The University of Queensland

Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content

Ganesamoorthy, Devika, Robertson, Alan James, Chen, Wenhan, Hall, Michael B., Cao, Minh Duc, Ferguson, Kaltin, Lakhani, Sunil R., Nones, Katia, Simpson, Peter T. and Coin, Lachlan J. M. (2022). Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content. BMC Cancer, 22 (1) 85, 85. doi: 10.1186/s12885-021-09160-1

High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing

Ganesamoorthy, Devika, Yan, Mengjia, Murigneux, Valentine, Zhou, Chenxi, Cao, Minh Duc, Duarte, Tania P. S. and Coin, Lachlan J. M. (2020). High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing. F1000Research, 9, 1084. doi: 10.12688/f1000research.25693.1

Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy

Zhang, Ping, Ganesamoorthy, Devika, Nguyen, Son Hoang, Au, Raymond, Coin, Lachlan J. and Tey, Siok-Keen (2020). Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy. Journal for ImmunoTherapy of Cancer, 8 (1) e000299, 1-13. doi: 10.1136/jitc-2019-000299

Phase I trial of inducible caspase 9 T cells in adult stem cell transplant demonstrates massive clonotypic proliferative potential and long-term persistence of transgenic T cells

Zhang, Ping, Raju, Jyothy, Ullah, Md Ashik, Au, Raymond, Varelias, Antiopi, Gartlan, Kate H, Olver, Stuart D., Samson, Luke D., Sturgeon, Elise, Zomerdijk, Nienke, Avery, Judy, Gargett, Tessa, Brown, Michael P., Coin, Lachlan J., Ganesamoorthy, Devika, Hutchins, Cheryl, Pratt, Gary R, Kennedy, Glen A., Morton, A. James, Curley, Cameron I., Hill, Geoffrey R. and Tey, Siok-Keen (2019). Phase I trial of inducible caspase 9 T cells in adult stem cell transplant demonstrates massive clonotypic proliferative potential and long-term persistence of transgenic T cells. Clinical Cancer Research, 25 (6), 1749-1755. doi: 10.1158/1078-0432.CCR-18-3069

Octapeptin C4 and polymyxin resistance occur via distinct pathways in an epidemic XDR Klebsiella pneumoniae ST258 isolate

Pitt, Miranda E., Cao, Minh Duc, Butler, Mark S., Ramu, Soumya, Ganesamoorthy, Devika, Blaskovich, Mark A. T., Coin, Lachlan J. M. and Cooper, Matthew A. (2018). Octapeptin C4 and polymyxin resistance occur via distinct pathways in an epidemic XDR Klebsiella pneumoniae ST258 isolate. The Journal of Antimicrobial Chemotherapy, 74 (3), 582-593. doi: 10.1093/jac/dky458

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing

Ganesamoorthy, Devika, Cao, Minh Duc, Duarte, Tania, Chen, Wenhan and Coin, Lachlan (2018). GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing. BMC Bioinformatics, 19 (1) 267, 267. doi: 10.1186/s12859-018-2282-3

npInv: accurate detection and genotyping of inversions using long read sub-alignment

Shao, Haojing, Ganesamoorthy, Devika, Duarte, Tania, Cao, Minh Duc, Hoggart, Clive J. and Coin, Lachlan J. M. (2018). npInv: accurate detection and genotyping of inversions using long read sub-alignment. BMC Bioinformatics, 19 (1) 261, 261. doi: 10.1186/s12859-018-2252-9

Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae

Pitt, Miranda E., Elliott, Alysha G., Cao, Minh Duc, Ganesamoorthy, Devika, Karaiskos, Ilias, Giamarellou, Helen, Abboud, Cely S., Blaskovich, Mark A. T., Cooper, Matthew A. and Coin, Lachlan J. M. (2018). Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae. Microbial Genomics, 4 (3) 000158. doi: 10.1099/mgen.0.000158

