Molecular Neuropathology Service

In May 2021, the Department of Clinical Neuropathology became part of an NHS/industry joint venture. The laboratory operations are now under the management of Synnovis LLP (a partnership between Guy’s and St Thomas’ and King’s College Hospital NHS Foundation Trusts, and SYNLAB UK and Ireland).

The Neuropathology department carries out around 800 molecular neuropathology tests per year. These include DNA and RNA testing of common brain tumour prognostic markers such as MGMT promoter methylation status and methylation arrays. The department also offers next-generation sequencing (NGS) of national test directory compliant gene panels associated with neurological tumours. It offers an RNA gene panel to detect gene fusion and has started a whole genome sequencing service in line with the Genomics Medicine Service Alliance.

The Molecular Neuropathology service is the designated laboratory within the South East Genomics Laboratory Hub offering molecular analysis of neurological malignancies.

Tests we perform

MGMT promotor methylation status

Testing for the methylation status of the O6-methylguanine DNA methyltransferase gene (MGMT) promoter methylation status performed using pyrosequencing technology and the therascreen MGMT pyro kit. This kit assesses four CpG sites, giving an average (%) methylation across the four.

Glioblastoma tumours with a methylated MGMT promoter are predictive of an improved response to alkylating chemotherapy (for example, temozolomide).

Turnaround time: 14 days from sample receipt

Methylation array

The molecular neuropathology department uses the Illumina 850k EPIC array to assess the DNA methylation status 850,000 individual CpG sites. The data is then processed via the ‘Molecular Neuropathology Classifier’ (MNP classifier), an algorithm developed the German Cancer Research Centre (Department of Neuropathology, University Hospital Heidelberg). This provides a tumour classification based on the methylation profile.

Turnaround time: 21 days from sample receipt

Multimodal NGS panel

The multimodal NGS panel assessed both DNA and RNA targets. Testing of the indicated genes is by the Qiagen QIAseq Multimodal Panel, using single primer extension with unique molecular indexes to assess a targeted DNA panel of 305 genes and a RNA panel of 76 genes associated with solid tumour fusions. Additional ‘virtual’ DNA panels may be applied as required, please contact the laboratory to discuss.

Samples are sequenced on an Illumina NextSeq2000, 2X150bp reads with a minimum coverage of 400x (minimum of 6 reads to make a mutation call). Variants at <2% are excluded from analysis and variants at <5% are not considered clinically significant and are therefore not reported. This test has been shown to have a minimum sensitivity of 98.3% for single nucleotide substitutions and small insertion/deletion variants for regions covered by >=400x with a 95% confidence interval.

Turnaround time: 21 days from sample receipt

NGS panels offered

Somatic Paediatric Neurological Tumours panel v5.0:

AKT1, ALK, ATRX, BCOR, BRAF, CDKN2A, CDKN2B, CTNNB1, DAXX, DDX3X, DICER1, DPYD, EZH2, FGFR1, FGFR4, IDH1, IDH2, KIT, MSH6, MYC, MYCN, NF1, NF2, NRAS, PDGFRA, PHOX2B, PIK3CA, PMS1, PMS2, PTCH1, PTCH2, PTEN, RAF1, RB1, SMARCA4, SMARCB1, SMARCE1, SMO, SUFU, TERT, TFE3, TP53, TSC1, TSC2, VHL, WT1, YAP1

Somatic Adult Neurological Tumours panel v5.0:

ATRX, BRAF, CDK4, CDK6, CDKN2A, CDKN2B, CTNNB1, DPYD, EGFR, FGFR3, H3C2, H3C3, H3F3A, H3F3B, IDH1, IDH2, KIAA1549, KRAS, MDM2, MDM4, MET, MYC, NF1, PDGFRA, PIK3CA, PIK3R1, PTEN, TERT, TP53, VHL

Germline Neurological Tumours panel v5.0:

AKT1, APC, ATM, BRCA1, BRCA2, DPYD, MLH1, MSH2, MSH6, NF1, NF2, PIK3CA, PMS1, PMS2, POLD1, POLE, PTCH1, PTCH2, PTEN, RAD51D, RB1, SMARCA4, SMARCB1, SUFU, TP53, TSC1, TSC2, VHL

RNA Neurological Tumours panel v5.0:

ABL1, AGK, AKAP9, ALK, ASPSCR1, BCOR, BCR, BRAF, BRD2, BRD3, BRD4, CBFB, CCDC6, CCNB3, CIC, DNAJB1, EGFR, EML4, ERBB3, ERG, ETV1, ETV6, EWSR1, FAM118B, FGFR1, FGFR2, FGFR3, FOXO1, FXR1, GNA11, HLA-A, HLA-B, HLA-C, KIAA1549, MACF1, MALAT1, MAML2, MET, MITF, MN1, MYB, MYBL1, MYC, MYH11, NFIB, NFIX, NPM1, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, NUTM2B, NUTM2E, PML, PRCC, PRKACA, PVT1, QKI, RAF1, RARA, RELA, RET, ROS1, RUNX1, RUNX1T1, SRGAP3, TFE3, TFEB, TMPRSS2, TPM3, TTYH1, WWTR1, YAP1, YWHAE, ZFTA

Gene Target as per National Genomic Test Directory Cancer 2021-22 v2, December 2021

1. Contact us in advance

Contact the Neuropathology Laboratory at King’s College Hospital on 020 3299 1957 or email us at [email protected] to let staff know when to expect delivery. The department is open from 8.30am to 5pm, Monday to Friday.

2. Sample requirements and request form

Either the FFPE block or ten unstained formalin fixed paraffin embedded (FFPE) tissue sections, cut at 10µm thick (from a representative block of tumour) are required for all molecular pathology tests. Alternatively, fresh tissue, preserved in RNALater can also be accepted instead of FFPE samples (please contact the laboratory for details).

Whole genome sequencing can only be performed on fresh tissue and this is the preferred sample type of the molecular laboratory. For histopathology, we recommend FFPE tissue, therefore in some cases samples need to be divided and the molecular laboratory has no option but to work with FFPE tissue. Formalin fixation should be reduced to a minimum time interval at neutral pH to try and preserve the nucleic acid for molecular studies.

If you have insufficient material or if you require multiple tests on the same samples, please call the laboratory on 020 3299 2375 to discuss any additional requirements prior to sending

Please complete the Molecular Neuropathology Request Form for all samples.

3. How to package and transport the sample

The unstained slides must be packed into clean slide carriers taped shut to ensure they are not damaged during transit. A letter explaining the clinical details should accompany the sample. Post in a padded envelope to:

Department of Clinical Neuropathology
1st Floor, Academic Neuroscience Centre
King’s College Hospital
Denmark Hill
London
SE5 9RS

Contact us

If you have any difficulties or questions, please contact Molecular Neuropathology on 020 3299 2375 or email us at [email protected]