Dr Paul James Leo

Ph.D

Senior Bioinformatician

Projects

Genetic profile of AML

Sequening the exomes and whole genomes of 150 AML cases in collaboartion with SA Pathology, PA Pathology, Queensland Heath and Complete Genomics

Next Generation Sequening in commom and rare diseases.

About me

I am Senior Bioinformatician at the University of Queensland Center for Clinical Genomics (UQCCG). This role involves the management and provision of Bioinformatics services and data analysis for UQCCG, including researchers at Queensland Brain Institute, UQ Centre for Clinical Research, and UQDI, as well as the Brown group at UQDI. In 2013 UQCCG was the largest next-generation sequencing center in the southern hemisphere sequencing over 4000 samples and is the world’s third largest genotyping center behind the Broad and Sanger institutes genotyping in excess of 20,00 samples/yr.

In this capacity I supervise three full time Bioinformaticians. I supervise Ph.D students and masters with bioinformatics and statistical genetics focused projects.

I maintain extensive academic, clinical and industry collaborations with researchers within UQDI, UQ, nationally and internationally where I provide key expertise in the analysis of large clinically focused datasets.

The themes of this research include the development of analysis of monogenic diseases, somatic celldiseases and rare variant discovery in complex diseases using next –generation sequencing and Gene discovery in complex diseases utilizing genome-wide association studies (genotyping chips and genomic imputation with common haplotypes).

The goals of this research are to characterise and understand the genetic origin of disease and to translate these finding into clinical practice.

Publications

McInerney-Leo A, Duncan EL, Leo PJ, Gardiner B, Bradbury L, Harris J, Clark G, Brown MA, Zankl A. COL1A1 C-propeptide cleavage site mutation causes high bone mass, bone fragility and jaw lesions: a new cause of gnathodiaphyseal dysplasia? Clin Genet (accepted May 2014)

Brown MA, Cremin K, Leo PJ, Harris J, De Smit E, Bradbury L, McKelvie P, Hill C, Hewitt A. Utility of temporal artery biopsy samples for genome-wide analysis of giant cell arteritis" Genes and Immunity, Accepted April 2014

Zhang L, Choi HJ, Estrada K, Leo PJ, Li J, Pei YF, Zhang Y, Lin Y, Shen H, Liu YZ, Liu Y, Zhao Y, Zhang JG, Tian Q, Wang YP, Han Y, Ran S, Hai R, Zhu XZ, Wu S, Yan H, Liu X, Yang TL, Guo Y, Zhang F, Guo YF, Chen Y, Chen X, Tan L, Zhang L,Deng FY, Deng H, Rivadeneira F, Duncan EL, Lee JY, Han BG, Cho NH, Nicholson GC, McCloskey E, Eastell R, Prince RL, Eisman JA, Jones G, Reid IR, Sambrook PN, Dennison EM, Danoy P, Yerges-Armstrong LM, Streeten EA, Hu T, Xiang S, Papasian CJ, Brown MA, Shin CS, Uitterlinden AG, Deng HW. Multistage genome-wide association meta-analyses identified two new loci for bone mineral density. Hum Mol Genet. 2014 Apr 1;23(7):1923-33.

McInerney-Leo AM, Marshall MS, Gardiner B, Benn DE, McFarlane J, Robinson BG, Brown MA, Leo PJ, Clifton-Bligh RJ, Duncan EL. Whole exome sequencing is an efficient and sensitive method for detection of germline mutations in patients with phaeochromcytomas and paragangliomas. Clin Endocrinol (Oxf). 2014 Jan;80(1):25-33.

Moayyeri A, Hsu YH, Karasik D, Estrada K, Xiao SM, Nielson C, Srikanth P, Giroux S, Wilson SG, Zheng HF, Smith AV, Pye SR, Leo PJ, et al. Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium. Hum Mol Genet. 2014 Jan 26.

McInerney-Leo AM, Marshall MS, Gardiner B, Coucke PJ, Van Laer L, Loeys BL, Summers KM, Symoens S, West JA, West MJ, Paul Wordsworth B, Zankl A, Leo PJ, Brown MA, Duncan EL. Whole exome sequencing is an efficient, sensitive and specific method of mutation detection in osteogenesis imperfecta and Marfan syndrome. Bonekey Rep. 2013 Dec 4;2:456.

