The history and geographic distribution of a KCNQ1 atrial fibrillation risk allele

The genetic architecture of atrial fibrillation (AF) encompasses low impact, common genetic variants and high impact, rare variants. Here, we characterize a high impact AF-susceptibility allele, KCNQ1 R231H, and describe its transcontinental geographic distribution and history. Induced pluripotent stem cell-derived cardiomyocytes procured from risk allele carriers exhibit abbreviated action potential duration, consistent with a gain-of-function effect. Using identity-by-descent (IBD) networks, we estimate the broad- and fine-scale population ancestry of risk allele carriers and their relatives. Analysis of ancestral migration routes reveals ancestors who inhabited Denmark in the 1700s, migrated to the Northeastern United States in the early 1800s, and traveled across the Midwest to arrive in Utah in the late 1800s. IBD/coalescent-based allele dating analysis reveals a relatively recent origin of the AF risk allele (~5000 years). Thus, our approach broadens the scope of study for disease susceptibility alleles to the context of human migration and ancestral origins.

Laser ablation sample preparation for atom probe tomography and transmission electron microscopy

Laser ablation is capable of removing large volumes of material with micron scale precision at very high speeds. This makes it an ideal tool for the initial stage of preparation of samples for atom probe and electron microscopy studies. However, the thermal nature of the laser ablation process is such that thermal and mechanical damage is induced in the samples in the form of zones of recrystallisation and stress induced deformation. For the analysis of nanometer-sized samples, such as those required for atom probe tomography and transmission electron microscopy, it is necessary to ensure that any damage induced during sample preparation will not introduce artefacts and that specimens are representative of the microstructure of the bulk sample. Here we have undertaken an analysis of the damage caused during sample preparation through a study of pure aluminium and phosphorous doped silicon wafers. Our findings indicate that recrystallisation and stress induced misorientations occur in pure aluminium at the micron scale, however, no detectable damage is observed in the silicon sample.

International HTA Experience with Targeted Therapy Approvals for Lung Cancer

OBJECTIVES

The aim of this study was to compare the listing success rates and time incurred to listing of recently approved lung cancer medications across Australia, Canada and England.

METHODS

A comparison between the three countries was performed with respect to the listing status, time incurred for listing and differences in recommendations made for cost effectiveness. Major uncertainties and limitations that compromise health technology assessment (HTA) recommendations were identified.

RESULTS

The listing success rate was found to be low across all three countries (33% Canada, 17% England and 8% Australia). Across the HTA agencies' reviews, comparators were either dissimilar or altered for effectiveness and/or economic analysis. Overall, limited evidence was found for all indications, and uncertainties were identified due to indirect analyses (70%) and survival extrapolation (100%). Although most of the indications were concluded to be not cost effective, some were subsequently listed (47%) at a reduced price and/or with a specific access programme.

CONCLUSIONS

This study demonstrated a low listing success rate for novel lung therapies internationally within different HTA jurisdictions. Major uncertainties that are resistant to available solutions seem to be common across different countries; thus, international solutions would be beneficial.

Clustering of 770,000 genomes reveals post-colonial population structure of North America

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies.

A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies

One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.

PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations

Identifying ancestry along each chromosome in admixed individuals provides a wealth of information for understanding the population genetic history of admixture events and is valuable for admixture mapping and identifying recent targets of selection. We present PCAdmix (available at https://sites.google.com/site/pcadmix/home ), a Principal Components-based algorithm for determining ancestry along each chromosome from a high-density, genome-wide set of phased single-nucleotide polymorphism (SNP) genotypes of admixed individuals. We compare our method to HAPMIX on simulated data from two ancestral populations, and we find high concordance between the methods. Our method also has better accuracy than LAMP when applied to three-population admixture, a situation as yet unaddressed by HAPMIX. Finally, we apply our method to a data set of four Latino populations with European, African, and Native American ancestry. We find evidence of assortative mating in each of the four populations, and we identify regions of shared ancestry that may be recent targets of selection and could serve as candidate regions for admixture-based association mapping.

Bayesian refinement of association signals for 14 loci in 3 common diseases

To further investigate susceptibility loci identified by genome-wide association studies, we genotyped 5,500 SNPs across 14 associated regions in 8,000 samples from a control group and 3 diseases: type 2 diabetes (T2D), coronary artery disease (CAD) and Graves' disease. We defined, using Bayes theorem, credible sets of SNPs that were 95% likely, based on posterior probability, to contain the causal disease-associated SNPs. In 3 of the 14 regions, TCF7L2 (T2D), CTLA4 (Graves' disease) and CDKN2A-CDKN2B (T2D), much of the posterior probability rested on a single SNP, and, in 4 other regions (CDKN2A-CDKN2B (CAD) and CDKAL1, FTO and HHEX (T2D)), the 95% sets were small, thereby excluding most SNPs as potentially causal. Very few SNPs in our credible sets had annotated functions, illustrating the limitations in understanding the mechanisms underlying susceptibility to common diseases. Our results also show the value of more detailed mapping to target sequences for functional studies.

