issued by United Kingdom Accreditation Service · robot and ABI 3130 X1 Genetic analyser and ABI 37300 Genetic analyser Using SOP’s SMD124 PCR and Sanger Mutation surveyor using

Assessment Manager: VB Page 1 of 24

Schedule of Accreditation issued by

United Kingdom Accreditation Service

2 Pine Trees, Chertsey Lane, Staines-upon-Thames, TW18 3HR, UK

9839

Accredited to

ISO 15189:2012

The Royal Marsden NHS Foundation Trust

Issue No: 001 Issue date: 04 September 2018

Haemato-Oncology Department

The Royal Marsden Hospital

15 Cotswold Road

Sutton

SM2 5PT

Contact: Sue Alexander

Tel: +44 (0)20 8661 3354

E-Mail: [email protected]

Testing performed at the above address only

DETAIL OF ACCREDITATION

Materials/Products tested

Type of test/Properties

measured/Range of measurement

Standard specifications/

Equipment/Techniques used

HUMAN BODY FLUIDS Molecular Haemato-Oncology

activities for the purpose of clinical diagnosis

Procedures documented in manufacturer’s equipment manuals in conjunction with documented in- house procedures by the following methods:

Fresh, frozen or fixed human tissue or cells (Blood and Bone marrow)

DNA Extraction

Unfixed tissue Qiagen Qiasymphony SP

Using SOP SMD01 Specimen reception and sample pre-processing SMD109 Cell separation for Chimerism analysis SMD102 DNA extraction Qiasymphony SMD25 DNA Extraction using QIAmp Blood mini kit QIAcube SMD70 DNA Extraction-QIAmp Midi Kit SMD90 Isolation of c.DNA from plasma specimens using the Roche Cobas sample preparation kit

Fixed tissue- FFPE Manual technique using SOP

SMD01 Specimen reception and sample pre-processing SMD73 DNA extraction using Qiagen kit

Fresh frozen tissue Manual process using SOP

SMD81_DNA extraction from fresh frozen tissue using Qiamp mini kit

9839

Accredited to ISO 15189:2012


United Kingdom Accreditation Service 2 P ine Trees , Cher t sey Lane, S ta i nes -upon-Thames , TW 18 3HR, UK



Testing performed at main address only







HUMAN BODY FLUIDS (cont’d) Molecular Haemato-Oncology

activities for the purpose of clinical diagnosis (cont’d)


Plasma Manual process SOP SMD69

separation of plasma from whole blood SMD67 Extraction of circulating free DNA from plasma using the Qiagen QIAmp circulating QIAmp circulating nucleic acid kit SMD90 Isolation of cfDNA from plasma specimens using Roche Cobas sample preparation kit

Qiagen QIASymphony SP: Using SOP SMD100 Extraction of cell- free DNA from plasma using the QIAsymphony SP instrument

Saliva DNA Extraction manual process

using SOP SMD 139 purification of DNA from the Oragene Saliva collection kit

Blood, bone marrow, biological fluids- unfixed tissue

RNA extraction Manual Process using SOP SMD01 Specimen reception and sample pre-processing SMD03 Extraction of RNA from biological samples (with QIAgen RNeasy mini kit)

Formalin fixed paraffin embedded tissues

RNA extraction Manual Process using SOP SMD01 Specimen reception and sample pre-processing SMD04 Extraction of RNA from FFPE tissues using Ambion’s Recover ALL nucleic acid purification kit

RNA derived from blood, bone marrow and biological fluids

cDNA synthesis-unfixed using Thermal cycler and SOP SMD11 cDNA Synthesis

9839
















RNA derived from formalin fixed paraffin embedded tissues

cDNA synthesis-fixed using Thermal cycler and SOP SMD109 cDNA Synthesis from FFPE derived RNA

Blood, bone marrow, biological fluids

Detection of fusion genes in acute leukaemias: AML Panel PML-RARA RUNX1-RUNX1T1 CBFB-MYH11 BCR-ABL1

RT-quantitative PCR for the detection of acute leukaemias using ABI 7500 Fast sequence detection system and SOP SMD05 RQ-PCR For detection and MRD Monitoring of translocation in acute leukaemias.

