Luminesce Alliance Publications

Functional Genomics Bustos F, Espejo-Serrano C, Segarra-Fas A, Toth R, Eaton AJ, Kernohan KD, Wilson MJ, Riley LG, Findlay GM. A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne–Kalscheuer syndrome. Scientific Reports. 2021 May 5;11(1):9560.

Bournazos AM, Riley LG, Bommireddipalli S, Ades L, Akesson LS, Al-Shinnag M, Alexander SI, Archibald AD, Balasubramaniam S, Berman Y, Beshay V. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genetics in Medicine. 2022 Jan 1;24(1):130-45.

Barroso-González J, García-Expósito L, Galaviz P, Lynskey ML, Allen JA, Hoang S, Watkins SC, Pickett HA, O’Sullivan RJ. Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell reports. 2021 Dec 7;37(10):110088.

Bouasker S, Patel N, Greenlees R, Wellesley D, Taie LF, Almontashiri NA, Baptista J, Alghamdi MA, Boissel S, Martinovic J, Prokudin I. Bi-allelic variants in WNT7B disrupt the development of multiple organs in humans. Journal of Medical Genetics. 2022 Jul 5.

Briere LC, Walker MA, High FA, Cooper C, Rogers CA, Callahan CJ, Ishimura R, Ichimura Y, Caruso PA, Sharma N, Brokamp E. A description of novel variants and review of phenotypic spectrum in UBA5-related early epileptic encephalopathy. Molecular Case Studies. 2021 Jun 1;7(3):a005827.

Chahine Karam F, Loi TH, Ma A, Nash BM, Grigg JR, Parekh D, Riley LG, Farnsworth E, Bennetts B, Gonzalez-Cordero A, Jamieson RV. Human iPSC-Derived Retinal Organoids and Retinal Pigment Epithelium for Novel Intronic RPGR Variant Assessment for Therapy Suitability. Journal of personalized medicine. 2022 Mar 21;12(3):502.

Chan DL, Rudinger-Thirion J, Frugier M, Riley LG, Ho G, Kothur K, Mohammad SS. A case of QARS1 associated epileptic encephalopathy and review of epilepsy in aminoacyl-tRNA synthetase disorders. Brain and Development. 2022 Feb 1;44(2):142-7.

Connolly K, Gonzalez-Cordero A. Modelling inner ear development and disease using pluripotent stem cells–a pathway to new therapeutic strategies. Disease Models & Mechanisms. 2022 Nov 1;15(11):dmm049593

Fernando M, Lee S, Wark JR, Xiao D, Lim BY, O’Hara-Wright M, Kim HJ, Smith GC, Wong T, Teber ET, Ali RR. Differentiation of brain and retinal organoids from confluent cultures of pluripotent stem cells connected by nerve-like axonal projections of optic origin. Stem Cell Reports. 2022 Jun 14;17(6):1476-92.

Javed A, Mattar P, Lu S, Kruczek K, Kloc M, Gonzalez-Cordero A, Bremner R, Ali RR, Cayouette M. Pou2f1 and Pou2f2 cooperate to control the timing of cone photoreceptor production in the developing mouse retina. Development. 2020 Sep 15;147(18):dev188730.

Lu R, Allen JA, Galaviz P, Pickett HA. A DNA-fiber protocol for single molecule analysis of telomere (SMAT) length and extension events in cancer cells. STAR protocols. 2022 Mar 18;3(1):101212.

McMahon R, Sibbritt T, Aryamanesh N, Masamsetti VP, Tam PP. Loss of Foxd4 Impacts Neurulation and Cranial Neural Crest Specification During Early Head Development. The Long Road to Building a Head: Smooth Travels and Accidents on the Journey From Patterning via Morphogenesis to Phenotype. 2022 Feb 1.

Mediati DG, Wong JL, Gao W, McKellar S, Pang CN, Wu S, Wu W, Sy B, Monk IR, Biazik JM, Wilkins MR. RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′ UTR required for intermediate vancomycin resistance. Nature communications. 2022 Jun 22;13(1):1-5.

Nelson N, Feurstein S, Niaz A, Truong J, Holien JK, Lucas S, Fairfax K, Dickinson J, Bryan TM. Functional genomics for curation of variants in telomere biology disorder associated genes, a systematic review. Genetics in Medicine. 2022 Dec 7.

Niaz A, Truong J, Manoleras A, Fox LC, Blombery P, Vasireddy RS, Pickett HA, Curtin JA, Barbaro PM, Rodgers J, Roy J. Functional interaction between compound heterozygous TERT mutations causes severe telomere biology disorder. Blood Advances. 2022 Apr 29.

O’Hara-Wright M, Gonzalez-Cordero A. Retinal organoids: a window into human retinal development. Development. 2020 Dec 15;147(24):dev189746.

O’Hara-Wright M, Mobini S, Gonzalez-Cordero A. Bioelectric Potential in Next-Generation Organoids: Electrical Stimulation to Enhance 3D Structures of the Central Nervous System. Front Cell Dev Biol. 2022 May 17;10:901652. doi: 10.3389/fcell.2022.901652. PMID: 35656553; PMCID: PMC9152151.

Okada T, McIlfatrick S, Hin N, Aryamanesh N, Breen J, St John JC. Mitochondrial supplementation of Sus scrofa metaphase II oocytes alters DNA methylation and gene expression profiles of blastocysts. Epigenetics & chromatin. 2022 Dec;15(1):1-20.

Ribeiro J, Procyk CA, West EL, O’Hara-Wright M, Martins MF, Khorasani MM, Hare A, Basche M, Fernando M, Goh D, Jumbo N. Restoration of visual function in advanced disease after transplantation of purified human pluripotent stem cell-derived cone photoreceptors. Cell reports. 2021 Apr 20;35(3).

