Tayside Molecular Genetics User Manual Page 1 of 11 User Manual East of Scotland Regional Molecular Genetics Service Human Genetics, Level 6 Ninewells Hospital and Medical School, Dundee DD1 9SY General Enquiries: 01382 632674 Fax: 01382 496382 Duty Scientist email:- [email protected] Head of Laboratory: Dr David Baty (01382 496271 [email protected]) Contact for Clinical Advice Consultant Geneticist: Dr David Goudie (01382 632035 [email protected]) Website: http://humangenetics.org.uk/ Laboratory operating hours Monday-Friday 8.30am-5pm Out of Hours Service is unavailable. Version No. p75.8 Tayside Molecular Genetics User Manual Page 2 of 11 CONTENTS: SAMPLE REFERRALS ............................................................................................... 3 SAMPLE TYPES ......................................................................................................... 3 SPECIMEN COLLECTION: ......................................................................................... 3 HIGH RISK SPECIMENS ............................................................................................ 4 SAMPLE TRANSPORT ............................................................................................... 4 SAMPLE STORAGE ................................................................................................... 4 REPORTING GUIDELINES ......................................................................................... 4 LABORATORY REPERTOIRE ................................................................................... 5 SCOTTISH CONSORTIUM REFERRAL LABORATORIES CONTACT DETAILS .. 10 OTHER UK REFERRAL LABS ................................................................................. 10 Version No. p75.8 Tayside Molecular Genetics User Manual Page 3 of 11 Sample referrals All samples should be accompanied by a Human Genetics request form, which can be downloaded from NHS Tayside Intranet either via the Human Genetics website, or from the Human Genetics section of Clinical Pathways/Information. It is also available on the Human Genetics Unit website hosted by the University of Dundee. It is the duty of the clinician/or other health professional to obtain consent from the patient (or patient’s representative) for genetic testing to be carried out. In submitting a sample, the clinician confirms that consent has been obtained: (a) for testing and storage, (b) for the use of this sample and the information generated from it to be shared with members of the patient’s family and their healthcare professionals (if appropriate). The following information must be supplied legibly with each sample: • • • • Patient's surname and forename (on sample and form) Patient's date of birth and gender or CHI (on sample and form) Name and address of the healthcare professional requiring report (on form) Analysis requested and reason for request (on form) NB: Samples received without 2 unique identifiers on the sample tube will be rejected. The patient postcode should also be provided as this is necessary for our records and external invoicing. If you are sending in a sample from an individual with a known family history please provide specific details of any known index case and mutation details if available. Please note that additional forms are required to be completed for some conditions eg breast and colon cancer, diabetes studies, familial hypercholesterolaemia, HOCM, and long QT syndrome. Please contact the Dundee Molecular Genetics Laboratory for details. Information can also be found on Staffnet at: http://staffnet.tayside.scot.nhs.uk/OurWebsites/HumanGenetics/index.htm Sample types Please see section “Laboratory Repertoire” for sample details for each condition. If in doubt, please contact the laboratory. NB: Clotted samples are not suitable for DNA/RNA extraction Specimen Collection: - Sample containers must be securely capped after filling Sample containers must not show visible external contamination by biological materials Sample containers must be well mixed to prevent clotting. Immediately after collection, gently invert each blood tube several times to distribute the EDTA throughout the sample. Dispose of sharps in a sharps bin after taking a blood sample Version No. p75.8 Tayside Molecular Genetics User Manual Page 4 of 11 High Risk Specimens Please note the laboratory does not have the containment facility