Blood, bone marrow, biological fluids

Detection of fusion genes in acute leukaemias: ALL and CML Panel BCR-ABL1 Etv6-RUNX1 TCF-PBX1 KNT2-AFF1 STIL-TAL1

RT-quantitative PCR for the detection of acute leukaemias using ABI 7500 Fast sequence detection system and SOP SMD05 RQ-PCR For detection and MRD Monitoring of translocation in acute leukaemias.

MRD analysis of acute leukaemia or

chronic myeloid leukaemia translocations

RT-quantitative PCR MRD analysis using ABI 7500 Fast sequence detection system and SOP SMD05 RQ-PCR For detection and MRD Monitoring of translocation in acute leukaemias.

Blood, bone marrow, biological fluids, DNA from external sources

Detection of SNPs according to Powerplex kit

PCR and fragment analysis for post Allogenic Chimerism and donor/recipient genotyping analysis using ABI Prism 3500 genetic analyser thermocycler and SOP SMD10 Post transplant Chimerism analysis using the Powerplex 16 kit (Promega)

9839
















Formalin fixed paraffin embedded tissues

Detection of fusion genes in soft tissue sarcomas

RT-PCR using ABI 7500 Fast sequence detection system and SOP SMD17 Real time PCR for detection of fusion genes in soft tissue sarcomas

B2M SS18-SSX1/2 (SSX1/2-SYT) PAX3-FOXO1 (PAX3-FKHR) PAX7-FOXO1 (PAX7-FKHR) EWSR1-ERG (EWS-ERG) EWSR1-FLI1 (EWS-FLI1) EWSR1-FLI1 (EWS-FLI1) EWSR1-ATF1 (EWS-ATF1) EWSR1-NR4A3 (EWS-CHN) TAF15-NR4A3 (TAF2N-CHN) EWSR1-CREB1 (EWS-CREB1) FUS-DDIT3 (FUS-CHOP) ASPSCR1-TFE3 (ASPL-TFE3) FUS-CREB3L2 JAZF1-SUZ12 (JAZF1-JJAZ1) ETV6-NTRK3 YWHAENUTM2A/B HEY1-NCOA2 Blood, bone marrow, biological fluids, DNA from external sources

NPM1 Exon 12 mutations PCR and Genescan analysis using ABI Prism 3500 genetic analyser thermocycler and SOP SMD12 NPM1 Mutation detection by PCR and Genescan

Peripheral blood and bone marrow, DNA from external sources

JAK2 V617F and CALR Exon 9 mutation detection

PCR and Genescan analysis using ABI Prism 3500 genetic analyser thermocycler and SOP SMD79 Detection of JAK2 V617F and CALR and MPL mutations in MPNs


MPL Exon 10 mutations PCR and Genescan analysis using ABI Prism 3500 genetic analyser thermocycler and SOP SMD79 Detection of JAK2 V617F and CALR and MPL mutations in MPNs

9839
















Formalin fixed paraffin embedded tissues, plasma

EGFR, BRAF and NRAS Mutations RT-PCR using Cobas z analyser 480 and SOP SMD41 Detection of EGFR mutations using the Cobas mutation test

SMD 123 detection of BRAF/NRAS Mutations using the Cobas

BRAF/NRAS mutation tests Formalin fixed paraffin embedded tissues, DNA from external sources

KIT/PDGFRA mutations SSCA Capillary electrophoresis and thermocycler and Hamilton Starlet robot ABI 3130 X1 Genetic analyser ABI 37300 Genetic analyser Using SOP’s SMD29 Detection of KIT/PDGFRA mutations by CE-SSCA SMD124 PCR and Sanger sequencing Mutation surveyor using SMD28

KIT/PDGFRA Mutations IDH Mutations SSCA Capillary electrophoresis and

thermocycler and Hamilton Starlet robot ABI 3130 X1 Genetic analyser ABI 37300 Genetic analyser Using SOP’s SMD103 Detection of IDH1 and IDH2 mutations by multiplex CE-SSC SMD124 PCR and Sanger sequencing Mutation surveyor using SMD28

