Publications

The following are publications, abstracts, posters and work in preparation using BioGrid Australia data.  The researchers using BioGrid Australia are generally working on multiple projects and so the list understates the achievements. If you would like to find out more about these publications please firstly contact the BioGrid Australia office- vicki.vlekkert@biogrid.org.au

Epilepsy

  1. Analysis and Validation of large scale SNP genotyping in pharmacogenetic analysis of anti-epileptic drugs.

    An abstract with the above title was presented at the Human Genetics Society of Australia meeting, Auckland, New Zealand, July, 2007.  Authors: Sheffield, L.J., Petrovski, S., Gasko, H., Szoeke, C.E.I., Goldstein, D.B., Cavalleri, G. & O’Brien, T.J.

  2. Association studies have been proposed as the way forward to locate important genetic changes in a number of conditions. In pharmacogenomics association studies can be used to study the occurrence of side effects or phamacoresistance. Single nucleotide polymorphisms (SNPs) are single base differences in DNA sequence in the population.  This is an example of studying the effect of failure of antiepileptics to control seizures in newly diagnosed epileptics.

    An abstract entitled “Utility of MRI in Adult First Seizure Patients -- Development & Validation of a Clinical Algorithm” was presented at at ANZAN (Australia New Zealand Association of Neurologists), Alice Springs, May 2007. Authors: Lowe, A.J., Kilpatrick, C.J., Yerra, R., Ghougassian, D.F., Matkovic, Z., & O’Brien, T.J.

    A Paper entitled “Use of Single Nucleotide Polymorphism (SNPs) in association studies” was presented at the Indo-Australian Conference on Human Variations and Pharmacogenomics, Manipal, India, March, 2007, and was submitted to Lancet Neurology.  Author: Sheffield, L.J.

  3. A large-scale multi-centre effort to map genetic variants for sporadic epilepsy syndrome and seizure types.

    A paper with the above title has been submitted to Lancet Neurology Journal, Vol 6, 2007. Authors: Gianpiero, L. Cavalleri, M., Weale M.E.., Shianna, K., Singh, R., Lynch, J., Grinton, B., Szoeke C., Murphy, K., Kinirons, P., O’Rourke, D.,  Ge, D.,  Depondt,C., Claeys, K.,  Gumbs, K., Walley, N., McNamara, J.,  Mulley, J.,  Linney, K.N.,  Sheffield, L., Radtke, R.,  Tate, S.K., Chissoe, S.,  Stanton, A.,  Graves, T.,  Hanna, M., Kalviainen, R., O'Brien, T.J., Sander, J.W.,  Duncan, J.S.,  Scheffer, I.E., Berkovic, S.F.,  Wood, N.W.,  Doherty, C.P., Delanty, N.,  Sisodiya, S.M., & Goldstein, D.
  4. How likely is a first epileptic seizure to be provoked by an external stimulus or to occur as an unprovoked seizure, and the frequency of those seizures re-occurring?

    An abstract entitled ‘First Seizure Clinic experience: Heterogeneity of patient population and prognosis’ was presented to the World Congress of Neurology (Sydney, 5–11 November 2005), and to the American Epilepsy Society and American Clinical Neurophysiology Society Joint Annual Meeting (Washington DC, 2–7 December, 2005). Authors: Yerra R, Kilpatrick C, Matkovic Z, King B, Rafael N, Hibbert M, Brand C, and O’Brien T. (Published in Epilepsia, Vol. 46, Suppl.8, 2005: page 360.)
  5. The most significant advance in the diagnosis of epilepsy has been the recognition of epileptic syndromes and diseases, which provides a proper medical diagnosis for patients with epileptic disorders.

  6. What is the accuracy of diagnosis of epilepsy based on the occurrence of a single seizure? 

    An abstract was presented at the World Congress of Neurology, which was held in Sydney (5–11 November 2005): ‘Syndromic diagnosis of epilepsy in the First Seizure Clinic population.’ Authors: Yerra R, Kilpatrick C, Matkovic Z, Belbin S, Rafael N, Hibbert M, Brand C, and O’Brien T.
  7. Can adverse responses to anti-epileptic drugs be predicted based on a patient’s genetic     profile? 

    A poster entitled ‘MDR1 Genotype, Seizure Occurrence and Adverse Drug Effects – Preliminary Data from the Australian Prospective AED Pharmaco-genetics Study’ was presented to an international epilepsy conference. Authors: O’Brien, T.J. et al.

