Haemato-Oncology

Genomic Laboratory Hub Services

In October 2018, the National Test Directory (NTD) for Cancer was published.

The National Test Directory is updated each year to ensure access to the latest diagnostics and treatments. The NTD specifies which genomic tests are commissioned by the NHS in England, the clinical indication for which they apply and the technology by which the tests will be delivered.

Access to genomic services for HaemOnc patients will continue to be through your Specialist Integrated Haematological Malignancy Diagnostic Service (SIHMDS).

The NE&Y GLH cover three regional SIHMDS groups:

North East Haematological Oncology Diagnostic Service

Sheffield Haematological Oncology Diagnostic Service

Haematological Malignancy Diagnostic Service Leeds

Genomic haemato-oncology diagnostics are funded centrally by NHSE and so referring Trusts will not be charged for these services if they refer testing to their designated local GLH.

Note. Non-genetic activity carried out within an SIHMDS is funded separately and will still be charged for.

The Haemato-Oncology Team

Prof John Snowden
HaemOnc Lead Clinician
0114 2713357
Paul.roberts16@nhs.net

Dr Catherine Cargo
HaemOnc Lead Clinician

Polly Talley
HaemOnc Lead Scientist
Polly.talley@nhs.net

Newcastle

Gavin Cuthbert
gavin.cuthbert@nhs.net

Angharad Goodman
angharad.goodman1@nhs.net

Sheffield

Rebecca Pollitt
rebeccapollitt@nhs.net

Harveer Cheema
harveer.cheema@nhs.net

Leeds

Paul Evans
paulevans@nhs.net

Phil Dean
philip.dean@nhs.net

HaemOnc Services

Within the HaemOnc test directory a number of rare diagnostic tests will be delivered by specified GLHs as part of a national network.

Where these tests are not completed within our GLH, please refer samples via your local SIHMDS where they will be appropriately routed to the agreed and appropriate GLH within the national network.

Tests that will be routed outside of the GLH include:

  • t(15;17) MRD testing
  • Rare non-standard breakpoint cases of t(8;21) and inv(16) for MRD testing
  • Rare NPM1 transcript MRD testing
  • FIP1L1/PDGFRA MRD testing
  • Rare BCR/ABL1 MRD testing
Those rare tests delivered within the NE&Y GLH as part of this national network are shown below:

Histiocytosis Service:

The Newcastle Histiocytosis Service is led by Prof Matt Collin, Chair of the National Histiocytosis Advisory Group.   The Newcastle team also manage the UK Histiocytosis Registry (funded by Histio UK and CRUK).

What is Histiocytosis?

Histiocytic disorders are a diverse group of rare neoplasms caused by somatic mutation and fusions of MAP kinase genes in cells of the macrophage/dendritic cell lineage.

The clinical entities include:

  • Langerhans cell histiocytosis,
  • Erdheim Chester disease,
  • Rosai Dorfman Destombes disease
  • Juvenile Xanthogranuloma
  • Indeterminate cell histiocytosis

Why is testing useful?

The clinical indications for genotyping in histiocytosis are:

  • BRAF inhibitors are highly effective for BRAF V600E-mutated disease
  • MEK inhibitors work for many BRAF-wild-type patients (depending upon the exact mutation)
  • Other kinase mutations are also directly targetable by an increasing array of small molecules.
  • Genotyping also has prognostic implications for risk of progression and neurological sequelae.

Genomic changes and testing

Clinically significant variants and fusions have been described in up to 90% of cases with histiocytic disorders.  About two-thirds of all cases have the BRAF V600E mutation that is detectable using a sensitive allele-specific PCR test.

The remainder of cases include BRAF and MAP2K1 insertion-deletion mutations (indels), mutations of CSF1R, RAS, PIK3CA, ARAF, MAP2K2, JAK3, KIT and fusions of BRAF, NTRK1, ALK and RET that require targeted NGS analysis.

Histiocytosis Service

In order to detect the spectrum of genetic abnormalities in histiocytic disorders, we offer a multi-component service:

  1. Highly sensitive targeted BRAF assay (allele specific PCR)
  2. 13 gene NGS panel (sub panel of paediatric NGS panel)
  3. RNA fusion panel

Samples required

Frozen Fresh tissue is recommended where possible.

FFPE: send two separate samples –
5x 10uM curls for DNA extraction (for BRAF and NGS panel testing) and
5x 10uM curls for RNA extraction (for RNA fusion panel testing) with a stated tumour cell content.

