Professor Anthony J. Brookes

Professor of Genetics

Tel: +44 (0)116 252 3401
Fax: +44 (0)116 252 3378

Email: ajb97@le.ac.uk

 

Personal details

I am Bioinformatics Group Leader at the University. Other professional appointments that I am involved with include; Director of the Leicester ‘Data-2-Knowledge-4-Practice’ Facility (DKP)Director of the Leicester ‘NUCLEUS’ Genomics Services FacilityCo-ordinator of the GEN2PHEN-Alliance and the I4Health NetworkPartner (for knowledge management and IT) in EU & IMI projects BioShaRE, EPAD, EMIF, eTOX, GCOF, RD-Connect (Associate), REQUITEand UK project COPD-MAPVice President of the Human Genome Variation Society (HGVS), Founding Member of the Human Variome Project (HVP), Principal Investigator for Genome Wide Association Study database ‘GWAS Central’International Steering Committee member for P3G International, Director for Oasis Genomics Ltd, UK among others.

 

Teaching

BS2064 (Bioinformatics)
MB3050 (Disease genetics)

Publications

    A 129 kb Deletion on Chromosome 12 Confers Substantial Protection Against Rheumatoid Arthritis, Implicating the Gene SLC2A3.
    C.D.Veal, K.E.Reekie, J.C.Lorentzen, L.Padyukov and A.J.Brookes. Human Mutation (2014) 35(2), 248-256 [doi: 10.1002/humu.22471].

    GWAS Central: A Comprehensive Resource For The Comparison And Interrogation Of Genome-Wide Association Studies.
    T.Beck, R.K.Hastings, S.Gollapudi, R.C.Free and A.J.Brookes. Eur. J. Hum. Genet (2014) 22, 949-952 [doi: 10.1038/ejhg.2013.274].

    A P3G Generic Access Agreement for Population Genomic Studies.
    B.M.Knoppers, R.Chisholm, J.Kaye and D.Cox (plus: P.Burton, A.J.Brookes, I.Fortier, P.Goodwin, J.Harris, K.Hveem, A.Kent, J.Little, P.Riegman, S.Ripatti, R.Stolk.). Nature Biotech. (2013) 31, 384-385 [doi:10.1038/nbt.2567].

    Automated Design Of Paralogue Ratio Test Assays For The Accurate And Rapid Typing Of Copy Number Variation.
    C.D.Veal, H.Xu, K.Reekie, R.Free, R.J.Hardwick, D.McVey, A.J.Brookes, E.J.Hollox and C.J.Talbot. Bioinformatics (2013) 29, 1997-2003.

    HGV2012: Leveraging Next-Generation Technology and Large Datasets to Advance Disease Research.
    N.Gonzaludo, H.X.Zheng, J.Wang, S.J.Chanock, L.Jin, S.Scherer, C.Wijmenga, P.Y.Kwok and A.J.Brookes. Hum Mutat. (2013), 34, 657-660.

    Improving Data And Knowledge Management To Better Integrate Healthcare And Research.
    M.Cases, L.I.Furlong, J.Albanell, R.B.Altman, R.Bellazzi, S.Boyer, A.Brand, A.J.Brookes, S.Brunak, T.W.Clark, J.Gea, P.Ghazal, N.Graf, R.Guigó, T.E.Klein, N.López-Bigas, V.Maojo, B.Mons, M.Musen, J.L.Oliveira, A.Rowe, P.Ruch, A.Shabo, E.H.Shortliffe, A.Valencia, J.VanDerLei, M.A.Mayer and F.Sanz. Journal of Internal Medicine (2013) 274, 321-328.

    A Mechanistic Basis For Amplification Differences Between Samples And Between Genome Regions.
    C.D.Veal, P.J.Freeman, K.Jacobs, O.Lancaster, S.Jamain, M.Leboyer, D.Albanes, R.R.Vaghela, I.Gut, S.J.Chanock and A.J.Brookes. BMC Genomics (2012) 13, 455 [doi:10.1186/1471-2164-13-455].

    Knowledge Engineering for Health: A new discipline required to bridge the 'ICT Gap' between research and healthcare.
    T.Beck, S.Gollapudi, S.Brunak, N.Graf, H.U.Lemke, D.Dash, I.Buchan, C.Díaz, F.Sanz and AJ.Brookes. Human Mutation (2012) 33, 797-802 (DOI: 10.1002/humu.22066).

    Observ-OM and Observ-TAB: Universal Syntax Solutions for the Integration, Search and Exchange of Phenotype And Genotype Information.
    T.Adamusiak, H.Parkinson, J.Muilu, E.Roos, J.VanDerVelde, G.A.Thorisson, M.Byrne, C.Pang, S.Gollapudi, V.Ferretti, H.Hillege, A.J.Brookes and M.A.Swertz. Human Mutation (2012) 33, 867-873 (DOI: 10.1002/humu.22070).