    An abstract expanding on the original poster was presented to World Congress of Neurology, Sydney 2005: “Pharmacogentics of neurocognitive side effects from newly commenced epileptic treatments.”

Neuropsychiatry

  1. Establish the validity and reliability of a cognitive – or brain function tool. MMIM has computerised and using NUCOG and incorporating the data.

    Paper accepted: The NUCOG: validity and reliability of a brief cognitive screening tool in neuropsychiatry patients. Australian and New Zealand Journal of Psychiatry 2006; 40: 995-1002, Authors: Walterfang, M.,  Siu, R., Velakoulis, D.

Gastroenterology

  1. ‘Relationship between disease severity, quality of life and health-care resource use in a cross-section of Australian patients with Crohn's disease’. Journal of Gastroenterology &  Hepatology. 2007, Jun 7; Authors: Gibson PR, Weston AR, Shann A, Florin TH, Lawrance IC, Macrae FA, Radford-Smith G.

  2. ‘Microsatellite instability markers for identifying early-onset colorectal cancers caused by germ-line mutations in DNA mismatch repair genes’. Clinical Cancer Research, 2007, May 15;13(10):2865-9.  Authors: Mead LJ, Jenkins MA, Young J, Royce SG, Smith L, St John DJ, Macrae F, Giles GG, Hopper JL, Southey MC.

  3. ‘Providing colonoscopy services for the National Bowel Cancer Screening Program’.
    Medical Journal of Australia. 2007 Mar 19;186(6):280-1. Macrae FA.

  4. What is the impact of pathology provider on factors such as the lymph node yield and determining the presence of lymph and vascular invasion in outcome prediction in colon?

    Abstracts submitted: ‘The quality of the pathology provider significantly impacts reporting of multiple prognostic factors in colon cancer’. American Society of Clinical Oncology - Gastrointestinal meeting, January 2007. Authors P. Gibbs, F. Barnett, J. Moore, A. Ryan, S. Ananda, M. Croxford, N. Reiger
  5. ‘A family with juvenile polyposis linked to the BMPR1A locus: Cryptic mutation or closely linked gene?’ Journal of  Gastroenterology and Hepatology; 2007 June 15; Authors: Chow E, Lipton L, Carvajal-Carmona LG, Arthur G, Bhathal P, Kaur G, Jaeger E, Woodford-Richens K, Howarth K, Tomlinson I, Macrae F.

    ‘A juvenile polyposis family with a cryptic BMPR1A mutation’. Royal Melbourne Hospital Research Week, 2006. An oral presentation was also given at Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005. It was also published in the Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A13.  Authors: Chow E, Arthur G, Bhathal P, Wood-Richens K, Carvajal L, Lipton L, Tomlinson I, Macrae F.

  6. Can we find a new Biomarker for Colorectal Cancer?

    Abstract submitted to Australian Gastroenterology Week 2006.  ‘P2X7: A New Biomarker for Colorectal Neoplasia’  Biosceptre International Ltd, Sydney; Anatomy & Histology, The University of Sydney.

    An oral presentation was also given at the Australian Gastroenterology Week, Adelaide, 2006. Authors: Kaur G, Chang WY, Zhiye S, Barden, J, Cumming G, Landgren A, Macrae F.  Colorectal Medicine & Genetics, and Pathology, Royal Melbourne Hospital 

  7. ‘A NOD2/CARD15 mutation predicts Crohn’s Disease aggression’. Royal Melbourne Hospital Research Week, 2006. An oral presentation was also given at Australian Gastroenterology Week, Adelaide, 2006. Authors: Bhullar M, Smith M, Sharpe K, Lewis P, Viney B, Brown G, Macrae F.

  8. ‘Initial experience of double balloon enteroscopy at RMH’. Royal Melbourne HospitalResearch Week, 2006 Authors: Brown GJE, Macrae FA.
    ‘Initial experience with double balloon enteroscopy at RMH’. Oral presentation, Australian Gastroenterology Week, Adelaide, 2006. Authors: Brown G, Macrae FA.

  9. ‘Dietary modulation of cancer related gene expression in the colon’.  Royal Melbourne Hospital Research Week, 2006. An oral presentation was also given at Australian Gastroenterology Week, Adelaide, 2006. Authors: Vlass A, Bostick R, Zhye Si, Sharpe K, Muir J, Macrae FA.