Riley, L.G., Rudinger‐Thirion, J., Frugier, M., Wilson, M., Luig, M., Alahakoon, T.I., Nixon, C.Y., Kirk, E.P., Roscioli, T., Lunke, S., Stark, Z., Wierenga, K.J., Palle, S., Walsh, M., Higgs, E., Arbuckle, S., Thirukeswaran, S., Compton, A.G., Thorburn, D.R. and Christodoulou, J. (2020), The expanding LARS2 phenotypic spectrum: HLASA, Perrault syndrome with leukodystrophy, and mitochondrial myopathy. Human Mutation. doi:10.1002/humu.24050

Riley, L.G., Waddell, L.B., Ghaoui, R. et al. Recessive DES cardio/myopathy without myofibrillar aggregates: intronic splice variant silences one allele leaving only missense L190P-desmin. Eur J Hum Genet 27, 1267–1273 (2019). https://doi.org/10.1038/s41431-019-0393-6

Villamizar O, Waters SA, Scott T, Saayman S, Grepo N, Urak R, Davis A, Jaffe A, Morris KV. Targeted activation of cystic fibrosis transmembrane conductance regulator. Molecular Therapy. 2019 Oct 2;27(10):1737-48.

Villamizar, O., Waters, S. A., Scott, T., Grepo, N., Jaffe, A., & Morris, K. V. (2021). Mesenchymal Stem Cell exosome delivered Zinc Finger Protein activation of cystic fibrosis transmembrane conductance regulator. Journal of Extracellular Vesicles, 10(3). doi:10.1002/jev2.12053

West EL, Majumder P, Naeem A, Fernando M, O’Hara-Wright M, Lanning E, Kloc M, Ribeiro J, Ovando-Roche P, Shum IO, Jumbu N. Antioxidant and lipid supplementation improve the development of photoreceptor outer segments in pluripotent stem cell-derived retinal organoids. Stem cell reports. 2022 Apr 12;17(4):775-88.

Westhaus A, Cabanes-Creus M, Jonker T, Sallard E, Navarro RG, Zhu E, Baltazar Torres G, Lee S, Wilmott P, Gonzalez-Cordero A, Santilli G. AAV-p40 bioengineering platform for variant selection based on transgene expression. Human Gene Therapy. 2022 May 6.

Xiao D, Kim HJ, Pang I, Yang P. Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. Bioinformatics. 2022 Apr 1;38(7):1956-63.

van Tilburg, C.M., Witt, R., Heiss, M. et al. INFORM2 NivEnt: The first trial of the INFORM2 biomarker driven phase I/II trial series: the combination of nivolumab and entinostat in children and adolescents with refractory high-risk malignancies. BMC Cancer 20, 523 (2020). https://doi.org/10.1186/s12885-020-07008-8

Computational Biology Data Program

Baker LA, Holliday H, Roden D, Krisp C, Wu SZ, Junankar S, Serandour AA, Mohammed H, Nair R, Sankaranarayanan G, Law AMK, McFarland A, Simpson PT, Lakhani S, Dodson E, Selinger C, Anderson L, Samimi G, Hacker NF, Lim E, Ormandy CJ, Naylor MJ, Simpson K, Nikolic I, O’Toole S, Kaplan W, Cowley MJ, Carroll JS, Molloy M, Swarbrick A, Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer. Breast Cancer Res. 2020 Jun 11;22(1):63

Bournazos AM, Riley LG, Bommireddipalli S, Ades L, Akesson LS, Al-Shinnag M, Alexander SI, Archibald AD, Balasubramaniam S, Berman Y, Beshay V. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genetics in Medicine. 2022 Jan 1;24(1):130-45.

Brunton H, Caligiuri G, Cunningham R, Upstill-Goddard R, Bailey UM, Garner IM, Nourse C, Dreyer S, Jones M, Moran-Jones K, Wright DW, Paulus-Hock V, Nixon C, Thomson G, Jamieson NB, McGregor GA, Evers L, McKay CJ, Gulati A, Brough R, Bajrami I, Pettitt SJ, Dziubinski ML, Barry ST, Grützmann R, Brown R, Curry E; Glasgow Precision Oncology Laboratory; Australian Pancreatic Cancer Genome Initiative, Pajic M, Musgrove EA, Petersen GM, Shanks E, Ashworth A, Crawford HC, Simeone DM, Froeling FEM, Lord CJ, Mukhopadhyay D, Pilarsky C, Grimmond SE, Morton JP, Sansom OJ, Chang DK, Bailey PJ, Biankin AV. HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer, Cell Reports, 2020 May 12, 31(6):107625 [MJ Cowley in APGI consortium author group]

Chen J, Nelson C, Wong M, Tee AE, Liu PY, La T, Fletcher JI, Kamili A, Mayoh C, Bartenhagen C, Trahair TN, Xu N, Jayatilleke N, Wong M, Peng H, Atmadibrata B, Cheung BB, Lan Q, Bryan TM, Mestdagh P, Vandesompele J, Combaret V, Boeva V, Wang JY, Janoueix-Lerosey I, Cowley MJ, MacKenzie KL, Dolnikov A, Li J, Polly P, Marshall GM, Reddel RR, Norris MD, Haber M, Fischer M, Zhang XD, Pickett HA, Liu T, Targeted Therapy of TERT-Rearranged Neuroblastoma with BET Bromodomain Inhibitor and Proteasome Inhibitor Combination Therapy. Clin Cancer Res. 2021 Mar 1;27(5):1438-1451. doi: 10.1158/1078-0432.CCR-20-3044, PMID: 33310889

Cipponi A, Goode DL, Bedo J, McCabe MJ, Pajic M, Croucher DR, Rajal AG, Junankar SR, Saunders DN, Lobachevsky P, Papenfuss AT, Nessem D, Nobis M, Warren SC, Timpson P, Cowley M, Vargas AC, Qiu MR, Generali DG, Keerthikumar S, Nguyen U, Corcoran NM, Long GV, Blay JY, Thomas DM, MTOR signaling orchestrates stress-induced mutagenesis facilitating adaptive evolution in human cancers, Science, 2020 Jun 5;368(6495):1127-1131

Clarke M, Mackay A, Ismer B, Pickles JC, Tatevossian RG, Newman S, Bale TA, Stoler I, Izquierdo E, Temelso S, Carvalho DM. Infant high-grade gliomas comprise multiple subgroups characterized by novel targetable gene fusions and favorable outcomes. Cancer discovery. 2020 Jul;10(7):942-63.

Cowley MJ, Liu Y, Oliver KL, Carvill GC, Myers CT, Gayevskiy V, Delatycki M, M Vlaskamp DR, Zhu Y, Mefford H, Buckley MF, Bahlo M, Scheffer IE, Dinger ME, Roscioli T. Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection, Human Mutation, 2019, 40(4):374–9

Davis RL, Kumar KR, Puttick C, Liang C, Ahmad KE, Edema-Hildebrand F, Park JS, Minoche AE, Gayevskiy V, Mallawaarachchi AC, Christodoulou J. Use of whole-genome sequencing for mitochondrial disease diagnosis. Neurology. 2022 Aug 16;99(7):e730-42.

