SW Thames Regional Genetics Laboratory, Jenner Wing, SGUL Cranmer Terrace London SW17 0RE Contact: Mr John Short Tel: +44 (0) 208 725 5332 Fax: +44 (0) 208 725 3440 E-Mail: swtrgl@stgeorges.nhs.uk Website: www.southwestthamesgenetics.nhs.uk Testing performed at the above address only DETAIL OF ACCREDITATION HUMAN TISSUE AND FLUIDS Amniotic fluid CVS Blood Solid tissues Other tissues / fluids Cytogenetic analysis for the purpose of clinical diagnosis Chromosome analysis for detection of aneuploidies and structural chromosome rearrangements for prenatal and postnatal diagnosis. Preparation of material for chromosome analysis by in-house methods - GEN-CYT-LAB-01 blood culture and harvest GEN-CYT-LAB-02 amniotic fluid culture and harvest GEN-CYT-LAB-03 CVS culture and harvest GEN-CYT-LAB-04 tumour culture and harvest GEN-CYT-LAB-05 tissue culture and harvest GEN-ALL-EQU-02 fridge, freezer and incubator use and maintenance GEN-CYT-LAB-06 slide preparation GEN-CYT-LAB-07 slide staining and banding GEN-CYT-EQU-05 Clearview coverslipping machine Analysis using Leica GSL120 automated capture station, Leica Cytovision workstations and analysis software using - GEN-CYT-LAB-08 Slide scanning using the GSL120 GEN-CYT-EQU-06 use of microscopes GEN-CYT-GEN-01 cytogenetic analysis, checking and reporting Assessment Manager: RB2 Page 1 of 9
HUMAN TISSUE AND FLUIDS Amniotic fluid CVS Blood Other tissues / fluids FFPE Cultured cells Buccal scrapes / saliva Amniotic fluid CVS Blood Other tissues / fluids FFPE Cultured cells Buccal scrapes / saliva Cytogenetic analysis for the purpose of clinical diagnosis Detection and analysis of genetic re-arrangements and/or genomic imbalance. DNA extraction using one or a combination of the techniques below (In-house procedures, commercial kits Chemagen MSN1, Maxwell 16, Nanodrop, QuBit, Biomek NX robot GEN-MOL-LAB-01 DNA extraction from blood GEN-MOL-LAB-02 Phenol Chloroform extraction GEN-MOL-LAB-03 DNA extraction from tissue, mouthwash, buccal scrapes, Oragene, FFPE GEN-MOL-LAB-23 DNA extraction using the Maxwell 16 IVD instrument GEN-MOL-LAB-04 DNA quantification GEN-MOL-EQU-03 Biomek NX robot use Fluorescent in situ hybridization (FISH) analysis of metaphase and interphase cells by GSL120 automated capture station, Cytovision workstations and Cytovision software GEN-CYT-LAB-14 FISH GEN-CYT-LAB-15 interphase FISH GEN-CYT-LAB-08 Slide scanning using the GSL120 GEN-CYT-EQU-06 use of microscopes GEN-CYT-GEN-01 cytogenetic analysis, checking and reporting Assessment Manager: RB2 Page 2 of 9
Amniotic fluid CVS Blood Other tissues / fluids FFPE Cultured cells Buccal scrapes / saliva Cytogenetic analysis for the purpose of clinical diagnosis Genome wide screen for copy number gain or loss of DNA by 8x60k Microarray profiling using OGT/Agilent technology and - GEN-CYT-LAB-16 array-cgh Benchwork GEN-CYT-LAB-18 prenatal array- CGH service process and workflow Analysed using InfoQuant cnfusion software GEN-CYT-LAB-17 array-cgh data handling GEN-CYT-GEN-02 array-cgh reporting procedure DNA extraction using one or a combination of the techniques below (In-house procedures, commercial kits Chemagen MSN1, Maxwell 16, Nanodrop, QuBit, Biomek NX robot - GEN-MOL-LAB-01 DNA extraction from blood GEN-MOL-LAB-02 Phenol Chloroform extraction GEN-MOL-LAB-03 DNA extraction from tissue, mouthwash, buccal scrapes, Oragene, FFPE GEN-MOL-LAB-23 DNA extraction using the Maxwell 16 IVD instrument GEN-MOL-LAB-04 DNA quantification Assessment Manager: RB2 Page 3 of 9
/RNA Detection of nucleotide variation (triplet repeats, microsatellites) for: Fragile X Myotonic Dystrophy types 1 and 2 (including TP-PCR and QP-PCR) Beckwith Weiderman, Wilms tumour, Silver Russell, isolated hemihypertrophy Huntington disease Identity / zygosity / maternal cell contamination (using Powerplex 16HS kit) Incontinentia Pigmentii Prader-Willi / Angelman s. UPD14 Y chromosome microdeletion PCR and electrophoretic analysis using ABI3130xl (including Assuragen AmplideX kit test for Fragile X) and Genemarker, Genemapper software - GEN-MOL-LAB-06 bisulphite modification of DNA GEN-MOL-LAB-07 Polymerase chain reaction GEN-MOL-EQU-02 ABI3130xl use GEN-MOL-DIS-02 11p15 disorders (including Silver Russell) GEN-MOL-DIS-06 - FMR1 disorders GEN-MOL-DIS-16 - Myotonic dystrophy type 1 GEN-MOL-DIS-17 - Myotonic dystrophy type 2 GEN-MOL-DIS-08 - Huntington disease GEN-MOL-DIS-09 Identity testing & DNA typing GEN-MOL-DIS-10 - Incontinentia Pigmentii GEN-MOL-DIS-19 - Prader-Willi / Angelman s GEN-MOL-DIS-21 - UPD14 GEN-MOL-DIS-23 - Y chromosome microdeletions reporting. Assessment Manager: RB2 Page 4 of 9