    Solving Bottlenecks In Data Sharing In The Life Sciences.
    R.Dalgleish, E.Molero, R.Kidd, M.Jansen, D.Past, A.Robl, B.Mons, C.Diaz, A.Mons and A.J.Brookes. Hum Mutat (2012) 33(10), 1494-1496 [doi: 10.1002/humu.22123].

    VarioML Framework for Comprehensive Variation Data Representation and Exchange.
    M.G.Byrne, I.F.A.C.Fokkema, O.Lancaster, T.Adamusiak, A.Ahonen-Bishopp, D.Atlan, C.Beroud, M.Cornell, R.Dalgleish, A.Devereau, G.Patrinos, M.A.Swertz, P.E.M.Taschner, G.A.Thorisson, M.Vihinen, A.J.Brookes and Juha Muilu. BMC Bioinformatics (2012) 13, 254 [doi:10.1186/1471-2105-13-254].

    Semantically enabling a genome-wide association study database.
    T.Beck, R.C.Free, G.A.Thorisson and A.J.Brookes. J. Biomed. Semantics (2012) 3, 9.

    Applying ontologies and exploring nanopublishing in a genome-wide association study database.
    T.Beck, G.A.Thorisson and A.J.Brookes. In SWAT4LS'11 Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences (2012) 1-2 (DOI: 10.1145/2166896.2166897).

    Towards a Roadmap in Global Biobanking for Health.
    J.R.Harris, P.Burton, B.M.Knoppers and K.Lindpaintner: plus, M.Bledsoe, A.J.Brookes, I.Budin-Ljøsne, R.Chisholm, D.Cox, M.Dechênes, I.Fortier, P.Hainaut, R.Hewitt, J.Kaye, J.Litton, A.Metspalu, B.Ollier, L.Palmer, A.Palotie, M.Pasterk, M.Perola, P.H.J.Riegman, G.vanOmmen, M.Yuille, K.Zatloukal. European J. Hum. Genet. (2012), 20, 1105-11 [doi: 10.1038/ejhg.2012.96].

    HGV2011: Personalized Genomic Medicine Meets The Incidentalome.
    M.A.W.Sayres, A.J.Brookes, S.J.Chanock, V.G.Cheung, L.Jin and P-Y.Kwok. Human Mutation (2012) 33, 582-585 (DOI: 10.1002/humu.22008).

    Navigating The Perfect [Data] Storm.
    M.J.Murtagh, G.A.Thorrison, S.G.Wallace, J.Kaye, I.Demir, I.Fortier, J.R.Harris, D.Cox, M.Deschênes, P.Laflamme, V.Ferretti, N.Sheehan, T.J.Hudson, A.Cambon-Thomsen, R.P.Stolk, B.M.Knoppers, P.R.Burton* and A.J.Brookes* (*equal contribution) [on behalf of the P3G Consortium, GEN2PHEN and BioSHARE-EU]. Norwegian J. Epidemiology (2012) 21, 203-209.

    Clarity and Claims in Variation/Mutation Databasing. [A response to: "MutaDATABASE: a centralized and standardized DNA variation database" by Bale et al., 2011].
    R.Dalgleish, W.S.Oetting, A.D.Auerbach, J.S.Beckmann, A.Cambon-Thomsen, A.Devereau, M.S.Greenblatt, G.P.Patrinos, G.R.Taylor, M.Vihinen and A.J.Brookes. Nature Biotechnology (2011) 29, 790-792 [DOI:10.1038/nbt.1961].

    An Informatics Project and Online 'Knowledge Centre' Supporting Modern Genotype-to-Phenotype Research.
    A.J Webb, G.A.Thorisson and A.J.Brookes (on behalf of the GEN2PHEN consortium). Human Mutation (2011) 32, 543-550. [DOI: 10.1002/humu.21469].

    Systems medicine and integrated care to combat chronic noncommunicable diseases.
    J.Bousquet, J.M.Anto, P.J.Sterk, I.M.Adcock, K.f.Chung, J.Roca, A.Agusti, C.Brightling, A.Cambon-Thomsen, A.Cesario, S.Abdelhak, S.E.Antonarakis, A.Avignon, A.Ballabio, E.Baraldi, A.Baranov, T.Bieber, J.Bockaert, S.Brahmachari, C.Brambilla, J.Bringer, M.Dauzat, I.Ernberg, L.Fabbri, P.Froguel, D.Galas, T.Gojobori, P.Hunter, C.Jorgensen, F.Kauffmann, P.Kourilsky, M.l.Kowalski, D.Lancet, C.LePen, J.Mallet, B.Mayosi, J.Mercier, A.Metspalu, J.H.Nadeau, G.Ninot, D.Noble, M.Öztürk, S.Palkonen, C.Préfaut, K.Rabe, E.Renard, R.g.Roberts, B.Samolinski, H.J.Schünemann, H-U.Simon, M.B.Soares, G.Superti-Furga, J.Tegner, S.Verjovski-Almeida, P.Wellstead, O.Wolkenhauer, E.Wouters, R.Balling, A.J.Brookes, D.Charron, C.Pison, Z.Chen, L.Hood, C.Auffray. Genome Medicine (2011) 3, 43.

