Pathology Services: A Practical Handbook (5 th Edition, 2008) Summary of Updates Updated (S/N 1 – 71) and Uploaded: Apr 2010 S/N Section # 1 INTRODUCTION Title COMMITTEE 2007 - 2010 Page/s 5 Update Under MEMBERS Effective Date 1 Mar 10 Amend: Dr Tien Sim Leng To: A/Prof Tien Sim Leng 2 1 THE ORGANISATION 11 Under LOCATION OF LABORATORIES Under Cytogenetics Lab 1 Mar 10 After Tel No. 63214678/50 Insert: Tel No. 63213632 3 1 THE ORGANISATION 12 Under PERSONNEL Under Professional Staff 1 Mar 10 CYTOGENETICS LAB After Lim Tse Hui Insert: Scientific Officer Karen See Hsu-Shien BSc (Hons) 1 4 1 THE ORGANISATION 14 Under PERSONNEL Under PROFESSIONAL STAFF 1 May 08 MOLECULAR LAB Amend: Head & Consultant Dr Lynette Oon Lin Ean BSc (Hons), MBBS, MRCP, FRCPA Senior Scientific Officer Dr Eileen Chen Xueqin B.Med, PhD Scientific Officer Ms Lim Kun Lee BSc (Hons), MSc To Head & Senior Consultant Dr Lynette Oon Lin Ean BSc (Hons), MBBS, MRCP, FRCPA Principal Scientific Officer Dr Eileen Chen Xueqin B.Med, PhD Senior Scientific Officer Ms Lim Kun Lee BSc (Hons), MSc 2 5 2 LABORATORY POLICIES & SERVICE INFORMATION 23 Under EXTERNAL QUALITY ASSESSMENT PROGRAMMES 1 Jan 2010 Under Molecular Delete : QCMD Toxoplasma gondii 6 2 LABORATORY POLICIES & SERVICE INFORMATION 25 Amend : CAP CMV and EBV Viral Load 2/year To CAP BKV, CMV and EBV Viral Load 2/year Insert: CAP HLA-B27 Typing Survey CAP EGFR CAP KRAS QCMD (JC virus and BK virus) QCMD (B19 virus DNA) QCMD (CMV DNA) QCMD (HHV6 DNA) QCMD (EBV DNA) QCMD (Clostridium difficile DNA) 2/year 2/year 2/year 1/year 1/year 1/year 1/year 1/year 1/year Under OPERATING HOURS 1 Apr 2010 Under OFFICE HOURS Delete Monday to Friday Saturday 8.30am - 5.30pm (Molecular Lab) 8.30am – 1.00pm (Molecular Lab) (The Molecular Laboratory will be following the same opening hours of the Department.) 3 7 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Biochemistry 70 Under CALL-BACK VALUES OF CRITICAL ANALYTES 18 Feb 10 Amend: Potassium Sodium Calcium Glucose pH (blood gas) Blood Ketone Digoxin Theophylline Paracetamol Salicylate Lithium <2.5 or <120 or <1.75 or <2.0 or <7.1 or >1.4 >2.5 >25.0 all results all results 2.0 >5.7 >160 >3.25 >25.0 >7.6 To Potassium Sodium Calcium Glucose pH (blood gas) Calcium,Ionic Blood Ketone Digoxin Theophylline Paracetamol Salicylate Lithium <2.5 or <120 or <1.75 or <2.5 or <7.1 or <0.80 or >1.4 >2.5 >25.0 all results all results >2.0 >5.7 >160 >3.25 >25.0 >7.6 >1.60 mmol/L mmol/L mmol/L mmol/L mmol/L mg/L mg/L mg/L mmol/L mmol/L mmol/L mmol/L mmol/L mmol/L mmol/L mmol/L mg/L mg/L mg/L mmol/L mmol/L 4 8 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Biochemistry 72 Under ALPHAFOETO PROTEIN (AFP) FRACTION 3 01 Jan 10 Amend: Reference interval : > 12 years: 0 – 14.9% : > 12 years: <10% To Reference interval 9 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Biochemistry 85 Under EVEROLIMUS, BLOOD 02 Nov 09 Amend: Method : Immunoassay To Method 10 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Biochemistry 88 : Liquid Chromatography/Tandem Mass Spectrometry Under HOMOCYSTEINE,PLASMA 16 Mar 10 Amend: Method : Colorimetry : Immunoassay To Method 5 11 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Biochemistry 94 Under METANEPHRINE,URINE 25 Feb 10 Amend: Reference Interval : : 3 – 8 years: 26-137 nmol/mmol creatinine 9 – 19 years: 18-126 nmol/mmol creatinine : : 3 – 8 years: 27-138 nmol/mmol creatinine 9 – 19 years: 19-126 nmol/mmol creatinine To Reference Interval 12 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Biochemistry 98 Under NORMETANEPHRINE,URINE 25 Feb 10 Amend: Reference Interval : : 3 – 8 years: 38-434 nmol/mmol creatinine 9 – 19 years: 28-359 nmol/mmol creatinine : : 3 – 8 years: 38-435 nmol/mmol creatinine 9 – 19 years: 29-360 nmol/mmol creatinine To Reference Interval 6 13 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics 122 After ‘CHROMOSOME ANALYSIS OF SOLID TUMOURS’ 1 Mar 10 [effect is to move the entry from pg 130-131 to pg122] Insert: