Next Generation Sequencing

Haemato-Oncology

The NE&Y GLH HeamOnc team deliver a variety of tests.

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

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