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Newcastle Laboratories

Cancer Services

Detection of acquired genetic abnormalities in haematological malignancies and solid tumours is of proven value in diagnosis, prognosis and monitoring. The objective of the Genomics Cancer Services is to identify clinically significant chromosome and other genetic changes by means of karyotype analysis, FISH and molecular techniques. Haemato-Oncology Genetic testing is delivered in conjunction with the Northern England Haemato-Oncology Diagnostic Service (NEHODS based in Blood Sciences, RVI (Tel 0191 282 5028)

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Cancer Genomics Enquiries

Tel: 0191 2418786
nuth.cancer.genomics@nhs.net
Newcastle Genetics Laboratory
Central Parkway
Newcastle upon Tyne
NE1 3BZ

Referral Forms

 

Key Cancer Genomics Contacts:

Cancer Genomics Lead Scientist:
Gavin Cuthbert FRCPath, Clinical Scientist – Genetics – nuth.cancer.genomics@nhs.net

Cancer Genomics Service Lead:
Angharad Goodman, Clinical Scientist – Genetics – nuth.cancer.genomics@nhs.net

Service Lead:
Laura Ions PhD DipRCPath, Clinical Scientist – Genetics – nuth.cancer.genomics@nhs.net

 

Yorkshire and North East Genomic Laboratory Hub (Y&NE GLH)

Newcastle Genetics Laboratory is part of the Yorkshire and North East Genomic Laboratory Hub (Y&N GLH).  For information of the NHS England Genomic Laboratory Hubs – see https://www.england.nhs.uk/genomics/genomic-laboratory-hubs/.

Genomic testing is delivered in accordance with the NHS England National Genomic Test Directory – https://www.england.nhs.uk/publication/national-genomic-test-directories/

Y&NE GLH Operational Director:
Dr Angie Silmon PhD
Y&NE GLH Laboratory Services Director
angela.silmon@nhs.net
Kath Smith FRCPath
Clinical Scientist – Genetics
kath.smith4@nhs.net
Y&NE GLH HaemOnc Scientific Lead:
Polly Talley FRCPath
Clinical Scientist – Genetics
polly.talley@nhs.net
Y&NE GLH Cancer Scientific Lead:
Paul Roberts FRCPath
Clinical Scentist – Genetics
paul.roberts16@nhs.net
Y&NE GLH Cancer Clinical Lead:
Dr Alastair Greystoke
Consultant Clinical Oncologist
alastair.greystoke@nhs.net

 

 

 

Diagnostic Techniques 

 

 

Karyotyping 

G-banded metaphase chromosome analysis (karyotyping) can identify genome-wide structural chromosome abnormalities including balanced translocations, inversion and can identify genomic complexity in living cells actively undergoing mitotic division.  It requires fresh samples (e.g. bone marrow aspirate, blood, lymph node biopsy) which need to be received within 24hrs of sampling).

Karyotyping studies can be completed with 72hrs in cases with urgent clinical necessity.  Please contact the lab. to highlight the need to urgent results. Non-urgent karyotyping is aimed to be reported in 21 days

If karyotype studies fail to yield metaphases we will attempt SNP array in all cases.  This may lead to a delay in reporting result in such cases.

 

FISH

Fluorescence in situ hybridisation (FISH) is generally carried out using commercial probesets on interphase cells from short term cell cultures (e.g. bone marrow or blood) or on FFPE (formalin fixed paraffin embedded) sections or cells released from FFPE blocks or curls. FISH can identify specific gene fusion events using either dual fusion (e.g. BCR-ABL1) or break –apart (e.g. MYC) probesets or deletion of tumour suppressor gene (e.g. TP53) or the presence of gene amplification (e.g. MYCN).  FFPE slide referrals must have an accompanying marked H&E slide and a stated tumour content.

FISH sensitivity varies depending on probe type but below 10-20% tumour content, FISH results may be uninformative.

FISH studies can be completed within 24hrs in cases in cases with urgent clinical necessity. Please contact the lab. to highlight the need to urgent results. All FISH is aimed to be reported in 7 days.

 

SNP Array 

Single Nucleotide Polymorphism array testing uses the CytoSNP 850k Bead arrays and can identify genome wide copy number changes (gains/losses/gene amplifications) and loss of heterozgosity (LOH).   Copy number changes below 5Mb and Copy neutral LOH below 10Mb are not reported.  Smaller imbalances in disease relevant genes will be report. SNP array testing cannot identify gene fusions.  SNP array can detect 10% abnormal cell content.  Normal result from tissue with low tumour content may be uninformative.

