Data

The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants—a multi-site prospective cohort study

The University of Western Australia
Davidson, Aimee L. ; Dressel, Uwe ; Norris, Sarah ; Canson, Daffodil M. ; Glubb, Dylan M. ; Fortuno, Cristina ; Hollway, Georgina E. ; Parsons, Michael T. ; Vidgen, Miranda E. ; Holmes, Oliver ; Koufariotis, Lambros T. ; Lakis, Vanessa ; Leonard, Conrad ; Wood, Scott ; Xu, Qinying ; McCart Reed, Amy E. ; Pickett, Hilda A. ; Al-Shinnag, Mohammad K. ; Austin, Rachel L. ; Burke, Jo ; Cops, Elisa J. ; Nichols, Cassandra B. ; Goodwin, Annabel ; Harris, Marion T. ; Higgins, Megan J. ; Ip, Emilia L. ; Kiraly-Borri, Catherine ; Lau, Chiyan ; Mansour, Julia L. ; Millward, Michael W. ; Monnik, Melissa J. ; Pachter, Nicholas S. ; Ragunathan, Abiramy ; Susman, Rachel D. ; Townshend, Sharron L. ; Trainer, Alison H. ; Troth, Simon L. ; Tucker, Katherine M. ; Wallis, Mathew J. ; Walsh, Maie ; Williams, Rachel A. ; Winship, Ingrid M. ; Newell, Felicity ; Tudini, Emma ; Pearson, John V. ; Poplawski, Nicola K. ; Mar Fan, Helen G. ; James, Paul A. ; Spurdle, Amanda B. ; Waddell, Nicola ; Ward, Robyn L.
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.6084/m9.figshare.c.6841086&rft.title=The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants—a multi-site prospective cohort study&rft.identifier=10.6084/m9.figshare.c.6841086&rft.publisher=Figshare&rft.description=Abstract Background Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer. Methods This multi-centre prospective study recruited 195 cancer-affected participants suspected to have a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing (WGS) and a comprehensive cancer virtual gene panel analysis were undertaken. Results Pathogenic variants consistent with the presenting cancer(s) were identified in 5.1% (10/195) of participants and pathogenic variants considered secondary findings with potential risk management implications were identified in another 9.7% (19/195) of participants. Health economic analysis estimated the marginal cost per case with an actionable variant was significantly lower for upfront WGS with virtual panel ($8744AUD) compared to standard testing followed by WGS ($24,894AUD). Financial analysis suggests that national adoption of diagnostic WGS testing would require a ninefold increase in government annual expenditure compared to conventional testing. Conclusions These findings make a case for replacing conventional testing with WGS to deliver clinically important benefits for cancer patients and families. The uptake of such an approach will depend on the perspectives of different payers on affordability.&rft.creator=Davidson, Aimee L. &rft.creator=Dressel, Uwe &rft.creator=Norris, Sarah &rft.creator=Canson, Daffodil M. &rft.creator=Glubb, Dylan M. &rft.creator=Fortuno, Cristina &rft.creator=Hollway, Georgina E. &rft.creator=Parsons, Michael T. &rft.creator=Vidgen, Miranda E. &rft.creator=Holmes, Oliver &rft.creator=Koufariotis, Lambros T. &rft.creator=Lakis, Vanessa &rft.creator=Leonard, Conrad &rft.creator=Wood, Scott &rft.creator=Xu, Qinying &rft.creator=McCart Reed, Amy E. &rft.creator=Pickett, Hilda A. &rft.creator=Al-Shinnag, Mohammad K. &rft.creator=Austin, Rachel L. &rft.creator=Burke, Jo &rft.creator=Cops, Elisa J. &rft.creator=Nichols, Cassandra B. &rft.creator=Goodwin, Annabel &rft.creator=Harris, Marion T. &rft.creator=Higgins, Megan J. &rft.creator=Ip, Emilia L. &rft.creator=Kiraly-Borri, Catherine &rft.creator=Lau, Chiyan &rft.creator=Mansour, Julia L. &rft.creator=Millward, Michael W. &rft.creator=Monnik, Melissa J. &rft.creator=Pachter, Nicholas S. &rft.creator=Ragunathan, Abiramy &rft.creator=Susman, Rachel D. &rft.creator=Townshend, Sharron L. &rft.creator=Trainer, Alison H. &rft.creator=Troth, Simon L. &rft.creator=Tucker, Katherine M. &rft.creator=Wallis, Mathew J. &rft.creator=Walsh, Maie &rft.creator=Williams, Rachel A. &rft.creator=Winship, Ingrid M. &rft.creator=Newell, Felicity &rft.creator=Tudini, Emma &rft.creator=Pearson, John V. &rft.creator=Poplawski, Nicola K. &rft.creator=Mar Fan, Helen G. &rft.creator=James, Paul A. &rft.creator=Spurdle, Amanda B. &rft.creator=Waddell, Nicola &rft.creator=Ward, Robyn L. &rft.date=2023&rft.relation=http://research-repository.uwa.edu.au/en/publications/b660764b-6c19-46be-a958-026afde249c1&rft.type=dataset&rft.language=English Access the data
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Abstract Background Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer. Methods This multi-centre prospective study recruited 195 cancer-affected participants suspected to have a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing (WGS) and a comprehensive cancer virtual gene panel analysis were undertaken. Results Pathogenic variants consistent with the presenting cancer(s) were identified in 5.1% (10/195) of participants and pathogenic variants considered secondary findings with potential risk management implications were identified in another 9.7% (19/195) of participants. Health economic analysis estimated the marginal cost per case with an actionable variant was significantly lower for upfront WGS with virtual panel ($8744AUD) compared to standard testing followed by WGS ($24,894AUD). Financial analysis suggests that national adoption of diagnostic WGS testing would require a ninefold increase in government annual expenditure compared to conventional testing. Conclusions These findings make a case for replacing conventional testing with WGS to deliver clinically important benefits for cancer patients and families. The uptake of such an approach will depend on the perspectives of different payers on affordability.

