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Effect of Genome-Wide Genotyping and Reference Panels on Rare Variants Imputation

j.urnal of Genetics and Genomics 2012年第10期39卷 545-550页

作者： Hou-Feng Zheng Martin Ladouceur Celia M.T. Greenwood j. brent richards Department of Medicine Human Genetics McGill University Montreal Quebec H3T 1E2 Canada Department of Epidemiology and Biostatistics Lady Davis Institute for Medical Research Jewish General Hospital Montreal Quebec H3T 1E2 Canada Research Center of Montreal Heart Institute Montreal Quebec HIT 1C8 Canada Department of Oncology McGill University Montreal Quebec H3T IE2 Canada Twin Research and Genetic Epidemiology King's College London London SE1 7EH United Kingdom

Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genome-wide genotypic arrays offers a cost-efficient strategy to achieve necessary sample sizes required for adequate statistical power. To estimate the performance of imputation of rare variants, we imputed 153 individuals, each of whom was genotyped on 3 different genotype arrays including 317k, 610k and 1 million single nucleotide polymorphisms （SNPs）, to two different reference panels： HapMap2 and 1000 Genomes pilot March 2010 release （1KGpilot） by using IMPUTE version 2. We found that more than 94% and 84% of all SNPs yield acceptable accuracy （info 〉 0.4） in HapMap2 and 1KGpilot-based imputation, respectively. For rare variants （minor allele frequency （MAF）〈5%）, the proportion of well- imputed SNPs increased as the MAF increased from 0.3% to 5% across all 3 genome-wide association study （GWAS） datasets. The proportion of well-imputed SNPs was 69%, 60% and 49% for SNPs with a MAF from 0.3% to 5% for 1M, 610k and 317k, respectively. None of the very rare variants （MAF 〈 0.3%） were well imputed. We conclude that the imputation accuracy of rare variants increases with higher density of genome-wide genotyping arrays when the size of the reference panel is small. Variants with lower MAF are more difficult to impute. These findings have important implications in the design and replication of large-scale sequencing studies.

关键词： Genotype imputation Genome-wide association study 1000 Genome Proj.ct HapMap Rare variant Common disease

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Experimental and analytical investigation on friction resistance force between buried coated pressurized steel pipes and soil

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Frontiers of Structural and Civil Engineering 2024年第4期18卷 615-629页

作者： Shaurav ALAM Tanvir MANZUR j.hn MATTHEWS Chris BARTLETT Erez ALLOUCHE brent KEIL j.hn KRAFT Department of Civil Engineering and Construction Engineering Technology Louisiana Tech UniversityRustonLA 71270USA Department of Civil Engineering Bangladesh University of Engineering and TechnologyDhaka 1000Bangladesh Georgia Tech Research Institute AtlantaGA 30332USA Stantec Inc. Edmonton T5J0K4Canada North West Pipe Company VancouverWA 98684USA

This paper presents an analytical approach for estimating frictional resistance to pipe movement at soil and external pipe surface of buried coated pressurized steel pipes relative to the internal thrust *** proposed analytical method was developed based on 36 experiments,which involved three coating types(cement mortar(CM),polyurethane type-I(PT-I),prefabricated plastic tape(PPT))on pipes’surfaces,three different soils(pea-gravel(PG),sand(S),silty-clay(SC)),and four simulated over burden depths above the pipe’s *** showed frictional resistance decreased with increasing over burden depth above the pipe’s *** degree of frictional resistance at the pipe-soil interface was found to be in the order of PG>SC>S for all coating variations and overburden *** coated pipe buried in all three types of soil produced significantly higher frictional resistance as compared to other coating *** on experimental data,the developed analytical introduced a dimensionless factor“Z”,which included effects of types of coatings,soil,and overburden depths for simplified rapid *** showed that the method provided a better prediction of frictional resistance forces,in comparison to previous analytical methods,which were barely close in predicting friction resistance for different coating variations,soil types,and overburden *** resistance force values reported herein could be considered conservative.

关键词： friction resistance force thrust force coated pressurized steel pipe soil type overburden depth

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The effects of selection for cold tolerance on cross-tolerance to other environmental stressors in Drosophila melanogaster

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Insect Science 2009年第3期16卷 263-276页

作者： Heath A. MacMillan j.llian P. Walsh brent j. Sinclair Department of Biology The University of Western Ontario London ON N6A 5B7 Canada

Cross tolerance, whereby tolerance to one environmental stress is correlated with tolerance to other stressors, is thought to be widespread in insects. We used lines of Drosophila melanogaster Meigen （Diptera： Drosophilidae） selected for survival at a 1-h exposure to -5℃ to examine the extent to which this selection results in increased tolerance to other stresses, including high and low temperatures, desiccation and starvation. While selection improved tolerance to acute cold exposure and survival at -5℃, there was little effect of selection regime on tolerance to other stressors. There was no correlation between tolerances to any of the stressors, suggesting different mechanisms of tolerance. This supports arguments that correlations between stress tolerances during selection experiments with D. melanogaster may be coincidental. The magnitude of heat-hardening was apparently constrained by basal tolerance among lines, but the magnitude of the rapid cold-hardening response was not correlated with basal cold tolerance, implying that the relationship between inducible and basal tolerances differs at high and low temperatures.

