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1.  Evaluation of Reference Genes for Quantitative Real-Time PCR in Oil Palm Elite Planting Materials Propagated by Tissue Culture 
PLoS ONE  2014;9(6):e99774.
Background
The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels.
Results
In this study, eight candidate reference genes selected from cDNA microarray study and literature review were evaluated comprehensively across 26 tissue culture samples using RT-qPCR. These samples were collected from two tissue culture lines and media treatments, which consisted of leaf explants cultures, callus and embryoids from consecutive developmental stages. Three statistical algorithms (geNorm, NormFinder and BestKeeper) confirmed that the expression stability of novel reference genes (pOP-EA01332, PD00380 and PD00569) outperformed classical housekeeping genes (GAPDH, NAD5, TUBULIN, UBIQUITIN and ACTIN). PD00380 and PD00569 were identified as the most stably expressed genes in total samples, MA2 and MA8 tissue culture lines. Their applicability to validate the expression profiles of a putative ethylene-responsive transcription factor 3-like gene demonstrated the importance of using the geometric mean of two genes for normalization.
Conclusions
Systematic selection of the most stably expressed reference genes for RT-qPCR was established in oil palm tissue culture samples. PD00380 and PD00569 were selected for accurate and reliable normalization of gene expression data from RT-qPCR. These data will be valuable to the research associated with the tissue culture process. Also, the method described here will facilitate the selection of appropriate reference genes in other oil palm tissues and in the expression profiling of genes relating to yield, biotic and abiotic stresses.
doi:10.1371/journal.pone.0099774
PMCID: PMC4057393  PMID: 24927412
2.  Chronic Infections of West Nile Virus Detected in California Dead Birds 
Abstract
During 2010 and 2011, 933 recently deceased birds, submitted as part of the dead bird surveillance program, tested positive for West Nile virus RNA at necropsy. The relative amount of RNA measured by qRT-PCR cycles ranged from 8.2 to 37.0 cycle threshold (Ct) and formed a bimodal frequency distribution, with maxima at 20 and 36 Ct and minima at 28–30 Ct. On the basis of frequency distributions among different avian species with different responses to infection following experimental inoculation, field serological data indicating survival of infection, and the discovery of persistent RNA in experimentally infected birds, dead birds collected in nature were scored as “recent” or “chronic” infections on the basis of Ct scores. The percentage of birds scored as having chronic infections was highest during late winter/spring, when all birds were after hatching year, and lowest during late summer, when enzootic transmission was typically highest as indicated by mosquito infections. Our data indicated that intervention efforts should not be based on dead birds with chronic infections unless supported by additional surveillance metrics.
doi:10.1089/vbz.2012.1097
PMCID: PMC3669600  PMID: 23488452
Surveillance; West Nile virus; Dead birds; Chronic infections; Overwintering
3.  Oil palm genome sequence reveals divergence of interfertile species in old and new worlds 
Nature  2013;500(7462):335-339.
Oil palm is the most productive oil-bearing crop. Planted on only 5% of the total vegetable oil acreage, palm oil accounts for 33% of vegetable oil, and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8 gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators1, which are highly expressed in the kernel. We also report the draft sequence of the S. American oil palm Elaeis oleifera, which has the same number of chromosomes (2n=32) and produces fertile interspecific hybrids with E. guineensis2, but appears to have diverged in the new world. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations which restrict the use of clones in commercial plantings3, and thus helps achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.
doi:10.1038/nature12309
PMCID: PMC3929164  PMID: 23883927
4.  Hormone therapy and Alzheimer disease dementia 
Neurology  2012;79(18):1846-1852.
Objectives:
Observational studies suggest reduced risk of Alzheimer disease (AD) in users of hormone therapy (HT), but trials show higher risk. We examined whether the association of HT with AD varies with timing or type of HT use.
Methods:
Between 1995 and 2006, the population-based Cache County Study followed 1,768 women who had provided a detailed history on age at menopause and use of HT. During this interval, 176 women developed incident AD. Cox proportional hazard models evaluated the association of HT use with AD, overall and in relation to timing, duration of use, and type (opposed vs unopposed) of HT.
Results:
Women who used any type of HT within 5 years of menopause had 30% less risk of AD (95% confidence interval 0.49–0.99), especially if use was for 10 or more years. By contrast, AD risk was not reduced among those who had initiated HT 5 or more years after menopause. Instead, rates were increased among those who began “opposed” estrogen-progestin compounds within the 3 years preceding the Cache County Study baseline (adjusted hazard ratio 1.93; 95% confidence interval 0.94–3.96). This last hazard ratio was similar to the ratio of 2.05 reported in randomized trial participants assigned to opposed HT.
