and hsCRP. A standardized activity questionnaire (HAES, habitual activity estimation score) was completed by all participants. EF was measured using PAT hyperemia ratios (PAT-HR) in all subjects. Results: HLS and controls were similar for baseline variables (mean age 23.2 ± 5 yrs; 23.4 ± 4.6 yrs, p=0.35). HLS were on average 9.9 ± 3.9 yrs post treatment. No differences in EF or cardiovascular risk factors were observed between HLS survivors and controls. However impaired EF, as evidenced by lower PAT-HR (1.66 ± 0.18 vs. 2.08 ± 0.38, p<0.01) was seen in HLS (n=13) who received mantle/mediastinal RT (mean RT dose 2657 ± 971 cGy) compared to controls. Mean cumulative anthracycline dose did not differ between HLS who did or did not receive RT (224.1 ± 65.4 vs. 253 ± 70.3 mg/m2 p=0.18). These differences were not explained by alterations in lipoproteins or hsCRP, however activity scores were significantly lower in HLS compared with young adult controls (2.01 ± 1.1 vs. 3.6 ± 1.2 hrs daily, p=0.02). Conclusions: Impaired EF was observed in a small group of HLS who received mediastinal RT as compared to those who did not. Cancer survivors at risk may benefit from early assessment of EF as a sub-clinical marker of CAD.

No significant financial relationships to disclose.

Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis

RATIONALE

Polymorphisms affecting Toll-like receptor (TLR)-mediated responses could predispose to excessive inflammation during an infection and contribute to an increased risk for poor outcomes in patients with sepsis.

OBJECTIVES

To identify hypermorphic polymorphisms causing elevated TLR-mediated innate immune cytokine and chemokine responses and to test whether these polymorphisms are associated with increased susceptibility to death, organ dysfunction, and infections in patients with sepsis.

METHODS

We screened single-nucleotide polymorphisms (SNPs) in 43 TLR-related genes to identify variants affecting TLR-mediated inflammatory responses in blood from healthy volunteers ex vivo. The SNP associated most strongly with hypermorphic responses was tested for associations with death, organ dysfunction, and type of infection in two studies: a nested case-control study in a cohort of intensive care unit patients with sepsis, and a case-control study using patients with sepsis, patients with sepsis-related acute lung injury, and healthy control subjects.

MEASUREMENTS AND MAIN RESULTS

The SNP demonstrating the most hypermorphic effect was the G allele of TLR1(-7202A/G) (rs5743551), which associated with elevated TLR1-mediated cytokine production (P < 2 x 10(-20)). TLR1(-7202G) marked a coding SNP that causes higher TLR1-induced NF-kappaB activation and higher cell surface TLR1 expression. In the cohort of patients with sepsis TLR1(-7202G) predicted worse organ dysfunction and death (odds ratio, 1.82; 95% confidence interval, 1.07-3.09). In the case-control study TLR1(-7202G) was associated with sepsis-related acute lung injury (odds ratio, 3.40; 95% confidence interval, 1.59-7.27). TLR1(-7202G) also associated with a higher prevalence of gram-positive cultures in both clinical studies.

CONCLUSIONS

Hypermorphic genetic variation in TLR1 is associated with increased susceptibility to organ dysfunction, death, and gram-positive infection in sepsis.

Sequence variation in the human transcription factor gene POU5F1

Background

POU5F1 expression is required to maintain stem cell pluripotency and for primordial germ cells to retain proliferative capability in embryonic development. Recent evidence suggests that POU5F1 may also be a testicular germ cell carcinoma (TGCC) oncogene, and POU5F1 variation may influence TGCC risk. As an important first step to a genetic association study, we sought to identify all common sequence variants in an 11.3 kb region containing POU5F1, and to describe the linkage disequilibrium patterns, using DNA from individuals of African-descent (AD) and European-descent (ED).

Results

A higher number of polymorphisms was observed in the AD (n = 102) versus ED (n = 82) population. Among the 41 observed haplotypes, 21 (51%) and 12 (29%) were unique to the AD and ED populations, respectively, while 8 (20%) were observed in both. The number of tagging polymorphisms necessary to explain at least 80% of common variation (minor allele frequency ≥ 0.10) due to the remaining untyped polymorphisms was 17 for an AD and 10 for an ED population, providing a 4.0- and 7.0-fold gain in genotyping efficiency for characterizing nucleotide variation, respectively.

