Garvan Institute of Medical Research

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Deveson, I. W.; Gong, B.; Lai, K.; LoCoco, J. S.; Richmond, T. A.; Schageman, J.; Zhang, Z.; Novoradovskaya, N.; Willey, J. C.; Jones, W.; Kusko, R.; Chen, G.; Madala, B. S.; Blackburn, J.; Stevanovski, I.; Bhandari, A.; Close, D.; Conroy, J.; Hubank, M.; Marella, N.; Mieczkowski, P. A.; Qiu, F.; Sebra, R.; Stetson, D.; Sun, L.; Szankasi, P.; Tan, H.; Tang, L. Y.; Arib, H.; Best, H.; Burgher, B.; Bushel, P. R.; Casey, F.; Cawley, S.; Chang, C. J.; Choi, J.; Dinis, J.; Duncan, D.; Eterovic, A. K.; Feng, L.; Ghosal, A.; Giorda, K.; Glenn, S.; Happe, S.; Haseley, N.; Horvath, K.; Hung, L. Y.; Jarosz, M.; Kushwaha, G.; Li, D.; Li, Q. Z.; Li, Z.; Liu, L. C.; Liu, Z.; Ma, C.; Mason, C. E.; Megherbi, D. B.; Morrison, T.; Pabon-Pena, C.; Pirooznia, M.; Proszek, P. Z.; Raymond, A.; Rindler, P.; Ringler, R.; Scherer, A.; Shaknovich, R.; Shi, T.; Smith, M.; Song, P.; Strahl, M.; Thodima, V. J.; Tom, N.; Verma, S.; Wang, J.; Wu, L.; Xiao, W.; Xu, C.; Yang, M.; Zhang, G.; Zhang, S.; Zhang, Y.; Shi, L.; Tong, W.; Johann, D. J., Jr.; Mercer, T. R.; Xu, J.; Group, Seqc Oncopanel Sequencing Working

NATURE BIOTECHNOLOGY 39 (9) :1115-1128, 2021 10.1038/s41587-021-00857-z

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Gong, B.; Li, D.; Kusko, R.; Novoradovskaya, N.; Zhang, Y.; Wang, S.; Pabon-Pena, C.; Zhang, Z.; Lai, K.; Cai, W.; LoCoco, J. S.; Lader, E.; Richmond, T. A.; Mittal, V. K.; Liu, L. C.; Johann, D. J., Jr.; Willey, J. C.; Bushel, P. R.; Yu, Y.; Xu, C.; Chen, G.; Burgess, D.; Cawley, S.; Giorda, K.; Haseley, N.; Qiu, F.; Wilkins, K.; Arib, H.; Attwooll, C.; Babson, K.; Bao, L.; Bao, W.; Lucas, A. B.; Best, H.; Bhandari, A.; Bisgin, H.; Blackburn, J.; Blomquist, T. M.; Boardman, L.; Burgher, B.; Butler, D. J.; Chang, C. J.; Chaubey, A.; Chen, T.; Chierici, M.; Chin, C. R.; Close, D.; Conroy, J.; Coleman, J. C.; Craig, D. J.; Crawford, E.; Del Pozo, A.; Deveson, I. W.; Duncan, D.; Eterovic, A. K.; Fan, X.; Foox, J.; Furlanello, C.; Ghosal, A.; Glenn, S.; Guan, M.; Haag, C.; Hang, X.; Happe, S.; Hennigan, B.; Hipp, J.; Hong, H.; Horvath, K.; Hu, J.; Hung, L. Y.; Jarosz, M.; Kerkhof, J.; Kipp, B.; Kreil, D. P.; Labaj, P.; Lapunzina, P.; Li, P.; Li, Q. Z.; Li, W.; Li, Z.; Liang, Y.; Liu, S.; Liu, Z.; Ma, C.; Marella, N.; Martin-Arenas, R.; Megherbi, D. B.; Meng, Q.; Mieczkowski, P. A.; Morrison, T.; Muzny, D.; Ning, B.; Parsons, B. L.; Paweletz, C. P.; Pirooznia, M.; Qu, W.; Raymond, A.; Rindler, P.; Ringler, R.; Sadikovic, B.; Scherer, A.; Schulze, E.; Sebra, R.; Shaknovich, R.; Shi, Q.; Shi, T.; Silla-Castro, J. C.; Smith, M.; Lopez, M. S.; Song, P.; Stetson, D.; Strahl, M.; Stuart, A.; Supplee, J.; Szankasi, P.; Tan, H.; Tang, L. Y.; Tao, Y.; Thakkar, S.; Thierry-Mieg, D.; Thierry-Mieg, J.; Thodima, V. J.; Thomas, D.; Tichy, B.; Tom, N.; Garcia, E. V.; Verma, S.; Walker, K.; Wang, C.; Wang, J.; Wang, Y.; Wen, Z.; Wirta, V.; Wu, L.; Xiao, C.; Xiao, W.; Xu, S.; Yang, M.; Ying, J.; Yip, S. H.; Zhang, G.; Zhang, S.; Zhao, M.; Zheng, Y.; Zhou, X.; Mason, C. E.; Mercer, T.; Tong, W.; Shi, L.; Jones, W.; Xu, J.

GENOME BIOLOGY 22 (1) :109, 2021 10.1186/s13059-021-02315-0

Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination

Whiteley, S. L.; Holleley, C. E.; Wagner, S.; Blackburn, J.; Deveson, I. W.; Marshall Graves, J. A.; Georges, A.

PLOS GENET 17 (4) :e1009465, 2021 10.1371/journal.pgen.1009465

Sequencing Strategies for Fusion Gene Detection

Heyer, E. E.; Blackburn, J.