Conclusions:
Association of HT use and risk of AD may depend on timing of use. Although possibly beneficial if taken during a critical window near menopause, HT (especially opposed compounds) initiated in later life may be associated with increased risk. The relation of AD risk to timing and type of HT deserves further study.
doi:10.1212/WNL.0b013e318271f823
PMCID: PMC3525314  PMID: 23100399
5.  Induced Pluripotent Stem Cells from Patients with Huntington’s Disease Show CAG Repeat Expansion Associated Phenotypes 
Cell stem cell  2012;11(2):264-278.
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded stretch of CAG trinucleotide repeats that results in neuronal dysfunction and death. Here, the HD consortium reports the generation and characterization of 14 induced pluripotent stem cell (iPSC) lines from HD patients and controls. Microarray profiling revealed CAG expansion-associated gene expression patterns that distinguish patient lines from controls, and early onset versus late onset HD. Differentiated HD neural cells showed disease associated changes in electrophysiology, metabolism, cell adhesion, and ultimately cell death for lines with both medium and longer CAG repeat expansions. The longer repeat lines were however the most vulnerable to cellular stressors and BDNF withdrawal using a range of assays across consortium laboratories. The HD iPSC collection represents a unique and well-characterized resource to elucidate disease mechanisms in HD and provides a novel human stem cell platform for screening new candidate therapeutics.
doi:10.1016/j.stem.2012.04.027
PMCID: PMC3804072  PMID: 22748968
6.  ZIP14 Zinc Transporter Downregulation and Zinc Depletion in the Development and Progression of Hepatocellular Cancer 
Purpose
Hepatocellular cancer (HCC) is a deadly and most rapidly increasing cancer in the USA and worldwide. The etiology and factors involved in development of HCC remain largely unknown. A marked decrease in zinc occurs in HCC. Its role and involvement in HCC has not been identified. We investigated the relationship of cellular zinc changes to the development of malignancy, and the identification of potential zinc transporters associated with the inability of hepatoma cells to accumulate zinc.
Methods
The detection of relative zinc levels in situ in normal hepatic cells vs. hepatoma was performed on normal and HCC tissue sections. ZIP1, 2, 3, and 14 transporters were identified by immunohistochemistry.
Results
Intracellular zinc levels are markedly decreased in HCC hepatoma cells vs. normal hepatic cells in early stage and advanced stage malignancy. ZIP14 transporter is localized at the plasma membrane in normal hepatocytes, demonstrating its functioning for uptake and accumulation of zinc. The transporter is absent in the hepatoma cells and its gene expression is downregulated. The change in ZIP14 is concurrent with the decrease in zinc. ZIP1, 2, 3 are not associated with normal hepatocyte uptake of zinc, and HCC zinc depletion. HepG2 cells exhibit ZIP14 transporter. Zinc treatment inhibits their growth.
Conclusions
ZIP14 downregulation is likely involved in the depletion of zinc in the hepatoma cells in HCC. These events occur early in the development of malignancy possibly to protect the malignant cells from tumor suppressor effects of zinc. This provides new insight into important factors associated with HCC carcinogenesis.
doi:10.1007/s12029-011-9269-x
PMCID: PMC3724761  PMID: 21373779
Hepatocellular cancer; Zinc; ZIP transporters; ZIP14; Zinc transporters
7.  A high-resolution 15,000Rad radiation hybrid panel for the domestic cat 
Summary
The current genetic and recombination maps of the cat have less than 3,000 markers and a resolution limit greater than 1 Mb. To complement the first generation domestic cat maps, support higher resolution mapping studies, and aid genome assembly in specific areas as well as in the whole genome, a 15,000Rad radiation hybrid (RH) panel for the domestic cat was generated. Fibroblasts from the female Abyssinian cat that was used to generate the cat genomic sequence were fused to a Chinese hamster cell line (A23), producing 150 hybrid lines. The clones were initially characterized using 39 STR and 1536 SNP markers. The utility of whole genome amplification (WGA) in preserving and extending RH panel DNA was also tested using ten STR markers; no significant difference in retention was observed. The resolution of the 15,000Rad RH panel was established by constructing framework maps across ten different 1 Mb regions on different feline chromosomes. In these regions, two-point analysis was used to estimate RH distances, which compared favorably with the estimation of physical distances. The study demonstrates that the 15,000Rad RH panel constitutes a powerful tool for constructing high-resolution maps, having an average resolution of 40.1 kb per marker across the ten 1 Mb regions. In addition, the RH panel will complement existing genomic resources for the domestic cat, aid in the accurate reassemblies of the forthcoming cat genomic sequence, and support cross-species genomic comparisons.
doi:10.1159/000339416
PMCID: PMC3480197  PMID: 22777158
8.  Risk Factors for Smoking among Adolescent Survivors of Childhood Cancer: A Report from the Childhood Cancer Survivor Study 
Pediatric blood & cancer  2011;58(3):428-434.
Background
Few studies have examined risk factors for smoking among adolescent survivors of childhood cancer. The present study reports on the rate of smoking and identifies factors associated with smoking in a sample of adolescent survivors from the Childhood Cancer Survivor Study (CCSS).