Dreyer SB, Pinese M, Jamieson NB, Scarlett CJ, Colvin EK, Pajic M, Johns AL, Humphris JL, Wu J, Cowley MJ, Chou A, Nagrial AM, Chantrill L, Chin VT, Jones MD, Moran-Jones K, Carter CR, Dickson EJ, Samra JS, Merrett ND, Gill AJ, Kench JG, Duthie F, Miller DK, Cooke S, Aust D, Knösel T, Rümmele P, Grützmann R, Pilarsky C, Nguyen NQ, Musgrove EA, Bailey PJ, McKay CJ, Biankin AV, Chang DK, Precision Oncology in Surgery: Patient Selection for Operable Pancreatic Cancer (2020), Annals of Surgery, 2020 Aug;272(2):366-376.

Dreyer SB, Upstill-Goddard R, Paulus-Hock V, Paris C, Lampraki EM, Dray E, Serrels B, Caligiuri G, Rebus S, Plenker D, Galluzzo Z, Brunton H, Cunningham R, Tesson M, Nourse C, Bailey UM, Jones M, Moran-Jones K, Wright DW, Duthie F, Oien K, Evers L, McKay CJ, McGregor GA, Gulati A, Brough R, Bajrami I, Pettitt S, Dziubinski ML, Candido J, Balkwill F, Barry ST, Grützmann R, Rahib L, Glasgow Precision Oncology Laboratory, Australian Pancreatic Cancer Genome Initiative, Johns A, Pajic M, Froeling FEM, Beer P, Musgrove EA, Petersen GM, Ashworth A, Frame MC, Crawford HC, Simeone DM, Lord C, Mukhopadhyay D, Pilarsky C, Tuveson DA, Cooke SL, Jamieson NB, Morton JP, Sansom OJ, Bailey PJ, Biankin AV, Chang DK. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer, Gastroenterology 2021 Jan 1; 160(1):362-377.e13. doi: 10.1053/j.gastro.2020.09.043. PMID: 33039466 [APGI consortium authorship]

Ewans LJ, Colley A, Gaston-Massuet C, et al, Pathogenic variants in PLOD3 result in a Stickler syndrome-like connective tissue disorder with vascular complications Journal of Medical Genetics, 2019, 56(9):629-638

Field MJ, Kumar R, Hackett A, Kayumi S, Shoubridge CA, Ewans LJ, Ivancevic AM, Dudding‐Byth T, Carroll R, Kroes T, Gardner AE. Different types of disease‐causing noncoding variants revealed by genomic and gene expression analyses in families with X‐linked intellectual disability. Human mutation. 2021 Jul;42(7):835-47.

Frazier AE, Compton AG, Kishita Y, Hock DH, Welch AE, Amarasekera SS, Rius R, Formosa LE, Imai-Okazaki A, Francis D, Wang M. Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus. Med. 2021 Jan 15;2(1):49-73.

Frederico IKS, Mesbah Ardakani N, Ryan AL, Cowley MJ, Wood BA Spitz Melanoma of Childhood With A Novel Promoter Hijacking Anaplastic Lymphoma Kinase (C2orf42-ALK) Rearrangement.. Am J Dermatopathol. 2021 Dec 1;43(12):972-975. doi: 10.1097/DAD.0000000000001972. PMID: 34001747.

Gamble LD, Purgato S, Henderson MJ, Di Giacomo S, Russell AJ, Pigini P, Murray J, Valli E, Milazzo G, Giorgi FM, Cowley M, Ashton LJ, Bhalshankar J, Schleiermacher G, Rihani A, Van Maerken T, Vandesompele J, Speleman F, Versteeg R, Koster J, Eggert A, Noguera R, Stallings RL, Tonini GP, Fong K, Vaksman Z, Diskin SJ, Maris JM, London WB, Marshall GM, Ziegler DS, Hogarty MD, Perini G, Norris MD, Haber M. A G316A Polymorphism in the Ornithine Decarboxylase Gene Promoter Modulates MYCN-Driven Childhood Neuroblastoma. Cancers. 2021 Apr 9;13(8):1807. doi: 10.3390/cancers13081807. PMID: 33918978

Gayevskiy V, Roscioli T, Dinger ME, Cowley MJ, Seave: a comprehensive web platform for storing and interrogating human genomic variation, Bioinformatics, 2019 Jan 1; 35(1):122-5

Khuong-Quang DA, Brown LM, Wong M, Mayoh C, Sexton-Oates A, Kumar A, Pinese M, Nagabushan S, Lau L, Ludlow LE, Gifford AJ. Recurrent SPECC1L–NTRK fusions in pediatric sarcoma and brain tumors. Molecular Case Studies. 2020 Dec 1;6(6):a005710.

Kim A, Kumar KR, Davis RL, Mallawaarachchi AC, Gayevskiy V, Minoche AE, Walls Z, Kim HJ, Jang M, Cowley MJ, Choi JH. Increased diagnostic yield of spastic paraplegia with or without cerebellar ataxia through whole-genome sequencing. The Cerebellum. 2019 Aug 15;18:781-90.

Kumar K, Cowley MJ, Davis R, Next generation sequencing and emerging technologies (2019), Seminars in Thrombosis and Haemostasis, 45(07): 661-673]

Kumar KR, Davis RL, Tchan MC, Wali GM, Mahant N, Ng K, Kotschet K, Siow S, Gu J, Walls Z, Kang C, Wali G, Levy S, Phua C Sen, Yiannikas C, Darveniza P, Chang FC, Morales-Briceño H, Rowe DB, Drew A, Gayevskiy V, Cowley MJ, Minoche A, Tisch S, Hayes M, Kummerfeld S, Fung VS, Sue CM, Whole genome sequencing for the genetic diagnosis of heterogeneous dystonia phenotypes (2019), Parkinsonism & Related Disorders 69:111-118

