Sheffield Children’s NHS Foundation Trust Department: Sheffield Diagnostic Genetics Service Title: Full A-Z List of Genetic Tests Document reference number: 413.001 Full A-Z List of Genetic Tests SHEFFIELD DIAGNOSTIC GENETICS SERVICE You can search for a test by typing into the ‘Find’ facility in the toolbar above and pressing enter. Click the ‘Find next’ icon to locate multiple entries within the document. *Gene content for Next Generation Sequencing (NGS) panels can be referenced at: https://www.sheffieldchildrens.nhs.uk/sdgs/next-generation-sequencing/ FISH tests listed under “F” starting with constitutional FISH tests listed by chromosome number 1-22,X,Y, followed by oncology FISH tests listed A-Z by gene name. ** Our turnaround times are listed here based on the recommendations of the Association for Clinical Genetic Science (http://www.acgs.uk.com/media/949852/acgs_general_genetic_laboratory_reporting_recommendations_2015.pdf) and are in calendar days. These may be altered locally based on specific Service Level Agreement or clinical urgency. Turnaround Test Specimen Type Volume Notes/Comments Time** Achondroplasia, hypchondroplasia and Blood 0.5-5ml 2-6 weeks thanatophoric dysplasia 0.25-1ml BM in 5-10ml of Acute Lymphoblastic Leukaemia Bone marrow/ transport medium 14 days (ALL) + FISH leukaemic blood OR 1ml BM/VB in Li Hep 0.25-1ml BM in 5-10ml of Acute Myeloid Leukaemia (AML) (+/- Bone marrow/ transport medium 14 days FISH) leukaemic blood OR 1ml BM/VB in Li Hep Adrenoleukodystrophy (ALD) Blood 0.5-5ml EDTA 2-6 weeks (X-linked) ALK Breakapart FISH (2p23) for lung PETS 2x4µm 7 days cancer – FISH only sections on slides Alpha thalassaemia Blood 0.5-5ml EDTA 2-4 weeks Alport Syndrome sequencing panel Blood 0.5-5ml EDTA 2-6 Weeks Alveolar rhabdomyosarcoma – FISH PETS 2x4µm 14 days only sections on slides Anaplastic large cell lymphoma, ALK PETS 2x4µm 21 days positive – FISH only sections on slides Androgen Insensitivity Syndrome Blood 0.5-5ml EDTA 2-6 weeks (Testicular Feminisation) Antithrombin Deficiency Blood 0.5-5ml EDTA 2-6 weeks 10-20ml sterile universal / Amniotic fluid / Aneuploidy Detection QF-PCR 3-4 fronds sterile universal in 3 days chorionic villus CVS culture medium Amniotic fluid Aneuploidy FISH test 2-5ml in sterile universal 2-3 days sample Apolipoprotein E (APOE) ) / Type III Blood 0.5-5ml EDTA 4 weeks Hyperlipoproteinaemia – E2 allele Array CGH (see microarray) - - - Ataxia Next Generation Sequencing panel (Please see Hereditary Ataxia - - - panel) Known mutations 10-20ml sterile universal / only, in Ataxia telangiectasia/ATR-Seckel Amniotic fluid / collaboration with 3-4 fronds sterile universal in 3 days syndrome prenatal testing chorionic villus Institute of Cancer CVS culture medium Studies, Birmingham Date of issue: 21/12/20 Version number: 22 Author: Sarah Aspey Authorised by: Richard Kirk Page 1 of 13 Sheffield Children’s NHS Foundation Trust Department: Sheffield Diagnostic Genetics Service Title: Full A-Z List of Genetic Tests Document reference number: 413.001 Bernard-Soulier syndrome (GP1BA, Blood 0.5-5ml EDTA 2-6 weeks GB1BB, GP9) Blood / Bone Send to Lab BCR-ABL1 Quantitation (RQ-PCR) 0.5-5ml EDTA 14 days