Schmidts M, Vodopiutz J, Christou-Savina S, Cortés CR, McInerney-Leo AM, Emes RD, Arts HH, Tüysüz B, D'Silva J, Leo PJ, Giles TC, Oud MM, Harris JA, Koopmans M, Marshall M, Elçioglu N, Kuechler A, Bockenhauer D, Moore AT, Wilson LC, Janecke AR, Hurles ME, Emmet W, Gardiner B, Streubel B, Dopita B, Zankl A, Kayserili H, Scambler PJ, Brown MA, Beales PL, Wicking C; UK10K, Duncan EL, Mitchison HM. Mutations in the gene encoding IFT dynein complex component WDR34 cause Jeune asphyxiating thoracic dystrophy. Am J Hum Genet. 2013 Nov 7;93(5):932-44.

Halbritter J, Bizet AA, Schmidts M, Porath JD, Braun DA, Gee HY, McInerney-Leo AM, Krug P, Filhol E, Davis EE, Airik R, Czarnecki PG, Lehman AM, Trnka P, Nitschké P, Bole-Feysot C, Schueler M, Knebelmann B, Burtey S, Szabó AJ, Tory K, Leo PJ, Gardiner B, McKenzie FA, Zankl A, Brown MA, Hartley JL, Maher ER, Li C, Leroux MR, Scambler PJ, Zhan SH, Jones SJ, Kayserili H, Tuysuz B, Moorani KN, Constantinescu A, Krantz ID, Kaplan BS, Shah JV; UK10K Consortium, Hurd TW, Doherty D, Katsanis N, Duncan EL, Otto EA, Beales PL, Mitchison HM, Saunier S, Hildebrandt F. Defects in the IFT-B component IFT172 cause Jeune and Mainzer-Saldino syndromes in humans. Am J Hum Genet. 2013 Nov 7;93(5):915-25.

McInerney-Leo AM, Schmidts M, Cortés CR, Leo PJ, Gener B, Courtney AD, Gardiner B, Harris JA, Lu Y, Marshall M; UK10K Consortium, Scambler PJ, Beales PL, Brown MA, Zankl A, Mitchison HM, Duncan EL, Wicking C. Short-rib polydactyly and Jeune syndromes are caused by mutations in WDR60. Am J Hum Genet. 2013 Sep 5;93(3):515-23.

Zheng HF, Duncan EL, Yerges-Armstrong LM, Eriksson J, Bergström U, Leo PJ, Leslie WD, Goltzman D, Blangero J, Hanley DA, Carless MA, Streeten EA, Lorentzon M, Brown MA, Spector TD, Pettersson-Kymmer U, Ohlsson C, Mitchell BD, Richards JB. Meta-analysis of genome-wide studies identifies MEF2C SNPs associated with bone mineral density at forearm. J Med Genet. 2013 Jul;50(7):473-8.

International Genetics of Ankylosing Spondylitis Consortium (IGAS), Cortes A, Hadler J, Pointon JP, Robinson PC, Karaderi T, Leo P, Cremin K, Pryce K, Harris J, Lee S, Joo KB, Shim SC, Weisman M, Ward M, Zhou X, Garchon HJ, Chiocchia G, Nossent J, Lie BA, Førre Ø, Tuomilehto J, Laiho K, Jiang L, Liu Y, Wu X, Bradbury LA, Elewaut D, Burgos-Vargas R, Stebbings S, Appleton L, Farrah C, Lau J, Kenna TJ, Haroon N, Ferreira MA, Yang J, Mulero J, Fernandez-Sueiro JL, Gonzalez-Gay MA, Lopez-Larrea C, Deloukas P, Donnelly P; Australo-Anglo-American Spondyloarthritis Consortium (TASC); Groupe Française d'Etude Génétique des Spondylarthrites (GFEGS); Nord-Trøndelag Health Study (HUNT); Spondyloarthritis Research Consortium of Canada (SPARCC); Wellcome Trust Case Control Consortium 2 (WTCCC2), Bowness P, Gafney K, Gaston H, Gladman DD, Rahman P, Maksymowych WP, Xu H, Crusius JB, van der Horst-Bruinsma IE, Chou CT, Valle-Oñate R, Romero-Sánchez  C, Hansen IM, Pimentel-Santos FM, Inman RD, Videm V, Martin J, Breban M, Reveille JD, Evans DM, Kim TH, Wordsworth BP, Brown MA. Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci. Nat Genet. 2013 Jul;45(7):730-8.

