TGL clinical User Guide

Transcription

1 TGL clinical User Guide The Institute of Cancer Research Brookes Lawley Building 15 Cotswold Road Sutton, Surrey SM2 5NG Page 1 of 7

2 TGL clinical This document describes the services provided by TGL clinical to internal and external users. The laboratory is situated in the Brookes Lawley Building, on the Sutton campus of the Institute of Cancer Research (ICR). TGL clinical provide a molecular diagnostic service for germline mutation analysis of genes that confer a predisposition to cancer. Uniquely TGL clinical provides an integrated laboratory and clinical interpretation service utilising expertise based at ICR and RMH to test for and interpret germline variation in cancer predisposition genes to aid and inform clinical management decisions. Staff list: Laboratory Director and Consultant Clinical Geneticist: Consultant Oncogeneticists: Clinical and Research Scientists: Scientific Officer: Database Manager: Statistician / Bioinformaticians: Operational Manager: Professor Nazneen Rahman Dr. Angela George Dr. Zoe Kemp Sheila Seal Dr. Shazia Mahamdallie Anthony Renwick Silvana Powell Emma Ramsay Bertha Adjei Anna Elliott Dr. Elise Ruark Dr. Shawn Yost Ann Strydom Page 2 of 7

3 Contact details: Laboratory contact: Postal address: Phone: TGLclinical laboratory Brookes Lawley Building The Institute of Cancer Research 15 Cotswold Road Sutton, Surrey SM2 5NG Website Hours of service: 9.00am to 5.00pm, Monday to Friday (excluding bank holidays). Out of hour s service: No out of hours service is provided. Samples received after 5.00pm will be processed the following working day. Instructions for completion of the request form: Please fill ALL the fields provided with the relevant demographic/clinical information. For patient details, stickers with the patient s information can be used. Similarly, stickers can be used for the Consultant and referring hospital information. If some information is unknown or not applicable please fill the field in with UNKNOWN and N/A, respectively, rather that leaving it blank. Samples with attached request forms that do not contain all the relevant information can be rejected by the lab or put on hold until a new and completely filled request form has been received. Clinical details, required investigations and family history should be filled in where possible. If in doubt please contact us on the laboratory or numbers given above. Consent: Upon receipt of samples, the laboratory assumes that appropriate consent has been obtained by the referring clinician. Page 3 of 7

4 Laboratory repertoire Test Genes included Cost A Cost B Turn-around time Panel tests Effective 1 st April 2017 BRCA panel BRCA1, BRCA % < 3 weeks Breast / Ovarian panel BRCA1, BRCA2, TP53, PALB2, PTEN, MLH1, MSH2, MSH6, STK11, % < 4 weeks BRIP1, RAD51C, RAD51D, ATM, CHEK2 Lynch panel MLH1, MSH2, MSH6, PMS2, EPCAM % < 4 weeks Polyposis panel APC, MUTYH % < 4 weeks Renal panel BAP1, FH, FLCN, MET, PTEN, SDHB, VHL % < 4 weeks Pheo / Para panel SDHB, SDHC, SDHD, SDHAF2, MAX, TMEM127, NF1, RET, VHL % < 4 weeks Melanoma panel CDKN2A, CDK % < 4 weeks Single gene tests Available for any gene included in a panel or one of the following genes: BUB1B, CDC73, CDH1, DICER1, MEN1, NF2, SMARCB1, SUFU, WT % < 3 weeks Specific mutation (predictive) tests Available for any gene listed above in a panel test or single test % < 2 weeks The full coding sequence and intron-exon boundaries are analysed for small variants and exon deletions and duplications, except PMS2 (exons 1-11 only), EPCAM (exon 9 CNV only) POLE, POLD1 (select mutations only). For further details see Cost A: UK NHS, UK self-funding, Middle and Low income countries (World bank classification) Cost B: Privately insured / funded, High income countries (World bank classification) cles/ world-bank-country-and-lending-groups Page 4 of 7

