Customer Manual. General instructions for molecular diagnostic tests

Transcription

1 Customer Manual General instructions for molecular diagnostic tests

2 Dear customer, CENTOGENE is a global leader in the field of genetic diagnostics for rare hereditary diseases with the largest test portfolio worldwide. Receiving samples from over 100 countries allows CENTOGENE a unique insight into epidemiological genetic differences, which is crucial in the interpretation of medical results. We focus strictly on offering quality molecular genetic diagnostics and biochemical/enzymatic analyses, underlined by our multiple international accreditations (ISO, CAP and CLIA). CENTOGENE s in-depth medical expertise is supported by the application of cutting-edge technologies, including next generation sequencing, whole exome sequencing (CentoXome ), whole genome sequencing (CentoGenome ) and innovative biomarkers for selected diseases. CENTOGENE has developed a comprehensive mutation database (CentoMD ) that is the cornerstone of our high quality diagnostic reporting and medical interpretation, supporting the interpretation process of each patient s sequencing data. In addition to diagnostic services for individual patients, we are also a pivotal partner to multiple renown industrial partners worldwide. Not all situations and questions will be answered here, but we are always available for answering your individual questions. Please do not hesitate to contact us directly with all of your questions and requests at dmqc@centogene.com All information and declarations of consent for our tests are also available on our website Contact information CENTOGENE AG Schillingallee Rostock Germany dmqc@centogene.com Phone: +49 (0) Fax: +49 (0) Web: 2

3 Contents Sample preparation 4 EDTA tube Filtercards Tissue sample Aminotic fluid Choronic villi Cord blood Purified DNA ctdna Sample transport 5 CentoCard : CENTOGENE s innovative solution Sample transport 6 Filtercards EDTA blood Cord blood Aminotic fluid Choronic villi Tissue samples Biochemical test orders 6-7 Sample requirement and stability 6-7 Required sample identification & information 7 Storage and archive of examined samples 7 Sample rejection policy 7 References 7 3

4 Sample preparation Proper preparation of the patient sample is the cornerstone for a quality analysis and diagnosis. In the following instructions, we describe precisely the requirements needed for the specific type of specimen and the amount needed to accurately perform testing. Our experts are always available to answer questions, please do not hesitate to contact us. The most common medium for receiving patient sample is blood, which is clinical routine and effective with the following considerations: The blood must be drawn under sterile conditions. An EDTA blood collection tube must be used and not reopened at any time. The blood cannot be decanted into an EDTA tube. The blood can be drawn using aspiration or vacuum methods. To ensure optimal mixing, the tubes should be filled to the mark on the tube. For molecular genetics, blood can be drawn at any time with no fasting or special time requirements. CENTOGENE offers an innovative solution for collecting as well as transporting blood samples in a simple and convenient manner with our unique filtercard system. More details on filtercard use are available in this manual and in our informational brochure available from our website ( Alternative methods of sample preparation Sample size: 3-5mL For newborns and small children 2ml is sufficient Please note: when ordering more than one panel, please contact CENTOGENE for confirmation of needed volume of blood to be submitted EDTA tube Sample size: 50µL of EDTA blood per circle (circles completely saturated) filled in circles, depending on the type of analysis ordered Please note: when ordering more than one or a large panel, please contact CENTOGENE for confirmation of needed number of filtercards to be submitted. Filtercard Sample size: 20mg Fresh frozen tissue shipped on dry ice Paraffin embedded tissue 25-50mg of tissue or 5-10 micron sections (thick) in a sterile tube Somatic Genomics 5-10µm with marked area of enriched tumor or tissue parraffin block for macrodissection (min. 50mg of tissue) Pathology report Fixation type accepted: 10% Formalin or 4% Paraformaldehyde or Frozen tissue from OCT-Cell blocks - Fresh Frozen Sample size: 10mL Clear no blood contamination Amniotic fluid Sample size: 10 villi Cleaned in RPMI media with fetal calf serum (FCS) Chorionic villi Please do not send tissue fixed in Bouins or gluteraldehyde. Ship in a sterile tube at room temperature - no cold pack required. Tissue sample Sample size: 3-5mL Sample size: 5µg (20µg in case of NGS panels) We accept purified DNA with a ratio of absorbance at 260 and 280nm (A260/280) in the range from Sample size: 10mL of blood shipped in cell-free DNA BCT STRECK tubes. Blood should not contain any other anti-coagulants or preservatives as this may cause coagulation. Please note: when ordering more than one panel, please contact CENTOGENE for confirmation of needed volume of blood to be submitted 4 Purified DNA ctdna Cord blood