Sparrow DB, McInerney-Leo A, Gucev ZS, Gardiner B, Marshall M, Leo PJ, Chapman DL, Tasic V, Shishko A, Brown MA, Duncan EL, Dunwoodie “Autosomal dominant spondylocostal dysostosis is caused by mutation in TBX6.” Hum Mol Genet. 2013 Apr 15;22(8): 1625-31.

Waddell N, Stein SR, Wagner SA, Bennett I, Djougarian A, Melana S, Jaffer S, Holland JF, Pogo BG, Gonda TJ, Brown MA, Leo P, Saunders NA, McMillan NA, Cocciardi S, Vargas AC, Lakhani SR, Chenevix-Trench G, Newman B, Francis GD. “Morphological and molecular analysis of a breast cancer cluster at the ABC Studio in Toowong.” Pathology. 2012 Aug;44(5):469-72. PMID: 22744170

Zheng HF, Tobias JH, Duncan E, Evans DM, Eriksson J, Paternoster L, Yerges-Armstrong LM, Lehtimäki T, Bergström U, Kähönen M, Leo PJ, Raitakari O, Laaksonen M, Nicholson GC, Viikari J, Ladouceur M, Lyytikäinen LP, Medina-Gomez C, Rivadeneira F, Prince RL, Sievanen H, Leslie WD, Mellström D, Eisman JA, Movérare-Skrtic S, Goltzman D, Hanley DA, Jones G, St Pourcain B, Xiao Y, Timpson NJ, Smith GD, Reid IR, Ring SM, Sambrook PN, Karlsson M, Dennison EM, Kemp JP, Danoy P, Sayers A, Wilson SG, Nethander M, McCloskey E, Vandenput L, Eastell R, Liu J, Spector T, Mitchell BD, Streeten EA, Brommage R, Pettersson-Kymmer U, Brown MA, Ohlsson C, Richards JB, Lorentzon M. WNT16 influences bone mineral density, cortical bone thickness, bone strength, and osteoporotic fracture risk. PLoS Genet. 2012 Jul;8(7):e1002745.

Estrada K, Styrkarsdottir U, Evangelou E, Hsu YH, Duncan EL, Ntzani EE, Oei L, Albagha OM, Amin N, Kemp JP, Koller DL, Li G, Liu CT, Minster RL, Moayyeri A, Vandenput L, Willner D, Xiao SM, Yerges-Armstrong LM, Zheng HF, Alonso N, Eriksson J, Kammerer CM, Kaptoge SK, Leo PJ, et al. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nat Genet. 2012 Apr 15;44(5):491-501.

Zankl A, Duncan EL, Leo PJ, Clark GR, Glazov EA, Addor MC, Herlin T, Kim CA, Leheup BP, McGill J, McTaggart S, Mittas S, Mitchell AL, Mortier GR, Robertson SP, Schroeder M, Terhal P, Brown MA. Multicentric carpotarsal osteolysis is caused by mutations clustering in the amino-terminal transcriptional activation domain of MAFB. Am J Hum Genet. 2012 Mar 9;90(3):494-501.

Brooks K, Oakes V, Edwards B, Ranall M, Leo P, Pavey S, Pinder A, Beamish H, Mukhopadhyay P, Lambie D, Gabrielli B. A potent Chk1 inhibitor is selectively cytotoxic in melanomas with high levels of replicative stress. Oncogene. 2013 Feb 7;32(6):788-96.

Škalamera D, Ranall MV, Wilson BM, Leo P, Purdon AS, Hyde C, Nourbakhsh E, Grimmond SM, Barry SC, Gabrielli B, Gonda TJ. A high-throughput platform for lentiviral overexpression screening of the human ORFeome. PLoS One. 2011;6(5):e20057.