to handle samples from individuals with confirmed or suspected prion diseases (eg vCJD) and tuberculosis. These samples will be discarded by the Laboratory. Sample transport Samples sent through the internal mail systems should be placed in sealed plastic bags, with the accompanying form in a separate compartment and folded to display the lab address clearly without exposing patient details. To send blood samples through the post, Royal Mail approved packaging must be used. This is available from the laboratory on request. All samples should be sent to the address shown on the front cover of this manual. Samples from NHS Highland are delivered either by DX Couriers or Royal Mail. Microbiology maintains a generic policy for van transport (NB141) of samples between PRI and Ninewells, with Genetics and other laboratories as copyholders. For optimum DNA/RNA extraction: • Blood and saliva samples should preferably be received by the laboratory within 3 working days of being taken and stored in the fridge prior to sending. • Blood samples for BCR-ABL testing should be collected in EDTA and should be received by the laboratory within 24hrs of sampling. • Urine samples should preferably be received by the laboratory within 48hrs of sampling. • Fresh tissue should be sent in appropriate transport media; please contact the laboratory for information. Please note that DNA/RNA quality may be affected by delays in transit which may compromise the testing. Sample storage Most DNA/RNA samples will be stored indefinitely unless otherwise requested. Please contact the laboratory for details. Please note additional testing may be requested at any time (i.e. no time limit) on stored samples by contacting the Duty Scientist e-mail account [email protected]. This is dependent on the quality/quantity of remaining archived sample. Reporting guidelines Written results will be sent to the healthcare professional specified on the request form. Only in certain circumstances will a report be available via FAX or e-mail (for e-mailing reports the recipient must have an nhs.net account); please contact the laboratory. Version No. p75.8 Tayside Molecular Genetics User Manual Page 5 of 11 Laboratory repertoire Disorder Acral peeling skin syndrome; APSS Autosomal dominant polycystic kidney disease; ADPKD Gene(s)/MutationsTested TGM5 approx 76% of the individuals clinically diagnosed as peeling skin syndrome are found to carry TGM5 mutations PKD1/PKD2 Sample requirement 3ml blood in EDTA (>1ml from infants) TAT Screen 40 working days 3ml blood in EDTA (>1ml from infants) Screen 40 working days TGM1 / ALOX12B. Mutations in TGM1 are detected in approx 45% of the individuals diagnosed with lamellar ichthyosis or non-bullous ichthyosis PKHD1 3ml blood in EDTA (>1ml from infants) Screen 40 working days 3ml blood in EDTA (>1ml from infants) Screen 40 working days Asthma Β2-adrenergic receptor; p.Gly16Arg change 20 working days Bullous congenital ichthyosiform erythroderma; BCIE KRT1 / KRT10 Biotinidase deficiency BTD Capillary malformations RASA1 Cerebral cavernous malformation; CCM KRIT1 / CCM2 / CCM3 Detects approx. 75% in familial cases CF29v2 kit will detect 29 of the most common mutations in the Northern European population Detects >80% of CF mutations in Scottish Caucasian population Intron 8 polyT test if appropriate APC 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA Screen 40 working days Tumour Block>50% tumour preferred 40 working days Tumour Block>50% neoplastic cell 40 working days Autosomal recessive congenital ichythosis; ARCI Autosomal recessive polycystic kidney disease; ARPKD Cystic fibrosis; CF Colorectal cancer; familial adenomatous polyposis; FAP Colorectal cancer – Lynch syndrome/HNPCC –High Risk family history Colorectal cancer-medium risk ? Lynch syndrome Colorectal cancer-medium risk ? Lynch syndrome MLH1 (MSH2/MSH6 automatically tested in Edinburgh) MSI & IHC for MLH1, MSH2, MSH6 and PMS2. Samples showing MSI and loss of MLH1 will be screened for the BRAF p.V600E mutation MLH1 methylation analysis under validation for tumour tissue showing MSI and loss of Version No. p75.8 Notes (or at least 100ul of DNA with conc. >50ng/ul) (or at least 100ul of DNA with conc. >50ng/ul) Screen 40 working days Screen 40 working days Screen 40 working days Screen 40 working days 20 working days Screen 40 working days Please provide details of the