关键词： chill coma cold tolerance cross-tolerance desiccation heat shock high temperature laboratory selection longevity rapid cold hardening starvation

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Lack of support for Rensch＇s rule in an intraspecific test using red flour beetle （Tribo/ium castaneum） populations

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Insect Science 2017年第1期24卷 133-140页

作者： Oliver Y. Martin Lukasz Michalczyk Anna L. Millard brent C. Emerson Matthew j. G. Gage School of Biological Sciences University of East Anglia Norwich Research Park Norwich NR4 7T J United Kingdom ETH Zurich Experimental Ecology Institute of Integrative Biology D-USYS Universitatsstrasse 16 CH-8092 Zurich Switzerland Department of Entomology Institute of Zoology Jagiellonian University Gronostajowa 9 30-387 Krakow Poland Island Ecology and Evolution Research Group (IPNA-CSIC) CIAstrofisico Francisco Sanchez 3 38206 La Laguna Tenerife Canary Islands Spain

Rensch＇s rule proposes a universal allometric scaling phenomenon across species where sexual size dimorphism （SSD） has evolved： in taxa with male-biased dimorphism, degree of SSD should increase with overall body size, and in taxa with female-biased dimorphism, degree of SSD should decrease with increasing average body size. Rensch＇s rule appears to hold widely across taxa where SSD is male-biased, but not consistently when SSD is female-biased. Furthermore, studies addressing this question within species are rare, so it remains unclear whether this rule applies at the intraspecific level. We assess body size and SSD within Tribolium castaneum （Herbst）, a species where females are larger than males, using 21 populations derived from separate locations across the world, and maintained in isolated laboratory culture for at least 20 years. Body size, and hence SSD patterns, are highly susceptible to variations in temperature, diet quality and other environmental factors. Crucially, here we nullify interference of such confounds as all populations were maintained under identical conditions （similar densities, standard diet and exposed to identical temperature, relative humidity and photoperiod）. We measured thirty beetles of each sex for all populations, and found body size variation across populations, and （as expected） female-biased SSD in all populations. We test whether Rensch＇s rule holds for our populations, but find isometry, i.e. no allometry for SSD. Our results thus show that Rensch＇s rule does not hold across populations within this species. Our intraspecific test matches previous interspecific studies showing that Rensch＇s rule fails in species with female-biased SSD.

关键词： allometry body size Coleoptera sexual selection sexual size dimorphism Tenebrionidae

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A novel method to fabricate TiAl intermetallic alloy 3D parts using additive manufacturing

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Defence Technology（防务技术） 2017年第2期13卷 72-76页

作者： j.j.S. Dilip H. Miyanaj. Austin Lassell Thomas L. Starr brent Stucker Rapid Prototyping Center Department of Industrial EngineeringUniversity of LouisvilleLouisvilleKY 40292USA Department of Chemical Engineering University of LouisvilleLouisvilleKY 40292USA 3DSIM 1794 Olympic ParkwaySuite 110Park CityUT 84098USA

The present work explores the feasibility of fabricating porous 3D parts in TiAl intermetallic alloy directly from Tie6Ale4V and Al powders. This approach uses a binder j.tting additive manufacturing process followed by reactive sintering. The results demonstrate that the present approach is successful for realizing parts in TiAl intermetallic alloy.

关键词： Additive manufacturing Binder j.tting Intermetallic Titanium aluminide Reactive sintering

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Ineffective esophageal motility is associated with acute rej.ction after lung transplantation independent of gastroesophageal reflux

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World j.urnal of Gastroenterology 2023年第21期29卷 3292-3301页

作者： Wai-Kit Lo brent Hiramoto Hilary j.Goldberg Nirmal Sharma Walter W Chan Division of Gastroenterology Hepatology and EndoscopyBrigham and Women's HospitalBostonMA 02115United States Division of Pulmonary and Critical Care Medicine Brigham and Women's HospitalBostonMA 02115United States