Ma A, Grigg JR, Flaherty M, Smith J, Minoche AE, e, Nash BM, Ho G, Gayagay T, Lai T, Farnsworth E, Hackett EL, Slater K, Wong K, Holman KJ, Jenkins G, Cheng A, Martin F, Brown NJ, Leighton SE, Amor DJ, Goel H, Dinger ME, Bennetts B, Jamieson RV. Genome sequencing in congenital cataracts improves diagnostic yield. Hum Mutat. 2021 Jun 8. doi: 10.1002/humu.24240. Online ahead of print. PMID: 34101287

Ma A, Yousoof S, Grigg JR, Flaherty M, Minoche AE, Cowley MJ, Nash BM, Ho G, Gayagay T, Lai T, Farnsworth E, Hackett EL, Fisk K, Wong K, Holman KJ, Jenkins G, Cheng A, Martin F, Karaconji T, Elder JE, Enriquez A, Wilson M, Amor DJ, Stutterd CA, Kamien B, Nelson J, Dinger ME, Bennetts B, Jamieson RV, Revealing hidden genetic diagnoses in the ocular anterior segment disorders, Genetics in Medicine, 2020 Oct;22(10):1623-1632

Mallawaarachchi AC, Furlong TJ, Shine J, Harris PC, Cowley MJ. Population data improves variant interpretation in Autosomal Dominant Polycystic Kidney Disease. Genetics in Medicine, 2019, 21(6):1425-1434

Mallawaarachchi AC, Lundie B, Hort Y, Schonrock N, Senum SR, Gayevskiy V, Minoche AE, Hollway G, Ohnesorg T, Hinchcliffe M, Patel C. Genomic diagnostics in polycystic kidney disease: an assessment of real-world use of whole-genome sequencing. European Journal of Human Genetics. 2021 May;29(5):760-70.

Massey S, Guo Y, Riley LG, Van Bergen NJ, Sandaradura SA, McCusker E, Tchan M, Thauvin-Robinet C, Thomas Q, Moreau T, Davis M. Expanding the Allelic Heterogeneity of ANO10-Associated Autosomal Recessive Cerebellar Ataxia. Neurology Genetics. 2023 Feb 1;9(1).

Mayoh, C., Gifford, A.J., Terry, R. et al. A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer. Genome Med 15, 20 (2023). https://doi.org/10.1186/s13073-023-01170-x

McCabe MJ, Pinese M, Chan CL, Sheriff N, Thompson TJ, Grady J, Wong M, Gauthier ME, Puttick C, Gayevskiy V, Hajdu E. Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases. Molecular Case Studies. 2019 Apr 1;5(2):a003764.

McCabe, M.J., Gauthier, ME.A., Chan, CL. et al. Development and validation of a targeted gene sequencing panel for application to disparate cancers. Sci Rep 9, 17052 (2019). https://doi.org/10.1038/s41598-019-52000-3

Minoche AE, Horvat C, Johnson R, Gayevskiy V, Morton SU, Drew AP, Woo K, Statham AL, Lundie B, Bagnall RD, Ingles J, Semsarian C, Seidman JQ, Seidman CE, Dinger ME, Cowley MJ, Fatkin D. Response to: Functional analysis of DES-p.L398P and RBM20-p.R636C – Correspondence to “Genome sequencing as a first-line genetic test in familial dilated cardiomyopathy”, Genetics in Medicine, 2019, 21(5):1248-1249

Minoche AE, Lundie B, Peters GB, Ohnesorg T, Pinese M, Thomas DM, Zankl A, Roscioli T, Schonrock N, Kummerfeld S, Burnett L, Dinger ME, Cowley MJ. ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data. Genome Med. 2021 Feb 25;13(1):32. doi: 10.1186/s13073-021-00841-x, PMID: 33632298 [senior author]

Mueller SA, Gauthier MA, Blackburn J, Grady JP, Kraitsek S, Hajdu E, Dettmer MS, Dahlstrom JE, Lee CS, Luk PP, Yu B, Giger R, Kummerfeld S, Clark JR, Gupta R*, Cowley MJ*, Molecular patterns in salivary duct carcinoma identify prognostic subgroups. Modern Pathology, 2020 Oct;33(10):1896-1909 [co-senior-author]

Mueller SA, Gauthier ME, Ashford B, Gupta R, Gayevskiy V, Ch’ng S, Palme CE, Shannon K, Clark JR, Ranson M, Cowley MJ. Mutational patterns in metastatic cutaneous squamous cell carcinoma. Journal of investigative dermatology. 2019 Jul 1;139(7):1449-58.

Nagabushan S, Lau LMS, Barahona P, Wong M, Sherstyuk A, Marshall GM, Tyrrell V, Wegner EA, Ekert PG, Cowley MJ, Mayoh C, Trahair TN, Crowe P, Anazodo A, Ziegler DS. Efficacy of MEK inhibition in a recurrent malignant peripheral nerve sheath tumor. NPJ Precis Oncol. 2021 Feb 12;5(1):9. doi:10.1038/s41698-021-00145-8. PMID: 33580196

Nash BM, Loi TH, Fernando M, Sabri A, Robinson J, Cheng A, Eamegdool SS, Farnsworth E, Bennetts B, Grigg JR, Chung SK. Evaluation for Retinal Therapy for RPE65 Variation Assessed in hiPSC Retinal Pigment Epithelial Cells. Stem cells international. 2021 Dec 13;2021.

Nash BM, Ma A, Ho G, Farnsworth E, Minoche AE, Cowley MJ, Barnett C, Smith JM, Loi TH, Wong K, St Heaps L, Wright D, Dinger ME, Bennetts B, Grigg JR, Jamieson RV. Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies. Int J Mol Sci. 2022 Mar 31;23(7):3905. doi: 10.3390/ijms23073905. PMID: 35409265; PMCID: PMC8999823.

Palmer EE, Carroll R, Shaw M, Kumar R, Minoche AE, Leffler M, Murray L, Macintosh R, Wright D, Troedson C, McKenzie F, Townshend S, Ward M, Nawaz U, Ravine A, Runke CK, Thorland EC, Hummel M, Foulds N, Pichon O, Isidor B, Le Caignec C, Demeer B, Andrieux J, Albarazi SH, Bye A, Sachdev R, Kirk EP, Cowley MJ, Field M, Gecz J, RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features. Am J Hum Genet. 2020 Oct 28:S0002-9297(20)30363-3.

