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Application for laboratory to join the UK Genetic Testing Network For help and clarification in completing this form please contact the UKGTN project team UKGTN Project team: UK Genetic Testing Network c/o South East Commissioning Support Unit (SECSU) 15 Marylebone Rd London NW1 5JD e-mail: [email protected] Tel: 020 3350 4999 Fax: 020 3350 4458 Please refer to the ‘Process and Criteria for UKGTN Laboratory Membership as a Diagnostic or Technical Service Provider’ document before completing this application form. Date of application What type of UKGTN membership is being applied for: a) Diagnostic membership Yes/No b) Technical membership Yes/No Laboratory details Laboratory name Laboratory Address Laboratory phone number Laboratory fax number Laboratory e-mail address Laboratory Web address Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 1 Organisational details Head of Laboratory Tel Number Fax Number Email address Signature of Head of Laboratory Owning Institution Name and Address of Chief Executive of owning institution Signature of Chief Executive Please note that for NHS organisations, the UKGTN will inform the relevant NHS commissioners should the laboratory become a member. Name of Lead NHS commissioner for the service Email address Commissioning organisation e.g. NHS England specialised commissioning hub or CCG Name and email address for NHS Contracts lead in the owning organisation Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 2 APPLICANTS MUST COMPLY WITH THE FOLLOWING MANDATORY REQUIREMENTS PRIOR TO MAKING AN APPLICATION UKGTN requires laboratories applying for diagnostic category status to be accredited by either CPA/UKAS or to be accredited to ISO15189. Laboratories applying as technical members need to be accredited to ISO17025. Instructions for completion Applications for diagnostic membership where the laboratory has full CPA/UKAS or is accredited to ISO15189, please complete: Section A Appendx 1 Notification of tests laboratory wishes to offer Appendix 2 Declaration of Interests Applications for technical provider membership where the laboratory is accredited with ISO17025 please complete: Section B Appendx 1 Notification of tests laboratory wishes to offer Appendix 2 Declaration of Interests Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 3 Section A – to be completed by applicants with full CPA/UKAS accreditation or accredited to ISO15189 and applying for diagnostic provider status 1.1 Accreditation Is the laboratory accredited with CPA? Yes/No (if Yes please go to question 1.2) Is the laboratory accredited to ISO15189? Yes/No (if Yes please go to question 1.3) 1.2 Accreditation – CPA What is the CPA reference number? What is the CPA discipline? When was the last inspection? Were all the tests that are being proposed for service (appendix 1) declared at the time of the last inspection using the current methodology? Yes/No If no please provide details here; Accreditation – ISO 1.3 What is the ISO certification number? What is the date on the most recent schedule of accreditation? Were all the tests that are being proposed for service (appendix 1) declared at the time of the last inspection using the current methodology? 2. 3. Yes/No If no please provide details here; Reporting times Please complete the proforma in appendix 1, please make a copy of the blank form and use a separate form for each test to be offered on the network stating: the levels of service offered (e.g. mutation screening / confirmation of known mutations / gene tracking / prenatal etc), reporting times (in calendar days) for both urgent and non-urgent referrals and percentage compliance to the reporting times for the last full financial year prior to application. Information on monitoring activity data There needs to be a minimum dataset for monitoring purposes, to include reporting times, number of tests per annum, geographic data on referrals (in the form of resident postcodes) to monitor equity of access and audit and outcome data to monitor effectiveness of service. Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 4 3.1 3.2 Association for Clinical Genetics Science (ACGS) Please indicate whether or not you return audit data to the ACGS: Yes/No Laboratory report activity data Service area: Cytogenetic Please provide data for 1st April to 31st March of the most recent financial year listing the number of reports issued for each of the bands. See Appendix 3 for information on the Genetic Units System used to assign tests to bands. GenU Band Number of Samples / Reports Please DO NOT multiply number of reports by weight A (sample prep) A (liquid nitrogen storage and/or cell export) B C D E F G NOT APPLICABLE H NOT APPLICABLE Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 5 Service area: Molecular Please give data for 1st April to 31st March of the most recent financial year listing the number of reports issued for each of the bands. See Appendix 3 for information on the Genetic Units System used to assign tests to bands. GenU Band Number of Samples A (all DNA/RNA extractions for service work) A (extract for research only exclude GeL work) A (extract for GeL work only) A (sample export) A (return of paraffin blocks) Number of Molecular Genetic Reports provided in each band GenU Band Inherited / Sporadic disorders (excluding NGS panels but including single gene tests that use NGS technology) B C NOT APPLICABLE D Inherited / Sporadic disorders NGS PANELS ONLY NOT APPLICABLE NOT APPLICABLE NOT APPLICABLE Acquired disorders (excluding NGS panels) NOT APPLICABLE Acquired disorders NGS PANELS ONLY NOT APPLICABLE NOT APPLICABLE NOT APPLICABLE E F G H 3.3 Resident postcodes for reports issued Please provide an estimate of the proportion of reports in which the resident postcode has been provided for reports issued in the last most recent financial year. % Please confirm if the data on resident postcodes and/or dates of birth/NHS numbers for every report where the laboratory did the analysis is easily extracted to an Excel spread sheet for submission to NHS Digital for the UKGTN Review of Genetic Testing rates as described in the Data Provision Notice https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/522519/Da ta_Provision_Notice__Genetic_Testing_rates.pdf Yes/No NHS England has issued Directions for NHS Digital to collect this data and it is a legal requirement for all UKGTN member laboratories to submit this data on an annual basis. If you are unable to do this please contact the UKGTN team before continuing any further with this application. Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 6 4. Clinical environment The applicant laboratory needs to demonstrate that the laboratory has management arrangements and a critical mass capable of providing a supportive environment for a specialist service. This includes advice on clinical interpretation and reporting. In the box below, please describe what arrangements you have in place to access clinical advice to interpret the clinical significance of results and to make counselling services available to patients and their families. 5. Research and development activity The applicant laboratory should have a relationship with at least one University Department with expertise in genetics with an expectation that it would, through its University links, attract research grants and carry out research. 5.1 Links to University Departments In the box below, please give details of University Departments or others with whom you have research links (expand the box as required). 5.2 Collaborations resulting in diagnostic testing services Please specify any tests that you have introduced into your laboratory in the past two years and advise which of these have been as a result of collaborations with a University department as listed in 5.1 (expand the box as required). 5.3 New techniques/technologies Please specify any new techniques/technologies that you have introduced into your laboratory in the past two years and advise which of these have been as a result of collaborations with a University department as listed in 5.1(expand the box as required). Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 7 5.4 Current research projects Please list current research projects/collaborations and how they are funded. Current research projects/collaborations Description of how project/collaboration is funded 5.5 Publications Please list the publications that your laboratory contributed to in the last financial year 6. Dissemination of information on availability of services It is mandatory for the applicant laboratory to complete UKGTN audit/activity reviews as required and I agree to provide information when requested. In order to facilitate equal access to services, I agree that the applicant laboratory, as part of the UKGTN, will provide information to the UK Genetic Testing Network using standardised formats provided by them where applicable. I agree to update the test information provided for this laboratory on the UKGTN website. I agree to inform the UKGTN of any changes to the laboratory services including changes in service provision, technology, organisational structures and appropriate research structures. I understand that if I do not provide information when requested that UKGTN membership may be removed. Signed: Name (print): Position: Date: Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 8 Section B – to be completed by applicants applying to be Technical Providers and accredited to ISO17025 1. External Quality Assurance Evidence of participation in the relevant formal EQA schemes will be required by the UK Genetic Testing Network Laboratory Membership & Audit Working Group. 1.1 EQA schemes In the box below (expand as required) please list the external quality assurance schemes in which you participate. 1.2 Performance with EQA Have you been contacted by a Scheme Organiser with regard to persistent poor performance in the last 12 months? Yes/No If yes, in the box below (expand as required), please provide details. 2. Support from owning Institution Applicant laboratories need to demonstrate the support from their owning institution to provide stability and quality of service including infrastructure, space and services. Arrangements for paying capital charges must be transparent and the host must indicate that this will lead to a planned and timely programme of capital (equipment) replacement. In the box below (expand as required) please provide details of the support you receive from your owning institution with respect to infrastructure, space and service requirements and a timely programme of capital (equipment) replacement. Please detail the process by which the management of the owning institution and the laboratory interact e.g. type and frequency of meetings Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 9 3. Provision of a robust and sustainable service The applicant laboratory needs to demonstrate that it can provide a reliable service. Considerations include staffing (vacancies, maternity/long and short term sick leave, holidays and training), technical considerations (planning for technical failure) and contingency plans for major incidents. 3.1 Staffing Structure For NHS organisations Please provide in a separate document the staffing structure (details as at April 1st of the year of application) and indicate the Agenda for Change band for each position and whether or not the current post holder is HCPC registered. For non-NHS organisations Please provide in a separate document the staffing structure (details as at April 1st of the year of application) and indicate whether the current post holder for each position is HCPC registered. 3.2 Staffing absence In the box below (expand as required) please describe how you deal with vacancies, maternity/long and short term sick leave, holidays and training. 3.3 Major incidents In the box below (expand as required) please describe how you plan for technical failures and major incidents. 