 

Sanger Sequencing 

Conventional Sanger DNA sequencing has a sensitivity of 20% mutant allele frequency (which equates to 40% tumour content for a heterozygous variant).  A normal result from tissue with a tumour content below 40% may be uninformative.

 

Agena Mass ARRAY (Targeted mutation testing)

The Agena MassARRAY uses mass spectrometry technology (MALDI-TOF – Matrix-assisted laser desorption/ionisation – time of flight) to identify specific DNA variants in a sensitive, high throughput and cost effective manner.  Agena testing has a sensitivity of 5% mutant allele frequency (which equates to approx. 10% tumour content.

 

Targeted PCR Fragment Analysis 

PCR Fragment analysis identifies genetic abnormalities by examination of PCR product size.  For instance FLT3 internal tandem duplications (FLT3-ITD) are identified as abnormally large sized fragments compared to the wild type product.  Please note that normal results using PCR fragment analysis in samples with below 20% tumour content (10% allele frequency) may be uninformative.

 

RT-PCR (Reverse transcriptase PCR)

Reverse transcriptase PCR detect gene fusions using cDNA generated from RNA.  Our repertoire includes primer sets which are designed to detec specific gene fusion events in a variety of soft tissue sarcomas and other tumours.  Our service generally combines FISH and RT-PCR together to reduce the risk of false negative findings which are seen when using FISH or RT-PCR testing alone. Negative results for FISH and RT-PCR may lead to RNA fusion panel testing (see below). Contact the laboratory for information on the RT-PCR service.

 

qRT-PCR (Quantitative RT-PCR)

Quantitative RT-PCR (qRT-PCR) is used for monitoring of BCR-ABL major break point. The ipogen BCR-ABL1 Mbcr IS-MMR kit is used to detect ~95% of the BCR-ABL fusion transcripts seen in CML – specifically the e13a2 and e14a2 breakpoints. This test will not detect minor breakpoint transcripts.

 

Myeloid NGS

Next Generation Sequencing (NGS) is available for myeloid disorders (AML, MDS, MPN) and is delivered via our links with the YNE-GLH laboratory in Leeds.  DNA extracted in Newcastle is sent for Myeloid NGS testing in Leeds and the data returned for analysis in Newcastle and integration into the HaemoSys records.

 

Whole Genome Sequencing 

Whole genome sequencing (WGS) is available for an expanding range of referrals (contact laboratory for eligibility). Fresh tumour and germline samples are sent to the NHS Genome Sequencing Centre, Hinxton and data is returned to the laboratory for analysis and reporting.

WGS results are discussed at the appropriate GLH GTAB and integrated reports issued by the relevant Consultant Pathologist

 

RNA fusion panel

The Illumina TruSight RNA Fusion Panel uses targeted Next Generation Sequencing (NGS) to detect fusions within 507 pan-cancer genes and identifying the (known or novel) partner gene. RNA is extracted from FFPE (5 x 10µM curls preferred), fresh or frozen tissue. The RNA fusion panel has been validated down to a sensitivity of 2% tumour content.

 

 

 

Northern England Haematological Oncology (HaemOnc) Diagnostic Service (NEHODS)

 

 

Haematological Oncology samples:

Please send all Haematological Oncology samples to the Northern England Haematological Oncology Diagnostic Service (NEHODS) reception:

NEHODS laboratory, Blood Sciences
Level 3, Leazes Wing
Royal Victoria Infirmary
Richardson Road
Newcastle upon Tyne
NE1 4LP
0191 282 5028
tnu-tr.nehods@nhs.net

Please use HaemoSys to request testing. If HaemoSys is not available – please use this form

 

 

 

 

Introduction about the NEHODS service 

The Northern England Haemato-Oncology Diagnostic Service (NEHODS) brings together expertise in haematology, flow cytometry, cytogenetics, molecular genetics and immunophenotyping.

With a centralised specimen reception at the Royal Victoria Infirmary and integrated laboratory services, NEHODS aims to improve outcomes for patients within Northern England by providing cost-effective and timely results for diagnosis, prognostication and monitoring of haematological malignancies.

We provide fully integrated laboratory reports for Clinical Haematologists across the region.

All NEHODS Genetic test requesting must be done in conjunction with the NEHODS Clinical Team.  Additional genetic testing in order to complete the diagnosis may be requested by NEHODS Clinical team.

All Haemato-oncology genetics reports are integrated with other patient results using HaemoSys.