PCR products Thermocycler and Hamilton Starlet

robot and ABI 3130 X1 Genetic analyser and ABI 37300 Genetic analyser Using SOP’s SMD124 PCR and Sanger Mutation surveyor using SMD28

9839
















Formalin fixed paraffin embedded tissues, DNA from external sources

Next generation sequencing Thermal cycler, tape station 2200 Illumina MiSeq and NGS Platform and ABI 7500 Fast sequence detection system using SOP SMD134 Nextera S rapid capture enrichment protocol

SMD 138 Nextera SMP2 target capture analysis

SMD133 Sequencing on NextEsq500

AKT1 ALK BRAF CCND1 CCND2 CCND3 CCNE1 CDK2 CDK4 CDKN2A CNTL EGFR ERBB2 FGFR2 FGFR3 HRAS KRAS MET NF1 NRAS NTRK1 PIK3CA PTEN RB1 RET ROS1 STK11 SWAP TSC1 TSC2

9839
















BRAF

KRAS NRAS PIK3CA TP53

Next generation sequencing Thermal cycler, tape station 2200 and Illumina MiSeq and NGS Platform using SOP SMD66 NGS MiSeq TSCA Set up and SMD 136 TSCA NGS analysis of CRC panel SMD132 Variant interpretation and classification

SMD131 Variant studio SMD 133 Sequencing on NextSeq500


Targeted capture Nimblegen Baits assay

Next generation sequencing Thermal cycler, tape station 2200 Illumina MiSeq NGS Platform ABI 7500 Fast sequence detection system using SOP SMD74: Targeted capture of DNA using KAPA Hyperplus Prep kit and Nimblegen BaitsSMD91 Somatic mutations report

SMD132 Variant interpretation and classification

SOP SMD78 Molecular diagnostics laboratory NGS analysis of BRCA1 and 2 in ovarian cancer SMD130 Alamut, SMD131 Variant studio, SMD133 Sequencing on NextSeq500

ABL1 ABCA1 ACVR1 AKT1 AKT2 AKT3 ALK AMER1 ANKRD26 ANTXR2 APC ARAF ARID1A

9839
















Blood, bone marrow, biological fluids, DNA from external sources (cont’d)

Targeted capture Nimblegen Baits assay (cont’d)




ARID1B ASXL1 ATM ATRX AURKA B2M BAP1 BCL2 BCOR BCORL1 BIRC3 BOD1L BRAF BRCA1 BRCA2 BRCC3 BRIP1 BTG1 BTK C19MC CALR CARD11 CASP8 CBL CBLB

9839





















CCND1 CCND2 CCND3 CCNE1 CCNE2 CD274 CD79A CD79b CDH1 CDK12 CDK2 CD4 CDK6 CDKN1A CDKN1B CDKN2A CDKN2B CDKN2C CEBPA CHEK2 CIC CKDN1B CKS1B CREBBP CRLF1

9839





















CSF3R CSNK1A1 CTCF CTNNB1 CUX1 CXCR4 DAXX DCLRE1C DDR2 DDX1 DDX3X DDX41 DICER1 DIS3 DNMT3A DNMT3B DOCK2 DROSHA EBF1 EGFR EGR ELMO1 EP300 ERBB2 ERBB3

9839





















ERBB4 ESR1 ETNK1 ETV6 EZH2 F2R FADD FAM46C FANCL FAT1 FBXW7 FGF10 FGFR1 FGFR2 FGFR3 FGFR4 FLT3 FOXL2 FOXO1 FRS2 FUBP1 GATA1 GATA2 GATA3 GLI2

9839





















GNA11 GNAQ GNAS GNB1 GPRC5A H3F3A H3F3B HIST1H1B_1 HIST1H1C_1 HIST1H1D_1 HIST1H1E_1 HIST1H3B HIST1H3C HIST2H3C HRAS ID3 IDH1 IDH2 IGF1R IGF2 IKZF1 IL3RA IL7R IRF1 IRF4

9839





















JAK1 JAK2 JAK3 KDM6A KIT KLF2 KMT2A KMT2C KMT2D KMT2E KRAS LAMB4 LUC7L2 MAP2K1 MAP2K2 MAP2K4 MAP3K1 MAP3K14 MAPK1 MCL1 MDM2 MDM4 MEF2B MET MLH1