3.4 Sample storage In the box below (expand as required) please describe the facilities that you have for long-term storage of samples and your policy for long term storage. Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 10 4. Technical and scientific environment The applicant laboratory needs to demonstrate that the lab has management arrangements and a critical mass capable of providing a supportive environment for a specialist service. This includes support for technical trouble shooting and a scientific and management objective setting environment capable of absorbing and integrating new scientific and technical developments. 4.1 Technical In the box below (expand as required), please describe the support you have in place to deal with technical trouble shooting 4.2 Scientific In the box below (expand as required), please provide information on the scientific and management arrangements you have in place to allow for the integration of new scientific and technical developments into your service. 5. Research and development activity It is recommended that the applicant laboratory should have a formal relationship with at least one University Department with expertise in genetics although it is recognised that this is not a requirement for Technical Service Providers. 5.1 Links to University Departments In the box below, please give details of University Departments or others with whom you have research links (expand the box as required). Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 11 5.2 Collaborations resulting in diagnostic testing services Please specify any tests that you have introduced into your laboratory in the past two years and advise which of these have been as a result of collaborations with a University department as listed in 5.1 (expand the box as required). 5.3 New techniques/technologies Please specify any new techniques/technologies that you have introduced into your laboratory in the past two years and advise which of these have been as a result of collaborations with a University department as listed in 5.1(expand the box as required). 5.4 Current research projects Please list current research projects/collaborations and how they are funded. Current research projects/collaborations 5.5 Description of how project/collaboration is funded Publications Please list the publications that your laboratory contributed to in the last financial year Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 12 6. Responsibility of service 6.1 Chain of responsibility In the box below (expand as required), please identify the chain of responsibility for any errors. 6.2 Legalities In the box below (expand as required), please demonstrate compliance to legal imperatives and the need for indemnification, which includes compliance with the 'In vitro diagnostic medical devices directive 98/79/EC' and the Human Tissue Act licensing arrangements. 6.3 Sub contracting In the box below (expand as required), please identify the lines of responsibility for subcontracting and provide information on any arrangements that are in place for subcontracting to another provider. 7. Services to be provided to UKGTN Diagnostic Laboratories Technical Service Providers are required to provide services to UKGTN Diagnostic Laboratories in order to maintain membership of UKGTN. 7.1 List of tests to be provided Using appendix 1 (please make as many copies as required), please provide a list of the services that will be available to UKGTN Diagnostic Laboratories. 7.2 Tests already provided to UKGTN Diagnostic Laboratories In the box below (expand as required), please list any tests that are already being provided to UKGTN Diagnostic Laboratories by stating the name of the test and the laboratories that are using these services Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 13 8. Dissemination of information on availability of services It is mandatory for the applicant laboratory to complete UKGTN audit/activity reviews as required and I agree to provide information when requested. In order to facilitate equal access to services, I agree that the applicant laboratory, as part of the UKGTN, will provide information to the UK Genetic Testing Network using standardised formats provided by them where applicable. I agree to inform the UKGTN of any changes to the laboratory services including changes in service provision, technology, organisational structures and appropriate research structures. I understand that if I do not provide information when requested that UKGTN membership may be removed. Signed: Name (print): Position: Date: Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 14 Appendix 1: Proforma for the notification of tests that the laboratory would like to offer to UKGTN. Laboratories applying for diagnostic membership will be required to submit Gene Dossiers (or additional provider forms where the test is already on the Directory) for tests that they wish to provide to the UKGTN once their application for membership has been accepted to pass stage 1. UKGTN tests must be provided as a national service. Please complete a separate form for each test – make copies as required. Service levels Qualifiers Sequencing of the entire coding region of a gene Reporting time target (Calendar days) Percentage of tests that met Reporting time target in last full financial year prior to application Price (£) - Price Note Please state whether price is per gene or for all genes Please provide notes e.g. if price is per gene or per combination of genes. To specify genes please list symbols e.g. BRCA1&BRCA2 Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Sequencing of the entire coding region of a gene PLUS copy number analysis Prenatal Diagnosis Sequencing of selected exons Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Mutation Scanning Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Targeted mutation analysis Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Testing for known mutations in family members Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Gene