Simulating the Dynamics of Targeted Capture Sequencing with CapSim

Cao, Minh Duc, Ganesamoorthy, Devika, Zhou, Chenxi and Coin, Lachlan J M (2017). Simulating the Dynamics of Targeted Capture Sequencing with CapSim. Bioinformatics (Oxford, England), 34 (5), 873-874. doi: 10.1093/bioinformatics/btx691

sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors

Chen, Wenhan, Robertson, Alan J., Ganesamoorthy, Devika and Coin, Lachlan J. M. (2017). sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors. Nucleic Acids Research, 45 (5) 1086, e34-e34. doi: 10.1093/nar/gkw1086

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

Cao, Minh Duc, Nguyen, Son Hoang, Ganesamoorthy, Devika, Elliott, Alysha G., Cooper, Matthew A. and Coin, Lachlan J. M. (2017). Scaffolding and completing genome assemblies in real-time with nanopore sequencing. Nature Communications, 8 (1) 14515, 14515. doi: 10.1038/ncomms14515

Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION (TM) sequencing

Cao, Minh Duc, Ganesamoorthy, Devika, Elliott, Alysha G., Zhang, Huihui, Cooper, Matthew A. and Coin, Lachlan J. M. (2016). Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION (TM) sequencing. Gigascience, 5 (1) 32, 32. doi: 10.1186/s13742-016-0137-2

Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae strain ATCC 700603

Elliott, Alysha G., Ganesamoorthy, Devika, Coin, Lachlan, Cooper, Matthew A. and Cao, Minh Duc (2016). Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae strain ATCC 700603. Genome Announcements, 4 (3) e00438-16. doi: 10.1128/genomeA.00438-16

Realtime analysis and visualisation of MinION sequencing data with npReader

Cao, Minh Duc, Ganesamoorthy, Devika, Cooper, Matthew A. and Coin, Lachlan J.M. (2015). Realtime analysis and visualisation of MinION sequencing data with npReader. Bioinformatics, 32 (5), 764-766. doi: 10.1093/bioinformatics/btv658

Use of copy number deletion polymorphisms to assess DNA chimerism

Bruno, Damien L., Ganesamoorthy, Devika, Thorne, Natalie P., Ling, Ling, Bahlo, Melanie, Forrest, Sue, Veenendaal, Marieke, Katerelos, Marina, Skene, Alison, Ierino, Frank L., Power, David A. and Slater, Howard R. (2014). Use of copy number deletion polymorphisms to assess DNA chimerism. Clinical Chemistry, 60 (8), 1105-1114. doi: 10.1373/clinchem.2013.216077

High-resolution microarray in the assessment of fetal anomalies detected by ultrasound

Charan, Poonam, Woodrow, Nicole, Walker, Sue P., Ganesamoorthy, Devika, McGillivray, George and Palma-Dias, Ricardo (2014). High-resolution microarray in the assessment of fetal anomalies detected by ultrasound. Australian and New Zealand Journal of Obstetrics and Gynaecology, 54 (1), 46-52. doi: 10.1111/ajo.12170

Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery

Chandrananda D., Thorne N.P., Ganesamoorthy D., Bruno D.L., Benjamini Y., Speed T.P., Slater H.R. and Bahlo M. (2014). Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery. PLoS ONE, 9 (1) e86993, e86993.1-e86993.14. doi: 10.1371/journal.pone.0086993

Application of a new molecular technique for the genetic evaluation of products of conception

Grati, Francesca R., Gomes, Denise Molina, Ganesamoorthy, Devika, Marcato, Livia, De Toffol, Simona, Blondeel, Eleonore, Malvestiti, Francesca, Loeuillet, Laurence, Ruggeri, Anna Maria, Wainer, Robert, Maggi, Federico, Aboura, Azzedine, Dupont, Celine, Tabet, Anne Claude, Guimiot, Fabien, Slater, Howard R., Simoni, Giuseppe and Vialard, Francois (2013). Application of a new molecular technique for the genetic evaluation of products of conception. Prenatal Diagnosis, 33 (1), 32-41. doi: 10.1002/pd.4004

Meeting the challenge of interpreting high-resolution single nucleotide polymorphism array data in prenatal diagnosis: Does increased diagnostic power outweigh the dilemma of rare variants?