9839





















MLH2 MPL MSH2 MSH6 MTOR MYC MYCL1 MYCN MYD88 MYOD1 NCOR1 NCOR2 NF1 NF2 NFE2 NFKBIE NOTCH1 NOTCH2 NOTCH3 NPM1 NRAS NRD1 NSD1 NT5C2 NUP98

9839





















OTX2 PALB2 PAX5 PBRM1 PDCD1LG2 PDGFRA PDGFRACN PHF6 PHOX2B PIGA PIK3CA PIK3CD PIK3R1 PLCG2 PMS1 PMS2 POLE POT1 PPM1D PRKAR1A PRPF8 PTCH1 PTCH2 PTEN PTPN11

9839





















PTPRT RAD21 RAD50 RAD51C RAD51D RAF1 RB1 RELAtx RET RFN43 RHOA RICTOR RIT1 ROS1 RUNX1 SAMHD1 SETBP1 SETD2 SF1 SF3B1 SH2B3 SMAD2 SMAD3 SMAD4 SMARCA2

9839





















SMARCA4 SMARCB1 SMARCE1 SMC1A SMC3 SMO SOCS1 SOX2 SRSF2 STAG2 STAT3 STAT5B SUFU TCF3 TCF7L2 TERT TET1 TET2 TFE3 TG TNFAIP3 TP53 TP63 TRAF2 TRAF3

9839





















TSC1 TSC2 U2AF1 U2AF2 UGT1A1 VHL WT1 WTX XPO1 YAP1 YES1 ZRSR2 Peripheral blood and bone marrow, DNA from external sources- unfixed tissue and Formalin fixed paraffin embedded tissues, DNA from external sources- fixed tissue

IG Gene re-arrangements Thermal cycler and Hamilton Starlet robot and ABI 3500 Genetic analyser using SOP’s SMD09 B and T cell detection by PCR and Genescan

TCR Gene re-arrangements Thermal cycler and Hamilton Starlet

robot and ABI 3500 Genetic analyser using SOP’s SMD09 B and T cell detection by PCR and Genescan

9839
















Peripheral blood and bone marrow, DNA from external sources- unfixed tissue

Ig Variable regions in chronic Lymphocytic leukaemia

Thermal cycler and ABI 3500 Genetic analyser Using SOP’s SMD16 Analysis of the mutational status of the IVGH Genes

Formalin fixed paraffin embedded tissues, DNA from external sources-fixed tissue

Rare mutations in the following: QX200 Automated Droplet generator PX1 PCR plate sealer DG32 Automated droplet generator cartridges, C1000 touch thermal cycler with 96 well deep well reaction module QX200 Droplet reader PC and Quantasoftware using SOP SMD115 Multiplex ddPCR for plasma match, SMD117 Multiplex ddPCR for PIPA, SMD94 Copy number variation detection of FGFR2 using droplet digital PCR

AKT1 E17K ALK APC ARDI1A ATM BRAF ESR1 Multiplex 1 ESR1 Multiplex 2 HER2 Multiplex 1 HER2 Multiplex 2 HER2 Multiplex 3 HRAS H3F3A KRAS MYOD1 NOTCH1 NRAS PIK3CA PIK3CA Exon 20 Mix PIK3CA Exon 9 Mix PTEN PTPN11 RET SMARCA4 TP53

9839
















Blood, bone marrow, CSF, Biopsies including fine needle aspirates, other body fluids

Diagnosis and monitoring of haematological malignancy and bone marrow failure syndromes

Microscopic examination/morphological assessment of stained material using Hematek automated staining machine using modified Wright’s stain Shandon Cytocentrifuge II and SOP Immuno 4 Specimen reception Immuno 5 Film preparation and staining Immuno 18 Processing tissue biopsies and body fluids Immuno 25 Immuno-morphology report Immuno 45 Cytospin preparation Immuno 46 Microscope use and maintenance Immuno 54 Hematek staining machine Immuno 67 Iron staining

9839














activities for the purpose of clinical

diagnosis (cont’d)


Blood, bone marrow, CSF, Biopsies including fine needle aspirates, other body fluids