Term pregnancies and the clinical characteristics of multiple sclerosis: a population based study

OBJECTIVE

Pregnancy has a well documented effect on relapse risk in multiple sclerosis (MS). Prospective studies have reported a significant decline by two-thirds in the rate of relapses during the third trimester of pregnancy and a significant increase by two-thirds during the first 3 months postpartum. However, it is unclear as to whether there are any long term effects on disability.

METHODS

Data were collated from clinical records and family histories systematically collected from the University of British Columbia MS Clinic.

RESULTS

Clinical and term pregnancy data were available from 2105 female MS patients. MS patients having children after MS onset took the longest time to reach an Expanded Disability Status Scale (EDSS) score of 6 (mean 22.9 years) and patients having children before MS onset were the quickest (mean 13.2 years). However, these effects were not related to term pregnancy and were fully accounted for by age of MS onset.

CONCLUSIONS

Pregnancy had no effect on the time to reach an EDSS score 6. As MS predominantly affects women of childbearing age, women with MS can be reassured that term pregnancies do not appear to have any long term effects on disability.

Development of syntax in a retarded girl using procedures of imitation, reinforcement, and modelling

Three experiments demonstrated the development and generalized use of a singular and plural declarative sentence in a child initially lacking sentence form responses. In each experiment, an adult(s) served as a language model(s), and consequences (sweets) were provided for imitation of the model. During training trials, an item(s) was displayed first to the model(s) then to the subject; these displays were accompanied by requests to label the item(s). Generalization was assessed by a number of probe trials that were periodically interspersed among training trials. During these trials, the subject was requested to label the displayed item(s) without any preceding labelling response from the model. Using these procedures, generalized use of a singular sentence ("That is one-") resulted in Experiment I, and generalized use of a plural sentence ("These are two-") resulted in Experiment II. In Experiment III, two models (a singular and a plural sentence model) were made available to the subject but imitation of only one model was reinforced during any one condition. Results indicated the subject labelled probe (generalization) items with the same sentence form that was modelled and reinforced during training trials.

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to play an important role in genetic susceptibility to common disease. To address this we undertook a large direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed ~19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated ~50% of all common CNVs larger than 500bp. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell-lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease, IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis, and type 1 diabetes, and TSPAN8 for type 2 diabetes, though in each case the locus had previously been identified in SNP-based studies, reflecting our observation that the majority of common CNVs which are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs which can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.

Potential utility of angiotensin II receptor blockers in the treatment of estrogen receptor positive infiltrating ductal carcinoma

Abstract #2125

Despite significant advances in diagnosis and treatment, breast cancer remains the world's leading cause of cancer mortality in women. In this study we employed differential expression analysis tools to mine the BioExpress®(1) database of transcriptional profiles and found that Angiogtensin II receptor 1 (AT1-R) mRNA expression was highly correlated with expression of estrogen receptor alpha (ERα) in biopsies from patients with infiltrating ductal carcinoma (IDC). Specifically, AT1-R transcript was up-regulated 12.5 fold in ER+ primary IDC relative to ER- primary IDC (P = 0.0001).
 Experiments using ER+ (T47D) and ER– (HCC1143) breast cancer cell lines derived from human mammary gland ductal carcinoma demonstrated that only the ER+ line responded to angiotensin II-mediated growth stimulation, and this effect was dramatically suppressed in a concentration dependent manner by AT1-R blockers (ARBs). Additional cell culture experiments evaluating eight cell lines derived from IDC further validated the concept that co-expression of both ERα and AT1-R was required for responsiveness to angiotensin II-induced cell proliferation. We have also found that ARBs significantly enhanced the anti-proliferative activity of both tamoxifen, an ER modulator, and formestane, an aromatase inhibitor. Most importantly, we have shown in a T47D tumor xenograft model that ARBs, candesartan and irbesartan, dose-dependently inhibited tumor progression in NODScid mice. Currently, we are evaluating the synergistic/additive effects of ARBs with tamoxifen in additional T47D xenograft models.
 In conclusion, our data provides evidence that ARBs may have utility in the prevention and treatment of ER+ IDC. These observations further validate reports that ARBs may suppress tumor cell proliferation, angiogenesis, and cancer progression. To our knowledge our findings represent the first example of a potential means to stratify a patient population for ARB-based tumor therapy using a clinically accepted biomarker, findings which may have significant clinical implications for the treatment of IDC.
 1) BioExpress® is a knowledgebase of human disease biology comprising over 20,000 individual patient samples profiled over the entire human transcriptome representing > 400 disease states including approximately 200 human breast cancer samples (169 diagnosed as IDC) and 68 normal breast tissue controls.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2125.

