The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

被引：157

作者：

Groza, Tudor ^{[1
,2
]}

Koehler, Sebastian ^{[3
]}

Moldenhauer, Dawid ^{[3
,4
]}

Vasilevsky, Nicole ^{[5
]}

Baynam, Gareth ^{[6
,7
,8
,9
,10
]}

Zemojtel, Tomasz ^{[3
,11
]}

Schriml, Lynn Marie ^{[12
,13
]}

Kibbe, Warren Alden ^{[14
]}

Schofield, Paul N. ^{[15
,16
]}

Beck, Tim ^{[17
]}

Vasant, Drashtti ^{[18
]}

Brookes, Anthony J. ^{[17
]}

Zankl, Andreas ^{[2
,19
,20
]}

Washington, Nicole L. ^{[21
]}

Mungall, Christopher J. ^{[21
]}

Lewis, Suzanna E. ^{[21
]}

Haendel, Melissa A.

Parkinson, Helen ^{[18
]}

Robinson, Peter N. ^{[3
,22
,23
,24
]}

机构：

[1] Univ Queensland, Sch Informat Technol & Elect Engn, St Lucia, Qld 4072, Australia

[2] Garvan Inst Med Res, Sydney, NSW 2010, Australia

[3] Charite, Inst Med & Human Genet, D-13353 Berlin, Germany

[4] Univ Appl Sci, D-35390 Giessen, Germany

[5] Oregon Hlth & Sci Univ, Lib, Portland, OR 97239 USA

[6] Univ Western Australia, Sch Paediat & Child Hlth, Perth, WA 6840, Australia

[7] Murdoch Univ, Inst Immunol & Infect Dis, Perth, WA 6150, Australia

[8] Off Populat Hlth Genom, Publ Hlth & Clin Serv Div, Dept Hlth, Perth, WA 6004, Australia

[9] King Edward Mem Hosp, Genet Serv Western Australia, Perth, WA 6008, Australia

[10] Telethon Kids Inst, Perth, WA 6008, Australia

[11] Polish Acad Sci, Inst Bioorgan Chem, PL-61704 Poznan, Poland

[12] Univ Maryland, Sch Med, Dept Epidemiol & Publ Hlth, Baltimore, MD 21201 USA

[13] Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA

[14] NCI, Ctr Biomed Informat & Informat Technol, Rockville, MD 20850 USA

[15] Univ Cambridge, Dept Physiol Dev & Neurosci, Cambridge CB2 3EG, England

[16] Jackson Lab, Bar Harbor, ME 04609 USA

[17] Univ Leicester, Dept Genet, Leicester LE1 7RH, Leics, England

[18] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England

[19] Childrens Hosp Westmead, Acad Dept Med Genet, Sydney, NSW 2145, Australia

[20] Univ Sydney, Discipline Genet Med, Sydney Med Sch, Sydney, NSW 2145, Australia

[21] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA

[22] Max Planck Inst Mol Genet, D-14195 Berlin, Germany

[23] Charite, Berlin Brandenburg Ctr Regenerat Therapies, D-13353 Berlin, Germany

[24] Free Univ Berlin, Dept Math & Comp Sci, Inst Bioinformat, D-14195 Berlin, Germany

来源：

AMERICAN JOURNAL OF HUMAN GENETICS | 2015年 / 97卷 / 01期

基金：

澳大利亚研究理事会; 英国医学研究理事会;

关键词：

GENOME-WIDE ASSOCIATION; RISK LOCI; GENETIC-VARIANTS; DATABASE; SUSCEPTIBILITY; DISORDERS; MEDICINE; RESOURCE; BIOLOGY; NETWORK;

D O I：

10.1016/j.ajhg.2015.05.020

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million Pub Med abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.

引用

页码：111 / 124

页数：14

共 85 条

[71] Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders [J].

Soden, Sarah E. ;

Saunders, Carol J. ;

Willig, Laurel K. ;

Farrow, Emily G. ;

Smith, Laurie D. ;

Petrikin, Josh E. ;

LePichon, Jean-Baptiste ;

Miller, Neil A. ;

Thiffault, Isabelle ;

Dinwiddie, Darrell L. ;

Twist, Greyson ;

Noll, Aaron ;

Heese, Bryce A. ;

Zellmer, Lee ;

Atherton, Andrea M. ;

Abdelmoity, Ahmed T. ;

Safina, Nicole ;

Nyp, Sarah S. ;

Zuccarelli, Britton ;

Larson, Ingrid A. ;

Modrcin, Ann ;

Herd, Suzanne ;

Creed, Mitchell ;

Ye, Zhaohui ;

Yuan, Xuan ;

Brodsky, Robert A. ;

Kingsmore, Stephen F. .

SCIENCE TRANSLATIONAL MEDICINE, 2014, 6 (265)

[72] Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci [J].

Stahl, Eli A. ;

Raychaudhuri, Soumya ;

Remmers, Elaine F. ;

Xie, Gang ;

Eyre, Stephen ;

Thomson, Brian P. ;

Li, Yonghong ;

Kurreeman, Fina A. S. ;

Zhernakova, Alexandra ;

Hinks, Anne ;

Guiducci, Candace ;

Chen, Robert ;

Alfredsson, Lars ;

Amos, Christopher I. ;

Ardlie, Kristin G. ;

Barton, Anne ;

Bowes, John ;

Brouwer, Elisabeth ;

Burtt, Noel P. ;

Catanese, Joseph J. ;

Coblyn, Jonathan ;

Coenen, Marieke J. H. ;

Costenbader, Karen H. ;

Criswell, Lindsey A. ;

Crusius, J. Bart A. ;

Cui, Jing ;

de Bakker, Paul I. W. ;

De Jager, Philip L. ;

Ding, Bo ;

Emery, Paul ;

Flynn, Edward ;

Harrison, Pille ;

Hocking, Lynne J. ;

Huizinga, Tom W. J. ;

Kastner, Daniel L. ;

Ke, Xiayi ;

Lee, Annette T. ;

Liu, Xiangdong ;

Martin, Paul ;

Morgan, Ann W. ;

Padyukov, Leonid ;

Posthumus, Marcel D. ;

Radstake, Timothy R. D. J. ;

Reid, David M. ;

Seielstad, Mark ;

Seldin, Michael F. ;

Shadick, Nancy A. ;

Steer, Sophia ;

Tak, Paul P. ;

Thomson, Wendy .

