South East Haematological Malignancy Diagnostic Service

The South East Haematological Malignancy Diagnostic Service (SE-HMDS) provides a comprehensive, state-of-the-art regional service for the diagnosis and monitoring of haematological malignancies and, acquired and constitutional bone marrow failure syndromes. It serves South London and the South of England with a catchment population of over 6 million. This specialist service is fully compliant with the 2016 NICE guidelines (NG47) on Improving Outcomes in Haematological Cancer, including providing integrated diagnostic reporting, contributing to local and regional MDT meetings and to Genomic Tumour Advisory Boards (GTABs). Diagnostic services are provided by a number of laboratories, including immunophenotyping, cytogenetic and molecular genetics services and histopathology. Our laboratories are UKAS accredited to ISO 15189:2012 and participate in external quality assurance schemes. 

In addition, the laboratories also provide testing within the clinical trials setting and have a broad research, development and innovation portfolio enabling rapid adoption of new tests and technologies into routine clinical practice. 

The SE-HMDS is involved in training clinicians and scientific staff and has an active programme of education with both live and recorded webinars available to the SE-GLH via the KHP website.

Genomic tests within SE-HMDS are commissioned and funded by NHS England, via the South East GLH, and follow the National Genomic Test Directory. Genomic testing for inherited haematological conditions, including inherited bone marrow failure syndromes, is performed by the Red Cell Centre.

The principles of the HMDS are predicated on a single point of referral for all samples/requests, performing the right test at the right time. We then integrate all the test results as one diagnostic report, as closely aligned to the World Health Organisation (WHO) classification of haematological malignancies as possible. We routinely review results/test referrals, and reflex additional testing, as part of this process, and are grateful to our referrers for providing comprehensive clinical information (including blood tests results) in order to perform the correct tests and provide an accurate diagnosis.

Tests offered and turnaround times

Expert review of MGG and Perl’s stained slides with full report (2 working days). 

Fully UKAS accredited Next Generation Flow cytometry (NGF) for the following indications:

  • Identification and diagnosis of acute and chronic haematological malignancies (5 days, urgent 24 hour provisional reports available on request)
  • Measurable Residual Disease (MRD) monitoring for CLL, ALL, AML and MM (5 days)
  • MDS integrated flow scoring (5 days)
  • PNH diagnosis and monitoring (5 days)
  • Rapid FISH for APL PML::RARA (3 days)
  • Rapid FISH for CML BCR::ABL1 (3 days)
  • Rapid FISH for ALL (3 days)
  • Rapid FISH for Burkitt lymphoma (3 days)
  • Rapid FISH panel for diagnosis of AML with recurrent genetic abnormalities (where indicated) (4 days)
  • Rapid FISH panel for secondary AML (4 days)
  • FISH panel for ABL class fusions in B-/T-ALL (14 days)
  • FISH panel for eosinophilia (21 days)
  • FISH panel for high-risk MDS (21 days)
  • FISH for MCL IGH::CCND1 & TP53 (21 days)
  • FISH panel for NHL (21 days)
  • FISH panel for plasma cell neoplasms (21 days)
  • FISH panel for T-PLL (21 days)

Full chromosome analysis by metaphase cytogenetics (14 / 21 days).

For CLL, MDS, MPN, MDS/MPN and ALL neoplasms (15 days).

All cases of CLL for treatment will have both SNP-Array karyotyping to detect copy number abnormalities and a lymphoid gene panel (including TP53 mutation analysis), to assess potential resistance to conventional treatment.

  • BCR-ABL1 Multiplex (5 days)
  • FLT3 /NPM1 mutation analysis – includes FLT-3 ITD and TKD (5 days)
  • KIT mutation detection (high sensitivity analysis for systematic mastocytosis only) EDTA (20 days)*
  • JAK2 V617F mutation quantitation where appropriate (5 days)
  • BRAF V600E mutation detection (10 days)
  • MYD88 L265P mutation detection (10 days). Lymphoid gene panel is the preferred test, but single gene analysis can be performed where this is limited material (e.g. CSF)
  • IgVH resequencing. This test is performed in the advanced diagnostics lab, see histopathology section
  • Myeloid gene panel [MGP45] (30 days)