individual’s ethnic origin when referring them for CF testing. Tayside Molecular Genetics User Manual Page 6 of 11 MLH1. Colorectal cancer – MutYH associated polyposis; MAP Colorectal cancer/polyps Colorectal cancer metastatic MutYH Analysed for 2 common mutations (p.Tyr179Cys and p.Gly396Asp). If one mutation found then full screen performed POLE and POLD1 common mutations KRAS codons 12, 13 and 61 NRAS codons 12, 13 and 61 BRAF codon 600 if requested Common trisomies - neonates T13 / T18 / T21 Common trisomies - prenatals T13 / T18 / T21 Congenital hypothyroidism TITF1 Crigler-Najjar syndrome; CN1 /2+UGT1A1 promotor variant UGT1A1 Deafness – non syndromic GJB2 sequencing and GJB6 deletions Deafness –aminoglycoside related deafness Mitochondrial mutation m.1555A>G may be screened for if evidence of aminoglycoside use or maternally inherited transmission Dystonia; early onset primary DYT1 Epidermolysis bullosa simplex; EBS KRT5 & KRT14 Epidermolytic Palmoplantar keratoderma; EPPK KRT1, KRT9 Ferguson-Smith Syndrome TGFBR1 mutation screening Gilbert syndrome UGT1A1 promoter repeat Gastrointestinal stromal tumours; GIST cKIT / PDGFRA selected exons / BRAF codon 600 Glomuvenous malformations; GVM 4 common glomulin mutations reported to account for 70% of mutations in GLMN families HFE; p.Cys282Tyr and p.His63Asp Approximately 90% of affected individuals are Haemochromatosis Version No. p75.8 content preferred 3ml blood in EDTA Screen 40 working days 3ml blood in EDTA Tumour Block>50% neoplastic cell content preferred >1ml EDTA from infants Amniotic fluid or Chorionic villus sampling 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 20 working days 7 working days 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) Tumour Block>40% tumour preferred 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA ** 20 working days oncologists must complete KRAS referral form 7 working days 2 working days Screen 40 working days Screen 40 working days Screen 20 working days 20 working days Screen 40 working days Screen 40 working days Screen 40 working days 20 working days Screen 40 working days Biopsies will be done rapidly on request Screen 40 working days 20 working days **Mouthwash samples should be provided for Tayside Molecular Genetics User Manual Page 7 of 11 homozygous (carry 2 copies) for the p.C282Y mutation Hirschsprung disease RET Holoprosencephaly SHH Hypo-/hypercalaemic periodic paralysis Selected mutations in the CACNA1S / SCN4A genes HOKPP1-approx 80% of cases will have one of the screened for mutations HYPP- approx 70% of cases will have one of the screened for mutations CFTR (Intron 8 polyT test if appropriate) / Y-chromosome deletions Infertility / azoospermia / CBAVD Ichthyosis bullosa of Siemens (IBS) KRT2 Ichthyosis vulgaris (IV) FLG 4 common mutations in European populations Loeys-Dietz TGFBR1 / TGFBR2 Lung cancer EGFR mutation analysis Lymphoma B-cells IGH and IGK T-cells TCRB and TCRG FBN1 / TGFBR1 / TGFBR2 Marfan syndrome; MFS recently transfused individuals 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) Screen 40 working days 3ml blood in EDTA (>1ml from infants) 20 working days 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) Tumour Block>50% neoplastic cell content preferred Tumour Block or cut sections 3ml blood in EDTA (>1ml from infants) Screen 40 working days Screen 40 working days Screen 40 working days Screen 40 working days Screen 40 working days 7 working days 20 working days Screen 40 working days Medium chain acyl-CoA dehydrogenase deficiency; MCADD ACADM 3ml blood in EDTA (>1ml from infants) Screen 40 working days Melanoma cKIT selected exons/ BRAF common mutations / NRAS codons 12, 13 and 61 Multiple endocrine neoplasia type 1; MEN1 Menin exons 2-10. In familial cases where no sequencing mutation is detected a DNA sample can be forwarded to Tumour Block>50% neoplastic cell content preferred 3ml blood in EDTA (>1ml from infants) BRAF/NRAS 7 working days/cKIT Screen 20 working days Screen 40 working days Version No. p75.8 Please provide details of the individual’s ethnic origin when referring them for CF testing. (or at least 100ul of DNA with conc. >50ng/ul) Urgent referrals will be reported within 5 working days for the common c.985A>G mutation. Tayside Molecular Genetics User Manual Page 8 of 11 Multiple endocrine neoplasia type 2; MEN2 Mitochondrial disorders Maturity onset diabetes of the