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Survey of diagnostic laboratories highlights need for improved standards in somatic genomic testing and reporting

European Journal of Human Genetics (2026) Cite this article

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A Comment to this article was published on 14 May 2026

Abstract

There is a growing international need to support somatic genomic testing, standardised variant curation and improved patient access to molecular profiling for somatic conditions, including cancer. We conducted a survey of scope, curation, reporting and sharing practices of diagnostic laboratories performing somatic testing in Australia and New Zealand. Laboratories with accreditation (n = 41) were invited in 2023 to complete a semi-structured, 25-question interview. Responses were received for 27 laboratories (66% response rate) offering solid tumour, haematological malignancy and non-cancer services. Only 36% of laboratories offered tests capturing the full breadth of variants, from single-nucleotide variants to gene fusions. Knowledge sharing was rare, with only one laboratory submitting variant classifications to a public knowledge base. Most laboratories (96%) conducted somatic testing in oncology. Of cancer laboratories, 35% offered testing considered capable of comprehensive genomic profiling (CGP). Almost half of cancer laboratories had already adopted the 2022 ClinGen/CGC/VICC oncogenicity guidelines, and 84% were using AMP/ASCO/CAP 2017 clinical significance guidelines. Only 47% of mixed discipline cancer laboratories reported biomarkers such as tumour mutational burden, with wide variation in reporting of matched therapy options. Our study has generated a unique overview of somatic laboratory practices in the region, and areas for global standardisation in somatic molecular testing and reporting. We also provide a model for practice and guideline uptake assessment, for application by other country-wide networks. This is particularly relevant in anticipation of CGP mainstreaming, with the increasing complexity of sequencing interpretation for laboratories and clinicians.

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Fig. 1: Breakdown of somatic testing offered by participating laboratories.
The alternative text for this image may have been generated using AI.
Fig. 2: Testing scope and sequencing details of laboratories.
The alternative text for this image may have been generated using AI.
Fig. 3: Variant curation guideline usage of cancer laboratories.
The alternative text for this image may have been generated using AI.
Fig. 4: Inclusion of tumour statuses and therapy options in cancer somatic testing reports.
The alternative text for this image may have been generated using AI.

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Data availability

The datasets supporting the current study have not been deposited in a public repository as a result of restrictions on the sharing of non-aggregate data outlined in the Shariant Terms of Use.

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Acknowledgements

The authors would like to thank all of the laboratories who participated in this survey and the somatic expansion of Shariant. We also thank representatives of the Human Genetics Society of Australasia Cancer Special Interest Group, SA Pathology and genomiQa for their feedback during drafting of the survey template, and/or promotion of the project.

Funding

Shariant Australasia (including funding for GP, ET and JA) was supported by Australian Genomics (NHMRC grants GNT1113531, GNT2000001 and GNT2035846). ABS was supported by NHMRC fellowship funding (APP177524).

Author information

Authors and Affiliations

  1. Australian Genomics, Melbourne, VIC, Australia

    Grace Pendlebury, Emma Tudini & James Andrews

  2. Population Health, QIMR Berghofer, Brisbane, QLD, Australia

    Grace Pendlebury, Emma Tudini & Amanda B. Spurdle

  3. Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia

    James Andrews

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  1. Grace Pendlebury
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  2. Emma Tudini
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  3. James Andrews
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  4. Amanda B. Spurdle
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Contributions

Survey conduction: GP, ET. Data analysis: GP, ET, JA. Manuscript drafting and editing: GP, ET, ABS.

Corresponding author

Correspondence to Amanda B. Spurdle.

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Competing interests

The authors declare no competing interests.

Ethical approval

This study was conducted under QIMR Berghofer HREC project approval P3447. No patients were recruited for this study. Participation by genomics professionals in the survey was voluntary, and consent considered implicit through completion of the survey interview. Respondents were informed that their answers would remain confidential and reported only in aggregated summary form outside of the study coordinators. Respondents were also given the opportunity to revise responses after the survey interview.

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Pendlebury, G., Tudini, E., Andrews, J. et al. Survey of diagnostic laboratories highlights need for improved standards in somatic genomic testing and reporting. Eur J Hum Genet (2026). https://doi.org/10.1038/s41431-026-02049-2

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