Palmer EE, Hong S, Al Zahrani F, Omar Hashem M, Aleisa F, Ahmed H, Kandula T, Macintosh R, Minoche AE, Puttick C, Gayevskiy V, Drew A, Cowley MJ, Dinger M, Rosenfeld JA, Cho M, Hamad M, Shinawi M, Andrews M, Jones M, Lindstrom K, Kayani S, Snyder M, Villanueva MM, Roscioli T, P Kirk E, Bye A, Merzaban J, Jaremko L, Jaremko M, Sachdev RK, Alkuraya FS, Arold ST. De novo variants disrupting the HX repeat motif of ATN1 cause a non-progressive neurocognitive disorder with recognisable facial features and congenital malformations,  AJHG, 2019, 104(3):542–52.

 

Palmer EE, Sachdev R, Macintosh R, Melo US, Mundlos S, Righetti S, Kandula T, Minoche AE, Puttick C, Gayevskiy V, Hesson L. Diagnostic yield of whole genome sequencing after nondiagnostic exome sequencing or gene panel in developmental and epileptic encephalopathies. Neurology. 2021 Mar 30;96(13):e1770-82.

Pinese M, Lacaze P, Rath EM, Stone A, Brion MJ, Ameur A, Nagpal S, Puttick C, Husson S, Degrave D, Cristina TN, Kahl VFS, Statham AL, Woods RL, McNeil JJ, Riaz M, Barr M, Nelson MR, Reid CM, Murray AM, Shah RC, Wolfe R, Atkins JR, Fitzsimmons C, Cairns HM, Green MJ, Carr VJ, Cowley MJ, Pickett HA, James PA, Powell JE, Kaplan W, Gibson G, Gyllensten U, Cairns MJ, McNamara M, Dinger ME, Thomas DM. The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly, Nature Communications, 2020 Jan 23;11(1):435.

R Rius, NJ Van Bergen, AG Compton, LR Riley, M Kava, S Balasubramaniam, DJ Amor, M Fanjul-Fernandez, MJ Cowley, M Fahey, MK Koenig, GM Enns, TY Tan, DR Thorburn, J Christodoulou, Clinical spectrum and functional consequences associated with bi-allelic pathogenic PNPT1 variants (2019), J Clinical Medicine, 8(11):19

Riley LG, Cowley MJ, Gayevskiy V, Minoche AE, Puttick C, Thorburn DR, Rius R, Compton AG, Menezes MJ, Bhattacharya K, Coman D. The diagnostic utility of genome sequencing in a pediatric cohort with suspected mitochondrial disease. Genetics in Medicine. 2020 Jul;22(7):1254-61.

Rius R, Compton AG, Baker NL, Welch AE, Coman D, Kava MP, Minoche AE, Cowley MJ, Thorburn DR, Christodoulou J. Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases. Genes. 2021 Apr 20;12(4):607. doi: 10.3390/genes12040607. PMID: 33924034

Rius R, Cowley MJ, Riley L, Puttick C, Thorburn DR, Christodoulou J. Biparental inheritance of mitochondrial DNA in humans is not a common phenomenon. Genet Med. 2019 Dec;21(12):2823-2826. doi: 10.1038/s41436-019-0568-0. Epub 2019 Jun 7. PMID: 31171843

Rius R, Riley LG, Menezes M, Compton AG, Van Bergen NJ, Gayevskiy V, Cowley MJ, Cummings BB, Adams L, Thorburn DR, Christodoulou J, Cryptic intronic NBAS variant reveals the genetic basis of recurrent liver failure in a child, Mol Genet Metab, 2019, 126(1):77–82.

Rudaks LI, Watson E, Oboudiyat C, Kumar KR, Sullivan P, Cowley MJ, Davis RL, Sue CM. Decompensation of cardiorespiratory function and emergence of anemia during pregnancy in a case of mitochondrial myopathy, lactic acidosis, and sideroblastic anemia 2 with compound heterozygous YARS2 pathogenic variants. American Journal of Medical Genetics Part A. 2022 Jul;188(7):2226-30.

Samaraweera SE, Wang PPS, Li KL, Casolari DA, Feng J, Pinese M, Maung KZY, Leo P, Cowley M, Perkins K, Smith AM, Ellis J, Wee A, Hiwase DK, Scott HS, Schreiber AW, Brown AL, Deans AJ, Ross DM, Moore AS, Gonda TJ, Hahn CN, D’Andrea RJ. Childhood Acute Myeloid Leukemia shows a high level of germline predisposition. Blood. 2021 Sep 14. doi: 10.1182/blood.2021012666.

Shale C, Cameron DL, Baber J, Wong M, Cowley MJ, Papenfuss AT, Cuppen E, Priestley P. Unscrambling cancer genomes via integrated analysis of structural variation and copy number. Cell Genomics, 2022 (Apr) 2:100112. https://doi.org/10.1016/j.xgen.2022.100112

Subhash VV, Huang L, Kamili A, Wong M, Chen D, Venn NC, Atkinson C, Mayoh C, Venkat P, Tyrrell V, Marshall GM, Cowley MJ, Ekert PG, Norris MD, Haber M, Henderson MJ, Sutton R, Fletcher JI, Trahair TN. Whole-genome sequencing facilitates patient-specific quantitative PCR-based minimal residual disease monitoring in acute lymphoblastic leukaemia, neuroblastoma and Ewing sarcoma. Br J Cancer. 2022 Feb;126(3):482-491. doi: 10.1038/s41416-021-01538-z. Epub 2021 Sep 1. PMID: 34471258; PMCID: PMC8810788.

Sullivan PJ, Gayevskiy V, Davis RL, Wong M, Mayoh C, Mallawaarachchi A, Hort Y, McCabe MJ, Beecroft S, Jackson MR, Arts P, Dubowsky A, Laing N, Dinger ME, Scott HS, Oates E, Pinese M, Cowley MJ. Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications. Genome Biol. 2023 May 17;24(1):118. doi: 10.1186/s13059-023-02936-7. PMID: 37198692; PMCID: PMC10190034.

Van Bergen NJ, Ahmed SM, Collins F, Cowley M, Vetro A, Dale RC, Hock DH, de Caestecker C, Menezes M, Massey S, Ho G. Mutations in the exocyst component EXOC2 cause severe defects in human brain development. Journal of Experimental Medicine. 2020 Oct 5;217(10).