BIOESSAYS 42 (7) :e2000016, 2020 10.1002/bies.202000016

Lymphoma Driver Mutations in the Pathogenic Evolution of an Iconic Human Autoantibody

Singh, M.; Jackson, K. J. L.; Wang, J. J.; Schofield, P.; Field, M. A.; Koppstein, D.; Peters, T. J.; Burnett, D. L.; Rizzetto, S.; Nevoltris, D.; Masle-Farquhar, E.; Faulks, M. L.; Russell, A.; Gokal, D.; Hanioka, A.; Horikawa, K.; Colella, A. D.; Chataway, T. K.; Blackburn, J.; Mercer, T. R.; Langley, D. B.; Goodall, D. M.; Jefferis, R.; Gangadharan Komala, M.; Kelleher, A. D.; Suan, D.; Rischmueller, M.; Christ, D.; Brink, R.; Luciani, F.; Gordon, T. P.; Goodnow, C. C.; Reed, J. H.

CELL 180 (5) :878-894 e19, 2020 10.1016/j.cell.2020.01.029

Use of synthetic DNA spike-in controls (sequins) for human genome sequencing

Blackburn, J.; Wong, T.; Madala, B. S.; Barker, C.; Hardwick, S. A.; Reis, A. L. M.; Deveson, I. W.; Mercer, T. R.

Nature Protocols 14 (7) :2119-2151, 2019 10.1038/s41596-019-0175-1

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

Singh, M.; Al-Eryani, G.; Carswell, S.; Ferguson, J. M.; Blackburn, J.; Barton, K.; Roden, D.; Luciani, F.; Giang Phan, T.; Junankar, S.; Jackson, K.; Goodnow, C. C.; Smith, M. A.; Swarbrick, A.

Nature Communications 10 (1) :3120, 2019 10.1038/s41467-019-11049-4

Crizotinib and Surgery for Long-Term Disease Control in Children and Adolescents With ALK-Positive Inflammatory Myofibroblastic Tumors

Trahair T, Gifford AJ, Fordham A, Mayoh C, Fadia M, Lukeis R, Wood AC, Santosh V, Walker RD, Blackburn J, Heyer EE, Mercer TR, Barbaric D, Marshall GM, MacKenzie KL.

JCO Precision Oncology 2019 10.1200/PO.18.00297

TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa

Blackburn, J.; Vecchiarelli, S.; Heyer, E. E.; Patrick, S. M.; Lyons, R. J.; Jaratlerdsiri, W.; van Zyl, S.; Bornman, M. S. R.; Mercer, T. R.; Hayes, V. M.

PROSTATE 79 (10) :1191-1196, 2019 10.1002/pros.23823

Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions

Hardwick, S. A.; Bassett, S. D.; Kaczorowski, D.; Blackburn, J.; Barton, K.; Bartonicek, N.; Carswell, S. L.; Tilgner, H. U.; Loy, C.; Halliday, G.; Mercer, T. R.; Smith, M. A.; Mattick, J. S.

Frontiers in Genetics 10 :309, 2019 10.3389/fgene.2019.00309

Diagnosis of fusion genes using targeted RNA sequencing

Heyer, E. E.; Deveson, I. W.; Wooi, D.; Selinger, C. I.; Lyons, R. J.; Hayes, V. M.; O'Toole, S. A.; Ballinger, M. L.; Gill, D.; Thomas, D. M.; Mercer, T. R.; Blackburn, J.

Nature Communications 10 (1) :1388, 2019 10.1038/s41467-019-09374-9

Chiral DNA sequences as commutable controls for clinical genomics

Deveson, I. W.; Madala, B. S.; Blackburn, J.; Barker, C.; Wong, T.; Barton, K. M.; Smith, M. A.; Watkins, D. N.; Mercer, T. R.

Nature Communications 10 (1) :1342, 2019 10.1038/s41467-019-09272-0

Universal Alternative Splicing of Noncoding Exons

Deveson, I. W.; Brunck, M. E.; Blackburn, J.; Tseng, E.; Hon, T.; Clark, T. A.; Clark, M. B.; Crawford, J.; Dinger, M. E.; Nielsen, L. K.; Mattick, J. S.; Mercer, T. R.

Cell Systems 6 (2) :p245-255, 2018 10.1016/j.cels.2017.12.005

Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes

Fleuren, E. D. G.; Vlenterie, M.; van der Graaf, W.; Hillebrandt-Roeffen, M. H. S.; Blackburn, J.; Ma, X.; Chan, H.; Magias, M. C.; van Erp, A.; van Houdt, L.; Cebeci, S.; van de Ven, A.; Flucke, U. E.; Heyer, E. E.; Thomas, D. M.; Lord, C. J.; Marini, K. D.; Vaghjiani, V.; Mercer, T.; Cain, J. E.; Wu, J.; Versleijen-Jonkers, Y. M. H.; Daly, R. J.

CANCER RESEARCH 77 (16) :4279-4292, 2017 10.1158/0008-5472.CAN-16-2550

Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination

Deveson, I. W.; Holleley, C. E.; Blackburn, J.; Marshall Graves, J. A.; Mattick, J. S.; Waters, P. D.; Georges, A.

Science Advances 3 (6) :e1700731, 2017 10.1126/sciadv.1700731

Damage-inducible intragenic demethylation of the human TP53 tumor suppressor gene is associated with transcription from an alternative intronic promoter

Blackburn, J. ; Roden, D. L. ; Ng, R. ; Wu, J. ; Bosman, A. ; Epstein, R. J.;

MOLECULAR CARCINOGENESIS 55 (12) :1940-1951, 2016