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

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journal 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 Project HapMap Rare variant Common disease

Anatomically realistic multiscale models of normal and abnormal gastrointestinal electrical activity

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World journal of Gastroenterology 2007年第9期13卷 1378-1383页

作者： Leo K Cheng Rie Komuro Travis M Austin martin L Buist Andrew j Pullan Bioengineering Institute The University of Auckland Private Bag 92019 Auckland 1142 New Zealand Division of Bioengineering National University of SingaporeSingapore Bioengineering Institute The University of Auckland Private Bag 92019 Auckland 1142 New ZealandDepartment of Engineering Science The University of Auckland

One of the major aims of the International Union of Physiological Sciences (IUPS) Physiome Project is to develop multiscale mathematical and computer models that can be used to help understand human health. We present here a small facet of this broad plan that applies to the gastrointestinal system. Specifically, we present an anatomically and physiologically based modelling framework that is capable of simulating normal and pathological electrical activity within the stomach and small intestine. The continuum models used within this framework have been created using anatomical information derived from common medical imaging modalities and data from the Visible Human Project. These models explicitly incorporate the various smooth muscle layers and networks of interstitial cells of Cajal (ICC) that are known to exist within the walls of the stomach and small bowel. Electrical activity within individual ICCs and smooth muscle cells is simulated using a previously published simplified representation of the cell level electrical activity. This simulated cell level activity is incorporated into a bidomain representation of the tissue, allowing electrical activity of the entire stomach or intestine to be simulated in the anatomically derived models. This electrical modelling framework successfully replicates many of the qualitative features of the slow wave activity within the stomach and intestine and has also been used to investigate activity associated with functional uncoupling of the stomach.

关键词： Model Bidomain Simulation Interstitial cells of Cajal Physiome GIOIE

Investigation of environmental and land use impacts in forested permafrost headwaters of the Selenga-Baikal river system,Mongolia-Effects on discharge,water quality and macroinvertebrate diversity

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International Soil and Water Conservation Research 2021年第4期9卷 605-619页

作者： martin Pfeiffer Georg Küstner Erdenetsetseg Erdenesukh Wolf von Tümpling jürgen Hofmann Department of Biogeography University of BayreuthUniversitätsstraße 3095447 BayreuthGermany Department of Aquatic Ecosystem Analysis and Management(ASAM) Helmholtz Centre for Environmental Research-UFZBrückstraße 3a39114 MagdeburgGermany Department of Ecology National University of MongoliaBaga toiruu 47Ulaanbaatar 210646Mongolia Department of Animal Ecology and Tropical Biology BiocenterJulius-Maximilians-Universität WürzburgAm Hubland97074 WürzburgGermany National Dong Hwa University No.1Sec.2Da Hsueh Rd.ShoufengHualien 97401Taiwan Central Laboratory for Water Analytics&Chemometrics Helmholtz Centre for Environmental Research-UFZBrückstrasse 3a39114 MagdeburgGermany Büro für Integrierten Gewässerschutz-BiG Werner-Voß-Damm 54 b12101 BerlinGermany

Headwater streams play a major role for provision of ecosystem services,*** *** investigated a high-altitude headwater catchment of the Kharaa River(including 411st-order rivers)to understand the impact of land cover(especially forest cover),environment and human usage on runoff,chemical water quality and macroinvertebrate fauna in a river basin under discontinuous permafrost conditions in an arid,sparsely populated region of *** verify our hypotheses that different landuses and environmental impacts in permafrost headwaters influence water quality,we investigated 105 sampling sites,37 of them at intermittent stream sections without water *** was positively impacted by land cover types steppe,grassland and forest and negatively by shrubland,forest burnt by wild fires(indicating a reduction of permafrost)and *** quality was affected by altitude,longitude and latitude,shrub growth and water *** diversity of macroinvertebrates was driven by water temperature,iron content of the water,flow velocity,and subbasin size(a.j.sted R^(2)=0.54).Sample plots clustered in three groups that differed in water chemistry,macroinvertebrate diversity,species composition and *** study confirms that steppes and grasslands have a higher contribution to runoff than forests,forest cover has a positive impact on water quality,and diversity of macroinvertebrates is higher in sites with less nutrients and *** excellent ecological status of the upper reaches of the Kharaa is severely threatened by forest fires and human-induced climate change and urgently needs to be conserved.