Conclusion

POU5F1 is highly polymorphic, however a smaller subset of polymorphisms can tag the observed genetic variation with little loss of information.

TagSNP analyses of the PON gene cluster: effects on PON1 activity, LDL oxidative susceptibility, and vascular disease

Paraoxonase 1 (PON1) activity is consistently predictive of vascular disease, although the genotype at four functional PON1 polymorphisms is not. To address this inconsistency, we investigated the role of all common PON1 genetic variability, as measured by tagging single-nucleotide polymorphisms (tagSNPs), in predicting PON1 activity for phenylacetate hydrolysis, LDL susceptibility to oxidation ex vivo, plasma homocysteine (Hcy) levels, and carotid artery disease (CAAD) status. The biological goal was to establish whether additional common genetic variation beyond consideration of the four known functional SNPs improves prediction of these phenotypes. PON2 and PON3 tagSNPs were secondarily evaluated. Expanded analysis of an additional 26 tagSNPs found evidence of previously undescribed common PON1 polymorphisms that affect PON1 activity independently of the four known functional SNPs. PON1 activity was not significantly correlated with LDL oxidative susceptibility, but genotypes at the PON1(-108) promoter polymorphism and several other PON1 SNPs were. Neither PON1 activity nor PON1 genotype was significantly correlated with plasma Hcy levels. This study revealed previously undetected common functional PON1 polymorphisms that explain 4% of PON1 activity and a high rate of recombination in PON1, but the sum of the common PON1 locus variation does not explain the relationship between PON1 activity and CAAD.

Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels

Elevated plasma levels of C-reactive protein (CRP), an inflammation-sensitive marker, have emerged as an important predictor of future cardiovascular disease and metabolic abnormalities in apparently healthy men and women. Here, we performed a systematic survey of common nucleotide variation across the genomic region encompassing the CRP gene locus. Of the common single-nucleotide polymorphisms (SNPs) identified, several in the CRP promoter region are strongly associated with CRP levels in a large cohort study of cardiovascular risk in European American and African American young adults. We also demonstrate the functional importance of these SNPs in vitro.

An association study of angiotensinogen polymorphisms with serum level and hypertension in an African-American population

OBJECTIVE

To evaluate the association of angiotensinogen (AGT) gene with AGT level and hypertension based on the overall genetic variation of the AGT gene in among African-Americans.

METHODS

All non-rare single nucleotide polymorphisms (SNPs) in AGT were identified by resequencing 24 individuals. Five tagging SNPs were selected based on the pairwised linkage disequilibrium (LD) pattern and were genotyped in 284 individuals. Association studies of AGT level and hypertension were performed using these five tagging SNPs.

RESULTS

No significant association with AGT level or hypertension was found in analyses of each of the five single SNPs. However, one of the haplotypes defined by these five SNPs was significantly associated with AGT level (P = 0.046), although this haplotype was not associated with hypertension.

CONCLUSIONS

Identification of genetic polymorphisms associated with risk of hypertension has been frustratingly difficult. Two strategies adopted to improve precision are the use of intermediate phenotypes and summarization of genetic information using haplotypes. These strategies appeared to yield a modest increase in precision at the AGT locus with respect to the physiological intermediate, but did not lead to significant association of the molecular markers with hypertension. Additional research is required to increase confidence in haplotype mapping as an epidemiological analysis tool.

Paraoxonase activity, but not haplotype utilizing the linkage disequilibrium structure, predicts vascular disease

OBJECTIVE

The effects of paraoxonase (PON1) activity and of genetic variation in the PON1 promoter and coding region on carotid artery disease (CAAD) were investigated.

METHODS AND RESULTS

We identified functional promoter polymorphisms and examined their effects in a cohort with and without CAAD. We used the full sequences in 23 white subjects to determine the linkage disequilibrium (LD) structure of the PON1 region and to direct the grouping of haplotypes for disease association testing. There are several discrete regions of the PON1 gene with strong local LD, but the useful levels of LD do not extend across the entire gene. Indeed, PON1-162/-108/55/192 haplotype did not predict additional variation in PON1 activities compared with the 4 genotypes separately. PON1 hydrolysis activity predicted CAAD status, but this was not attributable to the promoter or coding region polymorphisms or haplotype or to the effects of smoking or statin use on PON1 activity.

CONCLUSIONS

PON1 does not have LD across the gene, and use of haplotypes in association studies should consider the LD structure. PON1 activity predicts CAAD, yet 4 functional polymorphisms do not. Additional investigations of genetic and environmental factors that influence PON1 activity as a risk factor for vascular disease are warranted.

