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Institute of Precision Medicine & Bioinformatics

The Institute of Precision Medicine & Bioinformatics (IPM&B) was established in 2020 to enhance precision medicine (genomics and other omics) for patient care and research, and progress bioinformatics expertise and infrastructure within the District.

Precision medicine approaches utilise knowledge of an individual’s DNA, metabolomics, proteomics and other omics to identify the appropriate clinical interventions (treatments or preventive strategies) required to maintain health and wellbeing. The IPM&B’s vision is to ensure that the benefits of precision medicine are rapidly and effectively implemented into the clinical care of patients and their families at Sydney Local Health District.

Our Goals

  • Mainstreaming genomic testing across a growing number of disciplines, including respiratory and cardiovascular medicine, nephrology, immunology, neurology and rare genetic disorders via the mentoring of clinical champions in each discipline.
  • Expanding the range of personalised patient-specific therapies in cancer, including the ability to detect circulating tumour DNA (liquid biopsy).
  • Identifying at risk family members and using this knowledge to initiate early preventive or therapeutic interventions.
  • Prenatal screening and testing during pregnancy using non-invasive approaches.
  • Providing news and educational resources relevant to precision medicine, including the impact of artificial intelligence.
  • Building a Precision Medicine Consumer Group.

Research Themes

Scientist in a lab coat; performing tests in a lab
SydneyConnect Image: Scientist in the Medical Genomics laboratory

Our Researchers

Professor Ron Trent Director
Associate Professor Bing Yu Academic and Honorary Principal Hospital Scientist
Dr Anthony Cheong Genetic Pathologist
Dr Lisa Worgan Head, Clinical Genetics Service
Dr Amali Mallawaarachchi Clinical Geneticist
Dr Felicity Collins Clinical Geneticist
Dr Alison McLean Clinical Geneticist
Professor David Sullivan Head, Chemical Pathology
Dr Jay Ramanathan Staff Specialist (Clinical Pharmacology)
Dr Abdul Baten Genomics Bioinformatician
Dr Hugh French Genetic Pathology Registrar

Precision Oncology Research & Development

Associate Professor Bing Yu Academic and Honorary Principal Hospital Scientist
Cassandra Bruce Senior Hospital Scientist
Spiridoula Kraitsek Hospital Scientist
Jie Qian Hospital Scientist
Dan Chen Hospital Scientist

Clinical Trials in Familial Hypercholesterolaemia and Porphyria

Professor David Sullivan Head, Chemical Pathology
Professor Peter Stewart Clinical Director, Chemical Pathology
Kerry Kearins Registered Nurse, Study Coordinator
Darcie Kavanagh Registered Nurse
Nicole Lai Dietician

Selected Grants

Amount awarded Grant and project details
$4,951,985 MRFF, 2025-2030
Delivering benefit for all Australians in the new era of complete genomics.
Investigators: Mallawaarachchi A (CIJ).
$3,000,000 MRFF, 2023-2026
A national long-read genome sequencing program to improve rare disease diagnosis.
Investigator: Mallawaarachchi A (CII).
$1,000,000 MRFF Early to Mid-Career Researchers, 2022-2026
Harnessing nanopore sequencing technology to improve diagnosis of human disease.
Investigators: Mallawaarachchi A (CIC), Cheong A (CI),  French H (Associate Investigator).
$1,000,000 MRFF Genomics Health Future’s Mission, 2022-2026
Developing a long-read nanopore sequencing platform for Indigenous genomics.
Investigator: Mallawaarachchi A (CIE).
$3,000,000 MRFF Genomics Health Future’s Mission, 2021-2025
The Kidgen National Kidney Genomics Program.
Investigator: Mallawaarachchi A (CIF).
$2,572,403 MRFF, 2020-2026
Implementation of Metformin therapy to Ease Decline of Kidney Function in PKD.
Investigator: Mallawaarachchi A (CIJ).