Diagnosis and monitoring of

haematological malignancy and

bone marrow failure syndromes

Immunophenotyping by Flow cytometry and monoclonal antibodies with 8 colour FACS Canto II Flow cytometer SOP Immuno 4 Specimen reception Immuno 19 Operation of FACS Canto II Immuno 30 Start and end of day procedures Immuno 33 Reagent stock control Immuno 7 Testing and rationale and panels Immuno 8 B-Lymphoproliferative disorders Immuno 9 Mature T Cell disorders Immuno 10 Plasma cell dyscrasias Immuno 11 Acute leukaemias Immuno 17 MRD Detection Immuno 34 Antibody cocktail Preparation

Acute Leukaemia: AML, B-ALL and

T-ALL.

Chronic Myeloid disorders: MDS,

CML, CMML.

Mature Lymphoid Disorders: B & T

Lymphoproliferative

disorders, Lymphoma and

Plasma cell dyscrasias

Detection of the following markers:

CD1a CD2 CD3 CD4 CD5 CD7 CD8 CD10 CD11c CD13 CD14 CD15

9839
















Blood, bone marrow, CSF, Biopsies including fine needle aspirates, other body fluids (cont’d)

Diagnosis and monitoring of haematological malignancy and bone marrow failure syndromes (cont’d)

Immunophenotyping by Flow cytometry and monoclonal antibodies with 8 colour FACS Canto II Flow cytometer SOP Immuno 4 Specimen reception Immuno 19 Operation of FACS Canto II Immuno 30 Start and end of day procedures Immuno 33 Reagent stock control Immuno 7 Testing and rationale and panels Immuno 8 B-Lymphoproliferative disorders Immuno 9 Mature T Cell disorders Immuno 10 Plasma cell dyscrasias Immuno 11 Acute leukaemias Immuno 17 MRD Detection Immuno 34 Antibody cocktail Preparation

CD16 CD19 CD20 CD22 CD23 CD25 CD33 CD34 CD38 CD43 CD45 CD52 CD56 CD57 CD64 CD66b CD79a CD81 CD94 CD103 CD117 CD123 CD138

9839
















Blood, bone marrow, CSF, Biopsies including fine needle aspirates, other body fluids (cont’d)

Diagnosis and monitoring of haematological malignancy and bone marrow failure syndromes (cont’d)

Flow cytometry and monoclonal antibodies with 8 colour FACS Canto II Flow cytometer SOP Immuno 4 Specimen reception Immuno 19 Operation of FACS Canto II Immuno 30 Start and end of day procedures Immuno 33 Reagent stock control Immuno 7 Testing and rationale and panels Immuno 8 B-Lymphoproflierative disorders Immuno 9 Mature T Cell disorders Immuno 10 Plasma cell dyscrasias Immuno 11 Acute leukaemias Immuno 17 MRD Detection Immuno 34 Antibody cocktail Preparation

Acute Leukaemia: AML, B-ALL and

T-ALL.

Chronic Myeloid disorders: MDS,

CML, CMML.

Mature Lymphoid Disorders: B & T

Lymphoproliferative

disorders, Lymphoma and

Plasma cell dyscrasias

Immunophenotyping using the following markers

CD200 Bcl2 Epcam FMC7 HLA-DR IgM Kappa Ki67 Lambda MPO TCL1 TCR TdT

9839
















Blood Diagnosis and monitoring of

Paroxysmal Nocturnal Haemoglobinuria (PNH)

Flow cytometry and 8 colour FACS Canto II Flow cytometer SOP Immuno 66 PNH Detection

Using the following monoclonal

antibodies:

CD55 CD59 CD235a CD16 CD15 CD14 CD24 CD33 Flaer Alexa-488 Blood, stem cell harvest products (PB, BM, Cord blood)

Stem cell (CD34+) Enumeration Flow cytometry and 8 colour FACS Canto II Flow cytometer SOP Immuno 64 CD34 Enumeration

END

Documents

issued by United Kingdom Accreditation Service · robot and ABI 3130 X1 Genetic analyser and ABI 37300 Genetic analyser Using SOP’s SMD124 PCR and Sanger Mutation surveyor using