    Targeted Enrichment Of Genomic DNA Regions For Next-Generation Sequencing.
    F.Mertes, A.Elsharawy, S.Sauer, J.M.vanHelvoort, P.J.VanDerZaag, A.Franke, M.Nilsson, H.Lehrach and A.J.Brookes.. Brief Funct Genomics (2011) 10(6), 374-386.

    The MOLGENIS Toolkit: Rapid Prototyping Of Biosoftware At The Push Of A Button.
    M.A.Swertz, M.Dijkstra, T.Adamusiak, K.J.van der Velde, A.Kanterakis, T.E.Roos, J.Lops, G.A.Thorisson, D.Arends, G.Byelas, J.Muilu, A.J.Brookes, E.O.de Brock, R.C.Jansen and H.Parkinson. BMC bioinformatics (2010) 11(Suppl.12), S12 .

    Finding and sharing; New Approaches to Registries of Resources and Services for the Biomedical Sciences.
    D.Smedley, P.Schofield, C-K.Chen, V.Aidinis, C.Ainali, J.Bard, R.Balling, E.Birney, A.Blake, E.Bongcam-Rudloff, A.J.Brookes, G.Cesareni, J.Eppig, P.Flicek, G.Gkoutos, S.Greenaway, M.Gruenberger, J-K.Hériché, A.Lyall, A-M.Mallon, D.Muddyman, F.Reisinger, M.Ringwald, N.Rosenthal, K.Schughart, M.Swertz, G.A.Thorisson, M.Zouberakis and J.M.Hancock. Database (2010) 2010, baq014 DOI:10.1093/database/baq014.

    Locus Reference Genomic (LRG) sequences: an improved basis for describing human DNA variants.
    R.Dalgleish, P.Flicek, F.Cunningham, A.Astashyn, R.E.Tully, G.Proctor, Y.Chen, W.M.McLaren, P.Larsson, B.W.Vaughan, C.Béroud, G.Dobson, H.Lehväslaiho, P.E M.Taschner, J.T.denDunnen, A.Devereau, E.Birney, A.J.Brookes and D.R.Maglott. Genome Medicine (2010) 2, 24-30.

    Locus-specific database domain and data content analysis: Evolution and content maturation towards clinical use.
    C.Mitropoulou, AJ.Webb, K.Mitropoulos, AJ.Brookes and GP.Patrinos. Human Mutation (2010) 31, 1109-1116.

    HGV2009 Meeting: Bigger and better studies provide more answers and more questions.
    K.Reekie, A.Metspalu, S.J.Chanock, E.T.Liu, E.R.Mardis, S.W.Scherer, P-Y.Kwok and A.J.Brookes. Human Mutation (2010) 31, 886-888.

    The Human Variome Project (HVP) 2009 Forum "Towards Establishing Standards"..
    H.J.Howard, R.O.Horaitis, R.G.H.Cotton, J.T.denDunnen, M.Vihinen, R.Dalgleish, P.Robinson, A.J.Brookes, M.Axton, R.Hoffmann, S.V.Tavtigian and S.Tuffery-Giraud. Human Mutation (2010) 31, 366-367.

    Genotype-Phenotype Databases: Challenges and Solutions For The Post-Genomic Era.
    G.A.Thorisson, J.Muilu and A.J.Brookes. Nature Reviews Genetics (2009) 10, 9-18.

    Prepublication data sharing.
    E.Birney, T.J.Hudson, E.D.Green, C.Gunter, S.Eddy, J.Rogers, J.R.Harris and S.D.Ehrlich. Plus: R.Apweiler, C.P.Austin, L.Berglund, M.Bobrow, C.Bountra, A.J.Brookes, A.Cambon-Thomsen, N.P.Carter, R.L.Chisholm, J.L.Contreras, R.M.Cooke, W.L.Crosby, K.Dewar, R.Durbin, S.O.M.Dyke, J.R.Ecker, K.El.Emam, L.Feuk, S.B.Gabriel, J.Gallacher, W.M.Gelbart, A.Granell, F.Guarner, T.Hubbard, S.A.Jackson, J.L.Jennings, Y.Joly, S.M.Jones, J.Kaye, K.L.Kennedy, B.M.Knoppers, N.C.Kyrpides, W.W.Lowrance, J.Luo, J.J.MacKay, L.Martín-Rivera, W.R.McCombie, J.D.McPherson, L.Miller, W.Miller, D.Moerman, V.Mooser, C.C.Morton, J.M.Ostell, B.F.F.Ouellette, J.Parkhill, P.S.Raina, C.Rawlings, S.E.Scherer, S.W.Scherer, P.N.Schofield, C.W.Sensen, V.C.Stodden, M.R.Sussman, T.Tanaka, J.Thornton, T.Tsunoda, D.Valle, E.I.Vuorio, N.M.Walker, S.Wallace, G.Weinstock, W.B.Whitman, K.C.Worley, C.Wu, J.Wu, J.Yu. Nature (2009) 461, 168-170.

