Genomes and Genes
Affiliation: University of California
- Quantitative trait loci for hypercalciuria in a rat model of kidney stone diseaseRichard R Hoopes
Department of Medicine, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
J Am Soc Nephrol 14:1844-50. 2003..Identification of genes that contribute to hypercalciuria in this animal model should prove valuable in understanding idiopathic hypercalciuria and kidney stone disease in humans...
- R/qtlDesign: inbred line cross experimental designSaunak Sen
Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA
Mamm Genome 18:87-93. 2007..We give examples of software usage in real-life settings. The software is available at http://www.biostat.ucsf.edu/sen/software.html ...
- Selective genotyping and phenotyping strategies in a complex trait contextSaunak Sen
Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143 0560, USA
Genetics 181:1613-26. 2009..We use an information perspective to examine these experimental design issues in the broader context of complex traits and make recommendations on their use...
- Quantitative trait locus study design from an information perspectiveSaunak Sen
Department of Epidemiology and Biostatistics, University of California, San Francisco, 94143, USA
Genetics 170:447-64. 2005..Software for performing power calculations for backcross and F(2) intercross incorporating selective genotyping and marker spacing is available from http://www.biostat.ucsf.edu/sen...
- Impact of renal insufficiency on mortality in advanced lower extremity peripheral arterial diseaseANN M O'HARE
Division of Nephrology, Box 111J, Nephrology, VA Medical Center San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA
J Am Soc Nephrol 16:514-9. 2005..Death rates were particularly high among those with a GFR <30 ml/min per 1.73 m(2). This finding may be partly explained by their more frequent presentation with ischemic ulceration or gangrene rather than rest pain...
- Predictors of skin-related quality of life after treatment of cutaneous basal cell carcinoma and squamous cell carcinomaTina Chen
School of Medicine, University of California at San Francisco, San Francisco, USA
Arch Dermatol 143:1386-92. 2007..To identify predictors of skin-related quality of life (QOL) after treatment of nonmelanoma skin cancer (NMSC)...
- An angiotensin converting enzyme haplotype predicts survival in patients with end stage renal diseaseJames B Wetmore
The Department of Medicine, San Francisco VAMC University of California, San Francisco, CA 94121, USA
Hum Genet 120:201-10. 2006..This "protective" haplotype may encompass loci with functional significance in the ACE gene...
- Estrogen receptor genotype and risk of cognitive impairment in elders: findings from the Health ABC studyKristine Yaffe
Department of Psychiatry and Neurology, School of Medicine, San Francisco, CA 94121, USA
Neurobiol Aging 30:607-14. 2009..To determine whether variants in the estrogen receptors 1 (alpha) and 2 (beta) (ESR1 and ESR2) genes are associated with cognitive impairment in non-demented elderly men and women...
- Effect of secondhand smoke on asthma control among black and Latino childrenSam S Oh
Department of Medicine, University of California, San Francisco, CA 94158 2911, USA
J Allergy Clin Immunol 129:1478-83.e7. 2012....
- Childhood social and economic well-being and health in older ageSandra Moody-Ayers
San Francisco VA Medical Center, San Francisco, CA 94121, USA
Am J Epidemiol 166:1059-67. 2007..14, 1.64) participants but not Latinos. These findings suggest that childhood SES affects health status through midlife but the effects may abate in late life; its effects also may be weaker in Latinos than in Whites or Blacks...
- Renal insufficiency and use of revascularization among a national cohort of men with advanced lower extremity peripheral arterial diseaseANN M O'HARE
Department of Medicine, VA Medical Center, San Francisco, San Francisco, CA 94121, USA
Clin J Am Soc Nephrol 1:297-304. 2006..However, among patients with renal insufficiency, mortality is lowest for patients who receive a revascularization. Further studies are needed to determine the optimal care for this high-risk patient group...
- Strain background modifies phenotypes in the ATP8B1-deficient mouseSohela Shah
UCSF Liver Center, University of California San Francisco, San Francisco, California, United States of America
PLoS ONE 5:e8984. 2010..The ATP8B1-deficient mouse serves as an animal model of human ATP8B1 deficiency...
- A flexible estimating equations approach for mapping function-valued traitsHao Xiong
Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94143 0560, USA
Genetics 189:305-16. 2011..It provides a good compromise between model simplicity, statistical efficiency, and computational speed. We illustrate our method and its advantages using circadian mouse behavioral data...
- An african-specific functional polymorphism in KCNMB1 shows sex-specific association with asthma severityMax A Seibold
Department of Medicine, University of California San Francisco, San Francisco, CA 94143 2911, USA
Hum Mol Genet 17:2681-90. 2008..Female asthmatics may be insulated from the deleterious effects of the 818T allele by estrogen-mediated upregulation in BK channel activity...