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External Organisations
Queensland Institute of Medical Research; University of Queensland; Children's Medical Research Institute; Royal Brisbane and Women's Hospital; Royal Hobart Hospital; Peter Maccallum Cancer Centre; King Edward Memorial Hospital (Australia); Royal Prince Alfred Hospital; Monash Health; Liverpool Hospital; Department of Health (Western Australia); Royal Adelaide Hospital; Westmead Hospital; Prince of Wales Hospital; Royal Melbourne Hospital; University of Sydney
Associated Persons
Sarah Norris (Contributor); Rachel A. Williams (Contributor); John V. Pearson (Contributor)Aimee L. Davidson (Contributor); Uwe Dressel (Contributor); Daffodil M. Canson (Contributor); Dylan M. Glubb (Contributor); Cristina Fortuno (Contributor); Georgina E. Hollway (Contributor); Michael T. Parsons (Contributor); Miranda E. Vidgen (Contributor); Oliver Holmes (Contributor); Lambros T. Koufariotis (Contributor); Vanessa Lakis (Contributor); Conrad Leonard (Contributor); Scott Wood (Contributor); Qinying Xu (Contributor); Amy E. McCart Reed (Contributor); Hilda A. Pickett (Contributor); Mohammad K. Al-Shinnag (Contributor); Jo Burke (Contributor); Elisa J. Cops (Contributor); Cassandra B. Nichols (Contributor); Annabel Goodwin (Contributor); Marion T. Harris (Contributor); Megan J. Higgins (Contributor); Emilia L. Ip (Contributor); Catherine Kiraly-Borri (Contributor); Chiyan Lau (Contributor); Julia L. Mansour (Contributor); Melissa J. Monnik (Contributor); Abiramy Ragunathan (Contributor); Rachel D. Susman (Contributor); Sharron L. Townshend (Contributor); Alison H. Trainer (Contributor); Simon L. Troth (Contributor); Katherine M. Tucker (Contributor); Mathew J. Wallis (Contributor); Maie Walsh (Contributor); Ingrid M. Winship (Contributor); Felicity Newell (Contributor); Emma Tudini (Contributor); Nicola K. Poplawski (Contributor); Helen G. Mar Fan (Contributor); Paul A. James (Contributor); Amanda B. Spurdle (Contributor); Nicola Waddell (Contributor); Robyn L. Ward (Contributor)

Issued: 2023-09-19

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