Procedure
Participants included 307 adolescent survivors and 97 healthy siblings (ages 14-20) who completed a self-report survey of health, quality of life, and health behaviors.
Results
Smoking rates did not differ significantly between survivor and sibling groups (Ever Smokers: 28% vs. 33%, Recent Smokers: 10% vs. 9%, respectively). Ever smoking was significantly associated with peer smoking, smokers in the household, binging, suicidal behavior, and no history of CRT. There were significant interactions of peer smoking with gender and CRT for ever smoking and with binging for recent smoking. Recent smoking was more likely for survivors with other household smokers (RR=2.24, CI=1.21-4.16), past suicidality (RR=1.89, CI=1.00-3.56), and no CRT (RR=2.40, CI=1.12-5.17). Among survivors with few smoking friends, ever smoking was more likely for survivors with no CRT (RR=4.47, CI=1.43-13.9), and recent smoking was more likely among survivors who binged (RR=3.37, CI=1.17-9.71).
Conclusions
Despite the health risks associated with survivorship, nearly one in three adolescent survivors of childhood cancer has smoked. Exposure to other smokers, in particular, appears to increase the likelihood of smoking for some survivors. Providing smoking cessation programs targeted to family members, helping survivors choose nonsmoking friends, and teaching ways to resist smoking influences from peers may be important pathways for smoking prevention with adolescent survivors.
doi:10.1002/pbc.23139
PMCID: PMC3165077  PMID: 21618409
adolescents; childhood cancer; survivors; smoking
9.  MECHANISMS OF PREMATURE VASCULAR AGING IN CHILDREN WITH HUTCHINSON-GILFORD PROGERIA SYNDROME 
Hypertension  2011;59(1):92-97.
Hutchinson-Gilford progeria syndrome (HGPS) is a rare, segmental premature aging syndrome of accelerated atherosclerosis and early death from myocardial infarction or stroke. This study sought to establish comprehensive characterization of the fatal vasculopathy in HGPS and its relevance to normal aging. We performed cardiovascular assessments at a single clinical site on the largest prospectively studied cohort to date. Carotid-femoral pulse wave velocity was dramatically elevated (mean 13.00±3.83 m/s). Carotid duplex ultrasound echobrightness, assessed in predefined tissue sites as a measure of arterial wall density, was significantly greater than age- and gender-matched controls in the intima-media (P<0.02), near adventitia (P<0.003) and deep adventitia (P<0.01), as was internal carotid artery mean flow velocity (p<0.0001). Ankle-brachial indices were abnormal in 78% of patients. Effective disease treatments may be heralded by normalizing trends of these noninvasive cardiovascular measures. The data demonstrates that, along with peripheral vascular occlusive disease, accelerated vascular stiffening is an early and pervasive mechanism of vascular disease in HGPS. There is considerable overlap with cardiovascular changes of normal aging, which reinforces the view that defining mechanisms of cardiovascular disease in HGPS provides a unique opportunity to isolate a subset of factors influencing cardiovascular disease in the general aging population.
doi:10.1161/HYPERTENSIONAHA.111.180919
PMCID: PMC3248242  PMID: 22083160
Hutchinson-Gilford progeria syndrome; atherosclerosis; arteriosclerosis; arterial stiffness; lamin; aging
10.  Decreased zinc and downregulation of ZIP3 zinc uptake transporter in the development of pancreatic adenocarcinoma 
Cancer Biology & Therapy  2011;12(4):297-303.
Pancreatic adenocarcinoma is an untreatable deadly cancer. The factors involved in its early development remain unknown, which contributes to the absence of biomarkers for early detection of malignancy or at-risk subjects and the absence of efficacious therapeutic agents. Because zinc changes are implicated in some cancers, we determined if it might be involved in the development of pancreatic adenocarcinoma. With in situ Dithizone and Zinquin staining of normal pancreas and adenocarcinoma tissue sections, we show for the first time, a consistent major loss of zinc in ductal and acinar epithelium in adenocarcinoma compared with the normal epithelium. This decrease in zinc is evident in well-differentiated through poorly-differentiated stages of malignancy. Immunohistochemistry identified ZIP3 as the basilar membrane zinc uptake transporter in normal ductal/acinar epithelium; and that the transporter is absent in adenocarcinoma. In situ Rt-PCR revealed that ZIP3 gene expression is silenced in adenocarcinoma. The ZIP3 downregulation accompanied the loss of zinc in early and progressing malignancy. RREB1 transcription factor was downregulated along with ZIP3; and might be involved in the silencing of ZIP3 expression. Zinc treatment was cytotoxic to malignant Panc1 cells. The combination of concurrent zinc, ZIP3 and RREB-1 changes represent early events in the development of adenocarcinoma; and suggest that zinc might be a tumor suppressor of pancreatic cancer. This report provides the clinical foundation for further mechanistic studies that will provide important insight into pancreatic carcinogenesis, and can lead to the development of effective early biomarkers and effective therapeutic agents for pancreatic cancer.
doi:10.4161/cbt.12.4.16356
PMCID: PMC3173731  PMID: 21613827
pancreatic adenocarcinoma; zinc changes; ZIP3 transporter; RREB-1; ductal epithelium; acinar epithelium; Panc 1 cells; zinc inhibition cell growth
11.  Characterization and detection of cellular and proteomic alterations in stable stathmin-overexpressing, taxol-resistant BT549 breast cancer cells using offgel IEF/PAGE difference gel electrophoresis 
Mutation research  2010;722(2):154-164.