RAPID PRENATAL ANEUPLOIDY SCREENING, DOWN SYNDROME SCREENING AND SEX CHROMOSOME DETERMINATION WITH FLUORESCENCE IN SITU HYBRIDIZATION TEST Common indications : Advanced maternal age (≥ 35 years at EDD), Abnormal ultrasound findings, Positive maternal serum screening, Previous history of chromosome abnormality, Family history of Down syndrome, Parental anxiety Special instructions : This FISH test is usually requested in conjunction with conventional cytogenetic studies. Sample required : Amniotic fluid (3 mL), chorionic villi (5 mg), or fetal cord blood/neonate blood (0.5 mL) Method : Chromosome analysis as with Amniotic Fluid/Chorionic Villi or Fetal Cord Blood/Neonate Blood FISH assay using LSI 13 and 21, and CEP X, Y, and 18 DNA probes labelled with fluorophores are analysed under fluorescence microscopy. Test results : Normal or Abnormal, with the abnormalities listed. Findings are reported in accordance to the InternationalSystem for Human Cytogenetic Nomenclature (ISCN, 2009). Reference values : Individuals with a trisomy will show three signals of a particular DNA probe. Normal individuals will show two signals of each DNA probe. Females will show two signals of the X probe, males one signal of the X and Y probe each. Turnaround time : Within 3 days Day(s) test set up : Monday – Friday (office hours) 7 14 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics 122 After RAPID PRENATAL ANEUPLOIDY SCREENING, DOWN SYNDROME SCREENING AND SEX CHROMOSOME DETERMINATION WITH FLUORESCENCE IN SITU HYBRIDIZATION TEST 1 Mar 10 Insert : CHROMOSOME ANALYSIS WITH FLUORESCENCE IN SITU HYBRIDIZATION (FISH)TEST FOR MICRODELETION SYNDROMES Common Indications: This test is useful for patients suspected of PraderWilli (PW) / Angelman (AS), Di-George (DG) or Williams (WS) syndromes. Other microdeletion probes available include the SRY gene probe. Special Instructions: This FISH test is always used in conjunction with conventional cytogenetic studies. Contact the Cytogenetics laboratory before sending a specimen. Sample Required: Peripheral blood Method: Long-term culture to obtain metaphases. Probes used for metaphase and interphase FISH (PWS/AS, DGS or WS region DNA probes) are labeled with fluorophores and analysed under fluorescence microscopy. Test Results: Deleted or Not deleted. Nomenclature given is in accordance to the International System for Human Cytogenetic Nomenclature (ISCN, 2009). Reference Values: Individuals with a microdeletion will show two copies of the internal control signals but only one copy of the locus-specific signal for that region of interest. Turnaround Time: Within 1 week Day(s) Test Set Up: Monday – Saturday (office hours) 8 15 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics 123 -127 Delete Tests: 1Mar 10 INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION TEST WITH DUAL FUSION TRANSLOCATION PROBES - BCR/ABL1 INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST WITH DUAL FUSION TRANSLOCATION PROBES – ETO/AML1 INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TESTS WITH DUALCOLOUR BREAKAPART PROBES – CBFB (INV 16), MLL (11Q23), RARA (17Q21) IN ACUTE MYELOID LEUKAEMIA INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST WITH DUAL FUSION TRANSLOCATION PROBES – PML/RARA INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANEL TEST FOR CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANEL TEST FOR MULTIPLE MYELOMA (MM) INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANEL TEST FOR MYELODYSPLASTIC SYNDROME (MDS) INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION TESTS FOR OTHER HAEMATOLOGICAL MALIGNANCIES INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST FORANAPLASTIC LYMPHOMA KINASE (ALK) 9 16 4 SAMPLE COLLECTION & 123 - 127 After “CHROMOSOME ANALYSIS WITH FLUORESCENCE IN SITU HANDLING – SPECIAL HYBRIDIZATION (FISH)TEST FOR MICRODELETION SYNDROMES” INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES Insert: new FISH tests title “INTERPHASE FLUORESCENCE IN SITU & TEST RESULTS: HYBRIDIZATION (FISH) TEST FOR HAEMATOLOGICAL MALIGNANCIES” Cytogenetics Clinical Indications: Refer to Table 1. 