ALL MRD

MRD in paediatric ALL is completed in small number of centres (including Sheffield) in the UK. This testing is extensive and bespoke and adheres to strict quality control measures set by the Euro MRD group.

NHS England are keen that the distribution of ALL MRD testing fits the geography associated with the GLHs. This has involved a process of repatriation of cases from the Newcastle and Leeds region to Sheffield which began in March 2020 and was completed in December 2020. A small number of cases from Nottingham and Leicester we managed through the Sheffield service, but have also now been repatriated to the service associated with the East GLH.

Currently, discussion are underway as to what the process will be for the adult ALL MRD testing and whether this will follow a similar pathway to the paediatric MRD or whether a centralised process will be available.

AML MRD

The AML MRD testing includes the common NPM1 changes (types A, B & D) and t(8;21) and inv(16). These tests have been validated in Leeds in order to comply with the repatriation and consolidation requirements of these tests to the NE&Y GLH.

Myeloid and Lymphoid panels

In January 2019, all myeloid NGS testing laboratory work was transferred to Leeds making use of the existing Fluidigm myeloid NGS panel.  Distributed reporting is in place for this panel following agreement to a standardised format for analysis and reporting.

The myeloid NGS panel includes 26 genes listed here:
ASXL1, BCOR, CALR, CBL, CSF3R, DNMT3A, EZH2, FLT3, IDH1, IDH2, JAK2, KIT, NPM1, NRAS, MPL, KRAS, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, ZRSR2

SRSF2 is poorly covered on the NGS panel and is gap-filled using Sanger sequencing.

In June 2019, the lymphoid panel (liquid samples) was made available across the GLH. This panel covers genes specific to CLL, MZL and HCL, but as the Jan 2019 test directory only requests panel testing for TP53 currently, the uptake and use of this panel has remained low.

PanHaemOnc NGS panel

The NE&Y GLH HaemOnc team are working towards a bespoke panHaemOnc NGS panel designed to conform to NHS Englands plan to provide large panel NGS analysis. It will cover all genes on the Test Directory (TD), plus a number of additional genes of interest from a research or future planning perspective.

The panel was designed using Twist probes and library preparation to run on a NextSeq and has 258 genes known to be implicated in both myeloid and lymphoid disorders.

This is an ambitious aim, and we plan to manage this in a step-wise manner with the SNV analysis available on fresh samples first, and then working up the utility for FFPE samples and the use of the copy number analysis feature.

As of Dec 2020, the wet-work has been completed and is awaiting full analysis and further bioinformatics developments. We are planning to run the panel in parallel to the current myeloid and lymphoid panels, with a view to going live in April 2021.

The panHaemOnc NGS panel will cover a wide range of indications on the TD and we have been working on both testing algorithms, to ensure the most appropriate samples are tested, and , to ensure the analysis is directed, but not limited.

Virtual panels have been created to ensure that appropriate gene panels are assessed for each referral, but with aim of not limiting the analysis where differential diagnoses may be considered.

The first two panels to be implemented are the acute and myeloid panel and the lymphoid panels. All genes will have been sequenced, so there remains the option of going back to specific genes on the full panel if required.