Ganesamoorthy, D., Bruno, D. L., McGillivray, G., Norris, F., White, S. M., Adroub, S., Amor, D. J., Yeung, A., Oertel, R., Pertile, M. D., Ngo, C., Arvaj, A. R., Walker, S., Charan, P., Palma-Dias, R., Woodrow, N. and Slater, H. R. (2013). Meeting the challenge of interpreting high-resolution single nucleotide polymorphism array data in prenatal diagnosis: Does increased diagnostic power outweigh the dilemma of rare variants?. BJOG: An International Journal of Obstetrics & Gynaecology, 120 (5), 594-606. doi: 10.1111/1471-0528.12150

Molecular and clinical characterization of 25 individuals with exonic deletions of NRXN1 and comprehensive review of the literature

Bena, Frederique., Bruno, Damien L., Eriksson, Mats, van Ravenswaaij-Arts, Conny, Stark, Zornitza, Dijkhuizen, Trijnie, Gerkes, Erica, Gimelli, Stefania, Ganesamoorthy, Devika, Thuresson, Ann Charlotte, Labalme, Audrey, Till, Marianne, Bilan, Frederic, Pasquier, Laurent, Kitzis, Alain, Dubourgm, Christele, Rossi, Massimiliano, Bottani, Armand, Gagnebin, Maryline, Sanlaville, Damien, Gilbert-Dussardier, Brigitte, Guipponi, Michel, van Haeringen, Arie, Kriek, Marjolein, Ruivenkamp, Claudia, Antonarakis, Stylianos E., Anderlid, Britt Marie, Slater, Howard R. and Schoumans, Jacqueline (2013). Molecular and clinical characterization of 25 individuals with exonic deletions of NRXN1 and comprehensive review of the literature. American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics, 162 (4), 388-403. doi: 10.1002/ajmg.b.32148

Extending the scope of diagnostic chromosome analysis: Detection of single gene defects using high-resolution SNP microarrays

Bruno, Damien L., Stark, Zornitza, Amor, David J., Burgess, Trent, Butler, Kathy, Corrie, Sylvea, Francis, David, Ganesamoorthy, Devika, Hills, Louise, James, Paul A., O'Rielly, Darren, Oertel, Ralph, Savarirayan, Ravi, Prabhakara, Krishnamurthy, Salce, Nicholas and Slater, Howard R. (2011). Extending the scope of diagnostic chromosome analysis: Detection of single gene defects using high-resolution SNP microarrays. Human Mutation, 32 (12), 1500-1506. doi: 10.1002/humu.21581

Pathogenic aberrations revealed exclusively by single nucleotide polymorphism (SNP) genotyping data in 5000 samples tested by molecular karyotyping

Bruno, D. L., White, S. M., Ganesamoorthy, D., Burgess, T., Butler, K., Corrie, S., Francis, D., Hills, L., Prabhakara, K., Ngo, C., Norris, F., Oertel, R., Pertile, M. D., Stark, Z., Amor, D. J. and Slater, H. R. (2011). Pathogenic aberrations revealed exclusively by single nucleotide polymorphism (SNP) genotyping data in 5000 samples tested by molecular karyotyping. Journal of Medical Genetics, 48 (12), 831-839. doi: 10.1136/jmedgenet-2011-100372

Phenotypic variability of distal 22q11.2 copy number abnormalities

Tan, Tiong Yang, Collins, Amanda, James, Paul A., Mcgillivray, George, Stark, Zornitza, Gordon, Christopher T., Leventer, Richard J., Pope, Kate, Forbes, Robin, Crolla, John A., Ganesamoorthy, Devika, Burgess, Trent, Bruno, Damien L., Slater, Howard R., Farlie, Peter G. and Amor, David J. (2011). Phenotypic variability of distal 22q11.2 copy number abnormalities. American Journal of Medical Genetics, Part A, 155 (7), 1623-1633. doi: 10.1002/ajmg.a.34051

Further molecular and clinical delineation of co-locating 17p13.3 microdeletions and microduplications that show distinctive phenotypes

