Advanced Breast Cancer Testing
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Molecular testing of PIK3CA, AKT1 and PTEN for patients with advanced breast cancers

The June 2025 version of the National Cancer Test Directory includes an important update on the somatic testing of the genes PIK3CA, PTEN and AKT1 in selected cases of breast cancer.

Background to AKT1 and PTEN testing in breast cancer

This is to let you know of an addition to the molecular testing service for selected patients with advanced breast cancers in the NEY GLH which will go live from 23rd June 2025.  In the June 2025 version 13 of the national cancer test directory (see https://www.england.nhs.uk/publication/national-genomic-test-directories) somatic testing for variants in the AKT1 and PTEN genes 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)

Further Eligibility Criteria Essential targets only
M3.5 Essential targets: structural variants (fusions) – NTRK1, NTRK2, NTRK3

Clinical trials targets: Structural variants – ALK, BRAF, ROS1, MET (including exon 14 skipping)

 Patient’s clinical status means they are eligible for an NTRK inhibitor in the event an NTRK rearrangement is detected
M3.6* Essential targets: small variants and copy number variants – PIK3CA, AKT1, PTEN

Clinical trials targets:

Small variants – BRAF, ERBB2, MET exon 14 skipping                         Copy number variants – ERBB2, MET

 Molecular assessment will aid diagnosis or management.PIK3CA/AKT1/PTEN – As per NICE recommendations (TA816, TA1063) to guide treatment decisions in patients with ER positive, HER 2 negative advanced / metastatic breast cancer that are progressing on first line treatment with an aromatase inhibitor plus CDK 4/6 inhibitor.
*Note that currently we are unable to test for copy number variants in PIK3CA, AKT1, ERBB2 or MET. As indicated below, PTEN copy number calling validation is ongoing and will be reported in due course.

 

Around 40%-50% of patients with advanced breast cancer who are hormone receptor postive/HER2 negative have PIK3CA and AKT1 pathway variants. The recent availability via AstraZeneca of the drug Truqap (Capiversatib) to target those with PIK3CA/AKT1/PTEN variants, coupled with approval on the national cancer test directory, means that requesting for this test can now commence.

We will test for small variants and fusions in all the essential and clinical trials targets in table 1 in a single assay.

Please note that this assay is currently ONLY validated for detecting PTEN small variants and NOT PTEN copy number variants (approximately 40% of all PTEN loss of function variants). Validation of this assay is ongoing and expected to be completed by mid-July 2025. As such, any samples received between 23rd June and 14th July which do not have a PIK3CA or AKT1 variant will have PTEN CNV analysis activated and reported separately.

Sample requirements

What to send

  • We request samples with >20% estimated tumour cell percentage: please send one tube (Eppendorf or Universal) containing 5-10 x 10μm FFPE curls.
  • For samples with lower overall tumour percentage: if there is a region of the block with >20% tumour, please either; a. macrodissect tumour-rich regions and send in a single tube (preferred), or b. send 10 x 5μm slide mounted sections along with marked H&E with tumour rich area(s) marked.
  • If it is not possible to macrodissect out a tumour rich region >20%, please contact the laboratory for further guidance as to whether the sample can still be tested.

Where to send to

Samples should be sent to your local genomics laboratory (see table 2 below) using the GLH solid cancer referral form (Referral Forms – North East and Yorkshire Genomic Medicine Service North East and Yorkshire Genomic Medicine Service). Please ensure that it:

  • Includes email addresses for your Cell Path 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, including M code(s);
  • Clearly specifies tumour cell nuclei as a percent of nucleated cells.

Testing and reporting

Sequencing of samples will continue to be undertaken by the GLH in Leeds using the ThermoFisher Scientific Oncomine™ Precision Assay gene panel. Results will be reported by your local genomics laboratory in PDF format to the referring centre histopathology contacts provided. We will aim to issue reports within 14 days of sample receipt.

For any questions about the above changes, please contact the Sheffield cancer genomics team at [email protected].

Limitations of testing

Please note that this testing will not detect PIK3CA, AKT1, ERBB2 or MET copy number changes.

Implementation of Genomic Testing for ESR1

In December 2024 NICE approved Elacestrant for treating oestrogen receptor-positive HER2-negative advanced breast cancer with an ESR1 mutation.

You can read more about testing, eligibility and guidance here.

 

Below are details on how PIK3CA 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.