    HGVbaseG2P: A Central Genetic Association Database.
    G.A.Thorisson, O.Lancaster, R.C.Free, R.K.Hastings, P.Sarmah, D.Dash, S.Brahmachari and A.J.Brookes. Nucleic Acids Res. (2009) 37:D797-802.

    The Phenotype and Genotype Experiment Object Model (PaGE-OM): A Robust Data Structure for Information Related to DNA Variation.
    A.J.Brookes, H.Lehvaslaiho, J.Muilu, Y.Shigemoto, T.Oroguchi, T.Tomiki, A.Mukaiyama, A.Konagaya, T.Kojima, I.Inoue, M.Kuroda, H.Mizushima, G.A.Thorisson, D.Dash, H.Rajeevan, M.W.Darlison, M.Woon, D.Fredman, A.V.Smith, M.Senger, K.Naito and H.Sugawara. Human Mutation (2009) 30, 968-977.

    Genomic Variation in a Global Village: Report of the 10th Annual Human Genome Variation Meeting 2008..
    A.J.Brookes, S.J.Chanock, T.J.Hudson, L.Peltonen, G.Abecasis, P-Y.Kwok and S.W.Scherer. Human Mutation (2009) 30, 1134-1138 .

    Genetic Structure Of Copy Number Variants Revealed By Genotyping Single Sperm.
    M.Luo, X.Cui, D.Fredman, A.J.Brookes, M.A.Azaro, D.M.Greenawalt, G.Hu, H-Y.Wang, I.V.Tereshchenko, Y.Lin, Y.Shentu, R.Gao, L.Shen and H.Li. PLoS ONE (2009) 4, e5236.

    The Human Variome Project.
    R.G.H.Cotton, A.D.Auerbach, M.Axton, C.I.Barash, S.F.Berkovic, A.J.Brookes, J.Burn, G.Cutting, J.T.denDunnen, P.Flicek, N.Freimer, M.S.Greenblatt, H.J.Howard, M.Katz, F.A.Macrae, D.Maglott, G.Möslein, S.Povey, R.S.Ramesar, C.S.Richards, D.Seminara, T.D.Smith, M-J.Sobrido, J.H.Solbakk, R.E.Tanzi, S.V.Tavtigian, G.R.Taylor, J.Utsunomiya and M.Watson. Science (2008) 322, 861-862.

    Recommendations For Locus Specific Databases And Their Curation.
    R.G.H.Cotton, A.D.Auerbach, J.S.Beckmann, O.O.Blumenfeld, A.J.Brookes, A.E.Brown, P.Carrera, D.W.Cox, B.Gottlieb, M.S.Greenblatt, P.Hilbert, H.Lehvaslaiho, P.Liang, S.Marsh, D.W.Nebert, S.Povey, S.Rossetti, C.R.Scriver, M.Summar, D.R.Tolan, I.C.Verma, M.Vihinen and J.T.den Dunnen. Hum Mutation (2008) 29, 2-5.

    Association Of ADRB1 And UCP3 Gene Polymorphisms With Insulin Sensitivity But Not Obesity.
    S.Mottagui-Tabar, J.Hoffstedt, A.J.Brookes, H.Jiao, P.Arner and I.Dahlman. Hormone Res (2008) 69, 31-36.

    Defensins And The Dynamic Genome: What We Can Learn From Structural Variation At Human Chromosome Band 8p23.1.
    E.J.Hollox, J.C.K.Barber, A.J.Brookes and J.A.L.Armour. Genome Research (2008) 18, 1686-1697.

    SNPs Meet CNVs In Genome-Wide Association Studies: HGV2007 Meeting Report..
    X.Estivill, N.Cox, S.Chanock, P-Y.Kwok, S.W.Scherer and A.J.Brookes. PLoS Genet. (2008) 4, e1000068.

    MEGAPLEX PCR: A Strategy For Multiplex Amplification.
    L.Strömqvist-Meuzelaar, O.Lancaster, P.Pasche, G.Kopal and A.J.Brookes. Nature Methods (2007) 4, 835-837.

    Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis.
    G.Abecasis, P.K.Tam, C.D.Bustamante, E.A.Ostrander, S.W.Scherer, S.J.Chanock, P-Y.Kwok and A.J.Brookes. Nature Genet (2007) 39, 153-155.