关键词： Ecosystem services Ephemeroptera-Plecoptera-Trichoptera (EPT)complex GIS-based analysis IWRM-MoMo project Land use land cover(LULC) Natural reference state Runoff Self-purification capacity Stream water chemistry

Gene expression changes in dorsal root ganglia following peripheral nerve injury: roles in inflammation,cell death and nociception

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Neural Regeneration Research 2019年第6期14卷 939-947页

作者： Sarah L.martin Adam j.Reid Alexei Verkhratsky Valerio Magnaghi Alessandro Faroni Blond McIndoe Laboratories School of Biological SciencesUniversity of Manchester University Hospital of South Manchester Department of Plastic and BurnsManchester Faculty of Biology Medicine and HealthUniversity of Manchester Department of Pharmacological and Biomolecular Sciences Università degli Studi di Milano

Subsequent to a peripheral nerve injury, there are changes in gene expression within the dorsal root ganglia in response to the damage. This review selects factors which are well-known to be vital for inflammation, cell death and nociception, and highlights how alterations in their gene expression within the dorsal root ganglia can affect functional recovery. The majority of studies used polymerase chain reaction within animal models to analyse the dynamic changes following peripheral nerve injuries. This review aims to highlight the factors at the gene expression level that impede functional recovery and are hence are potential targets for therapeutic approaches. Where possible the experimental model, specific time-points and cellular location of expression levels are reported.

关键词： Gene expression polymerase chain reaction dorsal root ganglia inflammation nociception cell death peripheral nerve injury Schwann cells satellite glial cells nerve regeneration

An unusual mass arising from the vas deferens

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Asian journal of Andrology 2002年第3期4卷 236-236页

作者： A.Haq j.M. Orrell j.R.W. parry Departments of Urology and Pathology the Ipswich Hospital NHS Trust Ipswich UKDepartments of Urology and Pathology the Ipswich Hospital NHS Trust Ipswich UKDepartments of Urology and Pathology the Ipswich Hospital NHS Trust Ipswich UK

An 18-year-old man presented with a history of fightsided abdominal pain and weight loss. Clinical examination revealed the presence of a right-sided abdominal mass arising from the pelvis. Baseline haematological and biochemical investigations were normal. A computerized tomography scan revealed a 78×56 mm cystic mass indenting the right posterolateral aspect of the bladder. The right kidney was absent with a congenital anomaly and duplication of the inferior vena cava below the left renal vein. A dimercaptosuccinic acid (DMSA) scan revealed

关键词： An unusual mass arising from the vas deferens

Cenozoic diatreme field in Chubut （Argentina） as evidence of phreatomagmatic volcanism accompanied with extensive Patagonian plateau basalt volcanism？

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Episodes 2007年第3期30卷 217-223页

作者： Karoly Nemeth Ulrike martin Miguel j. Haller Viviana I. Alric Institute of Natural Resources Volcanic Risk Solutions M_asse_y Uniyer_sity Palmerston North New Zealand. Department of Mapping Geological Institute of Hungary Stefainia 14 Budapest H- 1143 Hungary. Geo-Zentrum an der KTB Am Bohrturm 2 92670 Windischeschenbach Germany. Universidad Nacional de la Patagonea San juan Bosco Bvard Brown 3700 （9120） Puerto Ma.dryn Argentina. Centro Nacional Patagenico-CONICET Bvard. Brown 3500 （9120） Puerto Madryn Argentina.