Stathmin/oncoprotein 18, a protein that regulates microtubule dynamics, is highly expressed in a number of tumors including leukemia, lymphoma, neuroblastoma, breast, ovarian, and prostate cancers. High stathmin levels have been associated with the development of resistance to the widely-used anticancer drug taxol (®Taxol, paclitaxel). The mechanisms of stathmin-mediated taxol resistance are not well-understood at the molecular level. To better understand the role of stathmin in taxol resistance, we stably overexpressed stathmin two-fold in BT549 human breast cancer cells and characterized several cell processes involved in the mechanism of action of taxol. After stable overexpression of stathmin, neither the cell doubling time nor the mitotic index was altered and the microtubule polymer mass was reduced only modestly (by 18%). Unexpectedly, microtubule dynamicity was reduced by 29% after stathmin overexpression, resulting primarily from reduction in the catastrophe frequency. Sensitivity to taxol was reduced significantly (by 44%) in a clonogenic assay, and stathmin appeared to protect the cells from the spindle-damaging effects of taxol. The results suggest that in the stably-stathmin overexpressing clones, compensatory gene expression occurred that resulted in normal rates of cell proliferation and prevented the increase in catastrophe frequency expected in response to stathmin. Stathmin overexpression protected the cells from taxol-induced abnormal mitoses, and thus induced taxol resistance. Using offgel IEF/PAGE difference gel electrophoresis, we identified a number of proteins whose expression is reduced in the taxol-resistant stathmin-overexpressing cell lines, including proteins involved in the cytoskeleton and cell structure, the stress response, protein folding, glycolysis, and catalysis.
doi:10.1016/j.mrgentox.2010.08.019
PMCID: PMC3017223  PMID: 20816848
stathmin; taxol; microtubule dynamics; proteomics; mitosis; resistance
12.  Cardiovascular Pathology in Hutchinson-Gilford Progeria: Correlation with the Vascular Pathology of Aging 
Objective
Children with Hutchinson–Gilford progeria syndrome (HGPS) exhibit dramatically accelerated cardiovascular disease (CVD) causing death from myocardial infarction or stroke between ages 7 and 20 years. We undertook the first histological comparative evaluation between genetically confirmed HGPS and the CVD of aging.
Methods and Results
We present structural and immunohistological analysis of cardiovascular tissues from two children with HGPS, who died of myocardial infarction. Both had features classically associated with the atherosclerosis of aging, as well as arteriolosclerosis of small vessels. Additionally, vessels exhibited prominent adventitial fibrosis, a previously undescribed feature of HGPS. Importantly, though progerin was detected at higher rates in the HGPS coronary arteries, it was also present in non-HGPS individuals. Between ages one month and 97 years, progerin staining increased an average of 3.34% per year (P<0.0001) in coronary arteries.
Conclusion
We find concordance between many aspects of cardiovascular pathology in both HGPS and geriatric patients. HGPS generates a more prominent adventitial fibrosis than typical CVD. Vascular progerin generation in young non-HGPS individuals, which significantly increases throughout life, strongly suggests that progerin has a role in the CV aging of the general population.
doi:10.1161/ATVBAHA.110.209460
PMCID: PMC2965471  PMID: 20798379
Progeria; cardiovascular disease; atherosclerosis; aging; progerin
13.  Resource Brief: The National Non-Human Primate DNA Bank 
Methods (San Diego, Calif.)  2009;49(1):3-4.
A National Non-Human Primate (NHP) DNA bank has been established by the National Primate Research Centers and the National Center for Research Resources, NIH, providing a new resource for comparative genomic studies. The collection includes genomic DNA samples from macaques, chimpanzees, baboons, vervets, marmosets, sooty mangabeys and titi monkeys. The repository includes DNAs from 697 unrelated animals, suitable for comparing allele representation within and between species. Another 474 DNAs are derived from family trios (dam, sire, off spring), and are useful for verifying the segregation of genetic variants. The National NHP DNA Bank includes specified holdings within each of the 8 National Primate Research Centers, though detailed information on the entire collection is available through a common website.
doi:10.1016/j.ymeth.2009.07.011
PMCID: PMC3172814  PMID: 19706346
non-human primate; monkey; macaque; genomic DNA; DNA bank; comparative genetics
14.  Defining the Ideal Injection Techniques When Using 5-mm Needles in Children and Adults 
Diabetes Care  2010;33(9):1940-1944.