1. A Dual Colour Dual Fusion translocation (DF) probe detects the juxtaposition of one gene locus with its translocation gene partner. The translocation event produces a fusion of the two genes on the derivative chromosomes. 2. A Dual Colour Breakapart (BA) probe detects disruptions to gene sequences that are known to be involved in translocations with another partner or disruptions due to other rearrangements such as an inversion. 3. An Extra Signal Dual Colour translocation (ES) probe detects the translocation between the genes of its translocation partners. 4. Single Colour Enumeration probes comprise locus specific identifier probes or centromeric probes and detect interstitial deletions or loss/gain of a whole chromosome. Special instructions: Interphase FISH test may be requested in conjunction with conventional cytogenetic studies or as a standalone test depending on the disease status. The FISH assay should preferably be done on diagnostic cases prior to treatment so as to determine the baseline pattern. Specimen required: Blood or Bone marrow in sodium/lithium heparin 1 Mar 10 10 16 4 cont’d 123 - 127 Method: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES Test results: & TEST RESULTS: Cytogenetics Fluorescence In Situ Hybridization using direct-labelled FISH DNA probes and analysed under fluorescence microscopy 8 Normal or abnormal signal pattern depending on the probe construction: 1. Dual Fusion (DF) probe: Typical abnormal signal pattern is 2 fusions, 1 red and 1 green pattern. Variant pattern is outside the normal range. 2. Breakapart (BA) probe: Typical abnormal signal pattern is 1 fusion, 1 red and 1 green pattern. Variant pattern is outside the normal range. 3. Extra Signal (ES) probe: Typical abnormal signal pattern is 1 fusion, 2 red signals and 1 green pattern. Variant pattern is outside the normal range. 4. Enumeration probe: Loss or Gain of FISH signal. FISH findings are reported in accordance to the International System for Human Cytogenetic Nomenclature (ISCN, 2009). Reference values: Please refer to Table 2 for the normal cut-off level for each probe. Turnaround Time: Within 1 week Day(s) test set up: Monday – Saturday (office hours) 11 17 4 SAMPLE COLLECTION & 123 - 127 After “INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST HANDLING – SPECIAL FOR HAEMATOLOGICAL MALIGNANCIES” INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES Insert: new FISH tests title “INTERPHASE FLUORESCENCE IN SITU & TEST RESULTS: HYBRIDIZATION (FISH) PANEL TESTS FOR MULTIPLE MYELOMA, Cytogenetics MULTIPLE MYELOMA HYPERDIPLOIDY, B-CELL CHRONIC LYMPHOCYTIC LEUKAEMIA (B-CLL) AND MYELODYSPLASTIC SYNDROME (MDS)” Clinical Indications: 1 Mar 10 Many cytogenetic abnormalities are subtle or are found in non-dividing cells that only interphase FISH can be used to elucidate instead of conventional cytogenetics. FISH panels offered by the laboratory include: 1. 2. 3. 4. Multiple Myeloma: Expanded MM FISH panel can be used to detect multiple chromosome aberrations found in multiple myeloma. Hyperdiploidy Multiple Myeloma: If hyperdiploidy is suspected in multiple myeloma, MM hyperdiploidy FISH panel can be offered. B-cell Chronic Lymphocytic Leukaemia: CLL FISH panel can be used to detect the multiple aberrations that are often found in clonal B-cells. Myelodysplastic Syndrome: MDS FISH panel are used to detect MDS. Special Instructions: The FISH panel test is charged as separate test from the accompanying cytogenetic test. Three to five DNA probes are used in the panel test. Specimen required: Blood or bone marrow in sodium/lithium heparin. For Bcell CLL, the preferred specimen is peripheral blood. Method: Fluorescence In Situ Hybridization using direct-labelled FISH DNA probes and analysed under fluorescence microscopy. Refer to Table 3 for the probes used in each panel. 