Short User Guide and Request Form - Oxford Molecular Diagnostics
Contents
1. Prenatal Diagnosis of sickle cell disease B thalassaemia and Hb H Bart s hydrops fetalis available by prior arrangement with the laboratory Turnaround time 3 5 working days CPA Accredited Medical Laboratory Oxford Biomedical Research Centre National Institute for Reference No 1040 Health Research Haemato Molecular Diagnostic Service User Guide Version 5 03 12 2013 Page 4 of 11 OXFORD Ri Molecular Diagnostics Centre Oxford University Hospitals INHS NHS Trust 3 Iron Regulation Indications family history of iron overload unexplained high ferritin Indications Test Specimen Turnaround Time Required On all patients with suspected HFE gene mutation analysis 4ml EDTA 2 weeks C282Y H63D peripheral blood Haemochromatosis Hyperferritinaemia with normal SLC40A gene Ferroportin 4ml EDTA 2 8 weeks serum iron and Transferrin IRE 5 UTR of FTL gene peripheral blood depending on saturation FTL gene complexity Hereditary Hyperferritinaemia Carrier and full genetic screening by cataract syndrome sequencing Patients with iron overload HFE2 HAMP SLC40A1 TFR2 and 4ml EDTA 2 8 weeks lethargy liver disease HFE gene mutation analysis peripheral blood depending on a meee Dosage analysis MLPA for COMPIEMLY xi pclae ai ne partial complete HFE HFE2 HAMP E Mesy rena TFR2 and SLC40A1 gene cee deletions duplications Juvenile haemochromatosis Severe iron overload diabetes2. cardiomyopathy endocrine problems hypogonadotrophic hypogonadism Asian patients with suspected HFE2 and HAMP mutation analysis 4ml EDTA 2 8 weeks HC first then the rest of the genes peripheral blood depending on sip les rade Apera sal Dosage analysis MLPA for complexity ie ome re ne PrO Sers partial complete HFE HFE2 HAMP Seda ee TFR2 and SLC40A1 gene M esas deletions duplications Iron overload negative for the 2 HOS Tean Repnlatory Gene pau 4ml EDTA 8 weeks North E is based on the following gene sets ibheral blood Common Sora pee TFR2 SLC40A1 HFE HFE2 HAMP P amp Pneral 0100 muon TF FTL IRE of FTL SLCIIA2 Non Caucasians with TMPRSS6 HEPH FTH CP ALAS2 unexplained iron overload BMP4 BMP6 SMAD4 CPA Oxford Biomedical Research Centre National Institute for Health Research Haemato Molecular Diagnostic Service User Guide Accredited Medical Laboratory Reference No 1040 Version 5 03 12 2013 Page 5 of 11 OXFORD Ri Molecular Diagnostics Centre Oxford University Hospitals INHS NHS Trust Indications Test Specimen Turnaround Time Required Tron regulatory iron deficiency N GS TSCA Iron Regulatory Gene uae 4ml EDTA ao anaemia IRIDA unexplained is based on the following gene sets peripheral blood anaemia Hyperferritinaemia Hereditary Hyperferritinaemia Cataract Syndrome HHCS Atransferrinaemia Aceruloplasminaemia Hereditary ferritinopathy X linked Siderobl
3. 3 D Health Research Haemato Molecular Diagnostic Service User Guide Version 5 03 12 2013 Page 9 of 11 OXFORD Ri Molecular Diagnostics Oxford University Hospitals LYZKJ Centre NHS Trust Disorder Tests Specimen Required Turnaround Time Fluid 5 10 ml as appropriate Please note blood bone marrow smears should be unstained PNH FLAER CD14 CD24 CD59 Blood 10ml EDTA and or Usually processed Bone marrow 1 2 ml within 24 hours EDTA CSF and Pleural Fluid 5 10 ml as appropriate Please note blood bone marrow smears should be unstained Results are communicated by e mail and telephone All results are discussed at the MDT meetings and authorised weekly 5 Solid Tumours Identification of clinically actionable mutations utilising the COBAS system or tumour profiling using a clinically validated NGS based Cancer Panel Disorder Tests Specimen Required Turnaround Time Colorectal Cancer KRAS BRAF NRAS 10 x Sum sections mounted on 5 working days 50 gene NGS cancer panel unstained slides Lung Cancer EGFR KRAS EML4 ALK 10 x Sum sections mounted on 5 working days 50 gene NGS cancer panel unstained slides For EML4 ALK 3x Sum unstained sections on coated slides Melanoma BRAF NRAS 10 x Sum sections mounted on 5 working days 50 gene NGS cancer panel unstained slides Other Cancer 50 gene NGS cancer panel 10 x Sum sections mounted on 10 working days unstained