OBJECTIVE
We aimed to establish the ideal injection techniques using 5-mm needles to reliably inject insulin into the subcutaneous fat in both children and adults and to quantify the associated pain and leakage of the test medium.
RESEARCH DESIGN AND METHODS
A total of 259 subjects (122 children/adolescents and 137 adults) were injected with sterile air corresponding to 20 IU insulin (200 μl) with 32-G 5-mm needles at 90° or 45°, in the abdomen and thigh, and with or without a pinched skin fold. Injection depth was assessed via ultrasonography. Subjects rated pain on a visual analog scale. Test medium injections into the abdomen and thigh (0.2–0.6 ml) were also administered to assess injection leakage.
RESULTS
Among children, 5.5% of injections were intramuscular (IM) and 0.5% were intradermal, while in adults, the incidence was 1.3 and 0.6%, respectively. The frequency of IM injections was greater in boys and negligible among adult women. Subcutaneous fat thickness was the primary predictor of the likelihood of IM injections (P < 0.001). A third of all patients reported experiencing no pain during insulin injection, with children/adolescents experiencing considerably more discomfort than adults. Some leakage of medium was observed, but was unrelated to injection volume and was generally minimal.
CONCLUSIONS
5-mm needles are reliably inserted into subcutaneous fat in both adults and children. These needles were associated with reduced pain and minimal leakage. We recommend an angled injection with a pinched skin fold for children, while in adults, the technique should be left to patient preference.
doi:10.2337/dc10-0871
PMCID: PMC2928337  PMID: 20585002
15.  A Content Analysis of Displayed Alcohol References on a Social Networking Web Site 
Purpose
Exposure to alcohol use in media is associated with adolescent alcohol use. Adolescents frequently display alcohol references on Internet media such as social networking websites (SNSs). The purpose of this study was to conduct a theoretically-based content analysis of older adolescents’ displayed alcohol references on a SNS.
Methods
We evaluated 400 randomly selected public MySpace profiles of self-reported 17 to 20-year-olds from zip codes representing urban, suburban and rural communities in one Washington county. Content was evaluated for alcohol references suggesting: 1) explicit versus figurative alcohol use, 2) alcohol-related motivations, associations and consequences, including references that met CRAFFT problem drinking criteria. We compared profiles from four target zip codes for prevalence and frequency of alcohol display.
Results
Of 400 profiles, 225 profiles (56.3%) contained 341 references to alcohol. Profile owners who displayed alcohol references were mostly male (54.2%) and White (70.7%). The most frequent reference category was explicit use (49.3%), the most commonly displayed alcohol use motivation was peer pressure (4.7%). Few references met CRAFFT problem drinking criteria (3.2%). There were no differences in prevalence or frequency of alcohol display among the four sociodemographic communities.
Conclusions
Despite alcohol use being illegal and potentially stigmatizing in this population, explicit alcohol use is frequently referenced on adolescents’ MySpace profiles across several sociodemographic communities. Motivations, associations and consequences regarding alcohol use referenced on MySpace appear consistent with previous studies of adolescent alcohol use. These references may be a potent source of influence on adolescents, particularly given that they are created and displayed by peers.
doi:10.1016/j.jadohealth.2010.01.001
PMCID: PMC2907358  PMID: 20638009
Adolescent; Internet; Alcohol; Media; Social Networking Web Sites; Content Analysis
16.  AGRICOH: A Consortium of Agricultural Cohorts 
AGRICOH is a recently formed consortium of agricultural cohort studies involving 22 cohorts from nine countries in five continents: South Africa (1), Canada (3), Costa Rica (2), USA (6), Republic of Korea (1), New Zealand (2), Denmark (1), France (3) and Norway (3). The aim of AGRICOH, initiated by the US National Cancer Institute (NCI) and coordinated by the International Agency for Research on Cancer (IARC), is to promote and sustain collaboration and pooling of data to investigate the association between a wide range of agricultural exposures and a wide range of health outcomes, with a particular focus on associations that cannot easily be addressed in individual studies because of rare exposures (e.g., use of infrequently applied chemicals) or relatively rare outcomes (e.g., certain types of cancer, neurologic and auto-immune diseases). To facilitate future projects the need for data harmonization of selected variables is required and is underway. Altogether, AGRICOH provides excellent opportunities for studying cancer, respiratory, neurologic, and auto-immune diseases as well as reproductive and allergic disorders, injuries and overall mortality in association with a wide array of exposures, prominent among these the application of pesticides.
doi:10.3390/ijerph8051341
PMCID: PMC3108113  PMID: 21655123
agriculture; cohort studies; consortium, pesticides; occupational exposures
17.  Enhanced Statistical Tests for GWAS in Admixed Populations: Assessment using African Americans from CARe and a Breast Cancer Consortium 
PLoS Genetics  2011;7(4):e1001371.