Examination of behavioral deficits triggered by targeting BDNF in fetal or postnatal brains of mice

Human and animal studies have implicated brain-derived neurotrophic factor (BDNF) in the etiology of psychiatric disorders. It is expressed in limbic regions of the brain associated with the regulation of emotionality during fetal development and in the adult animal. To further our understanding of the role of BDNF in the modulation of mood and to distinguish its prenatal and postnatal functions, we investigated and contrasted behavioral changes elicited by its depletion from fetal or postnatal brains of mice. Two corresponding lines of BDNF conditional knockout mice were subjected to a battery of behavioral tests assessing locomotor, depressive, aggressive and anxiety-related behaviors. We found that both lines of mutants were dramatically hyperactive during the light and dark cycles and hyperaggressive. They also exhibited a depression-like phenotype in the tail suspension test but not in the forced swim test. Interestingly, depletion of BDNF from the fetal brain had more pronounced effects on aggressive and depressive-like behaviors and led to deficits in 5-HT(2A) receptor content in the medial frontal cortex, highlighting the importance of this neurotrophin during development. We conclude that expression of BDNF both pre- and postnatally is essential for normal modulation of behavior by neural circuits in the adult animal.

Ligand density modulates eosinophil signaling and migration

Eosinophils are a major component of the inflammatory response in persistent airway inflammation in asthma. The factors that determine the retention of eosinophils in the airway remain poorly understood. Elevated levels of fibronectin have been observed in the airway of patients with asthma, and the levels correlate with eosinophil numbers. To determine if fibronectin density modulates eosinophil function, we investigated the effect of fibronectin and vascular cell adhesion molecule 1 (VCAM-1) density on eosinophil migration and signaling via the p38 and extracellular regulated kinase (ERK)-mitogen-activated protein kinase (MAPK) signaling pathways. There was a dose-dependent inhibition of eosinophil spreading and migration on increasing concentrations of fibronectin but not VCAM-1. In addition, activation of p38 MAPK was inhibited at high fibronectin but not high VCAM-1 concentrations, and ERK activity was slightly reduced at high VCAM-1 and fibronectin concentrations. Together, the results demonstrate that fibronectin but not VCAM-1 inhibits eosinophil migration and signaling.

Differential transcription efficiency of two Ig VH promoters in vitro

Each Ig variable region gene segment is transcribed from its own unique promoter. While all of these promoters share common consensus elements that contribute to the B cell-specific expression of these genes, the DNA sequence of each promoter is distinct. In this study, we have directly compared the transcription efficiencies of two murine heavy chain (VH) promoters in a murine B cell in vitro transcription system. We found that the promoters differed in both transcription efficiency and the ability to bind specific protein complexes. While some of the transcription differences may be attributed to differences in basal promoter elements, the spacing between the octamer and the heptamer consensus elements was found to be important. Others have reported a direct correlation between transcription efficiency and the probability that individual variable region gene segments will rearrange. Our studies may be of direct importance to those interested in identifying B cell-specific transcription factors and may ultimately help to explain differences in the expression of some VH gene segments.

Differential transcription efficiency of two Ig VH promoters in vitro

Each Ig variable region gene segment is transcribed from its own unique promoter. While all of these promoters share common consensus elements that contribute to the B cell-specific expression of these genes, the DNA sequence of each promoter is distinct. In this study, we have directly compared the transcription efficiencies of two murine heavy chain (VH) promoters in a murine B cell in vitro transcription system. We found that the promoters differed in both transcription efficiency and the ability to bind specific protein complexes. While some of the transcription differences may be attributed to differences in basal promoter elements, the spacing between the octamer and the heptamer consensus elements was found to be important. Others have reported a direct correlation between transcription efficiency and the probability that individual variable region gene segments will rearrange. Our studies may be of direct importance to those interested in identifying B cell-specific transcription factors and may ultimately help to explain differences in the expression of some VH gene segments.