Venn NC, Huang L, Hovorková L, Muskovic W, Wong M, Law T, Heatley SL, Khaw SL, Revesz T, Dalla Pozza L, Shaw PJ. Measurable residual disease analysis in paediatric acute lymphoblastic leukaemia patients with ABL-class fusions. British Journal of Cancer. 2022 Sep 1;127(5):908-15.

Whitehouse JP, Howlett M, Hii H, Mayoh C, Wong M, Barahona P, Ajuyah P, White CL, Buntine MK, Dyke JM, Lee S, Valvi S, Stanley J, Andradas C, Carline B, Kuchibhotla M, Ekert PG, Cowley MJ, Gottardo NG, Endersby R. A Novel Orthotopic Patient-Derived Xenograft Model of Radiation-Induced Glioma Following Medulloblastoma. Cancers, 2020 Oct 12;12(10):E2937

Wong M, Mayoh C, Lau LM, Khuong-Quang DA, Pinese M, Kumar A, Barahona P, Wilkie EE, Sullivan P, Bowen-James R, Syed M. Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer. Nature medicine. 2020 Nov;26(11):1742-53.

Zammit NW, Gray PE, Siggs OM, Yap JY, Russell A, Cultrone D, Warren J, Walters SN, Brink R, Zahra D, Burnett DL. Environmental and genetic disease modifiers of haploinsuffciency of A20. bioRxiv. 2022 Mar 20:2022-03.

Zammit NW, Siggs OM, Gray PE, Horikawa K, Langley DB, Walters SN, Daley SR, Loetsch C, Warren J, Yap JY, Cultrone D. Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity. Nature immunology. 2019 Oct;20(10):1299-310.

PREDICT Paediatric Cancer Predisposition Screening

Goudie C, Witkowski L, Cullinan N, Reichman L, Schiller I, Tachdjian M, Armstrong L, Blood KA, Brossard J, Brunga L, Cacciotti C. Performance of the McGill Interactive Pediatric OncoGenetic Guidelines for identifying cancer predisposition syndromes. JAMA oncology. 2021 Dec 1;7(12):1806-14.

Lau LM, Mayoh C, Xie J, Barahona P, MacKenzie KL, Wong M, Kamili A, Tsoli M, Failes TW, Kumar A, Mould EV. In vitro and in vivo drug screens of tumor cells identify novel therapies for high‐risk child cancer. EMBO Molecular Medicine. 2022 Apr 7;14(4):e14608.

Sylvester DE, Chen Y, Grima N, Saletta F, Padhye B, Bennetts B, Wright D, Krivanek M, Graf N, Zhou L, Catchpoole D. Rare germline variants in childhood cancer patients suspected of genetic predisposition to cancer. Genes, Chromosomes and Cancer. 2022 Feb;61(2):81-93.

Wong M, Mayoh C, Lau LM, Khuong-Quang DA, Pinese M, Kumar A, Barahona P, Wilkie EE, Sullivan P, Bowen-James R, Syed M. Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer. Nature medicine. 2020 Nov;26(11):1742-53

Paediatric Rare Diseases Predisposition Screening (Gene 2 Care)

Celse T, Tingaud-Sequeira A, Dieterich K, Siegfried G, Lecaignec C, Bouneau L, Fannemel M, Salaun G, Laffargue F, Martinez G, Satre V. OTX2 duplications: a recurrent cause of oculo-auriculo-vertebral spectrum. Journal of Medical Genetics. 2023 Jun 1;60(6):620-6.

Bustos F, Espejo-Serrano C, Segarra-Fas A, Toth R, Eaton AJ, Kernohan KD, Wilson MJ, Riley LG, Findlay GM. A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne–Kalscheuer syndrome. Scientific Reports. 2021 May 5;11(1):9560.

Nevin SM, Wakefield CE, Dadich A, LeMarne F, Macintosh R, Beavis E, Sachdev R, Bye A, Nunn K, Palmer EE. Hearing parents’ voices: A priority-setting workshop to inform a suite of psychological resources for parents of children with rare genetic epilepsies. PEC Innovation. 2022 Dec 1;1:100014.

Nevin, S. M., Wakefield, C. E., Schilstra, C. E., McGill, B. C., Bye, A., & Palmer, E. E. (2020). The information needs of parents of children with early-onset epilepsy: A systematic review. Epilepsy & Behavior, 112, 107382.

Palmer EE, Pusch M, Picollo A, Forwood C, Nguyen MH, Suckow V, Gibbons J, Hoff A, Sigfrid L, Megarbane A, Nizon M. Functional and clinical studies reveal pathophysiological complexity of CLCN4-related neurodevelopmental condition. Molecular psychiatry. 2023 Feb;28(2):668-97.

Robertson EG, Kelada L, Best S, Goranitis I, Grainger N, Le Marne F, Pierce K, Nevin SM, Macintosh R, Beavis E, Sachdev R. Acceptability and feasibility of an online information linker service for caregivers who have a child with genetic epilepsy: a mixed-method pilot study protocol. BMJ open. 2022 Oct 1;12(10):e063249.

Shah M, Selvanathan A, Baynam G, Berman Y, Boughtwood T, Freckmann ML, Parasivam G, White SM, Grainger N, Kirk EP, Ma AS. Paediatric genomic testing: Navigating genomic reports for the general paediatrician. Journal of Paediatrics and Child Health. 2022 Jan;58(1):8-15.

Strnadova I, Nevin SM, Scully JL, Palmer EE. The opinions and experiences of people with intellectual disability regarding genetic testing and genetic medicine: A systematic review. Genetics in Medicine. 2022 Mar 1;24(3):535-48.

Translation of Paediatric Precision Medicine Clinical Trials

Dedrick RM, Smith BE, Cristinziano M, Freeman KG, Jacobs-Sera D, Belessis Y, Whitney Brown A, Cohen KA, Davidson RM, van Duin D, Gainey A. Phage Therapy of Mycobacterium Infections: Compassionate-use of Phages in Twenty Patients with Drug-Resistant Mycobacterial Disease. Clinical Infectious Diseases. 2022 Jun 9.

D’Silva AM, Holland S, Kariyawasam D, Herbert K, Barclay P, Cairns A, MacLennan SC, Ryan MM, Sampaio H, Smith N, Woodcock IR. Onasemnogene abeparvovec in spinal muscular atrophy: an Australian experience of safety and efficacy. Annals of Clinical and Translational Neurology. 2022 Mar;9(3):339-50.