BACKGROUND Gastroesophageal reflux is associated with poorer outcomes after lung transplant,likely through recurrent aspiration and allograft *** prior studies have demonstrated a relationship between impedance-pH results and transplant outcomes,the role of esophageal manometry in the assessment of lung transplant patients remains debated,and the impact of esophageal dysmotility on transplant outcomes is *** particular interest is ineffective esophageal motility(IEM)and its associated impact on esophageal *** To assess the relationship between pre-transplant IEM diagnosis and acute rej.ction after lung *** This was a retrospective cohort study of lung transplant recipients at a tertiary care center between 2007 and *** with pre-transplant anti-reflux surgery were *** and reflux diagnoses were recorded from pre-transplant esophageal function ***-to-event analysis using Cox proportional hazards model was applied to evaluate outcome of first episode of acute cellular rej.ction,defined histologically per International Society of Heart and Lung Transplantation *** not meeting this endpoint were censored at time of post-transplant anti-reflux surgery,last clinic visit,or ***’s exact test for binary variables and student’s t-test for continuous variables were performed to assess for differences between *** Of 184 subj.cts(54%men,mean age:58,follow-up:443 person-years)met criteria for *** pulmonary fibrosis represented the predominant pulmonary diagnosis(41%).During the follow-up period,60 subj.cts(33.5%)developed acute *** all-cause mortality was 16.3%.Time-to-event univariate analyses demonstrated significant association between IEM and acute rej.ction[hazard ratio(HR):1.984,95%CI:1.03-3.30,P=0.04],confirmed on Kaplan-Meier *** multivariable analysis,IEM remained independently associated with acute rej.ction,even after c

关键词： Ineffective esophageal motility Esophageal hypomotility Esophageal manometry Gastroesophageal reflux disease Lung transplantation Acute rej.ction

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Patient Feedback for Acupuncture Practice Improvement:A Survey from Mayo Clinic

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Chinese j.urnal of Integrative Medicine 2017年第11期23卷 816-821页

作者： Barbara S Thomley Saswati Mahapatra brent A Bauer Molly j.Mallory LI Guang-xi Alexander Do Tony Y Chon Division of Operations Mayo Clinic HospitalAZ(85054)United States Integrative Medicine and Health Division of General Internal MedicineMayo ClinicMN(55902)United States

Obj.ctive： To understand patient satisfaction with acupuncture appointment duration for the first and subsequent appointments in the plan of care, time spent with the acupuncture provider, willingness to pay for longer duration appointments, and lack of insurance coverage. Methods： Patients who were referred for an acupuncture consult to the Center for Integrative Medicine at Mayo Clinic were asked to participate in the survey in August 2014. Patients were given paper survey at time of appointment check-in and entered into Research Electronic Data Capture Survey database tool to reveal patient-reported outcomes. Results： In total, 104 of 329 patients receiving acupuncture treatment responded to the survey with a 32% response rate. Insight and recommended changes to the duration of the initial and subsequent appointments were obtained. Most patients reported that time spent with the provider（76 cases, 74%） and appointment length（74 cases, 68%） were ＂j.st right＂. Seventy cases（70%） of respondents indicated that they wanted longer treatment. Patients reported return appointments with duration of 30 min was not enough. Fifty-three patients（62%） were willing to pay for additional costs not covered by insurance. Conclusions： We used patient feedback to assess the acupuncture practice in a complementary and integrative medicine program. Most patients referred for the acupuncture consult appeared to be satisfied with the current level of practice. These findings were used to establish a quality improvement plan that may be implemented to improve patient satisfaction with the acupuncture practice.

关键词： care survey health integrative medicine acupuncture practice

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Round spermatid inj.ction into human oocytes:a systematic review and meta-analysis

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Asian j.urnal of Andrology 2021年第4期23卷 363-369页

作者： brent M Hanson Taylor P Kohn Alexander W Pastuszak Richard T Scott j. Philip j.Cheng j.mes M Hotaling Department of Reproductive Endocrinology and Infertility IVI-Reproductive Medicine Associates of New JerseyBasking RidgeNJ 07920USA Department of Urology The Brady Urological Institute at Johns Hopkins UniversityBaltimoreMD 21287USA Department of Surgery University of Utah Center for Reconstructive Urology and Men's HealthSalt Lake CityUT 84108USA