Integrating outcomes measurement into clinical practice improvement across the continuum of care: a disease-specific episode of care model

This article describes a model for incorporating outcomes measurement into a comprehensive, continuum-wide clinical practice improvement program developed at Lovelace Health Systems (Albuquerque, N.M.). Created in 1993, the Lovelace Episode of Care Program currently includes nine disease-specific multidisciplinary teams that are working to improve care by addressing such issues as severity, appropriateness, efficiency, continuous quality improvement indicators, practice guidelines, care maps, and outcomes. Key features and advantages of the model are discussed, as well as implementation issues, successes, lessons learned, program restructuring and improvement, and applicability of the framework across diseases and health organizations.

Arrangement of repetitive sequences in the genome of herpesvirus Sylvilagus

Herpesvirus sylvilagus is a lymphotropic (type gamma) herpesvirus of cottontail rabbits (Sylvilagus floridanus). Analysis of virion DNA of herpesvirus sylvilagus has revealed that the genome consists of one stretch of about 120 kilobase pairs of internal, unique DNA flanked by a variable number of 553-base-pair tandem repeats. The G + C content of the repetitive DNA is extremely high (83%), as determined by sequencing. The organization of the herpesvirus sylvilagus genome is, therefore, similar to that of the primate lymphotropic viruses herpesvirus saimiri and herpesvirus ateles.

Dialysis in the management of pregnant patients with renal insufficiency

Successful pregnancy in patients on dialysis is uncommon because of a high rate of infertility and complications. The use of hemodialysis to manage pregnant patients needing dialysis has been well reported. However, to our knowledge, only 2 previous cases of pregnant patients using chronic ambulatory peritoneal dialysis (CAPD) have been reported. We discuss 14 pregnancies in 13 women in whom dialysis was used in the management of their pregnancies. Ten pregnancies were successful. Included are 5 successful pregnancies out of 8 managed with CAPD or chronic cycling peritoneal dialysis (CCPD). In comparing the cases managed with CAPD to those managed with hemodialysis, CAPD seems to offer several advantages. These include a more constant biochemical and extracellular environment for the fetus, higher hematocrit levels, infrequent episodes of hypotension, and no heparin requirement. In addition, intraperitoneal insulin facilitates the management of blood glucose in diabetics, and intraperitoneal magnesium facilitates the management of premature labor. Infection, loss of intraperitoneal volume, and loss of peritoneal clearances for solutes and water were not found to be problems.

Aortic root abscess. Initial experience using magnetic resonance imaging

The detection of aortic root abscess by magnetic resonance imaging has not been described previously. We report a patient with an aortic root abscess that was successfully diagnosed by magnetic resonance imaging and echocardiography. Computed tomography failed to detect the abscess. The patient recovered with antibiotic therapy. Based on this case and other reports in the literature, we advocate treating similar patients without surgery. We recommend magnetic resonance imaging as an investigational method where the diagnosis of aortic root abscess is ambiguous.

Sinus histiocytosis with massive lymphadenopathy: a case with unusual skin involvement and a therapeutic response to vinblastine-loaded platelets

A patient with sinus histiocytosis with massive lymphadenopathy had unusual skin lesions and progressive internal involvement. Both aspects responded dramatically to the administration of vinblastine-loaded platelets. Vinblastine-loaded, idiopathic thrombocytopenic purpura antibody-coated platelets are a rationale therapy for a disease characterized by the presence of actively phagocytosing histiocytes.

The effects of short- and long-term exposure of chick embryos to neutral red on the frequency of sister-chromatid exchange

The chick embryo was used to study the effects of neutral red (NR) on the frequency of sister-chromatid exchange (SCE) in specific tissues exposed to this mutagen for short and long periods as development proceeded. In short-term trials, aqueous NR at doses of 10, 25 and 100 micrograms was injected in 3-day and 6-day embryos. In each case, embryos were also treated with 5-bromodeoxyuridine (BrdU) for a 24-h period (two cell cycles) and harvested at 4 days and 7 days, resp. A long-term exposure (about 8 cell cycles) was achieved by exposing embryos to NR from day 3 to day 7 of incubation. At a NR dose of 25 micrograms, the chronic exposure resulted in a doubling of the rate of SCE (11.4/cell) over that observed in embryos exposed for only 24 h at either days 3-4 (6.0/cell) or days 6-7 (6.0/cell). At 100 micrograms of NR, the same relationship held with SCE rates of 14.2/cell for the chronic exposure versus rates of 8.0/cell (3-4 days) and 6.9/cell (6-7 days). At 10 micrograms of NR, no such accumulation of SCE occurred upon long-term treatment. These results show an enhanced SCE response upon growth of embryonic cells in the presence of NR for several days. This may be the result of the persistence of past lesions with the addition of more lesions upon continued exposure to NR.