    Recommendations Of The 2006 Human Variome Project Meeting.
    R.G.Cotton, W.Appelbe, A.D.Auerbach, K.Becker, W.Bodmer, D.J.Boone, V.Boulyjenkov, S.Brahmachari, L.Brody, A.Brookes, A.F.Brown, P.Byers, J.M.Cantu, J.J.Cassiman, M.Claustres, P.Concannon, J.T.denDunnen, P.Flicek, R.Gibbs, J.Hall, J.Hasler, M.Katz, P.Y.Kwok, S.Laradi, A.Lindblom, D.Maglott, S.Marsh, C.M.Masimirembwa, S.Minoshima, A.M.deRamirez, R.Pagon, R.Ramesar, D.Ravine, S.Richards, D.Rimoin, H.Z.Ring, C.R.Scriver, S.Sherry, N.Shimizu, L.Stein, G.O.Tadmouri, G.Taylor and M.Watson. Nature Genetics (2007) 39, 433-436.

    DNA Diagnostics By Surface-Bound Melt-Curve Reactions.
    L.Strömqvist-Meuzelaar, K.Hopkins, E.Liebana and A.J.Brookes. J Molec Diagn (2007) 9:30-41.

    An International Case-Control Study Of Interleukin-4Ralpha, Interleukin-13 And Cyclooxygenase-2 Polymorphisms And Glioblastoma Risk.
    J.A.Schwartzbaum, A.Ahlbom, S.Lönn, B.Malmer, A.Wigertz, A.Auvinen, A.J.Brookes, H.Collatz-Christensen, R.Henriksson, C.Johansen, T.Salminen, M.J.Schoemaker, A.J.Swerdlow, W.Debinski and M.Feychting. Cancer Epidemiol, Biomarkers & Prevention (2007) 16, 2448-2454.

    Association Of Arthritis With A Gene Complex Encoding C-Type Lectin-Like Receptors.
    J.C.Lorentzen, L.Flornes, C.Eklöw, L.Bäckdahl, U.Ribbhammar, J.P.Guo, M.Smolnikova, E.Dissen, M.Seddighzadeh, A.J.Brookes, L.Alfredsson, L.Klareskog, L.Padyukov and S.Fossum. Arthritis Rheum (2007) 56, 2620-2632.

    Non-Synonymous SNPs: Validation Characteristics, Derived Allele Frequency Patterns, And Suggestive Evidence For Natural Selection.
    D.Fredman*, S.L.Sawyer*, L.Strömqvist, S.Mottagui-Tabar, K.K.Kidd, C.Wahlelstedt, S.J.Chanock and A.J.Brookes (*equal contribution). Human Mutation (2006) 27, 173-186.

    Quantitative Trait Loci In ABCA1 Modify Cerebrospinal Fluid Amyloid-Beta 1-42 And Plasma Apolipoprotein Levels.
    H.Katzov, A.M.Bennet, K.Höglund, B.Wiman, D.Lütjohann, A.J.Brookes, N.Andreasen, K.Blennow, U.DeFaire and J.A.Prince. J Hum Genet. (2006) 51:171-179.

    Systematic Replication Study Of Reported Genetic Associations In Prostate Cancer: Strong Support For Genetic Variation In The Androgen Pathway.
    S.Lindström, S.L.Zheng, F.Wiklund, B-A.Jonsson, H-O.Adami, K.A.Bälter, A.J.Brookes, J.Sun, B-L.Chang, W.Liu, G.Li, W.B.Isaacs, J.Adolfsson, H.Grönberg and J.Xu. The Prostate (2006) 66:1729-1743.

    Longitudinal Memory Performance During Normal Aging: Twin Association Models Of APOE And Other Alzheimer Candidates.
    C.A.Reynolds, J.A.Prince, L.Feuk, A.J.Brookes, M.Gatz and N.L.Pedersen. Behav Genet. (2006) 36, 185-194.

    A Quality Assessment Survey of SNP Genotyping Laboratories.
    P.Lahermo, U.Liljedahl, G.Alnaes, T.Axelsson, A.J.Brookes, P.Ellonen, P-H.Groop, C.Halldén, D.Holmberg, K.Holmberg, M.Keinänen, K.Kepp, J.Kere, P.Kiviluoma, V.Kristensen, C.Lindgren, J.Odeberg, P.Osterman, M.Parkkonen, J.Saarela, M.Sterner, L.Strömqvist, U.Talas, M.Wessman A.Palotie and A-C.Syvänen. Hum Mutation (2006) 27, 711-714.

    Rapid Melting Curve Analysis on Monolayered Beads for High-throughput Genotyping of Single Nucleotide Polymorphisms.
    A.Russom, S.Haasl, A.J.Brookes, H.Andersson and G.Stemme. Anal Chem. (2006) 78, 2220-2225.