4. 5 2 weeks Boel Igk Vk Jk Vk Kde intron Kde rearrangements BEEE Rolled clonality Sections IgL rearrangements using BIOMED 2 CE marked 4ml of primers aoni IgH incomplete D J rearrangements using BIOMED peripheral primers blood or bone marrow Lymphoma TCRB and TCRG and TCRD gene rearrangements DNA Minimum 5 2 weeks T cell using BIOMED 2 CE marked primers FFPE Rolled clonality Sections 4ml of EDTA peripheral blood or bone marrow Chronic Somatic hypermutation analysis using leader and DNA 4ml of 4 weeks lymphocytic biomed 2 primers EDTA pukami TP53 mutation analysis by FISH and sanger Blood or BM peripheral blood or sequencing slide DNA bone marrow Chronic BCR ABL t 9 22 by multiplex PCR and quantitative RNA 20ml of 2 weeks myeloid PCR EDTA leukaemia peripheral blood or 2ml of bone marrow CPA UNIVER OXFORD Oxford Biomedical Research Centre National Institute for Health Research Haemato Molecular Diagnostic Service User Guide Accredited Medical Laboratory Reference No 1040 Version 5 03 12 2013 Page 7 of 11 OXFORD Ri Molecular Diagnostics Centre Oxford University Hospitals INHS NHS Trust Disorder Test Sample Type Specimen Required Turnaround Time Myeloproliferativ e disorders JAK2 V617F mutation by allele specific PCR and pyrosequencing JAK2 Exon 12 and MPL W515 mutation analysis BCR ABL by multiplex PCR DNA DNA RNA 4ml of EDTA per
5. Required Carrier analysis and full genetic screen peripheral blood depending on Dosage analysis MLPA for complexity partial complete F9 gene deletions duplications VWD Detection of known VWF gene 4ml EDTA 2 8 weeks mutations by direct sequencing peripheral blood depending on Targeted VWF gene screening for Type complexity 2A 2B 2N and 2M by direct sequencing Full genetic screening for Type 1 and Type 3 VWD Dosage analysis MLPA for partial complete VWF gene deletions duplications Other Disorders F5 F7 F10 F11 FI3A by direct 4ml EDTA 2 8 weeks sequencing peripheral blood depending on Fibrinogenaemias a B and y genes complexity Antithrombin deficiency SERPINCI gene Carrier and full gene analysis Dosage analysis MLPA for partial complete F7 and SERPINCI gene deletions duplications 4ml EDTA Platelet Disorders peripheral blood May Hegglin anomaly MYH9 gene 2 8 weeks Glanzmann Thrombasthenia UTGA2B amp depending on ITGB3 genes complexity Bernard Soulier syndrome Gplba Gp9 and Gplbb genes Platelet type pseudo VWD Gplba gene Thrombophilia Factor V Leiden and prothrombin 20210 4ml EDTA 2 weeks mutations by multiplex PCR peripheral blood CPA Oxford Biomedical Research Centre National Institute for Health Research Haemato Molecular Diagnostic Service User Guide Accredited Medical Laboratory Reference No 1040 Version 5 03 12 2013 Page 3 of 11 OXFORD Ri Molecular Diagnostics Oxford Uni