Clinical Trials

Study Details
AROAPOC3-3001 Phase 3 Study to Evaluate the Efficacy and Safety of ARO-APOC3 in Adults with Familial Chylomicronemia Syndrome (X22-0061)
Sullivan, D (PI for RPA)
AROAPOC3-2003 Open label study of Elevated Triglycerides study (X22-0073)
Sullivan, D (PI for RPA)
Victorian 1 Prevent Outcomes study in ASCVD (X23-0221)
Sullivan, D (PI for RPA)
MK 0616-017 Phase 3 RCT Oral PCSK9 in adults with HeFH (X23-0301)
Sullivan, D (PI for RPA)
MK 616-015 Phase 3 outcomes study for MK0616 in reducing Major CV events in patients at high patients with high CV risk (X23-0429)
Sullivan, D (PI for RPA)
ISIS678354-CORE Randomized, Double-Blind, Placebo-Controlled, Phase 3 Study of ISIS 678354 Administered Subcutaneously to Patients with Severe Hypertriglyceridemia (X22-075)
Sullivan, D (PI for RPA)
CTQJ230A12301 (HORIZON) Phase 3 randomized double-blind, placebo-controlled, multicenter trial assessing the impact of lipoprotein (a) lowering with pelacarsen (TQJ230) on major cardiovascular events in patients with established cardiovascular disease (X20-0269)
Sullivan, D (PI for RPA)
AROANG3-2003 Phase 2 Study to Evaluate the Safety and Efficacy of ARO-ANG3 in Subjects with Homozygous Familial Hypercholesterolemia (HoFH) (X22-073)
Sullivan, D (PI for RPA)
AROAPOC3-2001 Double-Blind, Placebo-Controlled Phase 2b Study to Evaluate the Efficacy and Safety of ARO-APOC3 in Adults with Severe Hypertriglyceridemia (X21-0223)
Sullivan, D (PI for RPA)
20180109 Olpasiran trials of Cardiovascular Events And LipoproteiN(a) reduction – DOSE Finding Study (OCEAN[a]-DOSE)
Sullivan, D (PI for RPA)
20210057 Multicenter, Cross-sectional study to Characterize the distribution of lipoprotein(a) levels among patients with documented history of atherosclerotic cardiovascular disease (ASCVD)
Sullivan, D (PI for RPA)
DISC-1459-501 An Open-Label, Long-Term Study to Investigate the Safety, Tolerability, and Efficacy of DISC-1459 (Bitopertin) in Participants with Erythropoietic Protoporphyria (EPP)
Stewart, P (PI for RPA)
DISC-1459-202 A Phase 2, Randomized, Open Label Study of Bitopertin to Evaluate the Safety, Tolerability, Efficacy, and Protoporphyrin IX (PPIX) Concentrations in Participants with Erythropoietic Protoporphyria (EPP)
Stewart, P (PI for RPA)