Bruno, Damien L., Anderlid, Britt-Marie, Lindstrand, Anna, Van Ravenswaaij-Arts, Conny, Ganesamoorthy, Devika, Lundin, Johanna, Martin, Christa Lese, Douglas, Jessica, Nowak, Catherine, Adam, Margaret P., Kooy, R. Frank, Van Der Aa, Nathalie, Reyniers, Edwin, Vandeweyer, Geert, Stolte-Dijkstra, Irene, Dijkhuizen, Trijnie, Yeung, Alison, Delatycki, Martin, Borgstrom, Birgit, Thelin, Lena, Cardoso, Carlos, Van Bon, Bregje, Pfundt, Rolph, De Vries, Bert B. A., Wallin, Anders, Amor, David J., James, Paul A., Slater, Howard R. and Schoumans, Jacqueline (2010). Further molecular and clinical delineation of co-locating 17p13.3 microdeletions and microduplications that show distinctive phenotypes. Journal of Medical Genetics, 47 (5), 299-311. doi: 10.1136/jmg.2009.069906

Methylation of novel markers of fragile X alleles is inversely correlated with FMRP expression and FMR1 activation ratio

Godler, David E., Tassone, Flora, Loesch, Danuta Z., Taylor, Annette Kimball, Gehling, Freya, Hagerman, Randi Jenssen, Burgess, Trent, Ganesamoorthy, Devika, Hennerich, Debbie, Gordon, Lavinia, Evans, Andrew, Choo, K. H. and Slater, Howard Robert (2010). Methylation of novel markers of fragile X alleles is inversely correlated with FMRP expression and FMR1 activation ratio. Human Molecular Genetics, 19 (8) ddq037, 1618-1632. doi: 10.1093/hmg/ddq037

A genotype-first approach for the molecular and clinical characterization of uncommon de novo microdeletion of 20q13.33

Traylor, Ryan N., Bruno, Damien L., Burgess, Trent, Wildin, Robert, Spencer, Anne, Ganesamoorthy, Devika, Amor, David J., Hunter, Matthew, Caplan, Michael, Rosenfeld, Jill A., Theisen, Aaron, Torchia, Beth S., Shaffer, Lisa G., Ballif, Blake C. and Slater, Howard R. (2010). A genotype-first approach for the molecular and clinical characterization of uncommon de novo microdeletion of 20q13.33. PLoS ONE, 5 (8) e12462, e12462.1-e12462.7. doi: 10.1371/journal.pone.0012462

Development of a multiplex ligation-dependent probe amplification assay for diagnosis and estimation of the frequency of spinocerebellar ataxia type 15

Ganesamoorthy, Devika, Bruno, Damien L., Schoumans, Jacqueline, Storey, Elsdon, Delatycki, Martin B., Zhu, Danqing, Wei, Morgan K., Nicholson, Garth A., McKinlay Gardner, R. J. and Slater, Howard R. (2009). Development of a multiplex ligation-dependent probe amplification assay for diagnosis and estimation of the frequency of spinocerebellar ataxia type 15. Clinical Chemistry, 55 (7), 1415-1418. doi: 10.1373/clinchem.2009.124958

Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice

Bruno, D. L., Ganesamoorthy, D., Schoumans, J., Bankier, A., Coman, D., Delatycki, M., Gardner, R. J. M., Hunter, M., James, P. A., Kannu, P., McGillivray, G., Pachter, N., Peters, H., Rieubland, C., Savarirayan, R., Scheffer, I. E., Sheffield, L., Tan, T., White, S. M., Yeung, A., Bowman, Z., Ngo, C., Choy, K. W., Cacheux, V., Wong, L., Amor, D. J. and Slater, H. R. (2009). Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice. Journal of Medical Genetics, 46 (2), 123-131. doi: 10.1136/jmg.2008.062604

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

Cao, Minh Duc, Nguyen, Hoang Son, Ganesamoorthy, Devika, Elliott, Alysha, Cooper, Matthew and Coin, Lachlan J. M. (2016). Scaffolding and completing genome assemblies in real-time with nanopore sequencing.