Myeloid gene panel test overview: The sequencing method uses QiaSeq targeted amplicon and an Illumina NextSeq 550. Targets covered: ANKRD26 (all coding and 3′ UTR); ASXL1 (exon 12); BCOR (all coding); CALR (exon 9); CBL (exons 7+8+9); CEBPA (all coding); CSF3R (exons 13 to 18); CUX1 (all coding); DDX41 (all coding); DNMT3A (all coding); ETV6 (all coding); EZH2 (all coding); FLT3 (exons 14+15+20); GATA1 (all coding); GATA2 (all coding); HRAS (exons 2+3); IDH1 (exon 4); IDH2 (exon 4); IKZF1 (exons all coding); JAK2 (12+14); KIT (exons 2, 8 to 11, 13+17); KMT2A (all coding); KRAS (exons 2+3); MPL (exon 10); NF1 (all coding); NFE2 (all coding); NPM1 (exon 12); NRAS (exons 2+3); PHF6 (all coding); PPM1D (all coding); PTPN11 (exons 3+13); RAD21 (all coding); RUNX1 (all coding); SETBP1 (exon 4); SF3B1 (exons 12 to 16); SH2B3 (all coding); SRSF2 (exon 1); STAG2 (all coding); TET2 (all coding); TP53 (all coding); U2AF1 (exons 2+6); WT1 (exons 7+9); ZRSR2 (all coding). For regions with read depth >400x, the limit of detection = 5% clone size. For sub-optimal coverage (200-399x), this is 10%. In poorly covered regions, variants may be missed. These will be listed on the final report by gene name and location (hg19). This method is unable to reliably identify insertions/deletions over ~ 100 bp. Known variants below 5% frequency may be reported if clinically relevant. Novel variants are not reported below 5%. Variants of unknown significance (VUS) are not reported unless they aid diagnosis of clonal haemopoiesis.

  • Mini-MPN Panel (JAK2 V617F, JAK2 exon12, CALR and MPL)
  • Lymphoid gene panel (within 30 days)
  • Plasma cell disorders gene panel (30 days)
  • Histiocytic disorders gene panel (30 days)

Lymphoid/plasma cell/histiocytic gene panel test overview: The sequencing method uses QiaSeq targeted amplicon and an Illumina NextSeq 550. Targets covered: ARAF (all coding); ARID1A (all coding); BRAF exon 15; BTK (all coding); CARD11 (all coding); CREBBP (all coding); CXCR4 (all coding); DIS3 (all coding); DNMT3A (all coding); EP300 (all coding); ERBB3 (all coding); ETV6 (all coding); EZH2 (all coding); TENT5C (all coding); FBXW7 (all coding); FOXO1 (all coding); HRAS (exons 2 + 3); IDH2 (exon 4); IRF4 (all coding); KRAS (exons 2 + 3); MAP2K1 (all coding); MAP3K1 (all coding); MEF2B (all coding); MYD88 (exons 3 + 4 + 5); NOTCH1 (exon 34); NRAS (exons 2 + 3); PIK3CA (all coding); PIK3CD (exon9); PLCG2 (all coding); RHOA (all coding); STAT3 (exons 20 + 21); STAT5B (exons 14 + 15 + 16); TET2 (all coding); TP53 (all coding). For regions with read depth >400x, the limit of detection = 5% clone size. For sub-optimal coverage (200-399x), this is 10%. In poorly covered regions, variants may be missed. These will be listed on the final report by gene name and location (hg19). This method is unable to reliably identify insertions/deletions over ~ 100 bp. Known variants below 5% frequency may be reported if clinically relevant. Novel variants are not reported below 5%. Variants of unknown significance (VUS) are not reported unless they aid diagnosis of clonal haemopoiesis.

  • *Constitutional bone marrow failure gene panel (*will be forwarded and undertaken in the Red Cell Centre) (30 days).
WGS has the potential to detect all types of abnormalities (single nucleotide variants/mutations, copy number variants and structural changes) on both germline and tumour (somatic) samples. Findings from WGS are analysed by expert clinical scientists, compared to ‘standard of care’ testing and reported as part of our Genomic Tumour Advisory Board (GTAB), which makes recommendations to the referrer. 
The current indications for WGS are as follows:
  • Acute Myeloid Leukaemia
  • Acute Lymphoblastic Leukaemia
  • Acute Leukaemia of ambiguous lineage at initial diagnosis.

All patients who are eligible for WGS should be offered this test as standard, as per NHS England recommendations. 

It is mandatory for all WGS requests to include a tumour and germline (skin) sample, and be accompanied by a completed Record of Discussion form (see below). If a tumour sample alone has been confirmed to reside in the HMDS (e.g. if the diagnosis was not suspected, or RoD/germline sample not obtained at diagnosis), the germline sample and Record of Discussion form can be sent at a later date. More information can be found in this presentation.

