Whole genome sequencing improves tissue-of-origin diagnosis and treatment options for cancer of unknown primary

Richard J Rebello; Atara Posner; Ruining Dong; Owen W J Prall; Tharani Sivakumaran; Camilla B Mitchell; Aidan Flynn; Alex Caneborg; Catherine Mitchell; Sehrish Kanwal; Clare Fedele; Samantha Webb; Krista Fisher; Hui-Li Wong; Shiva Balachander; Wenying Zhu; Shannon Nicolson; Voula Dimitriadis; Nicholas Wilcken; Anna DeFazio; Bo Gao; Madhu Singh; Ian M Collins; Christopher Steer; Mark Warren; Narayan Karanth; Huiling Xu; Andrew Fellowes; Rodney J Hicks; Kym Pham Stewart; Charles Shale; Peter Priestley; Sarah-Jane Dawson; Joseph H A Vissers; Stephen B Fox; Penelope Schofield; David Bowtell; Oliver Hofmann; Sean M Grimmond; Linda Mileshkin; Richard W Tothill

doi:10.1038/s41467-025-59661-x

Whole genome sequencing improves tissue-of-origin diagnosis and treatment options for cancer of unknown primary

Nat Commun. 2025 May 20;16(1):4422. doi: 10.1038/s41467-025-59661-x.

Authors

Richard J Rebello^#^{1

2}, Atara Posner^#^{1

2}, Ruining Dong^{1

2}, Owen W J Prall³, Tharani Sivakumaran^{4

5}, Camilla B Mitchell^{1

2}, Aidan Flynn^{1

2}, Alex Caneborg^{1

2}, Catherine Mitchell^{3

5}, Sehrish Kanwal^{1

2}, Clare Fedele^{1

2}, Samantha Webb⁶, Krista Fisher⁶, Hui-Li Wong^{4

5}, Shiva Balachander³, Wenying Zhu^{1

2}, Shannon Nicolson^{1

2}, Voula Dimitriadis², Nicholas Wilcken⁷, Anna DeFazio^{7

8

9}, Bo Gao¹⁰, Madhu Singh¹¹, Ian M Collins¹², Christopher Steer¹³, Mark Warren¹⁴, Narayan Karanth¹⁵, Huiling Xu³, Andrew Fellowes³, Rodney J Hicks¹⁶, Kym Pham Stewart², Charles Shale¹⁷, Peter Priestley¹⁷, Sarah-Jane Dawson^{2

5

6}, Joseph H A Vissers^{1

2}, Stephen B Fox^{3

5}, Penelope Schofield^{5

18

19}, David Bowtell^{5

6}, Oliver Hofmann^{1

2}, Sean M Grimmond², Linda Mileshkin^{4

5

6}, Richard W Tothill^{20

21

22}

Affiliations

¹ Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia.
² Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia.
³ Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
⁴ Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
⁵ Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
⁶ Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
⁷ The Westmead Institute for Medical Research, Sydney, NSW, Australia.
⁸ Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia.
⁹ The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia.
¹⁰ Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, Australia.
¹¹ Department of Medical Oncology, Barwon Health Cancer Services, Geelong, VIC, Australia.
¹² Department of Medical Oncology, Southwest HealthCare, Warrnambool and Deakin University, Geelong, VIC, Australia.
¹³ Border Medical Oncology, Albury Wodonga Regional Cancer Centre, Albury NSW, Australia and UNSW School of Clinical Medicine, Rural Clinical Campus, Albury, NSW, Australia.
¹⁴ Department of Medical Oncology, Bendigo Health, Bendigo, VIC, Australia.
¹⁵ Division of Medicine, Alan Walker Cancer Centre, Darwin, NT, Australia.
¹⁶ The St Vincent's Hospital Department of Medicine, University of Melbourne, Melbourne, VIC, Australia.
¹⁷ Hartwig Medical Foundation, Sydney, NSW, Australia.
¹⁸ Department of Psychology, and Iverson Health Innovation Research Institute, Swinburne University, Melbourne, VIC, Australia.
¹⁹ School of Computing, Engineering and Mathematical Sciences, La Trobe University, Melbourne, VIC, Australia.
²⁰ Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia. rtothill@unimelb.edu.au.
²¹ Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia. rtothill@unimelb.edu.au.
²² Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. rtothill@unimelb.edu.au.

^# Contributed equally.

Abstract

Genomics can inform both tissue-of-origin (TOO) and precision treatments for patients with cancer of unknown primary (CUP). Here, we use whole genome and transcriptome sequencing (WGTS) for 72 patients and show diagnostic superiority of WGTS over panel testing (386-523 genes) in 71 paired cases. WGTS detects all reportable DNA features found by panel as well as additional mutations of diagnostic or therapeutic relevance in 76% of cases. Curated WGTS features and a CUP prediction algorithm (CUPPA) trained on WGTS data of known cancer types informs TOO in 71% of cases otherwise undiagnosed by clinicopathology review. WGTS informs treatments for 79% of patients, compared to 59% by panel testing. Finally, WGS of cell-free DNA (cfDNA) from patients with a high cfDNA tumour fraction (>7%), enables high-likelihood CUPPA predictions in 41% of cases. WGTS is therefore superior to panel testing, broadens treatment options, and is feasible using routine pathology samples and cfDNA.

MeSH terms

Aged
Algorithms
Biomarkers, Tumor / genetics
Female
Gene Expression Profiling
Genomics / methods
Humans
Male
Middle Aged
Mutation
Neoplasms, Unknown Primary* / diagnosis
Neoplasms, Unknown Primary* / genetics
Neoplasms, Unknown Primary* / therapy
Transcriptome
Whole Genome Sequencing* / methods

Substances

Biomarkers, Tumor