Detection of aneuploidy of chromosomes 13, 18, 21 or sex chromosomes Detection of triplet repeat expansions in genes beyond the detection limit of PCR for: Fragile X QF-PCR using ABI 3130 xl PCR System and analysis using Genemapper, Genemarker Software GEN-MOL-EQU-02 ABI3130xl use GEN-ALL-DIS-01 - Aneuploidy screening by QF-PCR GEN-MOL-LAB-22 QF-PCR analysis Southern blot analysis by agarose gel electrophoresis GEN-MOL-LAB-10 chemiluminescent Southern blot analysis GEN-MOL-DIS-06 - FMR1 associated disorders GEN-MOL-DIS-16 Myotonic dystrophy type 1 reporting. Assessment Manager: RB2 Page 5 of 9
Molecular analysis of DNA dosage of genes and exons for: 1p19q / MGMT glioma analysis 11p15-associated conditions including Beckwith Wiederman, Wilms tumour, Silver Russell, isolated hemihypertrophy BRCA 1 & 2 Marfan Sotos Li-Fraumeni MLPA using ABI3130xl and software (Coffalyser and GeneMarker) GEN-MOL-EQU-06 thermal cyclers GEN-MOL-EQU-02 ABI3130xl use GEN-MOL-LAB-17 MLPA GEN-MOL-LAB-18 MLPA statistical analysis (excluding 11p15, 1p19q and MGMT) GEN-MOL-LAB-19-11p15 MLPA GEN-MOL-LAB-1p19q MLPA GEN-MOL-LAB-21 - MGMT MLPA GEN-MOL-DIS-01 1p19q oligodendroglioma GEN-MOL-DIS-24 - MGMT GEN-MOL-DIS-02 11p15 disorders GEN-MOL-DIS-03 - Breast cancer GEN-MOL-DIS-13 Marfan GEN-MOL-DIS-25 Overgrowth s GEN-MOL-DIS-11 Li-Fraumeni reporting. Assessment Manager: RB2 Page 6 of 9
DNA and RNA profiling for detection of point mutations and small insertions and deletions of nucleotides in single genes for: Beckwith Wiederman, Wilms tumour, Silver Russell, isolated hemihypertrophy Breast cancer (BRCA1 & 2) CADASIL Costello Li-Fraumeni Lymphoedema distichiasis and associated disorders Marfan Marfanrelated disorders( Aortopathies ) Rasopathies (Noonan Spectrum disorderst) Sotos and associated overgrowth s IDH1&2 infiltrative glioma Sanger sequencing and analysis using ABI3730 and 3130xl and software (Sequence scanner, Mutation Surveyor, Alamut) GEN-MOL-LAB-07 Polymerase chain reaction GEN-MOL-LAB-12 Sanger sequencing of a PCR product GEN-MOL-LAB-14 analysis of sequencing data GEN-MOL-LAB-15 Alamut software GEN-MOL-EQU-01 ABI3730 use GEN-MOL-EQU-02 ABI3130xl use GEN-MOL-DIS-02 11p15 disorders GEN-MOL-DIS-03 - Breast cancer GEN-MOL-DIS-04 CADASIL GEN-MOL-DIS-11 Li-Fraumeni GEN-MOL-DIS-18 RASopathies (Noonan spectrum disorders) GEN-MOL-DIS-13 Marfan GEN-MOL-DIS-14 Marfan related disorders GEN-MOL-DIS-25 Overgrowth s GEN-MOL-DIS-26 hereditary primary lymphoedema GEN-MOL-DIS-27 IDH1&2 infiltrative glioma reporting Assessment Manager: RB2 Page 7 of 9
Detection of point mutations and small insertions and deletions of nucleotides in multiple genes for: Breast cancer (BRCA1 &2) Rasopathy panel (Noonan Spectrum Test) Overgrowth panel Lymphoedema panel Next generation sequencing based on Ion PGM, Ion Chef, OneTouch 2 and and analysis using software Sofia Genetics, IonReporter, TSS and Alamut GEN-MOL-LAB-24 Ion Torrent Ampliseq DNA Library preparation GEN-MOL-LAB-25 Ion Torrent template preparation and sequencing GEN-MOL-LAB-26 Next Generation Sequence data analysis GEN-MOL-LAB-14 analysis of sequencing data reporting. GEN-MOL-LAB-15 Alamut software Assessment Manager: RB2 Page 8 of 9
Cell Free DNA extracted from maternal blood Detection of trisomy 21,18 and 13 Non-invasive prenatal screening test CE Marked IONA test using - QiaSymphony SP DNA extractor, GX Touch, IonChef, IonProton, IONA computer - GEN-SAFE-LAB-02 Automated DNA extraction using the QiaSymphony GEN-SAFE-LAB-03 Sciclone automated library preparation GEN-SAFE-LAB-04- Fragment size analysis using the GX Touch GEN-SAFE-LAB-05 - Ion Chef setup GEN-SAFE-LAB-06 - Ion Proton: Cleaning, Initialization and Sequencing GEN-SAFE-LAB-07 SAFE Lab report generation and distribution procedure GEN-SAFE-LAB-08 Manual library preparation GEN-SAFE-LAB-09 Manual DNA extraction END Assessment Manager: RB2 Page 9 of 9