- Cosmopolitan and ethnic-specific replication of genetic risk factors for asthma in 2 Latino populationsJoshua M Galanter
Department of Medicine, University of California, San Francisco, CA 94143 2911, USA
J Allergy Clin Immunol 128:37-43.e12. 2011..We sought to examine the possibility that population-specific genetic risks contribute to this disparity...
- Quantitative trait loci affecting delta13C and response to differential water availibility in Arabidopsis thalianaNeil J Hausmann
University of California, Berkeley, Department of Integrative Biology, Berkeley, California 94720, USA
Evolution 59:81-96. 2005..We found several significant QTL-QTL interactions including three that exhibited environmental dependence. These results provide preliminary evidence for proposed genetic mechanisms underlying phenotypic plasticity...
- Geography matters: relationships among urban residential segregation, dialysis facilities, and patient outcomesRudolph A Rodriguez
San Francisco General Hospital, University of California, San Francisco, Veterans Affairs Medical Center, San Francisco, California 94110, USA
Ann Intern Med 146:493-501. 2007..However, the impact of residential segregation by race-a prominent feature of many U.S. cities--on outcomes of patients receiving dialysis and on facility performance has not been evaluated...
- Polypharmacy and prescribing quality in older peopleMichael A Steinman
Division of Geriatrics, San Francisco Veterans Affairs Medical Center, and Department of Medicine, University of California at San Francisco, California 94121, USA
J Am Geriatr Soc 54:1516-23. 2006..To evaluate the relationship between inappropriate prescribing, medication underuse, and the total number of medications used by patients...
- Conflicts and concordance between measures of medication prescribing qualityMichael A Steinman
Division of Geriatrics, San Francisco VA Medical Center and UCSF, San Franciso, California 94121, USA
Med Care 45:95-9. 2007..However, little is known about the relationship between these instruments or the concordance of their quality assessments when applied to the same group of patients...
- Sequence-based classification using discriminatory motif feature selectionHao Xiong
Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
PLoS ONE 6:e27382. 2011..Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is available at http://www.epibiostat.ucsf.edu/biostat/sen/dmfs/...
- Effects of hospital procedure volume and resident training on clinical outcomes and resource use in radical retropubic prostatectomy surgery in the Department of Veterans AffairsTse Sun Ku
Anesthesiology Service, Veterans Affairs Medical Center, San Francisco, California 94121, USA
J Urol 179:272-8; discussion 278-9. 2008....
- QTL analysis for discovery of genes involved in drug responsesSaunak Sen
University of California San Francisco, Department of Epidemiology and Biostatistics, San Francisco, CA 94143 0560, USA
Curr Drug Targets Infect Disord 4:53-63. 2004..Through an integrated approach, studies can move beyond the search for markers of resistance to instead characterize the predisposition of parasites to develop new resistances and cross-resistances...
- Mortality risk stratification in chronic kidney disease: one size for all ages?ANN M O'HARE
Department of Medicine, University of California San Francisco, VA Medical Center, San Francisco, 111J Nephrology, 4150 Clement Street, San Francisco, CA 94121, USA
J Am Soc Nephrol 17:846-53. 2006..73 m2 eGFR group...
- Bringing the war back home: mental health disorders among 103,788 US veterans returning from Iraq and Afghanistan seen at Department of Veterans Affairs facilitiesKaren H Seal
Department of Medicine, University of California, San Francisco, CA, USA
Arch Intern Med 167:476-82. 2007....
- Interleukin-1 gene cluster polymorphisms predict risk of ESRDJames B Wetmore
Department of Medicine, San Francisco VAMC University of California, San Francisco, California 94121, USA
Kidney Int 68:278-84. 2005..Inflammation is regulated in part by genes of the interleukin-1 (IL-1) gene cluster. We hypothesized that polymorphisms in this gene cluster may be associated with risk of end-stage renal disease (ESRD)...
- Polymorphisms of MLH1 in benign prostatic hyperplasia and sporadic prostate cancerYuichiro Tanaka
Department of Surgery Urology 112F, Veterans Affairs Medical Center, University of California, 4150 Clement St, San Francisco, CA 94121, USA
Biochem Biophys Res Commun 383:440-4. 2009..056) of cancer. This is the first report that demonstrates a protective effect for the race-related MLH1 polymorphism at codon 384 against prostate cancer and these results are important in understanding their role in this disease...
- Genome-wide DNA Methylation Profiling of CpG Islands in HypospadiasShweta Choudhry
Department of Urology, University of California, San Francisco, California
J Urol 188:1450-6. 2012..We assessed whether epigenetic modification of DNA methylation is associated with hypospadias in a case-control study of 12 hypospadias and 8 control subjects...