While genome-wide association studies (GWAS) have primarily examined populations of European ancestry, more recent studies often involve additional populations, including admixed populations such as African Americans and Latinos. In admixed populations, linkage disequilibrium (LD) exists both at a fine scale in ancestral populations and at a coarse scale (admixture-LD) due to chromosomal segments of distinct ancestry. Disease association statistics in admixed populations have previously considered SNP association (LD mapping) or admixture association (mapping by admixture-LD), but not both. Here, we introduce a new statistical framework for combining SNP and admixture association in case-control studies, as well as methods for local ancestry-aware imputation. We illustrate the gain in statistical power achieved by these methods by analyzing data of 6,209 unrelated African Americans from the CARe project genotyped on the Affymetrix 6.0 chip, in conjunction with both simulated and real phenotypes, as well as by analyzing the FGFR2 locus using breast cancer GWAS data from 5,761 African-American women. We show that, at typed SNPs, our method yields an 8% increase in statistical power for finding disease risk loci compared to the power achieved by standard methods in case-control studies. At imputed SNPs, we observe an 11% increase in statistical power for mapping disease loci when our local ancestry-aware imputation framework and the new scoring statistic are jointly employed. Finally, we show that our method increases statistical power in regions harboring the causal SNP in the case when the causal SNP is untyped and cannot be imputed. Our methods and our publicly available software are broadly applicable to GWAS in admixed populations.
Author Summary
This paper presents improved methodologies for the analysis of genome-wide association studies in admixed populations, which are populations that came about by the mixing of two or more distant continental populations over a few hundred years (e.g., African Americans or Latinos). Studies of admixed populations offer the promise of capturing additional genetic diversity compared to studies over homogeneous populations such as Europeans. In admixed populations, correlation between genetic variants exists both at a fine scale in the ancestral populations and at a coarse scale due to chromosomal segments of distinct ancestry. Disease association statistics in admixed populations have previously considered either one or the other type of correlation, but not both. In this work we develop novel statistical methods that account for both types of genetic correlation, and we show that the combined approach attains greater statistical power than that achieved by applying either approach separately. We provide analysis of simulated and real data from major studies performed in African-American men and women to show the improvement obtained by our methods over the standard methods for analyzing association studies in admixed populations.
doi:10.1371/journal.pgen.1001371
PMCID: PMC3080860  PMID: 21541012
18.  Attentional and executive dysfunction as predictors of smoking within the Childhood Cancer Survivor Study cohort 
Nicotine & Tobacco Research  2010;12(4):344-354.
Introduction:
Previous research has suggested that childhood cancer survivors initiate smoking at rates approaching those of healthy individuals, even though smoking presents unique risks to survivors. The present study explores whether the attentional and executive functioning (EF) deficits associated with cancer and treatment place survivors of childhood cancer at increased risk for smoking.
Methods:
Data from the Childhood Cancer Survivor Study were examined to identify concurrent and longitudinal correlates of tobacco use. We explored whether childhood attention problems and adulthood executive dysfunction were associated with smoking among adult survivors of childhood cancer.
Results:
Childhood attention problems emerged as a striking predictor of adult smoking nearly a decade later on average. Nearly half (40.4%) of survivors who experienced attention problems in childhood reported a history of smoking, a significantly higher rate of ever smoking, than reported by those without childhood attention problems (relative risk [RR] = 1.53, 95% CI = 1.31–1.79). Furthermore, they were nearly twice as likely to be current smokers in adulthood compared with those without childhood attention problems (RR = 1.71, 95% CI = 1.38–2.11). Similar associations were found between components of adult executive dysfunction and adult smoking.
Discussion:
Childhood cancer and treatment are associated with subsequent deficits in attention and EF. Early detection of these deficits will allow clinicians to identify patients who are at increased risk for smoking, an important step in promoting and maintaining health in this medically vulnerable population.
doi:10.1093/ntr/ntq004
PMCID: PMC2847073  PMID: 20154054
19.  The naked truth: Sphynx and Devon Rex cat breed mutations in KRT71 
Mammalian Genome  2010;21(9-10):509-515.
Hair is a unique structure, characteristic of mammals, controlling body homeostasis, as well as cell and tissue integration. Previous studies in dog, mouse, and rat have identified polymorphisms in Keratin 71 (KRT71) as responsible for the curly/wavy phenotypes. The coding sequence and the 3′ UTR of KRT71 were directly sequenced in randomly bred and pedigreed domestic cats with different pelage mutations, including hairless varieties. A SNP altering a splice site was identified in the Sphynx breed and suggested to be the hairless (hr) allele, and a complex sequence alteration, also causing a splice variation, was identified in the Devon Rex breed and suggested to be the curly (re) allele. The polymorphisms were genotyped in approximately 200 cats. All the Devon Rex were homozygous for the complex alterations and most of the Sphynx were either homozygous for the hr allele or compound heterozygotes with the Devon-associated re allele, suggesting that the phenotypes are a result of the identified SNPs. Two Sphynx carrying the proposed hr mutation did not carry the Devon-associated alteration. No other causative mutations for eight different rexoid and hairless cat phenotypes were identified. The allelic series KRT71+ > KRT71hr > KRT71re is suggested.