Duncan EL, Danoy P, Kemp JP, Leo PJ, McCloskey E, Nicholson GC, Eastell R, Prince RL, Eisman JA, Jones G, Sambrook PN, Reid IR, Dennison EM, Wark J, Richards JB, Uitterlinden AG, Spector TD, Esapa C, Cox RD, Brown SD, Thakker RV, Addison KA, Bradbury LA, Center JR, Cooper C, Cremin C, Estrada K, Felsenberg D, Glüer CC, Hadler J, Henry MJ, Hofman A, Kotowicz MA, Makovey J, Nguyen SC, Nguyen TV, Pasco JA, Pryce K, Reid DM, Rivadeneira F, Roux C, Stefansson K, Styrkarsdottir U, Thorleifsson G, Tichawangana R, Evans DM, Brown MA. Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk. PLoS Genet. 2011 Apr;7(4)

Burdon KP, Macgregor S, Hewitt AW, Sharma S, Chidlow G, Mills RA, Danoy P, Casson R, Viswanathan AC, Liu JZ, Landers J, Henders AK, Wood J, Souzeau E, Crawford A, Leo P, Wang JJ, Rochtchina E, Nyholt DR, Martin NG, Montgomery GW, Mitchell P, Brown MA, Mackey DA, Craig JE. “Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1.” Nat Genet. 2011 Jun;43(6):574-8. Epub 2011 May 1.

Zhao L, Glazov EA, Pattabiraman DR, Al-Owaidi F, Zhang P, Brown MA, Leo PJ, Gonda TJ. Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb. Nucleic Acids Res. 2011 Jun;39(11):4664-79.

Poth KJ, Guminski AD, Thomas GP, Leo PJ, Jabbar IA, Saunders NA. Cisplatin treatment induces a transient increase in tumorigenic potential associated with high interleukin-6 expression in head and neck squamous cell carcinoma. Mol Cancer Ther. 2010 Au;9(8):2430-9.

Cameron SR, Dahler AL, Endo-Munoz LB, Jabbar I, Thomas GP, Leo PJ, Poth K, Rickwood D, Guminski A, Saunders NA. Tumor-initiating activity and tumor morphology of HNSCC is modulated by interactions between clonal variants within the tumor. Lab Invest. 2010 Nov;90(11):1594-603.

Australo-Anglo-American Spondyloarthritis Consortium (TASC), Reveille JD, Sims AM, Danoy P, Evans DM, Leo P, Pointon JJ, Jin R, Zhou X, Bradbury LA, Appleton LH, Davis JC, Diekman L, Doan T, Dowling A, Duan R, Duncan EL, Farrar C, Hadler J, Harvey D, Karaderi T, Mogg R, Pomeroy E, Pryce K, Taylor J, Savage L, Deloukas P, Kumanduri V, Peltonen L, Ring SM, Whittaker P, Glazov E, Thomas GP, Maksymowych WP, Inman RD, Ward MM, Stone MA, Weisman MH, Wordsworth BP, Brown MA. Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci. Nat Genet. 2010 Feb;42(2):123-7.

Duan R, Leo P, Bradbury L, Brown MA, Thomas G. Gene expression profiling reveals a downregulation in immune-associated genes in patients with AS. Ann Rheum Dis. 2010 Sep;69(9):1724-9.

Gonda TJ, Leo P, Ramsay RG. Estrogen and MYB in breast cancer: potential for new therapies. Expert Opin Biol Ther. 2008 Jun;8(6):713-7.

D. Yevick, M. Reimer, H. Yaffe, P.J. Leo D.L. Peterson, S.Wang K.B Rochford, Frequency and Duration of Communication System Outages Resulting from Polarization Mode Dispersion IEEE Journal of Lightwave Technology , Vol 1 No. 1 p1-8 2008.

Cole NB, Dieuliis D, Leo P, Mitchell DC, Nussbaum RL. Mitochondrial translocation of alpha-synuclein is promoted by intracellular acidification. Exp Cell Res. 2008 Jun 10;314(10):2076-89.

Antonellis A, Lee-Lin SQ, Wasterlain A, Leo P, Quezado M, Goldfarb LG, Myung K, Burgess S, Fischbeck KH, Green ED. Functional analyses of glycyl-tRNA synthetase mutations suggest a key role for tRNA-charging enzymes in peripheral axons. J Neurosci. 2006 Oct 11;26(41):10397-406.

Chin C, Vuletic V, Kerman A. ,Chu S, Tiesinga E, Leo PJ and Williams C. J Precision Feshbach spectroscopy of Ultracold Cs2 Phys Rev A. Vol 70 No 1 p032701(2004)

Venturi, V, Leo PJ, Tiesinga, Williams CJ and Whittingham IB. Purely-long-range bound states of He(2s[^3]S) + He(2p[^3]P) Phys. Rev. A 68, 022706 (2003).