Turnaround time: 6 weeks

  • Histopathology evaluation – bone marrow trephine, lymph node, spleen, other tissues (3-7 days)
  • Second opinion with immunohistochemistry (3-7 days)
  • Immunohistochemistry only (24-48 hours)
  • FISH on FFPE tissue (2-3 days)
  • IGH and TCR clonality testing on liquid/tissue (10-14 days)
  • IGHV mutational status (10-14 days)

Please specify the recurrent genetic abnormality (RGA) on the request form. Send samples in EDTA and samples must arrive within 24 hours to minimise RNA degradation. PB and BM are required for NPM1 monitoring together with course number and dates of last chemotherapy/transplant. MRD samples should arrive Monday-Thursday and must arrive within 24 hours.

  • BCR-ABL1 major (P210) quantitation (5 days)
  • BCR-ABL1 minor (P190) quantitation (5 days)
  • Rare BCR-ABL transcripts*
  • ABL1 kinase domain mutation detection (30 days)
  • FIP1L1-PDGFRA translocation (20 days)*
  • PML-RARA translocation quantitation (5 days)
  • RUNX1-RUNXT1 translocation quantitation (5 days)
  • CBFB-MYH11 translocation quantitation (5 days)
  • NPM1 transcript monitoring (Paired PB 20ml and BM 5ml samples) (14 days)
  • ALL molecular MRD by IGH or TCR rearrangements*
  • FISH for known cytogenetic aberrations

Post-allogeneic stem cell transplant PB and BM chimerism analysis (5 days).

For allogeneic stem cell transplantation, paired peripheral blood and bone marrow samples are required. The bone marrow will have an ‘unfractionated’ chimerism assay and the peripheral blood will be cell selected for CD3 (T-lymphoid) and CD15 (myeloid) components. In some cases, a CD19 subfraction should be requested (B-ALL, CLL and some B-cell LPDs that were leukaemic pre-transplant).

*tests that are sent outside of the SE GLH.

Further details can be found in the comprehensive user guides. 

SE GLH: HMDS test request form

  • Please complete every section of the request form and make sure there are at least 3 patient identifiers included. Note that the NHS number is mandatory for ALL test requests.
  • Please indicate if urgent, including if rapid AML genetic tests required that will inform immediate management.
  • Please complete the sample log form and include with each package sent to SE-HMDS

This form can be printed and filled out by hand or completed electronically and then printed.

Record of Discussion forms

With all WGS requests, a record of discussion (RoD) form is mandatory for testing and release of results. This form facilitates a ‘patient choice’ model of consent which covers both the clinical implications of a test, as well as the research offer within the clinical pathway.

If you are requesting non-WGS testing please use the SE GLH RoD below for your patient choice.

Sample type and requirements

Please refer to the HMDS Test Request Form for sample type and requirements.

  1. Peripheral blood containing >=20% blasts morphologically
    • EDTA tube: Infant: 1 – 3mls; Paediatric >3mls; Adult 5 – 10mls
  2. Bone marrow aspirate
    • 2 ml in EDTA tube
  3. Other body fluid e.g. cerebrospinal fluid, ascites fluid, pleural fluid, pericardial or vitreous humour) could be used as tumour source in the absence of an appropriate peripheral blood or bone marrow sample.
    • Sterile Universal Container (SUC)


  1. Skin biopsy
  2. Saliva – usually tumour contaminated at presentation. (Not suitable in any suspected or confirmed Covid-19 patients)
    • Should only be collected at a time when it is confirmed that the patient is in remission by morphological, immunophenotypic or PCR-MRD assessment of the bone marrow.
    • Take saliva sample from patient: prepIT.L2P kit (from DNA Genotek) for DNA extraction from saliva samples collected in Oragene collection tubes (obtained from Anifa Pereira, Viapath, Molecular Genetics, 5th Floor Tower Wing, Guy’s Hospital, London, SE1 9RT)
  3. Peripheral Blood
    • Can only be used once the blood is cleared of blasts and the patient confirmed in a bone marrow remission by morphological, immunophenotypic or PCR-MRD assessment of the bone marrow. PB in EDTA: Infant: 1 – 3mls; Paediatric >3mls; Adult 5mls.
  4. Cultured fibroblasts
    • From a skin biopsy – will delay constitutional WGS by ~3 weeks whilst cultured
    • Link to request form – http://www.viapath.co.uk/departments-and-laboratories/genetics
    • Please make request clear that for “Fibroblast culture for WGS in Acute Leukaemia”, and forwarded after culture to GLH DNA Extraction and Plating Service
    • Must be placed in standard specimen bags with a Genomic Medicine Service test order form for Fibroblast culture
    • Sterile Universal containing Hams F10 medium (obtained from Marie Jackson, Consultant Clinical Scientist, Head of Service, Biochemical Genetics Laboratory)
    • Biopsies can be transported at ambient temperature to reach our lab within 24 hours. If taking on Friday afternoon or over the weekend they can be stored in a fridge (do not freeze!) and send on Monday morning.