12 17 4 cont’d 123 - 127 Test Results: SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES Reference Values: & TEST RESULTS: Cytogenetics Turnaround Time: Day(s) test set up: 18 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics 128 Positive or Negative for the FISH panel. FISH findings are reported in accordance to the International System for Human Cytogenetic Nomenclature (ISCN, 2009). Please refer to Table 4 for the normal cut-off level of each probe. Within 1 week Monday – Saturday (office hours) Under “INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION TEST FOR BREAST CANCER TISSUES USING HER2 (ERBB2) DNA PROBE” 1 Mar 10 Under Special instructions : Insert after “thickness”: on coated slides. The optimal fixation time in formalin should be between 6-48 hours. An accompanying Hematoxylin and Eosin stained slide with the tumour region marked out should be submitted together with at least 3 unstained sections. Amend: Reference values : To: Reference values : Normal specimens have a HER2 (ERBB2) to CEP 17 signal ratio of < 2.0. Specimens with amplification have a ratio of ≥ 2.0…. Normal specimens have a HER2 (ERBB2) to CEP 17 signal ratio of < 1.8. Specimens with amplification have a ratio of ≥ 2.2…. Amend: Turnaround time : 5 days (mean) To: Turnaround time : Within 1 week 13 19 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics 128-129 Delete Tests: 1Mar 10 INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST FOR EWING SARCOMA INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TESTS FOR LYMPHOMA (PARAFFIN SECTIONS) – OTHER PROBES INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST FOR MUCOSAASSOCIATED LYMPHOID TISSUE (MALT) TYPE LYMPHOMA 14 20 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics 129 After “INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION TEST FOR BREAST CANCER TISSUES USING HER2 (ERBB2) DNA PROBE” 1 Mar 10 Insert: new FISH tests title “INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST FOR LYMPHOMA AND SARCOMA ON PARAFFIN-EMBEDDED SECTIONS OR TISSUE IMPRINTS’ Clinical Indications: Refer to Table 1. Lymphoma probes include ALK breakapart (BA), BCL6 (BA), c-MYC (BA), IGH/c-MYC (DF), API2/MALT1 (DF), IGH/CCND1 (DF), IGH (BA), IGH/BCL2 (DF), MALT1 (BA). Sarcoma probes include EWSR1 (BA) and SYT (BA). Variant translocations can be detected using the breakapart probe (BA). Special Instructions: The FISH test is optimal with fresh tissue samples. Tissue sections should preferably be prepared between 4time in formalin should be between 6-48 hours. An accompanying Hematoxylin and Eosin stained slide with the tumour region marked out should be submitted together with at least 3 unstained sections. Specimen required: Freshly-cut tissue sections or tissue imprints. Bone marrow aspirates can only be used if there is lymphomatous involvement. Method: Fluorescence In Situ Hybridization using direct-labelled FISH DNA probes and analysed under fluorescence microscopy. Test results: Normal or abnormal signal pattern depending on the probe construction. 15 20 4 cont’d SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics 129 1. Dual Fusion (DF) probe: Typical abnormal signal pattern is 2 fusions, 1 red and 1 green pattern. Variant pattern is outside the normal range. 2. Breakapart (BA) probe: Typical abnormal signal pattern is 1 fusion, 1 red and 1 green pattern. Variant pattern is outside the normal range. FISH findings are reported in accordance to the International System for Human Cytogenetic Nomenclature (ISCN, 2009). Reference Values: Please refer to Table 2 for the normal cut-off level of each probe. Turnaround Time: Within 1 week Day(s) test set up: Monday – Saturday (office hours) 16 21 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics 130 Under “INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANEL TEST FOR GLIOMA” 1 Mar 10 Under Special instructions Insert after ‘thickness’: on coated slides. The optimal fixation time in formalin should