Our Publications

2024

Swart G, Fraser CL, Shingde M, Thompson EO, Mallawaarachchi A, Lawlor M, Ahmad K, Halmagyi GM. Mitochondrial DNA 13513G>A Mutation Causing Leber Hereditary Optic Neuropathy Associated With Adult-Onset Renal Failure. J Neuroophthalmol. 2024 Jun 1;44(2):190-194. PMID: 37477990. DOI: 10.1097/WNO.0000000000001946. Epub 2023 Jul 21. 
McCarthy HJ, Mallett AJ, Sullivan P, Cowley MJ, Mallawaarachchi AC. Beyond DNA sequencing: genetic kidney disorders related to altered splicing. Nephrol Dial Transplant. 2024 Jun 28;39(7):1056-1059. PMID: 38289833. DOI: 10.1093/ndt/gfae022
Dwyer LJ, Singhal N, Yu B, Kao S. Successful Osimertinib Rechallenge After Relapse Following Adjuvant Osimertinib: A Case Report. J Thorac Oncol. 2024 Apr;19(4):650-652. PMID: 38340108. DOI: 10.1016/j.jtho.2024.01.001. Epub 2024 Feb 9. 
El-Wahsh S, Fellner A, Hobbs M, Copty J, Deveson I, Stevanovski I, Stoll M, Zhu D, Narayanan RK, Grosz B, Worgan L, Cheong PL, Yeow D, Rudaks L, Hasan MM, Hayes VM, Kennerson M, Kumar KR, Hayes M. An Inversion Affecting the GCH1 Gene as a Novel Finding in Dopa-Responsive Dystonia. Mov Disord Clin Pract. 2024 May;11(5):582-585. PMID: 38497520; PMCID: PMC11078477. DOI: 10.1002/mdc3.14023. Epub 2024 Mar 18. 
Al-Shinnag M, Cheong PL, Goodwin A, Trent R, Yu B. Germline potential should not be overlooked for cancer variants identified in tumour-only somatic mutation testing. Pathology. 2024 Jun;56(4):468-472. PMID: 38627125. DOI: 10.1016/j.pathol.2024.03.001. Epub 2024 Mar 29. 
Parmar JM, McNamara EL, Lamont PJ, Kumar KR, Rick A, Stoll M, Cheong PL, Ravenscroft G. Two Novel Variants in PI4KA in a Family Presenting With Hereditary Spastic Paraparesis: A Case Report. Neurol Genet. 2024 Apr 25;10(3):e200152. PMID: 38685974; PMCID: PMC11057436. DOI: 10.1212/NXG.0000000000200152
Birkenhead K, Sullivan D, Trumble C, Spinks C, Srinivasan S, Partington A, Elias L, Hespe CM, Fleming G, Li S, Calder M, Robertson E, Trent R, Sarkies MN. Implementation of a primary-tertiary shared care model to improve the detection of familial hypercholesterolaemia (FH): a mixed methods pre-post implementation study protocol. BMJ Open. 2024 May 1;14(5):e082699. PMID: 38692720; PMCID: PMC11086381. DOI: 10.1136/bmjopen-2023-082699
Morley KC, Kranzler HR, Luquin N, Jamshidi N, Adams C, Montebello M, Tremonti C, Dali G, Logge W, Baillie A, Teesson M, Trent R, Haber PS. Topiramate Versus Naltrexone for Alcohol Use Disorder: A Genotype-Stratified Double-Blind Randomized Controlled Trial. Am J Psychiatry. 2024 May 1;181(5):403-411. PMID: 38706338. DOI: 10.1176/appi.ajp.20230666
Zhen XM, Twigg SM, Wu T, Tabet E, McGill MJ, Constantino M, Mallawaarachchi A, Luo C, Thillainadesan S, Rahman Y, Wong J. Diabetic ketoacidosis in an adult with beta-ketothiolase deficiency (BKD) involving a novel ACAT1 variant : first report of established diabetes in BKD and a review of the literature. Clin Diabetes Endocrinol. 2024 Jun 10;10(1):17. PMID: 38853254; PMCID: PMC11163784. DOI: 10.1186/s40842-024-00174-9
Mallawaarachchi AC, Fowles L, Wardrop L, Wood A, O'Shea R, Biros E, Harris T, Alexander SI, Bodek S, Boudville N, Burke J, Burnett L, Casauria S, Chadban S, Chakera A, Crafter S, Dai P, De Fazio P, Faull R, Honda A, Huntley V, Jahan S, Jayasinghe K, Jose M, Leaver A, MacShane M, Madelli EO, Nicholls K, Pawlowski R, Rangan G, Snelling P, Soraru J, Sundaram M, Tchan M, Valente G, Wallis M, Wedd L, Welland M, Whitlam J, Wilkins EJ, McCarthy H, Simons C, Quinlan C, Patel C, Stark Z, Mallett AJ. Genomic Testing in Patients with Kidney Failure of an Unknown Cause: A National Australian Study. Clin J Am Soc Nephrol. 2024 Jul 1;19(7):887-897. PMID: 38861662; PMCID: PMC11254024. DOI: 10.2215/CJN.0000000000000464. Epub 2024 May 3. 