marrow immediately BCR-ABL1 Tyrosine kinase domain Blood / Bone Send to Lab 0.5-5ml EDTA 21 days (TKD) analysis (Sanger sequencing) marrow immediately Beta thalassaemia Blood 0.5-5ml EDTA 2-4 weeks PETS 2x4µm Bladder cancer –FISH only 21 days sections on slides Inform lab prior to Blooms syndrome Blood 3-4ml Li Hep 28 days sample dispatch Bone marrow failure Next Generation Sequencing panel* - Diamond-Blackfan anaemia - Dyskeratosis congenital *see website for - Fanconi anaemia panel content. Blood 0.5-5ml EDTA 6-12 weeks - Myelodysplastic syndrome Sub-panels - Severe congenital available neutropenia - Thrombocytopenia with absent radii BRAF (V-raf murine sarcoma viral PETS 8x10µm oncogenes homolog B1) mutations sections in 7 days affecting codon 600 in melanoma and universal colorectal cancer 6 weeks full Hereditary Breast & Ovarian Cancer screen, 2 *see website for (BRCA1, BRCA2 & PALB2) Next Blood 0.5-5ml EDTA weeks panel content Generation Sequencing* & MLPA predictive PETS 2x4µm Contact Lab prior to Breast Cancer (Her2) - FISH only 7 days sections on slides referral Hereditary Breast & Ovarian Cancer *see website for Blood 0.5-5ml EDTA 12 weeks Extended Gene Panel* panel content Bruck syndrome (PLOD2) Blood 0.5-5ml EDTA 2-6 weeks PETS 2x4µm Burkitt lymphoma –FISH only 21 days sections on slides CALR Exon 9 mutation screen Blood/Bone marrow 0.5-5ml EDTA 2 weeks Carnitine Acylcarnitine Translocase Blood or 0.5-5ml EDTA 2-6 weeks (CACT) Deficiency Fibroblasts Carnitine Palmitoyl Transferase Type2 (CPT2) Deficency Blood or - c.338C>T p.Ser113Leu 0.5-5ml EDTA 2-6 weeks Fibroblasts common mutation - Full sequencing Cartilage-associated protein (CRTAP) Blood 0.5-5ml EDTA 2-8 weeks -autosomal recessive OI. Cerebral AD Arteriopathy with Subcortical Infarcts & Blood 0.5-5ml EDTA 2-6 weeks Leukoencephalopathy (CADASIL) CGH/microarray –see microarray - - - Chimerism post bone marrow/stem 0.5-5ml EDTA cell transplant (Sex matched/ Blood/Bone marrow (see below if lineage-specific 7 days Powerplex) analysis required) Date of issue: 21/12/20 Version number: 22 Author: Sarah Aspey Authorised by: Richard Kirk Page 2 of 13 Sheffield Children’s NHS Foundation Trust Department: Sheffield Diagnostic Genetics Service Title: Full A-Z List of Genetic Tests Document reference number: 413.001 Chimerism post bone marrow/stem 2-3ml Li Hep cell transplant (Sex mis-matched Blood/Bone marrow (see below if lineage-specific 7 days (FISH)) analysis required) Chimerism if lineage-specific analysis 0.5-1ml EDTA required (MACS separated fraction Blood only 7 days (IN ADDITION TO ABOVE) e.g. CD3+) Blood preferable Chimerism Pre transplant DNA but other samples 0.5-5ml EDTA - storage (donor or recipient) can be processed e.g. buccal swabs Chromosome – Adult (with or without Blood 2-3ml Li Hep 28 days FISH) Chromosome – Child (with or without Blood 1-2ml Li Hep 28 days FISH) * smaller samples can be attempted Chromosome – Neonate Blood 0.5 – 1ml* Li Hep 10 days but may reduce the likelihood of a successful result Chromosome (with or without FISH) Amniotic Fluid 10-20ml sterile universal 14 days PRENATAL sample Chromosome (with or without FISH) 3-4 fronds sterile universal in