5 Sample transport CentoCard : CENTOGENE s innovative solution CENTOGENE has optimized the extraction of DNA from dried blood spots on filtercards. This allows us to assure the quality of analyses for our full range of testing from patient sample received on filtercards, including full gene, deletion/duplication and even whole exome sequencing. Detailed instructions for optimal blood spot preparation are provided on the filtercard itself. The following are important points worth highlighting: All circles must be filled and saturated with blood. The cards must be allowed to air dry for 2 hours before being placed into an envelope. Can be sent via normal post/mail at room temperature. At no time should the prepared filtercards be refrigerated or sent on ice, dry ice or cold packs. This has the potential to produce a poor quality analysis. Recommended Method 1 Disinfect the patient s arm 2 Perform a venous blood draw following EDTA procedures 3 Transfer blood from syringe to filtercard 4 Continue this procedure until the 10 required blood spots are completely saturated Valid specimen Invalid specimen Specimen quality insufficient for testing Specimen not dry before mailing Specimen appears supersaturated Specimen exhibits serum rings 5

6 Sample transport Filtercards, EDTA blood, cord blood & saliva: Samples can be sent via regular mail at room temperature. Liquid blood is stable for up to 4 days during transport. Amniotic fluid: Min. 10mL samples placed into a sterile conical tube. These should be shipped overnight at room temperature. Care must be given that the sample does not freeze. Chorionic villi, and any tissue samples: These specimens need to be shipped in a minimum of 35mL of RPMI transport medium with fetal calf serum at room temperature. The samples must be shipped in a manner to secure that the sample does not freeze (not below +4 C) especially during winter months. Blood for ctdna analysis: Blood sample must be sent in the glass STRECK tubes as per manufacturer s recommendation. Samples must be shipped immediately after sampling and at no stage should be frozen. Blood samples collected in STRECK tubes can be shipped at room temperature as they are stable upto 14 days. Samples in glass STRECK tubes must be handled and shipped carefully to prevent any damage of the glass tubes during shipment. Biochemical Test Orders At CENTOGENE, although we have classical fluorimetric and spectrophotometric methods available upon request, the detection method of choice is mass spectrometry, more precisely high resolution multiple reaction monitoring mass spectrometry (high resolution MRM-MS). MRM-MS in combination with liquid chromatography provides high specificity, selectivity, precise quantification of the enzymatic products or of the biomarkers and requires minimal amount of biological sample (mainly dried blood spots). Biochemical tests can: (i.) assert the specific enzymatic activity, or (ii.) measure the levels of the endogenous substrate accumulated in the cells (biomarkers). Sample requirement and stability: Please note that an notification needs to be sent to CENTOGENE (dmqc@centogene.com) when a timesensitive specimen has been sent.! 6 Tests in dried blood spots (DBS): We recommend to send a full card (10 spots) prepared as described in chapter 4. The requested amount for one biochemical analysis (inclusive the control assay, no repetition) is 2 spots. NOTE: biomarkers are stable in dried blood spots for years; all enzymatic assays with the exception of MPS IVa are stable in DBS for at least 4 weeks; MPS IVa enzymatic assay must be performed within 10 days from card preparation (for more information about sample handling for MPS IVa analysis please contact our customer relation department or see our publication from C. Cozma et al. 2015). Alternatively you can send us 2mL EDTA blood and we will prepare the filter cards in our laboratories (EDTA blood sample can be send at ambient temperature).

7 Biomarker determination in plasma: We recommend to send 0.5mL plasma. The minimum amount requested for one biomarker determination (no repetition) is 100µL plasma. Note: plasma can be frozen - biomarkers levels are stable in plasma for at least 6 months. Alternatively you can send us 2mL EDTA blood and we will prepare the plasma in our laboratories (the EDTA blood sample for plasma preparation should arrive at our laboratories in Rostock, Germany on ice not frozen, within 2 days from sample collection). ARSA enzymatic activity in leucocytes: Please send a minimum of 8mL EDTA-blood. NOTE: The blood should arrive in at our laboratories in Rostock, Germany within 48-72h from the blood collection at ambient temperature. Additional services Required sample identification & information Sample material must be labeled with the following information: Full name of patient Date of birth Required documents include: A completely filled request form (requisition) with ordering physician s signature and date. Requisition must specify which tests are needed, the ordering physician and where the results need to be sent, too. Clinical information must be submitted. This enables our scientists to generate a complete and accurate report. Any previous test results or family history will facilitate and improve the quality of information contained in the final report, especially with respect to the future needs of the patient and their family. Signed consent from the patient and/or legal guardian. Contact information must be submitted on the requisition. Storage and archive of examined samples CENTOGENE archives and stores all test material for a minimum of 20 years, but only when we have signed consent on file. The patient agrees to this archiving with the signing of the declaration of consent form. The patient may withdraw his/her consent at any time and the sample will be destroyed. Rejection of sample All samples that are received without proper identification and where there is no possibility to correctly identify the specimen, have to be rejected. The referring physician will be notified and a new sample will need to be collected. In the case that no test is ordered or the order is unclear, we will accept a written order from the referring physician with a signed requisition. References * The effect of preparation, storage and shipping of dried blood spots on the activity of five lysosomal enzymes; Carole S. Elbin, Genzyme Corp. P.O Box 9322, Framingham MA, 01701, USA, 03/17/2011) *Upon request, documents can be made available 7

8 Please visit our website for more information: Contact details: CENTOGENE AG Schillingallee Rostock Germany Phone: +49 (0) Fax: +49 (0) CLIA #99D V2.6_August2016