  10. ‘Celecoxib reduces formation of sporadic colorectal adenomas: Results from the Adenoma Prevention with Celecoxib (APC) trial’. Royal Melbourne Hospital Research Week, 2006.
    An oral presentation was also given at Australian Gastroenterology Week, Adelaide, 2006.  Authors: Macrae F, Jones IT, Pizzey C, Bertagnolli M, Hawk E, Eagle C for the APC Trial Investigators

  11. ‘Cancer risks for carriers of germline mutations in hMLH1, hMSH2, hMSH6, and hPMS2: a population-based case-family study’. Royal Melbourne Hospital Research Week, 2006.. Authors: Macrae FA, Jenkins MA, Bagliettto L, Dowty JG, vanVliet C, Southey MC, St John DJB, Jass JR, Giles GG, Hopper JL.
     
  12. ‘Impact of familial adenomatous polyposis on young adults: attitudes toward genetic testing, support, and information needs’. Genetic Medicine. 2006 Nov; 8(11):697-703. Authors: Andrews L, Mireskandari S, Jessen J, Thewes B, Solomon M, Macrae F, Meiser B.

  13. ‘Analysis of 25 years of screening for colorectal neoplasia based on moderate familial risk’. Accepted for oral presentation Aust Gastroenterology Week, Adelaide, 2006.Authors: Macrae FA, Slattery M, Brown GJ, St John DJB, O’Dwyer M, Budd K

  14. ‘Capsule endoscopy, endoscopy and barium studies in Peutz Jeghers Syndrome and Juvenile Polyposis’. Oral presentation. Australian Gastroenterology Week, Adelaide, 2006. Authors: Macrae F, Stella D, Gibson RN, Cameron D, Catto-Smith A, Pizzey C, Brown G.

  15. ‘An updated mutation spectrum in an Australian series of Peutz Jeghers Syndrome patients provides further evidence for only one gene locus’. Oral presentation, Australian Gastroenterology Week, Adelaide, 2006.  Authors: Chow E, Scott RJ, Macrae FA et al.

  16. How accurate is the ‘blood in the stool’ test compared to colonoscopy?   - An evaluation of the sensitivity and specificity of FOBT compared to colonoscopy’.

    A poster, entitled ‘Sensitivity of faecal occult blood testing (FOBT) for asymptomatic colorectal cancer and advanced adenomas over a 25-year experience in colorectal cancer screening’ was presented at Australian Gastroenterology Week (Brisbane, 19­–22 October 2005).
    It was also presented at the International Gastroenterology Conference and at CSIRO’s Science for Breakfast briefing for Parliamentarians in Canberra, hosted by the Hon Dr Brendan Nelson (Minister for Education, Science and Training) on 30 November, 2005.
    It was also published in the, Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A34.   Authors: Macrae FA, Slattery MA, Brown GJ, O’Dwyer MA Murphy CG, Hibbert ME, and St.John DJ. The poster was the result of collaboration with CSIRO eHealth.

    ‘Sensitivity of faecal occult blood testing (FOBT) for asymptomatic colorectal cancer and advanced adenomas over a 25 year experience in colorectal cancer screening.’ Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005. Authors: Macrae FA, Slattery MA, Brown GJ, O’Dwyer MA, Murphy C, Hibbert ME, St John DJB.

  17. ‘Confocal endomicroscopy for detection of normal and diseased colonic mucosa in vivo’. American Gastroenterological Association Digestive Diseases Week, Chicago, 2005; Gastroenterology 2005; 128: 4(2)A-28.  Authors: Macrae FA, Polglase A, McLaren W, Murr E, Delaney P.

    ‘Confocal endomicroscopy’. OMED Colorectal Cancer Screening Meeting. May 15, 2005, Chicago Author: Macrae FA.

    ‘Confocal laser endomicroscopy offers a high negative predictive value vs. histology of biopsies at the time of endoscopy’. Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005; Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A45. Authors: Macrae F, Polglase AL, McLaren WJ, Murr E, Delaney PM.

  18. ‘Biallellic MYH mutations in patients with multiple colorectal adenomas’. Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005; Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A17. Authors: Chow E, Lipton L, Cowie S, Nasioulous S, Lynch E, D’Souza R, Du Sart D, Winship I, Macrae FA.

  19. ‘CAPP2: a trial of aspirin and resistant starch in people at risk of hereditary non polyposis colorectal cancer (HNPCC)’. Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005, J of Gastroenterology and Hepatology 2005; 20 (suppl) A18. Authors: Macrae FA, Ives PC, Winship I, Boussioutas A, Leggett B, Scott RJ, Spigelman A, Walpole I, Goldblatt J, Burn J.