6. Fluid 6 10 mids Myeloid antibodies CD13 CD14 appropriate Please note CD33 CD64 CD117 MPO CD11 blood bone marrow smears Others CD34 CD56 HLA DR should be unstained TdT CD41 NGZ Glycophorin A B CD3 CD5 CD10 CD19 CD20 Blood 10ml EDTA and or Usually processed lymphoproliferative CD23 CD38 CD79b kappa lambda Bone marrow 1 2 ml within 24 hours FMC7 EDTA CSF and Pleural Fluid 5 10 ml as appropriate Please note blood bone marrow smears should be unstained T NK CD2 CD3 CD4 CD5 CD7 CD8 Blood 10ml EDTA and or Usually processed lymphoproliferative CD16 CD19 CD56 kappa lambda Bone marrow 1 2 ml within 24 hours CD57 TCR CD25 a B y 6 EDTA CSF and Pleural Fluid 5 10 ml as appropriate Please note blood bone marrow smears should be unstained Hairy cell B lymphoproliferative panel CD11c Blood 10ml EDTA and or Usually processed leukaemia CD22 CD25 CD103 Bone marrow 1 2 ml within 24 hours EDTA CSF and Pleural Fluid 5 10 ml as appropriate Please note blood bone marrow smears should be unstained Multiple myeloma CD19 CD38 CD45 CD56 CD138 Blood 10ml EDTA and or Usually processed kappa lambda Bone marrow 1 2 ml within 24 hours EDTA CSF and Pleural y CPA GaWese eae Accredited Medical Laboratory x Oxford Biomedical Research Centre National Institute for Reference No 1040 0 gt 6 10
7. slides Specimen requirements 10 x 5um sections mounted on unstained slides or 5 if marked neoplastic area gt 2cn Multiple sections can be placed on a single side Please clean microtome blade and water bath thoroughly before cutting sections to avoid cross contamination and false positive results Please include a H amp E stained section from same block with tumour boundary marked Tissue in this ring should be gt 70 neoplastic Cytological material can be sent as for tissue blocks or send maximum available material smears touch preps etc on slides CPA Accredited Medical Laboratory pss AEs Oxford Biomedical Research Centre National Ii NHS Refi No 1040 x i ational Institute for ererence No 4 10 28D Health Research Haemato Molecular Diagnostic Service User Guide Version 5 03 12 2013 Page 10 of 11 OXFORD Ri Molecular Diagnostics Oxford University Hospitals LYZKJ Centre NHS Trust Genes included in the 50 gene panel BRAF FGFR1 CTNNB1 SMO JAK3 EZH2 KRAS ERBB2 CDKN2A SMAD4 AKT1 GNA11 NRAS MET ABL VHL KDR GNAQ PDGFRA FGFR3 NOTCH1 NPM1 ALK IDH2 PIK3CA FLT3 ATM MPL JAK2 SRC KIT RB1 ERBB4 GNAS MLHI1 APC PTEN CSFIR FGFR2 HNF1A HRAS CDH1 EGFR RET STK11 FBXW7 TP53 SMARCB1 PTPN11 IDH1 Consultant Haematologist Head of BRC NHS Translational Molecular Diagnostics Dr Anna Schuh MD PhD MRCP FRCPath Consultant Haematologist Dr Chris Hatton Consultant Clinical Scientist Scientific Lead Dr Sh
8. OXFORD Ri Molecular Diagnostics Oxford University Hospitals LYZKJ Centre NHS Trust Short User Guide Oxford BRC Haemato Molecular Diagnostic Service The Oxford University Hospitals NHS trust s department of Haematology provides a comprehensive molecular diagnostic service for a range of haematological conditions The services offered are divided into 4 main areas 1 Haemostasis Haemophilia and thrombophilia genetic testing 2 Haemoglobinopathies A national service offering extensive molecular investigation of a thalassaemia B thalalassaemia abnormal haemoglobins and the sickle cell syndromes 3 Iron Regulation Screening for the HFE gene mutations 4 Haemato oncology An integrated phenotypic immunophenotyping and molecular service for the management of haematological malignancies 5 Solid tumours Integrated pathology and genomics CE marked diagnostics of response prediction and cancer gene mutation panel utilising next generation sequencing This document is intended as a brief and provisional introduction to our services More detailed information on all aspects of our service can be obtained from our web site http www oxford translational molecular diagnostics org uk or requested by e mail from oxford molecularhaem nhs net General Information Laboratory address for specimen reception Molecular Haematology Level 4 John Radcliffe Hospital Headington Oxford OX3 9DU CPA Accreditation Accr