Leo PJ, Gray G, Simer and Rochford KB. State of Polarization Changes: Classification and Measurement Journal Lightwave Technology Vol 21 No. 10 p2189-2193 2003.

Peterson DL, Ward BC, Rochford KB, Leo PJ, Simer G. (2002) Polarization mode dispersion compensator field trial and field fiber characterization. Optics Express 10 (14): 614-621 JUL 15

Leo PJ, Peterson DL and Rochford KB. Estimation of system outage statistics due to polarization mode dispersion Technical Digest: Symposium on Optical Fiber Measurements, NIST Special Publication 988 p213 2002

Ayer AJ, Damask J, Gray G and Leo PJ. (2002) Mapping PMD quantifies system performance. WDM Solutions April 2002 p31

Leo PJ, Venturi V, Whittingham IB, Babb JF. (2001) Ultracold collisions of metastable helium atoms. Physical Review A 64 (4): art. no. 042710 Oct

Kerman AJ, Chin C, Vuletic V, Chu S, Leo PJ, Williams CJ, Julienne PS. (2001) Determination of Cs-Cs interaction parameters using Feshbach spectroscopy. Omptes Rendus De L Academie Des Sciences Serie IV Physique Astrophysique 2 (4): 633-639 Jun

Leo PJ, Julienne PS, Mies FH, Williams CJ. Collisional frequency shifts in 133Cs fountain clocks. Phys Rev Lett. 2001 Apr 23;86(17):3743-6.

Leo PJ, Peach G, Whittingham IB. (2000) Investigation of sodium-helium interaction potentials. Journal of Physics B-Atomic Molecular and Optical Physics 33 (21): 4779-4797 Nov 14

Leo PJ, Williams CJ, Julienne PS (2000) Collision properties of ultracold Cs-133 atoms. Physical Review Letters 85 (13): 2721-2724 Sep 25

Gensemer SD, Gould PL, Leo PJ, Tiesinga E, Williams CJ. (2000) Ultracold Rb-87 ground-state hyperfine-changing collisions in the presence and absence of laser light. Physical Review A 62 (3): art. no. 030702 Sep

Venturi V, Whittingham IB, Leo PJ, Peach G. (1999) Close-coupled calculation of collisions of magnetostatically trapped metastable helium atoms. Physical Review A 60 (6): 4635-4646 Dec

Leo PJ, Tiesinga E, Julienne PS, Walter DK, Kadlecek S, Walker TG. (1998) Elastic and inelastic collisions of cold spin-polarized Cs-133 atoms. Physical Review Letters 81 (7): 1389-1392 Aug 17

Leo PJ, Bell KL, Keenan FP. (1998) Photoionisation cross sections for Fe XVII. Astronomy and Astrophysics 333 (1): 385-388 May

Leo PJ; Mullamphy DFT; Peach G; Venturi V; Whittingham IB. (1998) Temperature dependence of the self-broadened 540.06 nm neon line. Acta Physica Polonica A, Vol 93, Iss 3, pp 459-464

Leo PJ; Mullamphy DFT; Peach G; Venturi V; Whittingham IB. (1997) Self-broadening of 2p(5)3p-2p(5)ns (n=5, 6) neon lines. Journal of Physics B-Atomic Molecular and Optical Physics, Vol 30, Iss 3, pp 535-545

Leo PJ; Mullamphy DFT; Peach G; Venturi V; Whittingham IB (1996) Self-broadening of non-resonance 2p(5)3s-2p(5)3p neon lines. Journal of Physics B-Atomic Molecular and Optical Physics, Vol 29, Iss 20, pp 4573-4585

Leo PJ; Mullamphy DFT; Peach G; Whittingham IB (1995) Close-coupled calculation of self-broadening of nonresonance 2p(5)3s-2p(5)3p neon lines. Journal of Physics B-Atomic Molecular and Optical Physics Vol 28, Iss 20, pp 4449-4458

Leo PJ; Peach G; Whittingham IB. (1995) Close-coupled calculation of self-broadening of helium triplet lines. Journal of Physics B-Atomic Molecular and Optical Physics, Vol 28, Iss 4, pp 591-607

Leo PJ; Mullamphy DFT; Peach G; Whittingham IB. (1992) Self-broadening of triplet lines of helium. Journal of Physics B-Atomic Molecular and Optical Physics, Vol25, Iss 6, pp 1161-1173

 

Research fields

Bioinformatics