Orthogonal standard-of-care (SOC) test data (cancer)

Microsatellite instability (MSI) for colorectal patients

MSI is the condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR).

Here we provide outcomes for Immunohistochemistry (IHC) standard-of-care test for four MMR genes: MLH1, MSH2, MSH6 and PMS2 for a subset of colorectal patients

This data can be used to validate tumour mutation burden cut-off and MSI signatures

Data is located at /gel_data_resources/main_programme/cancer_orthogonal_test_data/20200820/MSI.24042020.txt

HER2 status for breast cancer patients

The IHC gives a score of 0 to 3+ that measures the amount of HER2 protein on the surface of cells in a breast cancer tissue sample.

Score	Classification	Action
0 to 1+	HER2-negative
2+	borderline	it’s likely that a DDISH test will be done on a sample of the cancer tissue to determine if the cancer is HER2-positive. DDISH test uses two probes that hybridise to the HER2 gene and to centromere region of chromosome 17 (CEP17). Patient is considered HER2-positive if HER2/CEP17 ration is above 2.
3+	HER2-positive

This data can be used for validation of focal amplifications. Exact copy number is provided only for equivocal IHC samples that underwent second round of testing with DDISH

Data is located at /gel_data_resources/main_programme/cancer_orthogonal_test_data/20200820/HER2.28022020.txt

FISH tests for haematological cancers

This is a collection of FISH panels, RT-PCR test and cytogenetic reports for patients with haematological cancers

This data can be used for validation of copy number calling as well as for structural variants

Data is located at /gel_data_resources/main_programme/cancer_orthogonal_test_data/20200820/HAEM-FISH.25052020.txt