be between 6-48 hours. An accompanying Hematoxylin and Eosin stained slide with the tumour region marked out should be submitted together with at least 3 unstained sections. Amend: Reference values : To: Reference values : Losses of 1p36 and/or 19q13 regions equal to or greater than 25% of interphase cells, and/or a ratio of 1p36/1q25 and/or 19q13/19p13 of equal to or less than 0.8. Losses of 1p36 and/or 19q13 regions equal to or greater than 17.2% of interphase cells, and/or a ratio of 1p36/1q25 and/or 19q13/19p13 of equal to or less than 0.8. Amend: Turnaround time : 5 days (mean) To: Turnaround time : Within 1 week 17 22 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics After “INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANEL TEST FOR GLIOMA” 1 Mar 10 Insert: Table 1 - HAEMATOLOGY/ONCOLOGY FLUORESCENCE IN SITU HYBRIDIZATION (FISH) AVAILABLE PROBES FISH PROBES ALK BA 1p36 / 19q13 BCL6 BA IGH/FGFR3 DF EGR1 EGFR (HER-1) PROBE LOCATION 2p23 1p36 / 19q13 3q27 4p16.3 / 14q32 5q31 7p12 D7S486 CEP 8 c-MYC BA 7q31 Cen 8 8q24 IGH/c-MYC DF ETO/AML1 DF BCR/ABL1 DF CEP 9, 11, 15 8q24.1 / 14q32 8q22 / 21q22 9q34 / 22q11.2 Cen 9 / Cen 11/ Cen 15 11q23 11q22.3 11q21 / 18q21 11q13 / 14q32 MLL BA ATM API2/MALT1 DF CCND1 XT/IGH DF CLINICAL INDICATIONS Anaplastic Large Cell Lymphoma Gliomas DLCL, FL Multiple Myeloma MDS, AML Solid tumours: head and neck, ovarian, cervical, bladder, oesophageal, non-small cell lung cancer, breast MDS, AML AML, CML, MDS Burkitt's Lymphoma (include variants), ALL Burkitt's Lymphoma, ALL AML ALL, AML, CML Multiple Myeloma ALL, AML B-CLL MALT lymphoma, DLBCL Mantle Cell Lymphoma, B-Prolymphocytic Leukaemia, Plasma Cell Leukaemia, Splenic Lymphoma, CLL, Multiple Myeloma, B-lineage lymphocyte 18 22 4 cont’d SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics FISH PROBES CEP 12 TEL/AML1 ES RB1 PROBE LOCATION Cen 12 12p13 / 21q22 13q14 D13S25 IGH BA IGH/BCL2 DF 13q14 14q32 14q32 / 18q21 PML/RARA DF CBFB BA TP53 15q22 / 17q21.1 16q22 17p13.1 HER-2/neu (ERBB2) RARA BA MALT1 BA SYT BA D20S108 17q11.2q12 EWSRI BA 22q12 Probe 1. 2. 3. 17q21.1 18q21 18q11.2 20q12 CLINICAL INDICATIONS B-CLL B-ALL Multiple Myeloma, CLL, AML, MDS, CLD B-CLL Multiple Myeloma, ALL, CLL, NHL DLCL, FL AML AML Multiple Myeloma, B-CLL, ALL, AML, MDS, NHL Breast Cancer AML-M3 (include variants) MALT lymphoma, DLBCL Synovial sarcoma MDS, AML, polycythemia vera, chronic neutrophilic leukemia Ewing's sarcoma (include variants) Constructions: BA- Breakapart DF- Dual Fusion ES- Extra Signal 19 23 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics After Table 1, 1 Mar10 Insert: TABLE 2 - NORMAL CUT-OFF LEVEL FOR HAEMATOLOGICAL AND ONCOLOGY FISH PROBES PROBES ALK BCL6 EGFR (HER-1) / CEP 7 c-MYC IGH/c-MYC/CEP 8 ETO/AML1 BCR/ABL1 MLL ATM API2/MALT1 TEL/AML1 IGH IGH/BCL2 PML/RARA CBFB RARA MALT1 SYT EWSRI CONSTRUCTION BA BA Polysomy BA DF DF DF BA Loss DF ES BA DF DF BA BA BA BA BA CUT-OFF LEVEL % 3.77 3.08 21.65 1.48 1.48 1.48 1.48 2.34 7.39 1.48 1.48 5.67 1.48 1.48 2.34 3.08 2.33 5.66 7.39 20 24 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics After Table 2, 1 Mar 10 Insert: TABLE 3 - HAEMATOLOGICAL FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANEL TESTS FISH PANEL TESTS Expanded MM Panel FISH PROBES USED IGH/FGFR3 DF CCND1 XT/IGH DF RB1 TP53 IGH/MAF DF MM Hyperdiploidy Panel CEP 9 CEP 11 CEP 15 CLL Panel ATM CEP 12 D13S25 TP53 MDS Panel EGR1 D7S486 CEP 8 D20S108 21 25 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Cytogenetics After Table 3, 1 Mar 10 Insert: TABLE 4 - NORMAL CUT-OFF LEVEL FOR FISH PANEL PROBES EXPANDED MM PANEL CONSTRUCTION IGH/FGFR3 Cyclin D1 XT/IGH RB1 TP53 IGH/MAF DF DF Loss Loss DF MM HYPERDIPLOIDY PANEL CONSTRUCTION CEP 9 CEP 11 CEP 15 Gain Gain Gain CLL PANEL CONSTRUCTION ATM CEP 12 D13S25 TP53 Loss Gain Loss Loss MDS PANEL CONSTRUCTION EGR1 D7S486 CEP 8 D20S108 Loss Loss Gain Loss CUT-OFF LEVEL % 1.48 1.48 5.06 10.5 1.48 CUT-OFF LEVEL % 2.33 1.48 3.08 CUT-OFF LEVEL % 7.39 4.43 1.49 