NATURE GENETICS, 2010, 42 (06) :508-U56

[73] Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics [J].

Stranger, Barbara E. ;

Stahl, Eli A. ;

Raj, Towfique .

GENETICS, 2011, 187 (02) :367-383

[74] Detecting Drug Interactions From Adverse-Event Reports: Interaction Between Paroxetine and Pravastatin Increases Blood Glucose Levels [J].

Tatonetti, N. P. ;

Denny, J. C. ;

Murphy, S. N. ;

Fernald, G. H. ;

Krishnan, G. ;

Castro, V. ;

Yue, P. ;

Tsau, P. S. ;

Kohane, I. ;

Roden, D. M. ;

Altman, R. B. .

CLINICAL PHARMACOLOGY & THERAPEUTICS, 2011, 90 (01) :133-142

[75] Next-generation sequencing of nine atrial fibrillation candidate genes identified novel de novo mutations in patients with extreme trait of atrial fibrillation [J].

Tsai, Chia-Ti ;

Hsieh, Chia-Shan ;

Chang, Sheng-Nan ;

Chuang, Eric Y. ;

Juang, Jyh-Ming Jimmy ;

Lin, Lian-Yu ;

Lai, Ling-Ping ;

Hwang, Juey-Jen ;

Chiang, Fu-Tien ;

Lin, Jiunn-Lee .

JOURNAL OF MEDICAL GENETICS, 2015, 52 (01) :28-36

[76] Interactome Networks and Human Disease [J].

Vidal, Marc ;

Cusick, Michael E. ;

Barabasi, Albert-Laszlo .

CELL, 2011, 144 (06) :986-998

[77] Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis [J].

Voight, Benjamin F. ;

Scott, Laura J. ;

Steinthorsdottir, Valgerdur ;

Morris, Andrew P. ;

Dina, Christian ;

Welch, Ryan P. ;

Zeggini, Eleftheria ;

Huth, Cornelia ;

Aulchenko, Yurii S. ;

Thorleifsson, Gudmar ;

McCulloch, Laura J. ;

Ferreira, Teresa ;

Grallert, Harald ;

Amin, Najaf ;

Wu, Guanming ;

Willer, Cristen J. ;

Raychaudhuri, Soumya ;

McCarroll, Steve A. ;

Langenberg, Claudia ;

Hofmann, Oliver M. ;

Dupuis, Josee ;

Qi, Lu ;

Segre, Ayellet V. ;

van Hoek, Mandy ;

Navarro, Pau ;

Ardlie, Kristin ;

Balkau, Beverley ;

Benediktsson, Rafn ;

Bennett, Amanda J. ;

Blagieva, Roza ;

Boerwinkle, Eric ;

Bonnycastle, Lori L. ;

Bostrom, Kristina Bengtsson ;

Bravenboer, Bert ;

Bumpstead, Suzannah ;

Burtt, Noisel P. ;

Charpentier, Guillaume ;

Chines, Peter S. ;

Cornelis, Marilyn ;

Couper, David J. ;

Crawford, Gabe ;

Doney, Alex S. F. ;

Elliott, Katherine S. ;

Elliott, Amanda L. ;

Erdos, Michael R. ;

Fox, Caroline S. ;

Franklin, Christopher S. ;

Ganser, Martha ;

Gieger, Christian ;

Grarup, Niels .

NATURE GENETICS, 2010, 42 (07) :579-U155

[78] Precision phenotyping, panomics, and system-level bioinformatics to delineate complex biologies of atherosclerosis: Rationale and design of the "Genetic Loci and the Burden of Atherosclerotic Lesions" study [J].

Voros, Szilard ;

Maurovich-Horvat, Pal ;

Marvasty, Idean B. ;

Bansal, Aruna T. ;

Barnes, Michael R. ;

Vazquez, Gustavo ;

Murray, Sarah S. ;

Voros, Viktor ;

Merkely, Bela ;

Brown, Bradley O. ;

Warnick, G. Russell .

JOURNAL OF CARDIOVASCULAR COMPUTED TOMOGRAPHY, 2014, 8 (06) :442-451

[79] An update on ECARUCA, the European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations [J].

Vulto-van Silfhout, Anneke T. ;

van Ravenswaaij, Conny M. A. ;

Hehir-Kwa, Jayne Y. ;

Verwiel, Eugene T. P. ;

Dirks, Rita ;

van Vooren, Steven ;

Schinzel, Albert ;

de Vries, Bert B. A. ;

de Leeuw, Nicole .

EUROPEAN JOURNAL OF MEDICAL GENETICS, 2013, 56 (09) :471-474

[80] Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation [J].

Washington, Nicole L. ;

Haendel, Melissa A. ;

Mungall, Christopher J. ;

Ashburner, Michael ;

Westerfield, Monte ;

Lewis, Suzanna E. .

PLOS BIOLOGY, 2009, 7 (11)

← 1 2 3 4 5 6 7 8 9 →