Pan Haem Onc Panel Full Gene List

ABL1
BTG2
CDKN2C
EP300
HIST1H1C
IRF4
MGA
P2RY8
PTPN11
SPIB
UBA1
AKT1
BTK
CEBPA
ERBB2
HIST1H1D
IRF8
MPEG1
PAR1
PTPN6
SRSF2
UBR5
ALK
CALR
CHEK2
ERBB3
HIST1H1E
ITPKB
MPL
PAX5
PTPRC
STAG2
VAV1
ANKRD26
CARD11
CIITA
ETNK1
HIST1H2AC
JAK1
MSH2
PDCD1
PTPRD
STAT3
WHSC1/MMSET
ARAF
CASP8
CKS1B
ETV6
HIST1H2AG
JAK2
MSH6
PDCD1LG2
RAD21
STAT5B
WT1
ARID1A
CBFB
CNOT3
EZH2
HIST1H2AM
JAK3
MTOR
PDGFRA
RAD51
STAT6
XPO1
ARID1B
CBL
CRBN
FAS
HIST1H2BC
KDM6A
MYB
PDGFRB
RASA2
STK11
ZFP36L1
ARID2
CCND1
CREBBP
FAT1
HIST1H2BD
KIT
MYC
PDS5B
RB1
SUZ12
ZRSR2
ASXL1
CCND2
CSF1R
FAT3
HIST1H2BG
KLF2
MYD88
PHF6
RHOA
SYK
ASXL2
CCND3
CSF3R
FAT4
HIST1H2BK
KLHL6
NCOR2
PIGA
ROS1
TBL1XR1
ATM
CCNE1
CTCF
FBXO11
HIST1H3B
KMT2A
NF1
PIK3CA
RPS15
TCF3
ATRX
CCR6
CTNNB1
FBXW7
HIST1H3G
KMT2C
NF2
PIK3CB
RUNX1
TENT5C
B2M
CD22
CUL4B
FGFR1
HLA-A
KMT2D
NFATc1
PIK3CD
SETBP1
TERT
BCL10
CD274
CUX1
FGFR2
HLA-B
KRAS
NFE2
PIK3R1
SETD2
TET2
BCL11A
CD28
CXCR4
FGFR3
HLA-C
LAMB4
NFKB1
PIM1
SETDB1
THRAP3
BCL2
CD58
CYLD
FLT3
HRAS
LMO2
NFKB2
PLCG2
SF1
TLR2
BCL6
CD70
DDX3X
FOXO1
ID3
LTB
NFKBIA
POT1
SF3B1
TMEM30A
BCL7A
CD79A
DDX41
GATA1
IDH1
LUC7L2
NFKBIE
POU2AF1
SGK1
TNF
BCOR
CD79B
DIS3
GATA2
IDH2
MAP2K1
NFKBIZ
POU2F2
SH2B3
TNFAIP3
BCORL1
CD83
DNMT3A
GATA3
IKBKB
MAP2K4
NOTCH1
PPM1D
SMARCA4
TNFRSF14
BIRC2
CDK4
DTX1
GNA13
IKZF1
MAP3K1
NOTCH2
PRDM1
SMARCB1
TP53
BIRC3
CDK6
EBF1
GNAS
IKZF3
MECOM
NPM1
PRKCB
SMC1A
TRAF2
BLM
CDKN1B
EGFR
GNB1
IL2RG
MED12
NRAS
PRPF8
SMC3
TRAF3
BRAF
CDKN2A
EGR1
GPRC5A
IL7R
MEF2B
NSD2
PTCH1
SOCS1
U2AF1
BTG1
CDKN2B
EGR2-F
HIST1H1B
IRF1
MET
NTRK1
PTEN
SPEN
U2AF2

Acute & Myeloid Virtual Gene Panel

ANKRD26 GNB1 PTPN11
ASXL1 HRAS RAD21
BCOR IDH1 RUNX1
BCR-ABL (TKD) IDH2 SETBP1
CALR IKZF1 SF3B1
CBL (NM_005188.2) JAK2 SH2B3
CEBPA KIT SRSF2
CHEK2 KMT2C STAG2
CSF3R KRAS STAT3
CUX1 MLL-PTD STAT5B
DDX41 MPL TET2
DNMT3A NF1 TP53
ETNK1 NFE2 U2AF1
ETV6 NOTCH1 UBA1
EZH2 NPM1 WT1
FBXW7 NRAS ZRSR2
FLT3 PPM1D
GATA1 PTEN

Lymphoid Virtual Panel

ARID1A KLF2 )
ATM MAP2K1
BCL2 MEF2B
BIRC3 MYD88
BRAF NOTCH1
BTK NOTCH2
CARD11 PLCG2
CCND3 POT1
CD79B RHOA
CDKN1B RPS15
CREBBP SF3B1
CXCR4 STAT3
DNMT3A STAT5B
EP300 TCF3
EZH2 TET2
FOXO1 TNFAIP3
ID3 TP53
IDH2

NGS RNA fusion panel

The HaemOnc Test Directory includes a number of fusion genes. It is recognised that the majority of these can be detected cytogenetically, but the NHSE direction of travel is to have the provision to detect these via NGS panel.

Fusion NGS panels are indicated by the test directory for four disease groups, AML, ALL, Myeloma and Histiocytosis.

Newcastle have experience of running the Illumina Trusight RNA Fusion Panel. This panel covers 507 genes and includes at least one gene partner for the majority of HaemOnc fusions required by the Test Directory. IGH and TCR genes are not included. Although cytogenetics will continue to be offered for the majority of indications in the first instance, referral for this panel will be available for our users.

