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Estimating the costs of genomic sequencing in cancer control

Louisa G. Gordon, Nicole M. White, Thomas M. Elliott, Katia Nones, Anthony G. Beckhouse, Astrid J. Rodriguez-Acevedo, Penelope M. Webb, Xing J. Lee, Nicholas Graves, Deborah J. Schofield
2020 BMC Health Services Research  
Despite the rapid uptake of genomic technologies within cancer care, few studies provide detailed information on the costs of sequencing across different applications. The objective of the study was to examine and categorise the complete costs involved in genomic sequencing for a range of applications within cancer settings. We performed a cost-analysis using gross and micro-costing approaches for genomic sequencing performed during 2017/2018 across different settings in Brisbane, Australia.
more » ... uencing was undertaken for patients with lung, breast, oesophageal cancers, melanoma or mesothelioma. Aggregated resource data were captured for a total of 1433 patients and point estimates of per patient costs were generated. Deterministic sensitivity analyses addressed the uncertainty in the estimates. Estimated costs to the public health system for resources were categorised into seven distinct activities in the sequencing process: sampling, extraction, library preparation, sequencing, analysis, data storage and clinical reporting. Costs were also aggregated according to labour, consumables, testing, equipment and 'other' categories. The per person costs were AU$347-429 (2018 US$240-297) for targeted panels, AU$871-$2788 (2018 US$604-1932) for exome sequencing, and AU$2895-4830 (2018 US$2006-3347) for whole genome sequencing. Cost proportions were highest for library preparation/sequencing materials (average 76.8% of total costs), sample extraction (8.1%), data analysis (9.2%) and data storage (2.6%). Capital costs for the sequencers were an additional AU$34-197 (2018 US$24-67) per person. Total costs were most sensitive to consumables and sequencing activities driven by commercial prices. Per person sequencing costs for cancer are high when tumour/blood pairs require testing. Using the natural steps involved in sequencing and categorising resources accordingly, future evaluations of costs or cost-effectiveness of clinical genomics across cancer projects could be more standardised and facilitate easier comparison of cost drivers.
doi:10.1186/s12913-020-05318-y pmid:32493298 fatcat:flzu4ekqtnbgrgr5muvrilt5dy

The adaptive response of anaerobically grownSaccharomyces cerevisiaeto hydrogen peroxide is mediated by the Yap1 and Skn7 transcription factors

Anthony G. Beckhouse, Chris M. Grant, Peter J. Rogers, Ian W. Dawes, Vincent J. Higgins
2008 FEMS Yeast Research  
The molecular mechanisms involved in the ability of cells to adapt and respond to differing oxygen tensions are of great interest to the pharmaceutical, medical and fermentation industries. The transcriptional profiles reported in previous studies of cells grown under anaerobic, aerobic and dynamic growth conditions have shown significantly altered responses including induction of genes regulated by the oxidative stress transcription factor Yap1p when oxygen was present. The present study
more » ... igated the phenotypic changes that occur in cells when shifted from anaerobic to aerobic growth conditions and it was found through mutant analyses that the elevated activity of Yap1p during the shift was mediated by the phospholipid hydroperoxide-sensing protein encoded by GPX3. Cell viability and growth rate were unaffected even though anaerobically grown cells were found to be hypersensitive to low doses of the oxidative stress-inducing compound hydrogen peroxide (H 2 O 2 ). Adaptation to H 2 O 2 treatment was demonstrated to occur when anaerobically grown wild-type cells were aerated for a short time that was reliant on the Yap1p and Skn7p transcription factors.
doi:10.1111/j.1567-1364.2008.00439.x pmid:18795957 fatcat:3ogxxvmhgffl5fph2fdexdvbhm

Zinc starvation induces a stress response inSaccharomyces cerevisiae that is mediated by the Msn2p and Msn4p transcriptional activators

Victoria J. Gauci, Anthony G. Beckhouse, Victoria Lyons, Eric J. Beh, Peter J. Rogers, Ian W. Dawes, Vincent J. Higgins
2009 FEMS Yeast Research  
Strains were grown overnight to the mid-log phase (OD 600 nm = 0.5) at 30 1C, cells were harvested at 6000 g for 5 min and washed three times with distilled water.  ...  The complete raw microarray data set is available at the gene expression omnibus database (accession number: GSE11878). b-Gal assays b-Gal activity was measured as described (Rose & Botstein, 1983; Beckhouse  ...  The authors are grateful to G. Marchler for providing the CTT1-18/7x plasmid and C. Schüller for providing the HOG1 mutant strain for use in this study.  ... 
doi:10.1111/j.1567-1364.2009.00557.x pmid:19702872 fatcat:bkimlqlpvvgyzopxznn3gj4yhi