9. astic anaemia TFR2 SLC40A1 HFE HFE2 HAMP TF FTL IRE of FTL SLC11A2 TMPRSS6 HEPH FTH1 CP ALAS2 BMP4 BMP6 SMAD4 4 Haemato Oncology a Molecular Genetics minimum residual disease monitoring Molecular genetic testing uses PCR DNA and RT PCR RNA methodologies to detect common chromosomal abnormalities of clinical diagnostic or prognostic significance in malignant haematological conditions UN 0 Disorder Test Sample Type Specimen Turnaround Required Time Acute BCR ABL t 9 22 by multiplex PCR and quantitative RNA 20ml of 3 5 working lymphoblastic PCR EDTA days leukaemia peripheral blood or 2ml of bone marrow Acute NPM1 FLT3 ITD and D835TK DNA 4ml of 2 weeks Myeloid EDTA Leukaemia peripheral blood or bone marrow CPA IVER XFORD Oxford Biomedical Research Centre National Institute for Health Research Haemato Molecular Diagnostic Service User Guide Accredited Medical Laboratory Reference No 1040 Version 5 03 12 2013 Page 6 of 11 OXFORD Ri Molecular Diagnostics Oxford University Hospitals INHS Centre NHS Trust Disorder Test Sample Type Specimen Turnaround Required Time Acute PML RARA t 15 17 CBFB MYH11 type A RNA 20ml of 3 5 working Myeloid RUNX1 RUNXT1 EDTA days Leukaemia peripheral blood or 2ml of bone marrow Lymphoma IgH FR1 FR2 FR3 rearrangements DNA Minimum
10. edited Ref No 1040 Lab service hours 9 00 5 00 Monday to Friday Enquiries and information Website http www oxford translational molecular diagnostics org uk y CPA UNIVERSITY ie NHS Accredited Medical Laboratory 0 4 10 4D Oxford Biomedical Research Centre National Institute for Reference No 1040 Health Research Haemato Molecular Diagnostic Service User Guide Version 5 03 12 2013 Page l of 11 OXFORD Ri Molecular Diagnostics Oxford University Hospitals LVK Centre NHS Trust E mail for advice and enquiries oxford molecularhaem nhs net Haematology molecular genetics laboratory 01865 572769 Immunophenotyping laboratory 01865 572827 Fax 01865 572775 Clinical and BRC Research leads Dr Anna Schuh MD PhD MRCP FRCPath Dr Chris Hatton FRCP FRCPath Scientific Director Dr Shirley Henderson MSc PhD Business Manager Dr Nick Housby PhD Haematology Laboratory Manager Mr Dan Smith C Sci FIBMS Request Form and Samples All samples should be accompanied by a completed request form page 6 For haemoglobinopathy investigations a more detailed NHRL request form is available from our web site Specimens and forms should have a minimum of 4 patient identifiers including patient surname first name dob and hospital number Please provide as much clinical and laboratory information as possible including a brief clinical history and any others recent results ava
11. ilable on the patient Indicate on the form the sample type date of collection and the investigation that you are requesting Please remember to give full contact details for results and reports The sample type required for each investigation is shown in the appropriate section below All samples should be addressed to Molecular Haematology and sent to the specimen reception of the Haematology Laboratory at the John Radcliffe Hospital Level 4 Address is given in general information page 1 Investigations Offered 1 Haemostasis Disorder Tests Specimen Turnaround Time Required Haemophilia A FS gene intron 22 inversion inverse 4ml EDTA 2 8 weeks PCR peripheral blood depending on 7 FS gene intron 1 inversion inverse 4ml EDTA complexity pace nC peripheral blood 2 8 weeks FS amp mutations by direct sequencing Acne neon Carrier analysis and full genetic screen ee ie Dosage analysis MLPA for P y partial complete F8 gene deletions duplications Haemophilia B F9 mutations by direct sequencing 4ml EDTA 2 8 weeks CPA Renee NHS Accredited Medical Laboratory 0 4 10 4D Oxford Biomedical Research Centre National Institute for Reference No 1040 Health Research Haemato Molecular Diagnostic Service User Guide Version 5 03 12 2013 Page 2 of 11 OXFORD Ry Molecular Diagnostics Oxford University Hospitals INHS Centre NHS Trust Disorder Tests Specimen Turnaround Time