Kariyawasam, D.S., D’Silva, A.M., Vetsch, J., Wakefield, C.E., Wiley, V. and Farrar, M.A., 2021. “We needed this”: perspectives of parents and healthcare professionals involved in a pilot newborn screening program for spinal muscular atrophy. EClinicalMedicine, 33, p.100742.

Shih ST, Farrar MA, Wiley V, Chambers G. Newborn screening for spinal muscular atrophy with disease-modifying therapies: a cost-effectiveness analysis. Journal of Neurology, Neurosurgery & Psychiatry. 2021 Dec 1;92(12):1296-304.

Strauss KA, Farrar MA, Muntoni F, Saito K, Mendell JR, Servais L, McMillan HJ, Finkel RS, Swoboda KJ, Kwon JM, Zaidman CM. Onasemnogene abeparvovec for presymptomatic infants with three copies of SMN2 at risk for spinal muscular atrophy: the Phase III SPR1NT trial. Nature medicine. 2022 Jul;28(7):1390-7.

Strauss KA, Farrar MA, Muntoni F, Saito K, Mendell JR, Servais L, McMillan HJ, Finkel RS, Swoboda KJ, Kwon JM, Zaidman CM. Onasemnogene abeparvovec for presymptomatic infants with two copies of SMN2 at risk for spinal muscular atrophy type 1: the Phase III SPR1NT trial. Nature medicine. 2022 Jul;28(7):1381-9.

Integrated Data linkage

He WQ, Nassar N, Schneuer FJ, Lain SJ, Congenital Heart Disease Synergy Study group, Dunwoodie SL, Winlaw D, Giannoulatou E, Kirk E, Chapman G, Blue G. Examination of validity of identifying congenital heart disease from hospital discharge data without a gold standard: Using a data linkage approach. Paediatric and Perinatal Epidemiology. 2023.

Lain SJ, Blue GM, O’Malley BR, Winlaw DS, Sholler G, Dunwoodie SL, Nassar N, The Congenital Heart Disease Synergy Study group. Using novel data linkage of biobank data with administrative health data to inform genomic analysis for future precision medicine treatment of congenital heart disease. Intern J Pop Data Sci 2023;8(1).2150

Signorelli C, Schneuer FJ, Wakefield CE, McLoone JK, Trahair T, Cohn RJ, Nassar N. Hospitalizations in Australian children with neuroblastoma: A population‐based study. Cancer Medicine. 2023. May 1.

Economic Impact and Framework for Sustainable Implementation of Paediatric Precision Medicine in the Australian Health System (Cancer)

Owens, C.E.L., Tan, O., Kuroiwa-Trzmielina, J. et al. The economic costs of precision medicine for clinical translational research among children with high-risk cancer. npj Precis. Onc. 8, 224 (2024). https://doi.org/10.1038/s41698-024-00711-w

Rapport F, Smith J, O’Brien TA, et al. Development of an implementation and evaluation strategy for the Australian ‘Zero Childhood Cancer’ (Zero) Program: a study protocol. BMJ Open 2020;10:e034522. doi: 10.1136/bmjopen-2019-034522

Smith, J., Braithwaite, J., O’Brien, T. A., Smith, S., Tyrrell, V. J., Mould, E. V. A., Long, J. C., & Rapport, F. (2022). Re-Imagining the Data Collection and Analysis Research Process by Proposing a Rapid Qualitative Data Collection and Analytic Roadmap Applied to the Dynamic Context of Precision Medicine. International Journal of Qualitative Methods, 21.

Smith, J., Rapport, F., O’Brien, T.A. et al. The rise of rapid implementation: a worked example of solving an existing problem with a new method by combining concept analysis with a systematic integrative review. BMC Health Serv Res 20, 449 (2020).

Establishment of small-scale cGMP vector manufacturing for gene and cell therapy clinical trials

Hsu, K., Middlemiss, S., Saletta, F. et al. Chimeric Antigen Receptor-modified T cells targeting EphA2 for the immunotherapy of paediatric bone tumours. Cancer Gene Ther 28, 321–334 (2021). https://doi.org/10.1038/s41417-020-00221-4

Tumour Cell Death Indicator (A self-amplifying theranostic for treatment of cancer)

Ho Shon I, Hennessy T, Guille J, Gotsbacher MP, Lay AJ, McBride B, Codd R, Hogg PJ. A first-in-human study of [68Ga] Ga-CDI: a positron emitting radiopharmaceutical for imaging tumour cell death. European journal of nuclear medicine and molecular imaging. 2022 Oct;49(12):4037-47.

Shon IH, Hogg PJ. Imaging of cell death in malignancy: Targeting pathways or phenotypes?. Nuclear Medicine and Biology. 2023 Sep 1;124:108380.

Shon IH, Kumar D, Schreuder M, Guille J, Doan J, Sathikumar C, Van K, Chicco A, Hogg PJ. Preclinical assessment of [68Ga] Ga-Cell Death Indicator (CDI): a novel hsp90 ligand for positron emission tomography of cell death. Current Radiopharmaceuticals. 2021 Nov 21.

Curing genetic metabolic liver disease by precise genomic and epigenomic editing

Cunningham SC, van Dijk EB, Zhu E, Sugden M, Mandwie M, Siew S, Devanapalli B, Tolun AA, Klein A, Wilson L, Aryamanesh N, Gissen P, Baruteau J, Bhattacharya K, Alexander IE. Recapitulation of Skewed X-Inactivation in Female Ornithine Transcarbamylase-Deficient Primary Human Hepatocytes in the FRG Mouse: A Novel System for Developing Epigenetic Therapies. Hum Gene Ther. 2023 Sep;34(17-18):917-926. doi: 10.1089/hum.2023.011. Epub 2023 Sep 11. PMID: 37350098.

Capraro A, Wong SL, Adhikari A, Allan KM, Patel HR, Zhong L, Raftery M, Jaffe A, Yeang M, Aggarwal A, Wu L. Ageing impairs the airway epithelium defence response to SARS-CoV-2. BioRxiv. 2021 Apr 6:2021-04.