5 Cancer predisposition gene tests not performed by TGL clinical : When requests are received for cancer predisposition gene tests not offered by TGL clinical we will arrange testing by external providers. These providers will be selected based on their accreditation and known expertise for specific tests. When the results are received by TGL clinical, they are forwarded to the referring clinician with a clear indication as to the accreditation status of the external laboratory. Reporting times and accreditation status of the external labs are monitored by TGL clinical. DNA storage: We can store DNA from individuals for which no test is currently indicated, but for which it is considered possible that testing may be appropriate in the future. We do not store blood samples and thus if blood samples are received for storage the DNA is extracted and stored. Turnaround time standards TGL clinical strives to achieve the turnaround times outlined in the Laboratory repertoire table above which are all within the UK national target standards. Reporting of service and standards Where TGL clinical undertakes more than 10 tests per month for any individual institution a monthly report will be provided within the first seven working days of the following month, which will include information on the number of tests, the test type, the referring department and/or clinician, and the average turnaround times per test type Specimens required: Please send 2 x 9 ml of blood in PLASTIC EDTA tubes. Smaller volumes, for example from children, can be extracted if necessary, but we require a minimum of 2 ml. Samples should be sent on the day of collection and at ambient temperature. DNA samples can also be received. We strongly prefer to receive blood samples but if this is not possible, please contact the lab to discuss sending a saliva sample. Unsuitable samples: Clotted samples are occasionally unsuitable for molecular analysis, where possible the referring clinician will be informed and a new sample requested. Samples should be labelled with the patient first name and surname, D.O.B., hospital number and the date and time the sample was taken. The details on the sample tube must correspond to those on the request form. At least two unique identifiers are required. Page 5 of 7

6 Unidentifiable/Unlabelled/Broken samples will NOT be accepted. Where possible the referring clinician will be informed and a new sample requested. High risk blood samples (HIV, Hep B or C) received by TGL clinical must be indicated as such both on the blood tubes and the request form. These samples cannot be extracted by TGL clinical and so will be sent to an external provider for testing. This may in-turn affect the turnaround time for that specific sample. Please note that all DNA samples are stored indefinitely unless otherwise requested. Transportation of samples: At Royal Marsden Hospital, samples will be sent together with the request form from the phlebotomy unit to the Royal Marsden Hospital Central Pathology Department at the Sutton site, or can be delivered to TGL clinical pigeon hole at BLB reception. Samples should be dispatched as soon as possible after taking the sample. In the case of samples sent from the Chelsea site, they will be transported in the pathology containers on the RMH inter-site coach, to be delivered to the RMH Central Pathology. Samples will be then collected from the RMH Central Pathology and the BLB pigeon hole by laboratory staff and transported to the lab contained inside an opaque sample transportation bag. See the HSE guidance on biological agents Blood and DNA samples from external users should be sent by first class mail, please address specimens to the TGL clinical postal address given above. Any diagnostic sample sent to the laboratory should be sent in accordance with the UN3373 regulations and the P650 Packaging instruction ( Failure to abide by these regulations will result in the rejection of that sample by TGL clinical. Data protection: TGL clinical ensures secure and safeguarded storage of patient information and compliance with the Data Protection Act. Charges for tests: TGL clinical will provide notice of any charge in advance of any service being undertaken. Receipt of a test request by TGL clinical will be considered an agreement of that charge. Any changes in charges will be notified 3 months in advance of the change being effected. Quality control: All TGL clinical laboratory examination procedures that generate patient results include appropriate quality control measures. The results of all quality control samples are evaluated for every patient sample by an authorised member of staff prior to the release of the relevant patient results. Page 6 of 7

7 If during an individual examination process a quality control result is deemed to have failed and to invalidate patient results, then these patient results are repeated and are not released without successful accompanying quality control results. Reporting of Results: Reports are produced electronically and can be provided in either electronic or paper format according to the user s requirements. Reports can be printed to produce paper copies when requested but are stored within TGL clinical and routinely dispatched as electronic copies. Clinical interpretations: TGL clinical examination reports contain a clear explanation of the result and its clinical implications for the patient and their relatives. To obtain further clinical advice, contact the lab directly by to tgl@icr.ac.uk. Please note that TGL clinical does not offer any interpretation of results obtained from external providers. Queries and Complaints procedure: Any questions about test methodology, interpretation of the results or complaints should be notified by to tgl@icr.ac.uk, phone or by post to: TGLclinical laboratory Brookes Lawley Building The Institute of Cancer Research 15 Cotswold Road Sutton, Surrey SM2 5NG Queries will be responded to as soon as possible. Complaints will be acknowledged as being received within two working days. Feedback will be provided within seven working days and will include a timeline and process for more detailed consideration of the complaint if necessary. Page 7 of 7