Electronic supplementary material
The online version of this article (doi:10.1007/s00335-010-9290-6) contains supplementary material, which is available to authorized users.
doi:10.1007/s00335-010-9290-6
PMCID: PMC2974189  PMID: 20953787
20.  Surveillance for Breast Cancer in Women Treated with Chest Radiation for a Childhood, Adolescent or Young Adult Cancer: A Report from the Children's Oncology Group 
Annals of internal medicine  2010;152(7):444-W154.
Background
Women treated with therapeutic chest radiation may develop breast cancer.
Purpose
Summarize breast cancer risk and breast cancer surveillance in women following chest radiation for a pediatric or young adult cancer.
Data Sources
Studies from MEDLINE, EMBASE, Cochrane Library, and CINAHL (1966 through December 2008).
Study Selection
Articles selected to answer any of 3 questions: 1) What is the incidence and excess risk of breast cancer in women following chest radiation for a pediatric or young adult cancer? 2) For these women, are the clinical characteristics of the breast cancer and the outcomes following therapy different than for women with sporadic breast cancer in the general population? 3) What are the potential benefits and harms associated with breast cancer surveillance among women exposed to chest radiation?
Data Extraction
Three investigators independently extracted data and assessed study quality.
Data Synthesis
Standardized incidence ratios ranged from 13.3 to 55.5; cumulative incidence of breast cancer by 40–45 years of age ranged from 13–20%. Risk of breast cancer increased linearly with chest radiation dose. Available limited evidence suggests that the characteristics of the breast cancers in these women and the outcomes following diagnosis are similar to those in the general population; these breast cancers can be detected by mammography, though sensitivity is limited.
Limitations
Limitations include study heterogeneity, design and small sample size.
Conclusions
Women treated with chest radiation have a substantially elevated risk of breast cancer at a young age, which does not appear to plateau. Among this high risk population, there appears to be a benefit associated with early detection. Further research is required to better define the harms and benefits of lifelong surveillance.
doi:10.1059/0003-4819-152-7-201004060-00009
PMCID: PMC2857928  PMID: 20368650
21.  Increased thermoregulation in cold-exposed transgenic mice overexpressing lipoprotein lipase in skeletal muscle: an avian phenotype? 
Journal of lipid research  2008;49(4):870-879.
LPL is an enzyme involved in the breakdown and uptake of lipoprotein triglycerides. In the present study, we examined how the transgenic (Tg) overexpression of human LPL in mouse skeletal muscle affected tolerance to cold temperatures, cold-induced thermogenesis, and fuel utilization during this response. Tg mice and their nontransgenic controls were placed in an environmental chamber and housed in metabolic chambers that monitored oxygen consumption and carbon dioxide production with calorimetry. When exposed to 4°C, an attenuation in the decline in body temperature in Tg mice was accompanied by an increased metabolic rate (15%; P < 0.001) and a reduction in respiratory quotient (P < 0.05). Activity levels, the expression of uncoupling proteins in brown fat and muscle, and lean mass failed to explain the enhanced cold tolerance and thermogenesis in Tg mice. The more oxidative type IIa fibers were favored over the more glycolytic type IIb fibers (P < 0.001) in the gastrocnemius and quadriceps muscles of Tg mice. These data suggest that Tg overexpression of LPL in skeletal muscle increases cold tolerance by enhancing the capacity for fat oxidation, producing an avian-like phenotype in which skeletal muscle contributes significantly to the thermogenic response to cold temperatures.
doi:10.1194/jlr.M700519-JLR200
PMCID: PMC2660204  PMID: 18175800
metabolic rate; respiratory quotient; body temperature; fiber-typing; uncoupling proteins; activity; birds
22.  National Athletic Trainers' Association Position Statement: Preventing, Detecting, and Managing Disordered Eating in Athletes 
Journal of Athletic Training  2008;43(1):80-108.
Objective:
To present recommendations for the prevention, detection, and comprehensive management of disordered eating (DE) in athletes.
Background:
Athletes with DE rarely self-report their symptoms. They tend to deny the condition and are often resistant to referral and treatment. Thus, screenings and interventions must be handled skillfully by knowledgeable professionals to obtain desired outcomes. Certified athletic trainers have the capacity and responsibility to play active roles as integral members of the health care team. Their frequent daily interactions with athletes help to facilitate the level of medical surveillance necessary for early detection, timely referrals, treatment follow-through, and compliance.