Colony-Stimulating Factor-1 Promotes Kidney Growth and Repair via Alteration of Macrophage Responses

Maliha A. Alikhan, Christina V. Jones, Timothy M. Williams, Anthony G. Beckhouse, Anne L. Fletcher, Michelle M. Kett, Samy Sakkal, Chrishan S. Samuel, Robert G. Ramsay, James A. Deane, Christine A. Wells, Melissa H. Little (+2 others)
2011 American Journal of Pathology  
Littermate newborn mice were injected with either mouse recombinant CSF-1 protein (1 g/g of body weight; Chiron Corporation, Emeryville, CA) or vehicle (PBS).  ...  G: Csf1r-EGFP macrophages show a spindle-shaped structure, wrapping around newly developed structures.  ... 
doi:10.1016/j.ajpath.2011.05.037 pmid:21762674 pmcid:PMC3157188 fatcat:qml6t2ossnhdbguzok43lj7xnq

Essential Role of One-carbon Metabolism and Gcn4p and Bas1p Transcriptional Regulators during Adaptation to Anaerobic Growth ofSaccharomyces cerevisiae

Bonny M. Tsoi, Anthony G. Beckhouse, Cristy L. Gelling, Mark J. Raftery, Joyce Chiu, Abraham M. Tsoi, Lars Lauterbach, Peter J. Rogers, Vincent J. Higgins, Ian W. Dawes
2009 Journal of Biological Chemistry  
at 100,000 ϫ g for 1 h at 4°C.  ...  G. H. Braus (Georgia-Augusta University, Goettingen).  ... 
doi:10.1074/jbc.m809225200 pmid:19224916 pmcid:PMC2670125 fatcat:d7b5p7jh4zagfadveveaihb3k4

Page 284 of Psychological Abstracts Vol. 54, Issue 1 [page]

1975 Psychological Abstracts  
G., 92 Beagley, Gwyneth, 714 Bearde, Jon L., 2110 Beary, John F., 7 Beattie, Randall C Beatty, William w. hes aL 518 Beau aton, D., 519 Becker, Ernest, 1261 Becker, Michael, 634 Becker, Wayne M., 673 Beckhouse  ...  Anderson, Robsrt M Anderson, Thomas R, 516, 577 Andersson, Karin, 578, 579 Andreasen, Nancy J., 1260 Angelo, Robert L., 545 Anggard, Erik, 1588 Angrist, Shirley S., 897 Angst, J., Anstey, Edgar, 2024 Anthony  ... 

Page 1193 of Psychological Abstracts Vol. 44, Issue 7 [page]

1970 Psychological Abstracts  
L., 9830 Anderson, John A., 10920 Beckhouse, Lawrence S., 10267 Bouchal, M., 10633 Byrne, D., 10277, 10313 Anderson, John P., 9640 Beckman, Linda J., 10268 Boulton, D.  ...  L., 9572 Bojanovsky, J., 10633 Burdock, Eugene I1., 10720 Aleck, Adolph W., 11121 Bashir, Anthony S., 11003 Bok, Marcia H., 11117 Burgess, Robert L., 10302 Aleksandrovskii, V.  ... 

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Harukazu Suzuki, Alistair R R Forrest, Erik van Nimwegen, Carsten O Daub, Piotr J Balwierz, Katharine M Irvine, Timo Lassmann, Timothy Ravasi, Yuki Hasegawa, Michiel J L de Hoon, Shintaro Katayama, Kate Schroder (+148 others)
2009 Nature Genetics  
(g) The statistical significance of the regulatory edge from motif to promoter is calculated based on correlation of the promoter expression and motif activity profiles.  ...  A m,t e pn,t e p2,t e p1,t Expression of all promoters d a b c e f g 96 24 12 4 1 0 Time t (h) 5.8 6.0 6.2 6.4 6.6 6.8 Log-expression [log tpm] Promoter p  ... 
doi:10.1038/ng.375 pmid:19377474 pmcid:PMC6711855 fatcat:d5jwq2rbt5bfllsd4ej5tprnue

FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Tsugumi Kawashima, Miki Kojima (+166 others)
2017 Scientific Data  
Most of the RNAs were subjected to the automated HeliScopeCAGE protocol 7 , except for RNAs with less than 1 μg that were subjected to the manual protocol optimized for low quantity RNAs 8 .  ...  Of the collected RNAs, those with more than 1 μg, were measured by Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE)  ... 
doi:10.1038/sdata.2017.112 pmid:28850106 pmcid:PMC5574368 fatcat:cel5hhhtardinak67mbl2okvhe