Coffey MJ, McKay IR, Doumit M, Chuang S, Adams S, Stelzer-Braid S, Waters SA, Kasparian NA, Thomas T, Jaffe A, Katz T. Evaluating the Alimentary and Respiratory Tracts in Health and disease (EARTH) research programme: a protocol for prospective, longitudinal, controlled, observational studies in children with chronic disease at an Australian tertiary paediatric hospital. BMJ open. 2020 Apr 1;10(4):e033916.

Deshpande NP, Riordan SM, Gorman CJ, Nielsen S, Russell TL, Correa-Ospina C, Fernando BS, Waters SA, Castaño-Rodríguez N, Man SM, Tedla N. Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus. Genome Medicine. 2021 Dec;13:1-21.

Fawcett LK, Wakefield CE, Sivam S, Middleton PG, Wark P, Widger J, Jaffe A, Waters SA. Avatar acceptability: views from the Australian Cystic Fibrosis community on the use of personalised organoid technology to guide treatment decisions. ERJ open research. 2021 Jan 1;7(1).

Hewson CK, Capraro A, Wong SL, Pandzic E, Zhong L, Fernando BS, Awatade NT, Hart-Smith G, Whan RM, Thomas SR, Jaffe A. Novel Antioxidant Therapy with the Immediate Precursor to Glutathione, γ-Glutamylcysteine (GGC), Ameliorates LPS-Induced Cellular Stress in In Vitro 3D-Differentiated Airway Model from Primary Cystic Fibrosis Human Bronchial Cells. Antioxidants. 2020 Nov 30;9(12):1204.

Komalla V, Allam VS, Kwok PC, Sheikholeslami B, Owen L, Jaffe A, Waters SA, Mohammad S, Oliver BG, Chen H, Haghi M. A phospholipid-based formulation for the treatment of airway inflammation in chronic respiratory diseases. European Journal of Pharmaceutics and Biopharmaceutics. 2020 Dec 1;157:47-58.

Prentice BJ, Ooi CY, Strachan RE, Hameed S, Ebrahimkhani S, Waters SA, Verge CF, Widger J. Early glucose abnormalities are associated with pulmonary inflammation in young children with cystic fibrosis. Journal of Cystic Fibrosis. 2019 Nov 1;18(6):869-73.

Tran BM, Grimley SL, McAuley JL, Hachani A, Earnest L, Wong SL, Caly L, Druce J, Purcell DF, Jackson DC, Catton M. Air-liquid-interface differentiated human nose epithelium: a robust primary tissue culture model of SARS-CoV-2 infection. International Journal of Molecular Sciences. 2022 Jan 13;23(2):835.

Wong SL, Awatade NT, Astore MA, Allan KM, Carnell MJ, Slapetova I, Chen PC, Capraro A, Fawcett LK, Whan RM, Griffith R. Molcecular dynamics and functional characterization of I37R-CFTR lasso mutation provide insights into channel gating activity. Iscience. 2022 Jan 21;25(1):103710.

Wong SL, Awatade NT, Astore MA, Allan KM, Carnell MJ, Slapetova I, Chen PC, Setiadi J, Pandzic E, Fawcett LK, Widger JR. Molecular dynamics and theratyping in airway and gut organoids reveal R352Q-CFTR conductance defect. American Journal of Respiratory Cell and Molecular Biology. 2022 Jul;67(1):99-111.

A pipeline of accredited RNA Diagnostics

Bournazos AM, Riley LG, Bommireddipalli S, Ades L, Akesson LS, Al-Shinnag M, Alexander SI, Archibald AD, Balasubramaniam S, Berman Y, Beshay V. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genetics in Medicine. 2022 Jan 1;24(1):130-45.

Bryen SJ, Yuen M, Joshi H, Dawes R, Zhang K, Lu JK, Jones KJ, Liang C, Wong WK, Peduto AJ, Waddell LB. Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone. Human Genetics and Genomics Advances. 2022 Oct 13;3(4):100125.

Byrne AB, Arts P, Ha TT, Kassahn KS, Pais LS, O’Donnell-Luria A; Broad Institute Center for Mendelian Genomics; Babic M, Frank MSB, Feng J, Wang P, Lawrence DM, Eshraghi L, Arriola L, Toubia J, Nguyen H; Genomic Autopsy Study Research Network; McGillivray G, Pinner J, McKenzie F, Morrow R, Lipsett J, Manton N, Khong TY, Moore L, Liebelt JE, Schreiber AW, King-Smith SL, Hardy TSE, Jackson MR, Barnett CP, Scott HS. Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death. Nat Med. 2023 Jan;29(1):180-189.

Dawes R, Bournazos AM, Bryen SJ, Bommireddipalli S, Marchant RG, Joshi H, Cooper ST. SpliceVault predicts the precise nature of variant-associated mis-splicing. Nature Genetics. 2023 Feb 6:1-9.

Dawes R, Joshi H, Cooper ST. Empirical prediction of variant-activated cryptic splice donors using population-based RNA-Seq data. Nature communications. 2022 Mar 29;13(1):1-2.

Huq AJ, Thompson B, Bennett MF, Bournazos A, Bommireddipalli S, Gorelik A, Schultz J, Sexton A, Purvis R, West K, Cotter M. Clinical impact of whole-genome sequencing in patients with early-onset dementia. Journal of Neurology, Neurosurgery & Psychiatry. 2022 Jul 29.

Wong SL, Awatade NT, Astore MA, Allan KM, Carnell MJ, Slapetova I, Chen PC, Setiadi J, Pandzic E, Fawcett LK, Widger JR. Molecular dynamics and theratyping in airway and gut organoids reveal R352Q-CFTR conductance defect. American Journal of Respiratory Cell and Molecular Biology. 2022 Jul;67(1):99-111.

Wong WK, Bryen SJ, Bournazos A, Yasa J, Lemckert F, Bommireddipall S, Waddell LB, Menezes MP, Webster R, Davis M, Liang C. A genetic basis is identified in 74% cases of paediatric hyperCKaemia without weakness presenting to a tertiary paediatric neuromuscular centre. Neuromuscular Disorders. 2022 Sep 1;32(9):707-17.

Yuen M, Worgan L, Iwanski J, Pappas CT, Joshi H, Churko JM, Arbuckle S, Kirk EP, Zhu Y, Roscioli T, Gregorio CC. Neonatal-lethal dilated cardiomyopathy due to a homozygous LMOD2 donor splice-site variant. European Journal of Human Genetics. 2022 Apr;30(4):450-7