In Patagonia, Argentina, at the northern border of the Patagonian Cenozoic mafic plateau lava fields, newly discovered diatremes stand about I00 m above the sur- rounding plain. These diatremes document phreato- magmatic episodes associated with the formation of the volcanic fields. The identified pyroclastic and intrusive rocks are exposed lower diatremes of former phreato- magmatic volcanoes and their feeding dyke systems. These remotely located erosional remnants cut through Paleozoic granitoids and jurassic/Cretaceous alternating siliciclastic continental successions that are rela-

关键词：新生界火山地下水湿生植物玄武岩

Inflation Targeting and Inflation Persistence

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Economic and Political Studies 2015年第1期3卷 3-17页

作者： GEORGE j.BRATSIOTIS jAKOB MADSEN CHRISTOPHER martin the School of Social Sciences University of Manchester the Department of Economics Monash University the Department of Economics University of Bath

This paper argues that the adoption of an inflation target reduces the persistence of *** develop the theoretical literature on inflation persistence by introducing a Taylor Rule for monetary policy into a model of persistence and showing that inflation targets reduce inflation *** investigate changes in the time series properties of inflation in seven countries that introduced inflation targets in the late 1980s or early *** find that the persistence of inflation is greatly reduced or eliminated following the introduction of inflation targets.

关键词： Taylor Rule inflation targeting Phillips Curve inf

Liver transplantation for malignancy:current treatment strategies and future perspectives

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World journal of Gastroenterology 2014年第18期20卷 5331-5344页

作者： Christina Hackl Hans j Schlitt Gabriele I Kirchner Birgit Knoppke martin Loss Department of Surgery University Hospital Regensburg93053 RegensburgGermany Department of Internal Medicine I University Hospital Regensburg93053 RegensburgGermany Department of Pediatrics and juvenile Medicine University Hospital Regensburg93053 RegensburgGermany

In 1967,Starzl et al performed the first successful liver transplantation for a patient diagnosed with *** the following,liver transplantation was considered ideal for complete tumor resection and potential cure from primary hepatic *** reports of liver transplantation for primary and metastatic liver cancer however showed disappointing results and the strategy was soon ***1996,Mazzaferro et al introduced the Milan criteria,offering liver transplantation to patients diagnosed with limited hepatocellular *** then,liver transplantation for malignant disease is an ongoing subject of preclinical and clinical *** this context,several aspects must be considered:(1)Given the shortage of deceased-donor organs,long-term overall and disease free survival should be comparable with results obtained in patients transplanted for nonmalignant disease;(2)In this regard,living-donor liver transplantation may in selected patients help to solve the ethical dilemma of optimal individual patient treatment vs organ allocation justice;and(3)Ongoing research focusing on perioperative therapy and antiproliferative immunosuppressive regimens may further reduce tumor recurrence in patients transplanted for malignant disease and thus improve overall *** present review gives an overview of current indications and future perspectives of liver transplantation for malignant disease.

关键词： Hepatocellular Fibrolamellar Carcinoma Cholangiocellular Hepatoblastoma Liver metastases

No evidence for increased cell entry or antibody evasion by Delta sublineage AY.4.2

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Cellular & Molecular Immunology 2022年第3期19卷 449-452页

作者： Prerna Arora Amy Kempf Inga Nehlmeier Luise Graichen martin S.Winkler martin Lier Sebastian Schulz Hans-martin jäck Stefan Pöhlmann Markus Hoffmann Infection Biology Unit German Primate CenterKellnerweg 437077GöttingenGermany Faculty of Biology and Psychology Georg-August-University GöttingenWilhelmsplatz 137073GöttingenGermany Department of Anesthesiology University of Göttingen Medical CenterGeorg-August University GöttingenRobert-Koch-Straße 4037075GöttingenGermany Division of Molecular Immunology Department of Internal Medicine 3Friedrich-Alexander University Erlangen-NürnbergGlückstraße 691054ErlangenGermany

Since the beginning of the COVID-19 pandemic,multiple SARS-CoV-2 variants have *** some variants spread only locally,others,referred to as variants of concern,disseminated globally and became drivers of the *** SARS-CoV-2 variants harbor mutations relative to the virus circulating early in the pandemic,and mutations in the viral spike(S)protein are considered of particular relevance since the S protein mediates host cell entry and constitutes the key target of the neutralizing antibody *** a consequence,mutations in the S protein may increase SARS-CoV-2 infectivity and enable its evasion of neutralizing ***,mutations in the S protein can modulate viral transmissibility and pathogenicity.

关键词： SARS-CoV-2 AY.4.2 Delta Host cell entry Antibody evasion