12. ipheral blood or bone marrow 4ml of EDTA peripheral blood or bone marrow 20ml of EDTA peripheral blood or 2ml of bone marrow 2 weeks 4 weeks 2 weeks Haemopoietic Stem Cell Transplantation SNP Chimerism total white cell CD3 and CD34 positive cells DNA BM PB 4ml of EDTA peripheral blood or bone marrow 2 weeks Non Hodgkin s lymphomas NHL FISH studies for chromosomal rearrangements t 8 14 14518 11514 11518 255 del17p13 1 11q22 3 Performed only after histopathology review FFPE Slides BM PB FFPE Slide 4ml of EDTA peripheral blood or bone marrow 2 weeks Must arrive in lab within 36 hours of collection CPA Accredited Medical Laboratory Reference No 1040 National Institute for Health Research Oxford Biomedical Research Centre Version 5 03 12 2013 Page 8 of 11 Haemato Molecular Diagnostic Service User Guide OXFORD Ri Molecular Diagnostics Oxford University Hospitals LYZKJ Centre NHS Trust b Immunophenotyping Immunophenotyping is performed on a six channel Becton Flow Cytometer The following antibody panels are available Disorder Tests Specimen Required Turnaround Time Acute leukaemia T cell antibodies CD2 CD3 CD7 Blood 10ml EDTA and or Usually processed lt ithi x B cell antibodies CD10 CD19 Bone marrow 1 2 ml within 24 hours EDTA CSF and Pleural CD79a cytoplasmic i gM
13. irley Henderson PhD Address Molecular Haematology Level 4 John Radcliffe Hospital Headington Oxford OX3 9DU Sample reception 01865 572769 Sec 01865 572826 Immunophenotyping 01865 572827 Fax 01865 572775 Email molhaem ouh nhs uk Web site http www oxford translational molecular diagnostics org uk y CPA Accredited Medical Laboratory Oxford Biomedical Research Centre National Institute for Reference No 1040 Health Research Haemato Molecular Diagnostic Service User Guide Version 5 03 12 2013 Page 11 of 11
14. versity Hospitals LYZKJ Centre NHS Trust Prenatal diagnosis of haemophilia by DNA analysis available by prior arrangement with the laboratory Turnaround time 3 5 working days 2 Haemoglobinopathies This service is provided by the National Haemoglobinopathy Reference Laboratory which provides a tertiary referral service for all hospitals throughout the UK Ireland and abroad Genetic tests for all known haemoglobinopathy mutations are available Disorder Tests Specimen Turnaround Time Required a thalassaemia Detection of deletions using Gap PCR 2 4ml EDTA 2 6 weeks and MLPA Detection of non deletion a peripheral blood depending on mutations by a globin gene sanger complexity sequencing B thalassaemia Detection of non deletion mutations 2 4ml EDTA 2 6 weeks using sanger sequencing peripheral blood depending on pyrosequencing and ARMS PCR complexity Detection of deletions using MLPA and Gap PCR HPFH and 6f thalassaemia Detection of deletions by MLPA and 2 4ml EDTA 2 6 weeks Gap PCR Detection of non deletion peripheral blood depending on HPFH using sanger sequencing of the complexity gamma gene promoters Sickle cell disease Genotyping by sanger sequencing 2 4ml EDTA 2 6 weeks pyrosequencing and ARMS PCR peripheral blood depending on complexity Hb Variants Identification by sanger sequencing of 2 4ml EDTA 2 6 weeks the a B y and 6 globin genes peripheral blood depending on complexity
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