- Phenotypic landscape of a bacterial cellRobert J Nichols
University of California, San Francisco, 94143, USA
Cell 144:143-56. 2011....
- Mouse chromosome 7 harbors a quantitative trait locus for isoflurane minimum alveolar concentrationMichael Cascio
Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94143 0464, USA
Anesth Analg 105:381-5. 2007..The location on the genome of genes or other genetic elements controlling quantiative traits is called quantitative trait loci (QTLs). In this study we sought to detect a quantitative trait locus underlying isoflurane MAC in mice...
- Quality-of-life outcomes of treatments for cutaneous basal cell carcinoma and squamous cell carcinomaMary Margaret Chren
Dermatology Service, San Francisco Veterans Affairs Medical Center and the Department of Veterans Affairs, San Francisco, California 94121, USA
J Invest Dermatol 127:1351-7. 2007..2 (7.4, 12.9) after Mohs surgery, and 3.4 (-0.9, 7.6) after ED&C. We conclude that, for NMSC, quality-of-life outcomes were similar after excision and Mohs surgery, and both therapies had better outcomes than ED&C...
- Locating Ath8, a locus for murine atherosclerosis susceptibility and testing several of its candidate genes in mice and humansRon Korstanje
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
Atherosclerosis 177:443-50. 2004..We found a significant association between ANGPTL3 and atherosclerotic lesions (P < 0.05) in human. These results suggest that Angptl3 is involved in atherosclerosis susceptibility in both mouse and human...
- R/qtl: QTL mapping in experimental crossesKarl W Broman
Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
Bioinformatics 19:889-90. 2003..AVAILABILITY: The package is freely available at http://www.biostat.jhsph.edu/~kbroman/qtl...
- Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3h/HeJ inbred strains of mice. (2001)Wesley G Beamer
J Bone Miner Res 20:1701-12; discussion 1700. 2005
- Isolation and confirmation of a calcium excretion quantitative trait locus on chromosome 1 in genetic hypercalciuric stone-forming congenic ratsRichard R Hoopes
Department of Medicine, SUNY Upstate Medical University, 750 E Adams Street, Syracuse, NY 13210, USA
J Am Soc Nephrol 17:1292-304. 2006..This is the first QTL for hypercalciuria to be isolated in a congenic animal...
- Poor performance of bootstrap confidence intervals for the location of a quantitative trait locusAni Manichaikul
Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205-2179, USA
Genetics 174:481-9. 2006..Likelihood support intervals and approximate Bayes credible intervals, on the other hand, are shown to behave appropriately...
- Sequential quantitative trait locus mapping in experimental crossesJaya M Satagopan
Memorial Sloan Kettering Cancer Center, USA
Stat Appl Genet Mol Biol 6:Article12. 2007..We examine settings under which the two-stage analytic approach provides sufficient power to detect the putative QTLs...
- The timing of eruption of the primary dentition in Nigerian childrenMorenike Folayan
Department of Child Dental Health, Obafemi Awolowo University, Ile Ife 22005, Nigeria
Am J Phys Anthropol 134:443-8. 2007....
- Significance thresholds for quantitative trait locus mapping under selective genotypingAni Manichaikul
Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
Genetics 177:1963-6. 2007..A stratified permutation test should be used, with phenotypes shuffled separately within the genotyped and ungenotyped individuals...
- The X chromosome in quantitative trait locus mappingKarl W Broman
Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
Genetics 174:2151-8. 2006..We found suggestive evidence of linkage to the X chromosome, which would be viewed as strong evidence of linkage if the X chromosome was treated as an autosome. Our methods have been implemented in the package R/qtl...
- Genetic modifiers interact with Cpe(fat) to affect body weight, adiposity, and hyperglycemiaGayle B Collin
The Jackson Laboratory, Bar Harbor, Maine 04609, USA
Physiol Genomics 22:182-90. 2005....
- Mapping quantitative trait loci for vertebral trabecular bone volume fraction and microarchitecture in miceMary L Bouxsein
Orthopedic Biomechanics Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
J Bone Miner Res 19:587-99. 2004..Ultimately, identification of genes that regulate trabecular bone traits may yield important information regarding mechanisms that regulate mechanical integrity of the skeleton...
- Statistical Methods for Experimental Genome PopulationsSaunak Sen; Fiscal Year: 2007..We will develop statistical methods to construct and use these populations efficiently. Our methods will reduce experimental cost, and improve detection of causal genetic elements contributing to disease susceptibility. ..
- Statistical Methods for Experimental Genome PopulationsSaunak Sen; Fiscal Year: 2010..We will develop statistical methods to construct and use these populations efficiently. Our methods will reduce experimental cost, and improve detection of causal genetic elements contributing to disease susceptibility. ..