This panel is also used in to detect NTRK fusions in solid cancer – more information on the panel and how to order it can be found below.
NTRK Testing

HaemOnc Services

Within the HaemOnc test directory a number of rare diagnostic tests will be delivered by specified GLHs as part of a national network.

Where these tests are not completed within our GLH, please refer samples via your local SIHMDS where they will be appropriately routed to the agreed and appropriate GLH within the national network.

Tests that will be routed outside of the GLH include:

  • t(15;17) MRD testing
  • Rare non-standard breakpoint cases of t(8;21) and inv(16) for MRD testing
  • Rare NPM1 transcript MRD testing
  • FIP1L1/PDGFRA MRD testing
  • Rare BCR/ABL1 MRD testing
Those rare tests delivered within the NE&Y GLH as part of this national network are shown below:

Histiocytosis Service:

The Newcastle Histiocytosis Service is led by Prof Matt Collin, Chair of the National Histiocytosis Advisory Group.   The Newcastle team also manage the UK Histiocytosis Registry (funded by Histio UK and CRUK).

What is Histiocytosis?

Histiocytic disorders are a diverse group of rare neoplasms caused by somatic mutation and fusions of MAP kinase genes in cells of the macrophage/dendritic cell lineage.  The clinical entities include:

  • Langerhans cell histiocytosis,
  • Erdheim Chester disease,
  • Rosai Dorfman Destombes disease
  • Juvenile Xanthogranuloma
  • Indeterminate cell histiocytosis

 Why is testing useful?

The clinical indications for genotyping in histiocytosis are:

  • BRAF inhibitors are highly effective for BRAF V600E-mutated disease
  • MEK inhibitors work for many BRAF-wild-type patients (depending upon the exact mutation)
  • Other kinase mutations are also directly targetable by an increasing array of small molecules.
  • Genotyping also has prognostic implications for risk of progression and neurological sequelae.

Genomic changes and testing

Clinically significant variants and fusions have been described in up to 90% of cases with histiocytic disorders.  About two-thirds of all cases have the BRAF V600E mutation that is detectable using a sensitive allele-specific PCR test.

The remainder of cases include BRAF and MAP2K1 insertion-deletion mutations (indels), mutations of CSF1R, RAS, PIK3CA, ARAF, MAP2K2, JAK3, KIT and fusions of BRAF, NTRK1, ALK and RET that require targeted NGS analysis.

Histiocytosis Service

In order to detect the spectrum of genetic abnormalities in histiocytic disorders, we offer a multi-component service:

  1. Highly sensitive targeted BRAF assay (allele specific PCR)
  2. 13 gene NGS panel (sub panel of paediatric NGS panel)
  3. RNA fusion panel

Samples required

Frozen Fresh tissue is recommended where possible.

FFPE:  send two separate samples –
5x 10uM curls for DNA extraction (for BRAF and NGS panel testing) and
5x 10uM curls for RNA extraction (for RNA fusion panel testing) with a stated tumour cell content.

ALL MRD

MRD in paediatric ALL is completed in small number of centres (including Sheffield) in the UK. This testing is extensive and bespoke and adheres to strict quality control measures set by the Euro MRD group.

NHS England are keen that the distribution of ALL MRD testing fits the geography associated with the GLHs. This has involved a process of repatriation of cases from the Newcastle and Leeds region to Sheffield which began in March 2020 and was completed in December 2020. A small number of cases from Nottingham and Leicester we managed through the Sheffield service, but have also now been repatriated to the service associated with the East GLH.

Currently, discussion are underway as to what the process will be for the adult ALL MRD testing and whether this will follow a similar pathway to the paediatric MRD or whether a centralised process will be available.

AML MRD

The AML MRD testing includes the common NPM1 changes (types A, B & D) and t(8;21) and inv(16). These tests have been validated in Leeds in order to comply with the repatriation and consolidation requirements of these tests to the NE&Y GLH.

Myeloid and Lymphoid panels

In January 2019, all myeloid NGS testing laboratory work was transferred to Leeds making use of the existing Fluidigm myeloid NGS panel.  Distributed reporting is in place for this panel following agreement to a standardised format for analysis and reporting.