10.5 CUT-OFF LEVEL % 7.39 8.48 3.77 8.48 22 26 27 28 4 4 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 185 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 185 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS Amend ALPHABETICAL TEST LISTING – MOLECULAR LABORATORY 1 Jan 10 To ALPHABETICAL TEST LISTING – INFECTIOUS DISEASES 186 Under BK VIRUS LOAD (QUANTITATIVE) Amend: Turnaround time Day(s) test set up : 2 – 14 days : Monday To Turnaround time Day(s) test set up : 1 – 5 days : Monday and Wednesday Under CHLAMYDOPHILA (FORMERLY CHLAMYDIA) PNEUMONIAE & MYCOPLASMA PNEUMONIAE PCR (MULTIPLEX PCR 1, QUALITATIVE) Amend: Turnaround time Day(s) test set up : 2 – 7 days : Wednesday To Turnaround time Day(s) test set up : 1 – 4 days : Variable 1 Jan 10 1 Jan 10 23 29 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 187 Before CYTOMEGALOVIRUS (CMV) PCR (QUALITATIVE) Insert: CYTOMEGALOVIRUS (CMV) LOAD (QUANTITATIVE) Specimen required: Storage and transportation: Method: Test results: Turnaround Time: Day(s) test set up: 30 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 15 Dec 09 187 3-5 ml of whole blood in EDTA 0.5-1 mL CSF / aqueous / vitreous fluid Refrigerate sample until transfer to laboratory. Do not freeze. Send sample at 2-8C. Sample should reach the laboratory within 72 hours after collection. Real-time PCR (In-house) Detected (quantity reported in copies/mL), Not Detected or Inconclusive Linear Range: 220 – 2,200,000,000 (2.349.34 log) copies/mL 1 - 5 days Tuesday and Friday Under CYTOMEGALOVIRUS (CMV) PCR (QUALITATIVE) Amend: Turnaround time Day(s) test set up : 1 – 7 days : Wednesday To Turnaround time Day(s) test set up : 1 – 4 days : Variable 1 Jan 10 24 31 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 188 Under HEPATITIS B VIRUS (HBV) LOAD (QUANTITATIVE) Amend Specimen required To Specimen required Insert Method Amend Test results To Test results 1 Jan 10 : 6 - 10 mL blood in sterile EDTA container. Alternatively, at least 3 mL plasma (separated from EDTA-treated blood within 1 day of collection by centrifugation at 800-1600g for 20 minutes at room temperature) in a sterile screw-capped polypropylene tube. : 3 - 5 mL blood in sterile EDTA container or serum separation tube. Alternatively, at least 1.5 mL plasma or serum (separated within 1 day of collection by centrifugation at 800-1600g for 20 minutes at room temperature) in a sterile screw-capped polypropylene tube. : Real-Time PCR (Roche COBAS Ampliprep/Taqman version 2.0) : Quantity reported in copies/mL and/or IU/mL Reported range : 12 IU/mL to 1.1E+08 IU/mL Linear Range : 54.5 (Log 10 = 1.74) to at least 1.1E+08 (Log 10 = 8.03) IU/mL : Quantity reported in copies/mL and/or IU/mL Linear Range : 20 to 1.7 X 10 8 IU/mL (116 to 9.9X10 8 copies/mL) Lowest detection limit : 9 IU/mL 25 32 33 34 35 36 4 4 4 4 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 190 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 191 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 191 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 191 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 191 Under HEPATITIS C VIRUS PCR (QUALITATIVE) Amend: Turnaround time Day(s) test set up : 2 - 14 days : Wednesday To Turnaround time Day(s) test set up : 2 – 10 days : Variable Under HERPES SIMPLEX VIRUS (HSV) PCR (QUALITATIVE) Add: Turnaround time 1 Jan 10 1 Jan 10 : 1 - 4 days; next working day for CSF samples Delete entire test HLA-B27 TYPING BY PCR (QUALITATIVE) 1 Jan 10 (This test is moved under ALPHABETICAL LISTING – MISCELLANOUS MOLECULAR TESTS page 195) Delete entire test HUMAN INFLUENZA A & B PCR (QUALITATIVE) 26 Jan10 (This test is now incorporated together with Influenza A/H1N1/2009 as INFLUENZA MULTIPLEX PCR – see below) Delete entire test HUMAN INFLUENZA A/NOVEL H1N1 PCR (QUALITATIVE) 26 Jan 10 (This test is now incorporated together with Influenza A and B as INFLUENZA MULTIPLEX PCR – see below) 26 37 38 4 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 