    Towards Compendia of Negative Association Studies: An Example For Alzheimers Disease.
    M.E-L.Blomqvist, C.Reynolds, H.Katzov, L.Feuk, N.Andreasen, N.Bogdanovic, K.Blennow, A.J.Brookes and J.A.Prince. Hum Genet (2006) 119, 29-37.

    7th International Meeting On Single Nucleotide Polymorphism And Complex Genome Analysis: Ever Bigger Scans And An Increasingly Variable Genome.
    D.Rocha, I.Gut, A.J.Jeffreys, P-Y.Kwok, S.J.Chanock* and A.J.Brookes* (*equal contribution). Human Genetics (2006) 119, 451-456.

    MHC2TA is associated with differential MHC molecule expression and susceptibility to rheumatoid arthritis, multiple sclerosis and myocardial infarction.
    M.Swanberg, O.Lidman, L.Padyukov, P.Eriksson, E.Åkesson, M.Jagodic, A.Lobell, M.Khademi, O.Börjesson, C.M.Lindgren, P.Lundman, A.J.Brookes, J.Kere, H.Luthman, L.Alfredsson, J.Hillert, L.Klareskog, A.Hamsten, F.Piehl and T.Olsson. Nature Genetics (2005) 37, 486-494.

    Linkage Disequilibrium Patterns Vary Substantially Among Populations.
    S.L.Sawyer, N.Mukherjee, A.J.Pakstis, L.Feuk, J.R.Kidd, K.K.Kidd* and A.J.Brookes* (*equal contribution). Eur J Hum Genet (2005) 13, 677-686.

    Polymorphisms Associated With Asthma Are Inversely Related To Glioblastoma Multiforme.
    J.Schwartzbaum, A.Ahlbom, B.Malmer, S.Lönn, A.J.Brookes, H.Doss, W.Debinski, R.Henriksson and M.Feychting. Cancer Res. (2005) 65, 6459-6465.

    Comprehensive genetic evaluation of common E-cadherin sequence variants and prostate cancer risk: strong confirmation of functional promoter SNP.
    S.Lindström, F.Wiklund, B-A.Jonsson, H-O.Adami, K.Bälter, A.J.Brookes, J.Xu, S.L.Zheng, W.B.Isaacs, J.Adolfsson and H.Grönberg. Human Genetics (2005) 118,339-347.

    Sequence Variants Of IDE Are Associated With The Extent Of -Amyloid Deposition In The Alzheimer's Disease Brain.
    M.E.Blomqvist, K.Chalmers, N.Andreasen, N.Bogdanovic, G.K.Wilcock, N.J.Cairns, L.Feuk, A.J.Brookes, S.Love, K.Blennow, P.G.Keheo and J.A.Prince. Neurobiol Aging (2005) 26, 795-802.

    Mutation Screening Of A Haplotype Block Around The Insulin Degrading Enzyme Gene And Association With Alzheimer's Disease.
    L.Feuk*, S.McCarthy*, B.Andersson, J.A.Prince and A.J.Brookes (*equal contribution). Am J Med Genet (2005) 136, 69-71.

    Elevated Amyloid ß Protein (Aß42) and Late Onset Alzheimer's Disease are Associated with Single Nucleotide Polymorphisms in the Urokinase-Type Plasminogen Activator Gene.
    N.Ertekin-Taner, J.Ronald, L.Feuk, J.Prince, M.Tucker, L.Younkin, M.Hella, S.Jain, A.Hackett, L.Scanlin, J.Kelly, M.Kihiko-Ehman, M.Neltner, L.Hersh, M.Kindy, W.Markesbery, M.Hutton, M.deAndrade, R.C.Petersen, N.Graff-Radford, S.Estus, A.J.Brookes and S.G.Younkin. Hum Mol Genetic (2005) 14, 447-460.

    Human neuropeptide Y (NPY) signal peptide gain-of-function polymorphism is associated with increased body mass index: possible mode of function..
    B.Ding, B.Kull, Z.Liu, S.Mottagui-Tabar, H.Thonberg, H.F.Gu, A.J.Brookes, L.Grundemar, C.Karlsson, A.Hamsten, P.Arner, C-G.Östenson, S.Efendic, M.Monné, G.vonHeijne, P.Eriksson and C.Wahlestedt. Regul Pept. (2005) 127, 45-53.

    DNA, Diseases, and Databases: Disastrously Deficient.
    G.P.Patrinos and A.J.Brookes. Trends Genetics (2005) 21, 333-338.

    Special Issue: "Fundamental and Molecular Mechanisms of Mutagenesis". Special Section: "Single Nucleotide Polymorphisms (SNPs): Detection, Interpretation, and Applications". Paper: Genetic Association Analysis: Lessons From The Study Of Alzheimers Disease.
    A.J.Brookes and J.A.Prince. Mutation Research (2005) 573, 152-159.