Many azoospermic men do not possess mature spermatozoa at the time of surgical sperm *** study is a systematic review and meta-analysis evaluating outcomes following round spermatid inj.ction(ROSI),a technique which utilizes immature precursors of spermatozoa for *** electronic search was performed to identify relevant articles published through October *** cohort studies in English involving male patients who had round spermatids identified and used for fertilization with human oocytes were *** rate,pregnancy rate,and resultant delivery rate were assessed following ***-analysis outcomes were analyzed using a random-effects *** were extracted from 22 studies involving 1099 couples and 4218 embryo *** fertilization rate after ROSI was 38.7%(95%confidence interval[CI]:31.5%–46.3%),while the pregnancy rate was 3.7%(95%CI:3.2%–4.4%).The resultant delivery rate was low,with 4.3%of embryo transfers resulting in a delivery(95%CI:2.3%–7.7%).The pregnancy rate per couple was 13.4%(95%CI:6.8%–19.1%)and the resultant delivery rate per couple was 8.1%(95%CI:6.1%–14.4%).ROSI has resulted in clinical pregnancies and live births,but success rates are considerably lower than those achieved with mature *** this technique may be a feasible alternative for men with azoospermia who decline other options,couples should be aware that the odds of a successful delivery are greatly diminished and the prognosis is relatively poor.

关键词： azoospermia in vitro fertilization infertility spermatozoa testis

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低维生素D水平被当作癌症危险因子新的研究证据不支持补充维生素D能够预防癌症

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英国医学杂志中文版 2018年第2期21卷 65-66页

作者： Despoina Manousaki j.brent richards 任倩 Centre for Clinical Epidemiology Department of Epidemiology Lady Davis Institute for Medical ResearchJewish GeneralHospital McGill UniversityMontreal QuebecCanada Departments of Medicine Human GeneticsEpidemiology and Biostatistics JewishGeneral HospitalMcGill UniversityMontreal QuebecCanada Department of Twin Research and Genetic Epidemiology King's College LondonLondon UK 北京大学人民医院内分泌科

尽管仍存在争议，但是目前初级预防依然是临床上最有效的降低癌症负担的方式。其中一种很有潜力的策略就是治疗维生素D缺乏症，因为流行病学和动物实验研究发现低水平维生素D和癌症的风险增高相关2-30而且维生素D缺乏症患者比例达到总... 详细信息

尽管仍存在争议，但是目前初级预防依然是临床上最有效的降低癌症负担的方式。其中一种很有潜力的策略就是治疗维生素D缺乏症，因为流行病学和动物实验研究发现低水平维生素D和癌症的风险增高相关2-30而且维生素D缺乏症患者比例达到总人群的40％。并且很容易通过简单的血液检测进行诊断，

关键词：低维生素D 癌症预防措施临床研究

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A comparison of the relative efficiency of ICSI and extended culture with epididymal sperm versus testicular sperm in patients with obstructive azoospermia

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Asian j.urnal of Andrology 2020年第2期22卷 222-226页

作者： Scott j.Morin brent M Hanson Caroline R j.neau Shelby A Neal j.ssica N Landis Richard T Scott j. j.mes M Hotaling Reproductive Medicine Associates of New j.rsey 140 Allen RoadBasking RidgeNJ 07920USA Division of Reproductive Endocrinology and Infertility Department of Obstetrics and GynecologySidney Kimmel Medical College at Thomas Jefferson University833 Chestnut StreetPhiladelphiaPA 19107USA Foundation for Embryonic Competence 140 Allen RoadBasking RidgeNJ 07920USA Division of Urology Department of SurgeryUniversity of Utah School of Medicine30 N 1900 ESalt Lake CityUT 84132USA Department of Obstetrics and Gynecology University of Utah School of Medicine30 N 1900 ESalt Lake CityUT 84132USA.An abbreviated version of this manuscript was published and presented as an abstract at the American Society for Reproductive Medicine(ASRM)2017 Scientific Congress.

This is a retrospective cohort study comparing blastocyst transfer outcomes following intracytoplasmic sperm inj.ction utilizing epididymal versus testicular sperm for men with obstructive *** cases at a single center between 2012 and 2016 were *** approach was selected at the surgeon’s discretion and included microepididymal sperm aspiration or testicular sperm *** culture was exclusively utilized prior to *** primary outcome was live birth *** outcomes included fertilization rate,blastulation rate,euploidy rate,and implantation rate.A mixed effects model was ***-six microepididymal sperm aspiration cases and 93 testicular sperm extraction cases were *** live birth rate was equivalent(48.6%vs 50.5%,P=0.77).However,on mixed effects model,epididymal sperm resulted in a greater likelihood of fertilization(adj.sted OR:1.37,95%CI:1.05–1.81,P=0.02)and produced a higher blastulation rate(adj.sted OR:1.41,95%CI:1.1–1.85,P=0.01).As a result,the epididymal sperm group had more supernumerary blastocysts available(4.3 vs 3,Pj.ction following microepididymal sperm aspiration resulted in a greater number of usable blastocysts per ***,the true benefit of epididymal sperm may only be demonstrated via a comparison of cumulative pregnancy rates after multiple transfers from one cohort.

关键词： azoospermia intracytoplasmic sperm inj.ction male infertility testicular sperm extraction

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