192 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 193 After HUMAN PAPILLOMAVIRUS DNA (HPV) (QUALITATIVE) 26 Jan 10 Insert new test: INFLUENZA MULTIPLEX PCR (QUALITATIVE) Indications: This test detects Influenza A, B and Influenza A/H1N1/2009. Specimen Required: Nasal/ throat / nasopharyngeal swabs: Use only Dacron-tipped or Copan flocked swab. Send dry in sterile container or swab sheath. Storage & Transportation: Refrigerate sample until transfer to laboratory. Do not freeze. Send sample at 2-8°C (with an ice-pack). Sample must reach laboratory within 24 hours after collection. Method: Multiplex reverse-transcription Polymerase Chain Reaction (In-house real-time) Test Results: Detected, Not Detected or Inconclusive Turnaround Time: 1 working day Day(s) Test Set Up: Monday to Saturday Under NOROVIRUS PCR (QUALITATIVE) Amend: Turnaround time Day(s) test set up : 2 - 7 days : Monday To Turnaround time Day(s) test set up : 1 - 5 days : Tuesday and Thursday 1 Jan 10 27 39 40 41 4 4 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 193 194 195 Under PAN-ENTEROVIRUS PCR (QUALITATIVE) Amend: Turnaround time Day(s) test set up : 2 - 5 days : Wednesday To Turnaround time Day(s) test set up : 1 - 4 days : Wednesday and Friday Under TOXOPLASMA GONDII PCR (QUALITATIVE) Amend: Turnaround time Day(s) test set up : 2 - 8 days : Wednesday To Turnaround time Day(s) test set up : 1 - 4 days : Variable Under VARICELLA-ZOSTER VIRUS PCR (QUALITATIVE) Amend: Turnaround time Day(s) test set up : 1 – 7 days : Wednesday To Turnaround time Day(s) test set up : 1 - 4 days : Variable 1 Jan 10 1 Jan 10 1 Jan 10 28 42 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 195 After VARICELLA-ZOSTER VIRUS PCR (QUALITATIVE) 1 Feb 10 Insert: ALPHABETICAL LISTING – MOLECULAR ONCOLOGY TESTS Insert new test: KRAS MUTATION TEST Indications : This assay detects 7 KRAS mutations in codons 12 and 13 (exon 2) of the KRAS oncogene. The presence of these mutations correlates with a lack of response to certain EGFR inhibitor cancer therapies in metastatic colorectal cancer patients. Specimen Required: Paraffin embedded tissue block Method: Allele-specific real-time PCR assay employing Amplification Refractory Mutation System (ARMS) PCR Test Results: Detected, Not Detected or Inconclusive Turnaround Time: 3-15 days Day Test Set Up: Monday Day Test Reported: Thursday 29 43 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: MOLECULAR DIAGNOSTICS 195 After ALPHABETICAL LISTING – MOLECULAR ONCOLOGY TESTS 1Jan 2010 KRAS MUTATION TEST Insert: ALPHABETICAL LISTING –MISCELLANOUS MOLECULAR TESTS Insert test: HLA-B27 TYPING BY PCR (QUALITATIVE) Specimen required: Storage and transportation: Method: Test Result: Turnaround Time: Day(s)Test Set Up: 44 45 4 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 223 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 224 5 ml of whole blood in EDTA Refrigerate sample until transfer to laboratory. Do not freeze. Send sample at 2-8C. Sample should reach the laboratory within 72 hours after collection. In-house real-time polymerase chain reaction Detected, Not Detected or Inconclusive 2-8 days Tuesday Under CYTOMEGALOVIRUS (CMV) ANTIBODY 24 Nov 09 Amend Turnaround time : Anti-CMV IgM : <1 – 8 days Anti-CMV IgG : <1 – 4 days Under DENGUE VIRUS ANTIBODY 24 Nov 09 Amend Turnaround time : Anti-dengue IgM : <1 – 5 days Anti-dengue total : 3 – 15 days Day(s) test set up : Anti-Dengue total : Once a fortnight 30 46 47 48 49 50 51 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 224 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 226 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 226 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 227 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 228 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 228 Under EPSTEIN-BARR VIRUS (EBV) ANTIBODY 24 Nov 09 Amend Turnaround time : Anti-VCA IgM/IgG : <1 – 4 days Anti-VCA IgA : <1 – 7 days