Age related skeletal muscle response to electrical stimulation

We hypothesized that the conditioned muscles of elderly and growing organisms have different responses to electrical stimulation from that of young adult organisms. Five day old lambs, 1 year old sheep, and 8 year old elderly sheep were used for this investigation. The latissimus dorsi muscle (LDM) was partially mobilized and left in situ. Two electrodes were implanted and electrical stimulation (ES) was begun for 8 weeks; it was then stopped for 2 weeks. Biopsies were taken before ES, after 8 weeks of ES, and after the 2 week delay period. The LDM of old sheep has less fatigue resistance than the LDM of younger animals. Conditioned LDM of the lamb continued to be fatigue resistant after a 2 week delay compared with adult sheep. In all animals, lactate dehydrogenase (LDH) fraction five decreased and LDH-1 + 2 fractions increased after ES. After a 2 week delay, the data returned to baseline values only in adult animals. The percentage area occupied by mitochondria in old sheep was less after ES than in younger animals. In all animals, the mitochondrial area increased after ES and reverted to baseline values after the delay. The number of nuclei and fibers considerably increased after ES. Only in the lamb did the number of nuclei and fibers continue to be elevated after the delay. There are more changes in young skeletal muscle than in adult (1 year or 8 year old) muscle during ES, and they "remember" these properties. Elderly skeletal muscle does not convert to a fatigue resistant state as completely as adult skeletal muscle during a conventional 8 week ES protocol. It is necessary to change and prolong the ES protocol for elderly patients.

Pregnancy outcome following maternal use of the new selective serotonin reuptake inhibitors: a prospective controlled multicenter study

CONTEXT

Although a large number of women of reproductive age use new selective serotonin reuptake inhibitors (SSRIs) and half of all pregnancies are unplanned, no data exist on the safety of these agents for the human fetus.

OBJECTIVE

To assess fetal safety and risk of fluvoxamine, paroxetine, and sertraline.

DESIGN

A prospective, multicenter, controlled cohort study.

SETTING

Nine Teratology Information Service centers in the United States and Canada.

PATIENTS

All women who were counseled during pregnancy following exposure to a new SSRI and followed up by the participating centers. Controls were randomly selected from women counseled after exposure to nonteratogenic agents.

MAIN OUTCOME MEASURES

Rates of major congenital malformations.

RESULTS

A total of 267 women exposed to an SSRI and 267 controls were studied. Exposure to SSRIs was not associated with either increased risk for major malformations (9/222 live births [4.1%] vs 9/235 live births [3.8%] in the controls, relative risk, 1.06, 95% confidence interval, 0.43-2.62) or higher rates of miscarriage, stillbirth, or prematurity. Mean (SD) birth weights among SSRI users (3439 [505] g) were similar to the controls (3445 [610] g) as were the gestational ages (39.4 [1.7] weeks vs 39.4 [1.9] weeks).

CONCLUSION

The new SSRIs, fluvoxamine, paroxetine, and sertraline, do not appear to increase the teratogenic risk when used in their recommended doses.

Evaluation of the role of routine serial cranial computed tomography in the management of children with human immunodeficiency virus infection

OBJECTIVE

To review the impact of routine follow-up cranial computed tomography (CT) scans on the management of children with human immunodeficiency virus (HIV) infection.

DESIGN

Longitudinal data collected from 58 HIV-infected children followed in one center for mean of 3.8 +/- 1.8 years.

SETTING

HIV/AIDS pediatric program following over 90% of the identified HIV-infected children in one region in Canada.

RESULTS

The baseline CT scans showed intracranial abnormalities in 35 of 58 children (60%). In five children with basal ganglia calcifications (BGC) without cerebral atrophy, there has not been progressive encephalopathy. For the 43 children who had serial CT scans for routine follow-up, 34 (79%) had changes in the scans that were concordant with the clinical assessment. In all but five children with progressive ventricular and sulcal dilatation on CT scan, there was simultaneous clinical evidence of encephalopathy. Those five children were already on antiretroviral therapy, and therapy was not changed in response to the CT scan findings.

CONCLUSION

Baseline CT scans provide useful diagnostic and prognostic information. Further research is needed to evaluate the role of cranial CT imaging in the management of pediatric HIV encephalopathy.