Mallawaarachchi A, Biros E, Harris T, Bennetts B, Boughtwood T, Elliott J, Fowles L, Gardos R, Garza D, Goranitis I, Haas M, Huntley V, Jefferis J, Kassahn K, Leaver A, Lundie B, Lunke S, O'Connor C, Pratt G, Quinlan C, Shearman D, Soraru J, Sundaram M, Tchan M, Valente G, White J, Wilkins E, Alexander SI, Amir N, Best S, Gul H, Jayasinghe K, McCarthy H, Patel C, Stark Z, Mallett AJ. Shaping the future of kidney genetics in Australia: proceedings from the KidGen policy implementation workshop 2023. Hum Genomics. 2024 Aug 17;18(1):88. PMID: 39154021; PMCID: PMC11330018. DOI: 10.1186/s40246-024-00656-y
Jayasinghe K, Biros E, Harris T, Wood A, O'Shea R, Hill L, Fowles L, Wardrop L, Shalhoub C, Hahn D, Rangan G, Kevin L, Tchan M, Snelling P, Sandow R, Sundaram M, Chaturvedi S, Trnka P, Faull R, Poplawski NK, Huntley V, Garza D, Wallis M, Jose M, Leaver A, Trainer AH, Wilkins EJ, White S, Elbaum Y, Prawer Y, Krzesinski E, Valente G, Winship I, Ryan J, Whitlam J, Nicholls K, West K, Donaldson L, Johnstone L, Lewit-Mendes M, Kerr PG, Bodek S, Chakera A, MacShane M, Mincham C, Stackpoole E, Willis F, Soraru J, Pachter N, Bennetts B, Forbes TA, Mallawaarachchi A, Quinlan C, Patel C, McCarthy H, Goranitis I, Best S, Alexander S, Stark Z, Mallett AJ. Implementation and Evaluation of a National Multidisciplinary Kidney Genetics Clinic Network Over 10 Years. Kidney Int Rep. 2024 May 9;9(8):2372-2385. PMID: 39156154; PMCID: PMC11328548. DOI: 10.1016/j.ekir.2024.04.068.
Munif MR, Hart RA, Rafeek RAM, Mallawaarachchi AC, Anderson L, McMillan DJ, Sriprakash KS, Ketheesan N. Mechanisms that potentially contribute to the development of post-streptococcal glomerulonephritis. Pathog Dis. 2024 Feb 7;82:ftae024. PMID: 39341789; PMCID: PMC11556339. DOI: 10.1093/femspd/ftae024
Jiang A, Chen Y, Ning Y, Yu B, Wang H, Ma F, Xu C, Kang Y. MRI grading for informed clinical decision-making in Peutz-Jeghers syndrome patients with cervical lesions. Sci Rep. 2024 Oct 10;14(1):23731. PMID: 39390237; PMCID: PMC11467353. DOI: 10.1038/s41598-024-75227-1
Bennetts B, Ho G, Shin S, Cheong PL, Wotton T, Ranieri E, Pirreca S. Newborn Genomic Sequencing Needs Confirmation but Not Repeating. Children (Basel). 2024 Oct 25;11(11):1287. PMID: 39594862; PMCID: PMC11593300. DOI: 10.3390/children11111287
Austin R, Brown JS, Casauria S, Madelli EO, Mattiske T, Boughtwood T, Metke A, Davis A, Horton AE, Winlaw D, Das D, Soka M, Giannoulatou E, Rath EM, Haan E, Blue GM, Vohra J, Atherton JJ, van Spaendonck-Zwarts K, Cox K, Burnett L, Wallis M, Haas M, Quinn MCJ, Pachter N, Poplawski NK, Stark Z, Bagnall RD, Weintraub RG, Pantaleo SJ, Lunke S, De Fazio P, Thompson T, James P, Chang Y, Fatkin D, Macciocca I, Ingles J, Dunwoodie SL, Semsarian C, McGaughran J; Australian Genomics Cardiovascular Disorders Flagship. A multitiered analysis platform for genome sequencing: Design and initial findings of the Australian Genomics Cardiovascular Disorders Flagship. Genet Med Open. 2024 Mar 25;2:101842. PMID: 39669597; PMCID: PMC11613726. DOI: 10.1016/j.gimo.2024.101842
Mallawaarachchi AC, Hort Y, Wedd L, Lo K, Senum S, Toumari M, Chen W, Utsiwegota M, Mawson J, Leslie S, Laurence J, Anderson L, Snelling P, Salomon R, Rangan GK, Furlong T, Shine J, Cowley MJ. Somatic mutation in autosomal dominant polycystic kidney disease revealed by deep sequencing human kidney cysts. NPJ Genom Med. 2024 Dec 19;9(1):69. PMID: 39702469; PMCID: PMC11659627. DOI: 10.1038/s41525-024-00452-6
Mou SN, Rupa AA, Chowdhury MAA, Rahi ML, Baten A, Ali AA, Khan H, Amin MA, Islam MR. Current Chinese Science. 2024;4(3):202–213.

More Information

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