Anti-EA IgA : <1 – 7 days Under HEPATITIS C VIRUS (HCV) SEROLOGY 24 Nov 09 Amend Turnaround time : Anti-HCV IgG : <1 – 2 days Anti-HCV RIBA : <1 – 8 days Under HEPATITIS DELTA VIRUS ANTIBODY (ANTI-HDV TOTAL AB) 24 Nov 09 Amend Turnaround time : <1 – 7 days Under HEPATITIS E VIRUS (HEV) ANTIBODY 24 Nov 09 Amend Turnaround time : Negative report : <1 – 7 days Under HERPES SIMPLEX VIRUS (HSV) ANTIBODY 24 Nov 09 Amend Turnaround time : Anti-HSV IgM : Routine cases : <1 – 4 days Under HUMAN IMMUNODEFICIENCY VIRUS (HIV) ANTIBODY, SCREENING (includes Confirmation if reactive) 24 Nov 09 Amend Turnaround time : Routine screening non-reactive report : <1 – 2 days Confirmation of reactive results : 1 – 8 days 31 52 53 54 55 56 57 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 229 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 229 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 230 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 231 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 232 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 233 Under HUMAN IMMUNODEFICIENCY VIRUS (HIV) ANTIBODY, WESTERN BLOT 24 Nov 09 Amend Turnaround time : 1 – 8 days Under MEASLES ANTIBODY 24 Nov 09 Amend Turnaround time : Anti-Measles IgM : <1 – 8 days Anti-Measles IgG : <1 – 4 days Under MUMPS ANTIBODY 24 Nov 09 Amend Turnaround time : Anti-Mumps IgM or IgG : <1 – 4 days Under PARVOVIRUS ANTIBODY 24 Nov 09 Amend Turnaround time : IgM or IgG : <1 – 7 days Under RUBELLA ANTIBODY 24 Nov 09 Amend Turnaround time : 1 – 8 days Anti-Rubella IgM or IgG : <1 – 7 days Anti-Rubella total : 1 – 8 days Under SARS-CORONAVIRUS (SARS-COV) ANTIBODY 24 Nov 09 Amend Turnaround time : Anti-SARS IgM or IgG : <1 – 4 days 32 58 59 60 61 62 63 64 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 233 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 234 SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology SAMPLE COLLECTION & HANDLING – SPECIAL INSTRUCTIONS, LABORATORY TESTS, REFERENCE VALUES & TEST RESULTS: Virology 235 Under VARICELLA-ZOSTER VIRUS (VZV) ANTIBODY 24 Nov 09 Amend Turnaround time : Routine cases : Anti-VZV IgM : <1 – 4 days Anti-VZV IgG : <1 – 7 days Under CYTOMEGALOVIRUS ANTIGEN 24 Nov 09 Amend Turnaround time : <1 – 2 days 234 Under DENGUE VIRUS ANTIGEN 24 Nov 09 Amend Turnaround time : <1 – 4 days 234 Under HERPES SIMPLEX VIRUS AND VARICELLA-ZOSTER VIRUS ANTIGEN 24 Nov 09 Amend Turnaround time : >1 – 2 days Under MEASLES AND MUMPS ANTIGEN 24 Nov 09 Amend Turnaround time : <1 – 2 days 235 Under NOROVIRUS ANTIGEN 24 Nov 09 Amend Turnaround time : <1 – 7 days 235 Under RESPIRATORY VIRUS ANTIGEN 24 Nov 09 Amend Turnaround time : <1 – 2 days 33 65 7 TEST INDEX 276 After INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANELTEST FOR GLIOMA 1 Mar 10 Insert New FISH test: INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANEL TESTS FOR MULTIPLE MYELOMA, MULTIPLE MYELOMA HYPERDIPLOIDY, B-CELL CHRONIC LYMPHOCYTIC LEUKAEMIA (B-CLL) AND MYELODYSPLASTIC SYNDROME (MDS) 66 7 TEST INDEX 276 After INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) PANEL TESTS FOR MULTIPLE MYELOMA, MULTIPLE MYELOMA HYPERDIPLOIDY, B-CELL CHRONIC LYMPHOCYTIC LEUKAEMIA (B-CLL) AND MYELODYSPLASTIC SYNDROME (MDS 1 Mar 10 Insert new FISH test: INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST FOR HAEMATOLOGICAL MALIGNANCIES 67 7 TEST INDEX 276 After INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST FOR HAEMATOLOGICAL MALIGNANCIES 1 Mar 10 Insert new FISH test: INTERPHASE FLUORESCENCE IN SITU HYBRIDIZATION (FISH) TEST FOR LYMPHOMA AND SARCOMA ON PARAFFIN-EMBEDDED SECTIONS OR TISSUE IMPRINTS 68 7 TEST INDEX 275 Before CYTOMEGALOVIRUS (CMV) PCR (QUALITATIVE) 15 Dec 09 Insert new test: CYTOMEGALOVIRUS (CMV) LOAD (QUANTITATIVE) 69 7 TEST INDEX 276 Before INFLUENZA VIRUS ISOLATION 26 Jan 10 Insert new test: INFLUENZA MULTIPLEX PCR (QUALITATIVE) 34 70 7 TEST INDEX 277 After KETONE, BLOOD 1 Feb 10 Insert new test: KRAS MUTATION TEST 35