Molecular testing of PIK3CA for patients with advanced breast cancers.

In the April 2022 version 3 of the national cancer test directory (see national-genomic-test-directory-cancer-2021-22-v3-april-2022.xlsx-.xlsx (, somatic testing for variants in the PIK3CA gene was added for those patients with breast cancer where molecular testing will aid in patient diagnosis or management, as in the table below:

Test Code Target Gene(s) Test Scope Technology Further Eligibility Criteria
M3.6 PIK3CA Small variant detection Panel Molecular assessment will aid diagnosis or management

Around 40% of patients with advanced beast cancer who are hormone receptor positive/HER2 negative have PIK3CA variants. The recent availability via Novartis Oncology of the drug Piqray (alpelisib) to target those with PIK3CA variants, coupled with approval on the national cancer test directory, means that requesting for this test can now commence.

Below are details on how this testing is to be provided in the North East and Yorkshire by our Genomics Laboratory Hub.

Requests for testing should be made via your local Cellular Pathology laboratory that holds the tumour tissue. Samples for testing should then be sent to your local genomics laboratory where DNA extraction will be performed prior to the sequencing assay to assess PIK3CA status.

The local genomics lab will direct the testing and reporting as appropriate, so that they can act as your single point of call for any of your queries. Costs from your local genomics laboratory onward, including transport and test costs, are commissioned and paid for by NHSE directly to the GLH, so do not need to be paid for by the referring cellular pathology lab. However local centres will need to meet the cellular pathology costs of sample preparation and pre-analytical analysis (slide mark up, tumour % assessment etc.).Until a single GLH-wide referral form is available, we will accept requests on existing genetics lab forms. However, please ensure that the form:

  • Includes email addresses for your Cellular Pathology secretaries and pathologist. Results will be returned to the pathologist for integration into the full histopathology report and should not be acted upon out of context of those findings;
  • Clearly specifies which tests are needed;
  • Clearly specifies tumour cell nuclei as a percent of nucleated cells (in marked area if sections used).

FFPE curls are the preferred sample type for testing.For sample with >20% neoplastic cells, please send one tube (Eppendorf or Universal): containing 5-10 x 10μm FFPE curls.For samples with lower tumour content, please send 10 x 5μm slide mounted sections along with marked H&E with tumour rich area(s) marked.

The clinical trial assays for SOLAR-1 (NCT02437318) and BYLieve (NCT03056755) included the 11 frequently observed mutations in the PIK3CA gene (exon 7: C420R; exon 9: E542K, E545A, E545D [1635G>T only], E545G, E545K, Q546E, Q546R; and exon 20: H1047L, H1047R, H1047Y). The current assay we employ utilises ion torrent next generation sequencing technology via an Oncomime Focus panel. It can detect all of the mutations of PIK3CA in the SOLAR-1 and BYLieve trials, as well as other less common mutations. Outside of these 11 hotspots, while there is literature to support additional rare activating PIK3CA mutations, there is limited efficacy evidence available for alpelisib with these rarer mutations in advanced breast cancer- therefore treatment options should be a clinical decision based on review of the variant detected.

As with other genetic tests undertaken by the GLH, the result will be returned to the referring clinician by either email or uploaded to the electronic patient record as agreed by each referring Trust. We will aim to report results where possible within 7 calendar days of sample receipt.

If you have any questions about the specifics of testing please get in touch with one of us in the NEY GLH laboratories.