    Genotyping by dynamic heating of monolayered beads on a microheated surface.
    A.Russom, S.Haasl, A.Ohlander, T.Mayr, A.J.Brookes, H.Andersson, G.Stemme. Electrophoresis (2004) 25, 3712-3719.

    Lower rate of genomic variation identified in the trans-membrane domain of monoamine sub-class of Human G-Protein Coupled Receptors: The Human GPCR-DB Database.
    C.Wahlestedt, A.J.Brookes and S.Mottagui-Tabar. BMC Genomics (2004) 5, 91.

    Genetic Analysis of the RNASEL Gene in Hereditary, Familial and Sporadic Prostate Cancer.
    F.Wiklund, B-A.Jonsson, A.J.Brookes, L.Strömqvist, J.Adolfsson, M.Emanuelsson, H-O.Adami, K.Augustsson-Bälter and H.Grönberg. Clin Cancer Res (2004) 10, 7150-7156.

    Complex SNP-Related Sequence Variation In Segmental Genome Duplications.
    D.Fredman, S.J.White, S.Potter, E.E.Eichler, J.T.DenDunnen and A.J.Brookes.. Nature Genetics (2004) 36, 861-866.

    Quantitative Trait Loci Near the Insulin-Degrading Enzyme (IDE) Gene Contribute to Variation in Plasma Insulin Levels.
    H.F.Gu, S.Efendic, S.Nordman, C-G.Östenson, K.Brismar, A.J.Brookes and J.A.Prince. Diabetes (2004) 53, 2137-2142.

    Haplotype Block Structures Show Significant Variation Among Populations.
    N.Liu, S.L.Sawyer, N.Mukherjee, A.J.Pakstis, J.R.Kidd, K.K.Kidd, A.J.Brookes and H.Zhao. Genetic Epidemiol. (2004) 27, 385-400.

    Sequence variation in the proximity of IDE may impact age at onset of both Parkinson's disease and Alzheimer's disease.
    M.E-L.Blomqvist, P.A.Silburn, D.D.Buchanan, N.Andreasen, K.Blennow, N.Pedersen, A.J.Brookes, G.D.Mellick and J.A.Prince. Neurogenetics (2004) 5, 115-119.

    DFold: PCR Design that Minimizes Secondary Structure and Optimizes Downstream Genotyping Applications.
    D.Fredman, M.Jobs, L.Stromqvist and A.J.Brookes. Hum Mutation (2004) 24, 1-8.

    Common variants of ACE contribute to variable age-at-onset of Alzheimer's disease.
    P.G.Kehoe, H.Katzov, N.Andreasen, M.Gatz, G.K.Wilcock, N.J.Cairns, J.Palmgren, U.DeFaire, A.J.Brookes, N.L.Pedersen, K.Blennow and J.A.Prince. Hum Genet. (2004) 114, 478-483.

    Variants of CYP46A1 may interact with age and APOE to influence CSF Abeta42 levels in Alzheimer's disease.
    A.Johansson, H.Katzov, H.Zetterberg, L.Feuk, B.Johansson, N.Bogdanovic, N.Andreasen, B.Lenhard, A.J.Brookes, N.L.Pedersen, K.Blennow and J.A.Prince. Hum Genet. (2004) 114, 581-587.

    Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
    T. Imanishi et al,. PLoS Biology (2004) 2, 856-875.

    Genetic variants of ABCA1 modify Alzheimer disease risk and quantitative traits related to beta-amyloid metabolism.
    H.Katzov, K.Chalmers, J.Palmgren, N.Andreasen, B.Johansson, N.J.Cairns, M.Gatz, G.K.Wilcock, S.Love, N.L.Pedersen, A.J.Brookes, K.Blennow, P.G.Kehoe and J.A.Prince. Hum Mutation (2004) 23, 358-367.

    Genetic Variation In CTNNA3 Encoding Alpha-3 Catenin And Alzheimer's Disease.
    M.E.Blomqvist, N.Andreasen, N.Bogdanovic, K.Blennow, A.J.Brookes and J.A.Prince. Neurosci Lett. (2004) 358, 220-222.

    HGVbase: A Curated Resource Describing Human DNA Variation and Phenotype Relationships.
    D.Fredman, G.Munns, D.Rios, F.Sjöholm, M.Siegfried, B.Lenhard, H.Lehväslaiho and A.J.Brookes. Nucleic Acids Res. (2004) 32, D516-D519.

    A Novel Screen for Nuclear Mitochondrial Gene Associations with Parkinson's Disease.
    G.D.Mellick, P.A.Silburn, J.A.Prince and A.J.Brookes. J. Neural Transmission. (2004) 111, 191-199.

