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).

• 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)
• Rare translocations: (multiple KMT2A translocations: PICALM-MLLT10 DEK-NUP214, RUNX1- CBFA2T3, RUNX1-PRDM16, RUNX1-MECOM, NUP98-NSD1, NUP98-HOXA9, NUP98-KDM5A, NPM1-MLF1, KAT6A-CREBBP, KAT6A-NCOA2, FUS-ERG, CBFA2T3-GLIS2, MN1-ETV6, MNX1-ETV6, RANBP2-ALK, RUNX1-ZFPM2, ETV6-ABL, SSBP2-CSF1R, RAC1-NIPBL, ATAD5-LRR37B, EP300-CIC, COG5-EXOC4, FOXO4-KAT6B, MYB-GATA1, NIPBL-HOX89, NICOA2-PRDM14, ETV6-RPL31, TEC-MLLT10, DDX3X-MLLT10, SMARCA2-ETV6
• 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).