CVS 14 days PRENATAL CVS culture medium Chromosome (with or without FISH) Fetal blood 0.5-1ml Li Hep 10 days PRENATAL cordocentesis Chromosome (with or without FISH) Cord blood 1-3ml Li Hep 10 days POSTNATAL Placental biopsy at See our “additional cord insertion site, information” page Chromosome (with or without FISH) <1cm cubed Sterile tissue fetal membrane, 28 days for information FETAL LOSS culture medium pots villi and cord regarding sending biopsies samples 1-2mm cubed Chromosome (with or without FISH) Skin biopsy Sterile tissue culture medium 2-3 weeks pots Solid Tumour <1cm cubed Universal with 5- Chromosome (with or without FISH) 21 days Biopsy 10ml of transport medium Universal with 5-10ml of Chronic Lymphoproliferative Bone marrow/ transport medium 21 days Leukaemia (CLL) –FISH leukaemic blood OR BM/VB Li Hep If blood ONLY then FISH result will be Chronic Myeloid Leukaemia (CML) 0.25-1ml BM in 5-10ml of Bone marrow issued and bone Karyotyping &/or BCR-ABL1 FISH (at transport medium 7 days /leukaemic blood marrow sample diagnosis) OR 1ml BM/VB in Li Hep requested for karyotyping Chronic Myeloid Leukaemia (CML) 0.25-1ml BM in 5-10ml of Bone marrow Karyotyping &/or BCR-ABL1 FISH transport medium 14 days /leukaemic blood (monitoring) OR 1ml BM/VB in Li Hep Collagen 6 related myopath panel Blood 0.5-5ml EDTA 2-6 Weeks Colorectal Cancer (HNPCC/FAP) *see website for Blood 0.5-5ml EDTA 12 weeks Extended Gene Panel* panel content *see website for Connective Tissue Disorders Next panel content Blood 0.5-5ml EDTA 12 weeks Generation Sequencing Panel Sub-panels available Congenital thrombotic Blood 0.5-5ml EDTA 2-6 weeks thrombocytopenic purpura Date of issue: 21/12/20 Version number: 22 Author: Sarah Aspey Authorised by: Richard Kirk Page 3 of 13 Sheffield Children’s NHS Foundation Trust Department: Sheffield Diagnostic Genetics Service Title: Full A-Z List of Genetic Tests Document reference number: 413.001 (ADAMTS13 deficiency) 2-6 weeks Crigler-Najjar Syndrome types I and II Blood 0.5-5ml EDTA cfDNA testing for EGFR mutations Peripheral blood 10ml PB in Streck/Paxgene 7 days Preservative tubes (Relapse or diagnostic) preservative tubes can be supplied by the laboratory if required. Contact lab prior to sending Cutis Laxa sequencing panel Blood 0.5-5ml EDTA 2-6 weeks Blood or Dried Cystic fibrosis – 50-mutatIon panel 0.5-5ml EDTA 2 weeks bloodspots Cystic fibrosis – newborn screening - 4-mutation and 50-mutation Dried bloodspots 0.5-5ml EDTA 4 days panels Cystic fibrosis – newborn screening NGS pilot study Dried bloodspots 0.5-5ml EDTA 4 days - NGS panel (332 mutations) Dementia Next Generation * see website for Blood 0.5-5ml EDTA 12 weeks Sequencing Panel* panel content Dentatorubral-pallidoluysian atrophy Blood 0.5-5ml EDTA 4 weeks (DRPLA) Dermatofibrosarcoma protuberans – PETS 4x4µm 21 days FISH only sections on slides Diamond Blackfan Anaemia (RPS19) Blood 0.5-5ml EDTA 2-8 weeks Diamond Blackfan Anaemia (dosage Blood 0.5-5ml EDTA 8 weeks testing by MLPA) Dopa-responsive dystonia (Segawa Blood 0.5-5ml EDTA 2-8 weeks syndrome), dominant DYPD Blood 3-5mL EDTA 3 days Dystonia and Parkinsonism Next *see website for Blood 0.5-5ml EDTA 12 weeks