    Single Nucleotide Polymorphisms in the Proximal Promoter Region of the Adiponectin (APM1) Gene are Associated with Type 2 Diabetes in Swedish Caucasians.
    H.F.Gu, A.Abutaiti, C-G.Östenson, K.Humphreys, C.Wahlestedt, A.J.Brookes and S.Efendic. Diabetes (2004) 53 (supplement 1), S31-S35.

    The Association Of Three Amyloid-Related Candidates And Longitudinal Memory Performance In The Second Half Of The Life-Span.
    C.A.Reynolds, J.A.Prince, L.Feuk, A.J.Brookes, M.Gatz and N.L.Pedersen. Behav Genet (2004) 34, 657.

Research

Bioinformatics and Genomics Technologies in the Analysis of Human Genome Diversity and Disease

The human genome contains ~30,000 genes that together encode mankind’s ‘blueprint for life'. However, the detailed content of ‘the genome’ differs quite considerably between individuals. Many million single nucleotide polymorphisms (SNPs) distinguish one person’s DNA from that of another, along with thousands of very small to very large regions of structural variability and copy number variation (CNV) that affect genes and their intervening sequences. Chemical modifications of these sequences also occur, adding an additional layer of variability. All this variability contributes to making each person unique in their appearance and behavior, as well as in terms of the diseases they suffer and how they react to drugs.

Across the globe, major research projects endeavor to elucidate the biological mechanisms of action of genetic variation, and increasingly genome sequences are being tested in healthcare settings to inform diagnostic, prognostic and therapeutic approaches. This is especially true for rare inherited genetic disorders. Increasingly these efforts are using modern ‘next-generation sequencing’ (NGS) technologies that enable a whole genome to be sequenced within timeframes and budgets barely imaginable just a few years ago.

However, to benefit from the many opportunities raised by these advanced research and healthcare approaches, a range of new challenges must be met in terms of achieving effective data and knowledge management (capture, quality, storage, integration, analysis, discovery, sharing, visualisation), creating good informatics tools (standards, processing, databasing, utilisation) and information control (ethics, legalities, consent, sanctions). Furthermore, to be truly useful the devised solutions have to accommodate a diversity of approaches and constraints across nations, and the different requirements of research and healthcare settings.

Our laboratory program therefore has two areas of focus:

1) By local efforts and international collaboration, we explore previously unknown structural characteristics of the human genome, innovate new technologies for genome analysis, and investigate how the genome varies in normal and disease contexts.

2) We work within, often in a leadership capacity, major international consortia seeking to devise informatics solutions that will enable efficient and appropriate use of biomedical data and knowledge, especially aiming to bi-directionally bridge the divide between research and healthcare.

Wet-lab projects (as of September 2014) include:

• Transferring the Dynamic Allele-Specific Hybridisation (DASH) method onto micro-arrays, as a highly robust and generic method for targeted and quantitative DNA Diagnostics. This system tracks DNA melting in real time, thereby quickly and cost-effectively detecting all sequence variants down to 1% representation in all sequence contexts by means of standardised run conditions

• Using a range of advanced methods to characterise the melting behavior of the genome, in particular to create a high resolution map of regions that do not fully denature even at 130 degrees Celcius and which are consequently difficult or impossible to examine by standard procedures.

• Characterising a particular class of genome structural variation that is created in populations by a mutation process called ‘non-alleleic homologous recombination’. Importantly, we have shown these sequences are enriched for disease predisposing genes which consequently vary in copy number between individuals, and thereby we have found a possible major genetic contributor (giving many fold increased risk) to disease traits such as arthritis, dementia, and cancer, as well as normal differences such as heart rate.

Bioinformatics projects (as of September 2014) include:

• Developing new tools and strategies (Café Variome, OmicsConnect, eDAS) that will facilitate the comprehensive ‘discovery’ of where data or knowledge of interest exists when such data cannot be openly exposed (e.g., private patient data, sensitive commercial data, unpublished information). Particular use cases being explored include diagnostics and research pertaining to Rare Disease, connecting biobank datasets, cohort creation for clinical trials, and pre-competitive collaboration between pharmaceutical companies.

• Running the world’s largest open access Genome Wide Association Study database, ‘GWAS Central’, which provides a centralized compilation of summary level findings from all published genetic association studies, both large and small.

• Undertaking data collection and knowledge management for translational research consortia REQUITE and COPD-MAP.

 

Research Links

Search PubMed at the US National Library of Medicine for this author: Prof A. Brookes
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Contact Details

Department of Genetics
University of Leicester

Adrian Building
University Road
Leicester
LE1 7RH
United Kingdom
 

Tel: +44 (0)116 252 3374

Fax: +44 (0)116 252 3378

E Mail: genetics@le.ac.uk

 

Interim Head of Department

Professor Alison Goodall