[A nomogram of duplex ultrasound quantification of peripheral arterial stenoses. Studies of the cardiovascular model and in angiography patients]

BACKGROUND AND METHODS

Blood flow velocity measurements were performed with duplex ultrasound in vitro (flow phantom) and in 62 patients who underwent angiography due to peripheral vascular disease.

RESULTS

Intrastenotic peak systolic velocity (PSV) divided by proximally recorded PSV (peak velocity ratio, PVR) exhibited a strong correlation with percent diameter reduction: r2 = 0.86; N = 106 stenoses. A PVR value > or = 2.4 indicated a more than 50% stenosis with a sensitivity of 87% and a specificity of 94%. Calculation of PVR may normalize for patient variation and allow noninvasive quantification of lumen narrowing with high sensitivity and specificity. The intraobserver variability (95% CI) of stenosis quantification using PVR values was 10%. A nomogram simplifies estimation of lumen narrowing after measurement of intrastenotic and proximal PSV values.

CONCLUSION

Quantification of peripheral artery stenoses can be performed easily and noninvasively with duplex ultrasound using the peak velocity ratio (PVR).

Prospective multicentre study of pregnancy outcome after lithium exposure during first trimester

Lithium carbonate is an effective drug for prophylaxis and treatment of major affective disorders. In-utero exposure to lithium during the first trimester of pregnancy might be associated with an increased risk of cardiac malformations, especially the rare Ebstein's anomaly. We prospectively recruited and followed 148 women (mean age 30 years, SD 5 range 15-40) using lithium during the first trimester of pregnancy, who consulted four teratogen information centres in the USA and Canada. Pregnancy outcome was compared with that of controls matched for maternal age. We had complete follow-up of pregnancy outcome in 138 of 148 patients recruited. In the other 10, fetal echocardiograms were available but postnatal follow-up was not done. Mean daily dose of lithium was 927 mg (SD 340). Rates of major congenital malformations did not differ between the lithium (2.8%) and control (2.4%) groups. 1 patient in the lithium group chose to terminate pregnancy after Ebstein's anomaly was detected by a prenatal echocardiogram. There was 1 ventricular septal defect in the controls. Birthweight was significantly higher in the lithium-exposed infants than in the controls despite identical gestational ages (3475 [660] g vs 3383 [566] g, p = 0.02). The true difference in birthweight might have been even larger, since significantly more women using lithium than controls were cigarette smokers (31.8% vs 15.5%, p = 0.002). These results indicate that lithium is not an important human teratogen. Women with major affective disorders who wish to have children may continue lithium therapy, provided that adequate screening tests, including level II ultrasound and fetal echocardiography, are done.

Hemostatic evaluation of Sarns/3M-VAD implantation in calves

The authors evaluated the potential for thrombotic complications arising from implantation of a ventricular assist device (Sarns/3M-VAD) in four calves. Coagulation screening tests (prothrombin time [PT], partial thromboplastin time [PTT], thrombin time [TT]), fibrinogen levels, and antithrombin III functional activity were found to be of little value as predictors of the degree of activation of the hemostatic system. However, platelet counts, adenosine diphosphate (ADP)- and collagen-induced platelet aggregation, and thromboxane (TXB2) levels were good indicators of changes in platelet reactivity. Platelet counts (initial value 6 x 10(5) rose, and were associated with increased rate and extent of ADP- and collagen-induced platelet aggregation, which remained elevated during the entire 25 day postimplantation period. The first 5 days postimplantation revealed a typical acute inflammatory response, with increased platelet levels, but with TXB2 levels significantly decreased during this period. A monoclonal antibody based bovine D-dimer assay and Western blot studies indicated a small but significant increase in circulating bovine D-dimer, indicating localized fibrin formation and its dissolution.

Comparison of a topical mixture of lidocaine and prilocaine (EMLA) versus 1% lidocaine infiltration on wound healing

We compared a eutectic mixture of lidocaine and prilocaine (EMLA, Astra Pharmaceuticals, Inc) with 1% lidocaine infiltration to determine the effect on wound healing in a prospective single blind study using the rat model. Thirty-six wounds were assessed. No clinical or histologic evidence of infection or necrosis was present in any wound. Five wounds (two in the lidocaine and three in the EMLA group, P = 1.0) demonstrated a widened scar owing to healing by secondary intention following suture disruption. There was no significant difference between groups in the degree of inflammation (P = 0.08). We conclude that EMLA does not affect wound healing adversely and is comparable to 1% lidocaine infiltration in the animal model. Further study to determine its anesthetic effect in laceration repair is presently being undertaken.