young; (MODY) Exeter for MLPA RET selected exons 10,11,13,14,15,16 MtDNA common mutations causing MELAS, MERRF, NARP and LHON, & selected mutations associated with deafness and/or cardiomyopathy HNF1A, HNF4A and GCK Renal cysts and diabetes HNF1B Myeloproliferative neoplasms; MPN Myotonic dystrophy (DM1) JAK2; p.Val617Phe / then JAK2 exon 12 / CALR exon 9 / MPL exon 10 reflex testing as appropriate CAG repeat length Neurofibromatosis type 1; NF1 NF1 screen Occulopharyngeal muscular dystrophy; OPMD PABPN1 repeat Pachyonychia congenita Types I and II Hot-spots of the KRT6A, KRT6B, KRT6C, KRT16 and KRT17 genes PARK2 / LRRK2 / PINK1 Sequence analysis of PARK2 gene plus MLPA analysis for deletions of PARK1, PARK2, PARK5, PARK6, PARK7, PARK8 and ATP13A2 genes (kit can also detect LRRK2 p.Gly2019Ser mutation) Parkinson disease Pendred syndrome SLC26A4 / FOXI1 Phaeochromocytoma / Paraganglioma SDHB / SDHC / SDHD; TMEM127 / MEN2 / VHL / MAX PLP / GJA12. 50-60% of cases have a duplication of the PLP gene 30% of remaining cases have a point mutation EXOSC3 – common mutation only Pelizaeus-Merzbacher disease; PMD Pontocerebellar hypoplasia type1 Palmoplantar keratoderma; PPK K1, K5, K9, K10 Proximal symphalangism GDF5 / NOG1 Version No. p75.8 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) Screen 40 working days 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) Screen 40 working days 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 20 working days 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 20 working days 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) Screen 40 working days 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 20 working days 20 working days Urine sample for adult patients esp. if MELAS indicated. Must reach lab within 48 hours Screen 40 working days 20 working days Screen 40 working days (or at least 100ul of DNA with conc. >50ng/ul) Screen 40 working days Screen 40 working days Screen 40 working days Screen 40 working days Screen 40 working days Screen 40 working days Referrals accepted from neurology only Tayside Molecular Genetics User Manual Page 9 of 11 Thoracic aortic aneurysm and dissection (TAAD) ACTA2 Thrombophilia p.Arg506Gln / g.20210G>A Tuberous sclerosis TSC1 and TSC2 Von Hippel Lindau; VHL VHL Version No. p75.8 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) 3ml blood in EDTA (>1ml from infants) Screen 40 working days 20 working days Screen 40 working days Screen 40 working days Tayside Molecular Genetics User Manual Page 10 of 11 Scottish Consortium Referral Laboratories Contact Details North of Scotland Regional Genetics Service Polwarth Building, University of Aberdeen Medical School, Foresterhill, Aberdeen AB25 2ZD Phone 01224 553893 E-mail [email protected] South East Scotland Genetics Service Molecular Medicine Centre Western General Hospital Crewe Road Edinburgh EH4 2XU Phone 0131 651 1116 / 1270 E-mail [email protected] West of Scotland Genetics Service Laboratory Genetics Level 2B Laboratory Medicine Southern General Hospital Glasgow G514TF Phone 0141 354 9330 E-mail [email protected] Other UK Referral Labs The referral labs which we use most regularly send samples for testing include: Birmingham: West Midlands Regional Genetics Laboratory DNA laboratory Birmingham Women’s foundation Trust Birmingham B15 2TG 0121 627 2710 [email protected] Cardiff: All Wales Molecular Genetics Service Institute of Medical Genetics University Hospital of Wales Heath Park Cardiff CF14 4XW 029 2074 2641 [email protected] Version No. p75.8 Tayside Molecular Genetics User Manual Page 11 of 11 Guy’s London: Vipath Genetics Laboratories 5th Floor, Tower Wing Guy’s Hospital, Great Maze Pond London SE1 9RT 020 7188 1696/2582 [email protected] Manchester: Regional Genetics Laboratory Services Genetic Medicine 6th Floor, St Mary’s Hospital Oxford Road Manchester M13 9WL 0161 276 6122 Sheffield: Sheffield Diagnostic Genetics Service Sheffield Children’s NHS Foundation Trust Western Bank Sheffield S10 2TH 0114 2717003 [email protected] Addresses / Contact details of other UK laboratories Addresses / Contact details of other UK laboratories which we refer samples to can be obtained by contacting us directly, or follow this link to the UKGTN home page where you can search for test and laboratories: http://www.ukgtn.nhs.uk Version No. p75.8
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