  20. ‘Genome wide SNP genotyping with microarrays to detect novel colorectal cancer (CRC) genes using high throughput SNP microarrays’. Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005; Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A27. Authors: Hannan G, Saunders I, Macrae F, Young G.

  21. ‘Hyperplastic polyposis syndrome: phenotype and the role of MDB4 and MYH.’ Gastroenterological Society of Australia Australian Gastroenterology Week, Brisbane 2005; Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A28. Authors: Chow E, Barker M, Buchanan D, Young J, Leggett B, Lipton L, Winship I, Macrae F.

  22. ‘Survey of HNPCC management - analysis of responses from 18 international cancer centres’. Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005, Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A37. Authors: Chow E, Macrae F, Burn J, on behalf of respondents from 18 international ICG-HNPCC Familial Cancer Clinics

  23. ‘Capsule endoscopy for obscure anaemia at The Royal Melbourne Hospital’. Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005, J of Gastroenterology and Hepatology 2005; 20 (suppl) A42. Authors: Kiew KK, Brown GJE, Macrae FA. 

  24. ‘Development of self advancing endoscope: goals and outcomes’. Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005; Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A45. Authors: Soutorine M, Macrae FA, Waxman BP. 

  25. ‘Video capsule endoscopy (VCE): initial national experience after Medicare listing’. Gastroenterological Society of Australia, Australian Gastroenterology Week, Brisbane 2005, Journal of Gastroenterology and Hepatology 2005; 20 (suppl) A59. Authors: Kiew KK, Macrae FA for the Australian Capsule Endoscopy Group.

  26. ‘Photodynamic therapy in high grade dysplasia in Barrett’s oesophagus using 5 amino-laevulinic acid sensitization’. Gastroenterological Society of Australia, Annual Gastroenterology Week, Cairns 2004; Journal of Gastroenterology and Hepatology 2004; 19: A235. Authors: Macrae FA, Rajesekaram R, Thomas R.  

Colorectal Cancer and Diabetes                                                                                                         

  1. Is there an interaction between smoking, diabetes and CRC development?

    Letters accepted:  ‘Type 2 Diabetes Mellitus, Smoking and Colorectal Cancer". American Journal of Gastroenterology (2007 April;102(4):909-10), Authors: P Gibbs, S McLaughlin, IT Jones, I Faragher, I Skinner, M Croxford, J Johns, M Chapman, L Lipton

  2. Do those with diabetes have an increased risk of site specific Colorectal Cancer? Those with diabetes are more likely to have proximal colon cancer.

    A Letter to the Editor entitled Subsite-specific colorectal cancer in diabetic and non-diabetic patients has been published in Cancer Epidemiology, Biomarkers & Prevention (2005; 14: 1579–1582). The letter showcases the advantages of using the MMIM database. Authors: Lim E, Jones IT, Gibbs P, McLaughlan S, Faragher I, Skinner I, Chao MW, and Johns J.

Colorectal Cancer 

  1. A third of colorectal cancer occurs in the setting of familial risk. Family Cancer Clinics (FCC) counsel patients and families about risk reduction strategies and to perform genetic testing where appropriate. Is the referral process effective?

    Abstract submitted: Familial Colorectal Cancer - How Poor is our Pick-up?". American Society of Clinical Oncology - Gastrointestinal meeting, January 2007. Authors: LR Lipton, C Wong, P Gibbs, J Johns, I Faragher, I Jones, G Lindeman, F Macrae, E Lynch
  2. Quality of pathology reporting impacts on lymph node yield in colon cancer. Journal of Clinincal Oncology. 2007 Feb 1; 25(4):463; author reply 463-4.  Authors: Rieger NA, Barnett FS, Moore JW, Ananda SS, Croxford M, Johns J, Gibbs P.

  3. Is the number of lymph nodes collected in Colorectal Cancer patients a marker for the adequacy of the surgical, pathological or institutional care? The authors found that the pathologist has a significant influence on the number of lymph nodes reported following colon cancer surgery, and that improved lymph node yields can be obtained with appropriate intervention in pathology practice.

    Letters accepted. "The quality of pathology reporting impacts on lymph node yield in colon cancer". Journal of Clinical Oncology. 2007 Feb 1;25(4):463; author reply 463-4. Comment on: Journal of Clinical Oncology. 2006 Aug 1;24(22):3570-5. Authors: Reiger NA, Barnett FS, Moore JWE, Neo E, Badahdah F, Ryan AJ, Ananda SS, Croxford M, Johns J, Gibbs P.