 

 

NEHODS Clinical advice

NEHODS lab management

Chris Kettle
Operational Manager- Integrated and Precision Medicine
c.kettle@nhs.net

 

Dr Andrew McGregor
Consultant Haematologist
NEHODS
andrewmcgregor1@nhs.net
0191 2825028 (NEHODS laboratory)
DECT 48013 – (0191 2448013)

 

 

HaemOnc Testing

AML – karyotyping, FISH, FLT3/NPM1/CEBPA, Myeloid NGS if requested by NEHODS team

NB –  At present the FLT3 test cannot distinguish between FLT3-ITD high and FLT3-ITD low.

MPN – BCR/ABL1 FISH, karyotyping, MPN mutation analysis (JAK2, MPN, CALR)

ALL – FISH for risk stratifying gene fusions and SNP array for risk stratifying ploidy changes and UKALL CNa profile

MDS – karyotyping, Myeloid NGS if requested by NEHODS team

CLL – TP53 FISH, MLPA (11q, 12, 13q, 17p)

Myeloma – FISH on CD138+ cells for IGH/MAF and IGH/FGFR3 fusion, 1p/q and 17p copy number

Mantle cell lymphoma – IGH/CCND1 FISH, TP53 sequencing in +ve cases

Burkitt lymphoma – MYC FISH plus confirmation of IG-partner

Diffuse Large B-cell lymphoma – MYC, BCL6, BCL2 FISH. Confirmation of IG status of MYC partner in double- or triple-hit cases

CML MRD – qRT-PCR for BCR-ABL1 major breakpoint transcript and BCR-ABL mutation analysis

 

 

Medulloblastoma National Reference Laboratory

Clinical advice:
Prof Steve Clifford
Professor of Molecular Diagnostics, Lead for National Medulloblastoma Service
steve.clifford@newcastle.ac.uk

Dr Steve Crosier
Trial Sample Coordinator, Newcastle
s.crosier@nhs.net

Janet Thompson
NeuroOncology Coordinator, Cellular Pathology
janet.thompson8@nhs.net

 

Testing

MYCN – MYC, chromosome 6 FISH

– TAT 3 days

TP53 – CTNNB1 sequencing

-TAT 14 days

SNP array

– TAT 14 days

Paediatric NGS panel – (in development)

Methylation arrays  – (in development)

 

Neuroblastoma National Reference Centre

Clinical advice:
Professor Deborah Tweddle 
Consultant Paediatric Oncologist, Head of SIOPEN /CCLG National Neuroblastoma Reference Centre for Neuroblastoma Biology
deborah.tweddle@nhs.net

 

 

 

Pathology Clinical Advice 

 

Dr Katrina Wood
Consultant Histopathologist, Head of Department, Histopathology
katrina.wood1@nhs.net
Dr Petra Dildey
Consultant Histopatholgist, North of England Bone and Soft Tissue Tumour Service
petra.dildey@nhs.net
Dr Alastair Greystoke
Consultant Clinical Oncologist, YNE GLH Cancer Clincal Lead
alastair.greystoke@nhs.net
Dr Abhijit Joshi
Consultant Neuropathlogist
abhijit.joshi1@nhs.net

 

 

Pathology Oncology Samples

Pathology Oncology samples:
Please send all Pathology samples to:
Newcastle Genetics Laboratory
Central Parkway
Newcastle upon Tyne
NE1 3BZ
Referral forms link

Pathology Genetics can be requested directly for those services listed below. Referral of sarcoma genetic testing must be done in conjunction with the North of England Bone and Soft Tissue Tumour Service.

 

Paediatric Oncology and Sarcoma

Comprehensive service of RT-PCR and FISH.

Contact the laboratory. nuth.cancer.genomics@nhs.net

Non-small cell lung cancer

(available directly) – see Molecular Pathology referral form

Targeted mutation detection of 9 variants in EGFR and 12 variants in KRAS (details available on request) using Agena MassARRAY – TAT 5-7 days (14 day NHSE guideline) – email reporting

Colorectal cancer

(available directly) – see Molecular Pathology referral form

Targeted mutation detection of 28 variants in KRAS, 25 variants in NRAS and BRAF V600E  (details available on request) using Agena MassARRAY – TAT 5-7 days (14 day NHSE guideline) – email reporting

Melanoma

(available directly) – see Molecular Pathology referral form

Targeted mutation detection of 12 variants in BRAF and 25 variants in KRAS (details available on request) using Agena MassARRAY – TAT 5-7 days (14 day NHSE guideline) – email reporting

Gastrointestinal stromal tumour (GIST)

– see Molecular pathology referral form

Sanger sequencing for KIT and PDGFRA

– TAT 14 days

 

 

Key Contacts

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