Turnaround times

See above for each test’s turn-around time target. Please contact the relevant laboratory and/or HMDS reception if more urgent results are required. 

Acceptance criteria

Samples may be rejected for the following reasons:

  • Samples and request form do not show at least three identical patient identifiers
  • No patient name or mismatched name
  • The sample is in the incorrect collection media
  • The sample is not of sufficient volume
  • The sample is too old (greater than 3 days old for certain tests)
  • No NHS number – this is mandatory
  • No indication (YES/NO) of whether the sample is High Risk Pathogen on the form

It is the responsibility of the person collecting the sample to ensure it is correctly labelled.


Our web-based NHS results lookup is available at the following address: https://sehmds.synnovis.report/


To request access to this system please use the following online short form: https://forms.office.com/e/vHezuiPLSL


The final integrated report continues to be available via an emailed pdf to a departmental email meeting the secure email standard (DCB1596).


Lab address and opening hours

All samples and forms should be sent to the address below:

South East HMDS
c/o Central Specimen Reception
Synnovis Analytics
Ground Floor Bessemer Wing
King’s College Hospital
Denmark Hill, London SE5 9RS


For clinical enquiries

If you wish to discuss the results or have any clinical or scientific queries please contact the SE-HMDS Consultants between 9-5pm Monday to Friday.                kch-tr.KHMDC-consultants@nhs.net 

Dr Deborah Yallop (SE-HMDS Co-Director) – Deborah.yallop@nhs.net

Dr Shireen Kassam (SE-HMDS Co-Director) – Shireen.kassam@nhs.net

Dr Guy Hannah (SE-HMDS Consultant) –     guyhannah@nhs.net

Dr Prudence Hardefeldt (SE-HMDS Consultant) prudence.hardefeldt@nhs.net

Dr Henry Wood (SE-HMDS Consultant) henrywood@nhs.net

Additional laboratory contacts

SE-HMDS Central Specimen Reception

For result and general enquiries and to notify of urgent samples contact SE-HMDS CSR. 

Immunophenotyping Laboratory
020 3299 3003

Katy Jones (Head of Immunophenotyping Laboratory) – katy.jones28@nhs.net

Lauren Jamieson (Scientific Lead) – lauren.jamieson1@nhs.net

Charles Manogaran (Operations Lead) – charles.manogaran@nhs.net

Tissue Science
020 3299 3043

Histopathology kch-tr.histopathologyoffice@nhs.net

Advanced Diagnostics kch-tr.advanced-diagnositcs@nhs.net

Laboratory for Molecular Haemato-Oncology
020 7848 5809

Dr Nicholas Lea (Joint Lab. Director) – nlea@nhs.net

Dr Aytug Kizilors (Joint Lab. Director) – akizilors@nhs.net

Cytogenetics Laboratory
020 3299 7637

Frances Aldridge (Head of Cytogenetics) – frances.aldridge@nhs.net

Remi Oke (Operations Lead) – remi.oke1@nhs.net

Zoë Thorn (Operations Lead) – zoe.thorn@nhs.net

With any Whole Genome Sequencing (WGS) test ordered, a Record of Discussion (RoD) form will also need to be submitted. This document is to record the patient’s consent for genomic testing and their choice on taking part in research. Guidance on the patient choice conversation can be found here
This RoD form will be available for clinicians to download from this webpage. Once completed with the patient, it can be send to the lab with the corresponding test order form and sample.
Tests available to order will be listed in the National Genomic Test Directory. A test order form will soon be made available for clinicians on this webpage to download and complete. This form will include the address of the laboratory that the appropriate sample and completed form needs to be sent to.
Until the new Genomic Laboratory Service goes live, please continue to follow existing test order processes.
Later this year, the online test ordering tool for Whole Genome Sequencing will be integrated into the National Genomics Informatics System (NGIS) and clinicians will be able to search or filter to find a clinical indication, confirm eligibility criteria and start the test request process for their patient.