Application of Genome-Wide Expression Analysis To Identify Molecular Markers Useful in Monitoring Industrial Fermentations

V. J. Higgins, P. J. Rogers, I. W. Dawes
2003 Applied and Environmental Microbiology  
efflux YGL255w ZRT1 8.1 High-affinity zinc transport protein YLR130c ZRT2 7.7 Low-affinity zinc transport protein YDR284c DPP1 6.8 Diacylglycerol pyrophosphate phosphatase YGL121c GPG1 6.2 G  ...  to Schizosaccharomyces pombe sds23 YIR037w HYR1 5.1 Putative glutathione peroxidase Repressed by zinc depletion YOL086c ADH1 15 Alcohol dehydrogenase YMR116c ASC1 10 WD repeat protein (G-beta-like  ...  We thank Geoff Kornfeld and Anthony Beckhouse for support and assistance.  ... 
doi:10.1128/aem.69.12.7535-7540.2003 pmid:14660410 pmcid:PMC310037 fatcat:xdeniwsah5abzeo7on2zwkvgv4

Cells have distinct mechanisms to maintain protection against different reactive oxygen species: Oxidative-stress-response genes

G. W. Thorpe, C. S. Fong, N. Alic, V. J. Higgins, I. W. Dawes
2004 Proceedings of the National Academy of Sciences of the United States of America  
We thank Gabriel Perrone, Anthony Beckhouse, Cristy Gelling, Jia Qi Wang, and Thomas Felder for assistance and helpful discussions.  ... 
doi:10.1073/pnas.0305888101 pmid:15087496 pmcid:PMC404085 fatcat:kre3ilwxcradvoy5tl7dqtiuze

Identification of reference miRNAs in plasma useful for the study of oestrogen-responsive miRNAs associated with acquired Protein S deficiency in pregnancy

J. W. Tay, I. James, Q. W. Hughes, J. Y. Tiao, R. I. Baker
2017 BMC Research Notes  
Acknowledgments also extend to Dr Anthony Beckhouse at Bio-Rad Laboratories for extensive technical support in the optimisation of miRNA digital droplet PCR experiments.  ...  The extraction protocol was modified with an extended centrifugation time of 60 min at 13,000×g at the organic extraction step, and each RNA sample was eluted in 50 μL of hot elution (95 °C) buffer.  ...  Whole blood was centrifuged at 2000×g for 15 min within 4 h of blood collection to separate plasma from cells and platelets as previously described [18] , and the supernatant plasma was transferred into  ... 
doi:10.1186/s13104-017-2636-3 pmid:28743297 pmcid:PMC5526281 fatcat:i42ndnbvavbupgirhqqsuozjbm

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Shohei Noma (+480 others)
2021 Nature Communications  
Acknowledgements We thank Cédric Notredame, Anthony Mathelier, Oriol Fornes Crespo, Philip Richmond, Jean-Christophe Andrau, Diego Garrido Martin, Dimitri D.  ...  The cDNA synthesis was carried out by using 5 μg of total RNA or 1 μg of PAPed RNA with RT primer (5-TTTTTTTTUUUTTTTTVN-3) by PrimeScript II Reverse Transcriptase (TaKaRa Bio).  ...  Evaluating mismatched G bias at Illumina 5' end CAGE reads. Comparison between Heliscope vs. Illumina CAGE sequencing was performed as in de Rie et al. 38 .  ... 
doi:10.1038/s41467-021-23143-7 pmid:34078885 pmcid:PMC8172540 fatcat:ctyfp77e2fcejlamqa7s5ni2tq

Impact of Hydrogen Peroxide on Protein Synthesis in Yeast

Cecilia Picazo, Mikael Molin
2021 Antioxidants  
Anthony G Beckhouse et al. showed in 2008 that adaptation to H 2 O 2 treatment occurs when anaerobically grown wild-type cells are aerated for a short time and depends on the Yap1 and Skn7 transcription  ... 
doi:10.3390/antiox10060952 fatcat:t6fgrv5e3vedlljm5kz5mzlu6y

Alternatively Spliced Forms of Tollip Regulate Inflammatory Signalling in Macrophages

Lo, Yu-Lan (Sandra), University, My, Christine Wells
Anthony Beckhouse for discussions on experimental design; Ms Dipti Vijayan for her assistance with FACS and Dr.  ...  Anthony Beckhouse (University of Queensland). (A) Melt curves of human TOLLIP.A, TOLLIP.B and TOLLIP.C primers used for qRT-PCR.  ... 
doi:10.25904/1912/891 fatcat:fyyfpyqurnhlvlr72iazr4vu44
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