  4. Completion of therapy by Medicare patients with stage III colon cancer. Journal of National Cancer Institute. 2006 Nov 1;98(21):1582  Authors: Gibbs P, McLaughlin S, Skinner I, Jones I, Hayes I, Chapman M, Johns J, Lim L, Faragher I.

  5. Are those who come from a non-English speaking background diagnosed at the same stage and receive the same treatment as those from a non-English speaking background.

    Paper published in ANZ Journal of Surgery Vol. 76 Issue 7 Page 671 July 2006 entitled: ‘The Influence of Language Spoken on Colorectal Cancer Diagnosis and Management’. Authors: Rodrigues J, Lim E, McLaughlin S, Faragher I, Skinner I, Chao M, Croxford M, Chapman M, Johns J, Gibbs P (2006 in preparation).
     
  6. What percentage of patients in routine clinical practice fail to complete adjuvant treatment for stage III colon cancer and what are the associated factors?

    Re: Completion of therapy by Medicare patients with stage III colon cancer. The Journal of the National Cancer Institute. 2006 Nov 1;98 (21):1582. Authors: Gibbs P, McLaughlin S, Skinner I, Jones I, Hayes I, Chapman M, Johns J, Lim L, Faragher I.

  7. What are the surveillance practices, how is chemotherapy dosing calculated and what is the use of chemotherapy for treating metastases in colorectal cancer patients by medical and trainee oncologists?

    Chemotherapy dosing and the management of colorectal cancer: results of a nationwide survey. Oral presentation at the Medical Oncology Group Australia  Western Hospital, Victoria, August, 2006. Author: Field, K

  8. A multicentre analysis of the long-term outcomes of patients with localized rectal cancer treated with chemotherapy and/or radiotherapy alone due to medical inoperability or patient refusal. Poster presentation at the American Society of Clinical Oncology Annual Meeting in June 2006. Authors: Lim L, Chao M, Shapiro J, Millar J, Kipp D, Rezo A, Fong A, Jones IT, McLaughlin S, Gibbs P.

  9. In preparation: ‘A Single Institution Experience Of Adjuvant 5-Fluorouracil Based Chemotherapy For Stage III Colon cancer.’  Authors: Faragher I, Handolias D, McLaughlin S, Skinner I, Chao M, Chapman M, Johns J, Gibbs P.

  10. Synoptic Reporting – is a concise and standardized reporting method that includes all data needed for accurate staging, treatment, and prognosis in cancer.

    Papers presented Synoptic reporting in colorectal cancer". Australian Gastrointestinal Trials Group, September 14th 2006. Gibbs, P.
  11. In Press: Long-term outcomes of patients with localized rectal cancer treated with chemotherapy and/or radiotherapy alone due to medical inoperability or patient refusal. Authors: Lim L, Chao M, Shapiro J, Millar J. L., Kipp D, Rezo A, Fong A, Jones IT, McLaughlin S, Gibbs P.

Diabetes

  1. Molecular Medicine Informatics Model (MMIM) – setting up a new tool for diabetes research and quality assurance, Authors: Colman, P., Jerums, J.,  Cameron, F., Ward, G., Oats, J., Gasko, H., and Hibbert, M.E., Royal Melbourne, Austin and Repatriation, Royal Children’s, St. Vincent’s Hospital and Royal Women’s Hospitals. Abstract submitted to the Australian Diabetes Society Annual Scientific meeting which will be in Christchurch in September, 2007.

MMIM Technology                                                                                                                                

  1. The Molecular Medicine Informatics Model (MMIM). Paper/presentation to Healthgrid 2007. Geneva. From Genes to Personalised Healthcare: Grid Solutions for Life Sciences IOS Press 77-86; 2007. Authors: Hibbert, M.E., Gibbs, P., O’Brien, T., Colman, P., Merriel, R.,  Rafael, N., Georgeff, M.

  2. The Molecular Medicine Informatics Model (MMIM). Studies in Health Technology Informatics. 2007; 126:77-86. Authors: Hibbert M, Gibbs P, O'brien T, Colman P, Merriel R, Rafael N, Georgeff M.

  3. Overview of the MMIM architecture and system. Paper/presentation for HIC 2006 presented ‘Information Based Medicine and the Molecular Medicine Informatics Model (MMIM) Project’ Authors: Ross, B., Hadzanovic, L., Ientile, J.,  IBM Healthcare and Life Sciences, Australia, Robert Merriel, Marienne Hibbert, Melbourne Health.