Recommendations:
These recommendations are intended to provide certified athletic trainers and others participating in the health maintenance and performance enhancement of athletes with specific knowledge and problem-solving skills to better prevent, detect, and manage DE. The individual biological, psychological, sociocultural, and familial factors for each athlete with DE result in widely different responses to intervention strategies, challenging the best that athletics programs have to offer in terms of resources and expertise. The complexity, time intensiveness, and expense of managing DE necessitate an interdisciplinary approach representing medicine, nutrition, mental health, athletic training, and athletics administration in order to facilitate early detection and treatment, make it easier for symptomatic athletes to ask for help, enhance the potential for full recovery, and satisfy medicolegal requirements. Of equal importance is establishing educational initiatives for preventing DE.
PMCID: PMC2231403  PMID: 18335017
eating disorders; anorexia nervosa; bulimia nervosa; subclinical eating disorders; pathogenic weight control behaviors; female athlete triad; body image
23.  Strategies for Detecting Adverse Drug Events among Older Persons in the Ambulatory Setting 
Objective: To examine various strategies for the identification of adverse drug events (ADEs) among older persons in the ambulatory clinical setting.
Design: A cohort study of Medicare enrollees (n = 31,757 per month) receiving medical care from a large multispecialty group practice during a 12-month observation period (July 1, 1999 through June 30, 2000).
Measurements: Possible drug-related incidents occurring in the ambulatory clinical setting were detected using signals from multiple sources.
Results: During the tracking period, there were 1,523 identified ADEs, of which 421 (28%) were considered preventable. Across all sources, 23,917 signals were found; 12,791 (53%) were potential incidents that led to review of a patient's medical record and 2,266 (9%) were presented to physician reviewers. Although the positive predictive value (PPV) for reports from providers was high compared with other sources (54%), only 11% of the ADEs and 6% of the preventable ADEs were identified through this source. PPVs for other sources ranged from a low of 4% for administrative incident reports to a high of 12% for free-text review of electronic notes. Computer-generated signals were the source for 31% of the ADEs and 37% of the preventable ADEs. Electronic notes were the source for 39% of the ADEs and 29% of the preventable ADEs. There was little overlap in the ADEs identified across all sources.
Conclusion: Our findings emphasize the limitations of voluntary reporting by health care providers as the principal means for detection of ADEs and suggest that multiple strategies are required to detect ADEs in geriatric ambulatory patients.
doi:10.1197/jamia.M1586
PMCID: PMC524629  PMID: 15299000
24.  Fracture risk among First Nations people: a retrospective matched cohort study 
Background
Canadian First Nations people have unique cultural, socioeconomic and health-related factors that may affect fracture rates. We sought to determine the overall and site-specific fracture rates of First Nations people compared with non-First Nations people.
Methods
We studied fracture rates among First Nations people aged 20 years and older (n = 32 692) using the Manitoba administrative health database (1987–1999). We used federal and provincial sources to identify ethnicity, and we randomly matched each First Nations person with 3 people of the same sex and year of birth who did not meet this definition of First Nations ethnicity (n = 98 076). We used a provincial database of hospital separations and physician billing claims to calculate standardized incidence ratios (SIRs) and 95% confidence intervals (CIs) for each fracture type based on a 5-year age strata.
Results
First Nations people had significantly higher rates of any fracture (age- and sex-adjusted SIR 2.23, 95% CI 2.18–2.29). Hip fractures (SIR 1.88, 95% CI 1.61–2.14), wrist fractures (SIR 3.01, 95% CI 2.63–3.42) and spine fractures (SIR 1.93, 95% CI 1.79–2.20) occurred predominantly in older people and women. In contrast, craniofacial fractures (SIR 5.07, 95% CI 4.74–5.42) were predominant in men and younger adults.
Interpretation
First Nations people are a previously unidentified group at high risk for fracture.
doi:10.1503/cmaj.1031624
PMCID: PMC522652  PMID: 15477625
25.  Ethics roundtable debate: should a sedated dying patient be wakened to say goodbye to family? 
Critical Care  2003;7(5):335-338.
Intensivists have the potential to maintain vital signs almost indefinitely, but not necessarily the potential to make moribund patients whole. Current ethical and legal mandates push patient autonomy to the forefront of care plans. When patients are incapable of expressing their preferences, surrogates are given proxy. It is unclear how these preferences extend to the very brink of inevitable death. Some say that patients should have the opportunity and authority to direct their death spiral. Others say it would be impossible for them to do so because an inevitable death spiral cannot be effectively palliated. Humane principles dictate they be spared the unrelenting discomfort surrounding death. The present case examines such a patient and the issues surrounding a unique end-of-life decision.
doi:10.1186/cc2329
PMCID: PMC270714  PMID: 12974961
ethics; intensive care; palliative care; terminal care; withholding treatment

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