The myeloid NGS panel includes 26 genes listed here:
ASXL1, BCOR, CALR, CBL, CSF3R, DNMT3A, EZH2, FLT3, IDH1, IDH2, JAK2, KIT, NPM1, NRAS, MPL, KRAS, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, ZRSR2

SRSF2 is poorly covered on the NGS panel and is gap-filled using Sanger sequencing.

In June 2019, the lymphoid panel (liquid samples) was made available across the GLH. This panel covers genes specific to CLL, MZL and HCL, but as the Jan 2019 test directory only requests panel testing for TP53 currently, the uptake and use of this panel has remained low.

PanHaemOnc NGS panel

The NE&Y GLH HaemOnc team are working towards a bespoke panHaemOnc NGS panel designed to conform to NHS Englands plan to provide large panel NGS analysis. It will cover all genes on the Test Directory (TD), plus a number of additional genes of interest from a research or future planning perspective.

The panel was designed using Twist probes and library preparation to run on a NextSeq and has 258 genes known to be implicated in both myeloid and lymphoid disorders.

This is an ambitious aim, and we plan to manage this in a step-wise manner with the SNV analysis available on fresh samples first, and then working up the utility for FFPE samples and the use of the copy number analysis feature.

As of Dec 2020, the wet-work has been completed and is awaiting full analysis and further bioinformatics developments. We are planning to run the panel in parallel to the current myeloid and lymphoid panels, with a view to going live in April 2021.

The panHaemOnc NGS panel will cover a wide range of indications on the TD and we have been working on both testing algorithms, to ensure the most appropriate samples are tested, and , to ensure the analysis is directed, but not limited.

Virtual panels have been created to ensure that appropriate gene panels are assessed for each referral, but with aim of not limiting the analysis where differential diagnoses may be considered.

The first two panels to be implemented are the acute and myeloid panel and the lymphoid panels. All genes will have been sequenced, so there remains the option of going back to specific genes on the full panel if required.

Acute & Myeloid Virtual Gene Panel
ANKRD26 GNB1 PTPN11
ASXL1 HRAS RAD21
BCOR IDH1 RUNX1
BCR-ABL (TKD) IDH2 SETBP1
CALR IKZF1 SF3B1
CBL (NM_005188.2) JAK2 SH2B3
CEBPA KIT SRSF2
CHEK2 KMT2C STAG2
CSF3R KRAS STAT3
CUX1 MLL-PTD STAT5B
DDX41 MPL TET2
DNMT3A NF1 TP53
ETNK1 NFE2 U2AF1
ETV6 NOTCH1 UBA1
EZH2 NPM1 WT1
FBXW7 NRAS ZRSR2
FLT3 PPM1D
GATA1 PTEN
Lymphoid Virtual Panel
ARID1A KLF2 )
ATM MAP2K1
BCL2 MEF2B
BIRC3 MYD88
BRAF NOTCH1
BTK NOTCH2
CARD11 PLCG2
CCND3 POT1
CD79B RHOA
CDKN1B RPS15
CREBBP SF3B1
CXCR4 STAT3
DNMT3A STAT5B
EP300 TCF3
EZH2 TET2
FOXO1 TNFAIP3
ID3 TP53
IDH2

NGS RNA fusion panel

The HaemOnc Test Directory includes a number of fusion genes. It is recognised that the majority of these can be detected cytogenetically, but the NHSE direction of travel is to have the provision to detect these via NGS panel.

Fusion NGS panels are indicated by the test directory for four disease groups, AML, ALL, Myeloma and Histiocytosis.

Newcastle have experience of running the Illumina Trusight RNA Fusion Panel. This panel covers 507 genes and includes at least one gene partner for the majority of HaemOnc fusions required by the Test Directory. IGH and TCR genes are not included. Although cytogenetics will continue to be offered for the majority of indications in the first instance, referral for this panel will be available for our users.

This panel is also used in to detect NTRK fusions in solid cancer – more information on the panel and how to order it can be found below.
NTRK Testing

Genomic Multi-Disciplinary Team Meetings

In order to support the interpretation of genomic data and its integration within the clinical Multi-Disciplinary Team process a series of genomic advisory boards have been established.

These are multi-disciplinary teams who analyse the more complex genomic results which arise from testing for larger numbers of gene abnormalities.

GMT Meetings

National Genomic Test Directory

The 2020/2021 National Genomic Test Directory for rare and inherited disorders and cancer.

View Directory
Genomic Laboratory Hub Services