Tracking Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Targeted copy number analysis Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Whole genome analysis for copy number imbalance Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Chromosome analysis for balanced structural chromosome rearrangements Prenatal Diagnosis Chromosome instability (breakage) analysis Prenatal Diagnosis Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Postnatal Diagnosis Routine Postnatal Diagnosis Urgent Non Invasive Pre Natal Diagnosis Prenatal Diagnosis Please tick the QA schemes that are undertaken for this test: UKNEQAS (Disorder specific) EMQN (Disorder specific) No EQA scheme available Not participating Accredited Generic Technical Scheme Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 15 Appendix 2 DECLARATION OF INTEREST To be completed by Directors/senior staff of the organisation responsible for the laboratory I ..........................................................…………………………….declare that I currently have/do not have* interests which are material and relevant to the UKGTN service or any NHS organisations. *please delete as appropriate Interests which are relevant and material are: 1. Directorships, including non-executive Directorships, held in private companies or PLCs (with the exception of those of dormant companies) 2. Ownership or part ownership of private companies, businesses or consultancies likely or possibly seeking to do business with the NHS 3. Majority or controlling shareholdings in organisations likely or possibly seeking to do business with the NHS 4. A position of trust in a charity or voluntary organisation in the field of health and social care 5. Any other connection with a voluntary or other organisation contracting for NHS services My interests are listed below: Please state ‘nil’ if no interests are to be declared (Please note that the interest of members spouses or cohabiting partners should also be regarded as relevant) Signed ................................................ Date ................................................... Please sign, date and return with your application form to UKGTN Team c/o Sout East Commissioning Support Unit (SECSU) 15 Marylebone Rd London NW1 5JD Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 16 Appendix 3 Genetic Units (GenUs) system to record laboratory activity – 2016 version. Further advice on how to use the GenUs system is available from the UKGTN website at http://ukgtn.nhs.uk/our-work/ukgtn-reportsguidelines/genetic-units-genus/ Note internal transport of DNA/cell culture samples between co-located laboratories should not be counted as exports Band A GenU Score 1 General examples All DNA extractions to include o extract > test locally o extract > DNA banking All RNA extraction Sample receipt, booking in, and processing of all sample types. Covers: o Sample preparation, setting up of culture(s) and processing of sample to provide a cell suspension for cytogenetic analyses, processing of PET samples for FISH, DNA extraction Specific examples A 1 B 2 DNA/cell culture sample export Cell freezing/storage – long term liquid nitrogen storage Single amplicon (genotyping or sequencing) Embryo preparation of PGD analysis FISH only testing for constitutional or acquired samples with a single FISH hybridisation as the only test Follow up FISH testing for all sample types with a single FISH hybridisation as the only test Samples processed for both Cytogenetic and Molecular Genetic Studies are considered as separate. Interpretation/undertaking segregation of results from another laboratory. Re-issue of report for sample previously tested (repeat request for same test). Proband samples processed as a positive control for other family members An additional A is counted for any exports only of DNA or cell cultures Freezing/storage – this is a one-off charge for potentially long-term storage FraX PCR Haemochromatosis Factor V Jak2 HD (diagnostic and predictive tests) Other triplet disorders where a single PCR is required (eg SBMA) Y deletions FLT3 NPM1 Only includes preparation for testing. A single hybridisation can include two informative probes e.g. ATM/TP53 combination probe Follow up of microarray findings using a single FISH probe Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 17 Band C GenU Score 4 General examples Specific examples Genotyping 2-4 amplicons Sequencing: Very small gene with 2-4 exons/amplicons Sequencing: Predictive tests, confirmations and carrier tests MS-PCR MLPA with no other test (including DMD) Prenatal tests to include the MCC 1 lane on Southern Triplet disorders that require two PCRs (allele specific and TP-PCR) Identity/paternity tests Direct CVS analysis Rapid aneuploidy testing for +13, +18 and +21, X/Y (QF-PCR FISH) Follow up testing all sample types by karyotype, FISH, MLPA, targeted array and FISH (if 2-4 hybridisations) Kit based MLPA FISH only testing for constitutional or acquired samples with 2-4 FISH hybridisations Postnatal constitutional whole genome screen by karyotyping or array analysis without a rapid aneuploidy pre-screen includes. This includes any additional conventional staining or FISH tests requested/required including confirmation of array findings, if required, for the proband CF-ARMS, CF-OLA, CF-HT AS/PWS FraX if Southern blotted DM, Friedreich’s ataxia RT PCR BCR/ABL1 Includes slide making/banding and FISH preparation for all probe types Parental follow up samples: any method NB. proband sample acts as a positive control E.g. CLL FISH panel Haematology monitoring samples included as follow up 5-19 amplicons (MLPA to count as 2 amplicons when part of full screen) All linkage tests including UPD Prenatal constitutional whole genome screen by karyotyping or array analysis without a rapid aneuploidy pre-screen includes any additional conventional staining or FISH tests requested/required including array confirmation for the proband Postnatal constitutional whole genome screen by karyotyping or array analysis including a rapid aneuploidy pre-screen test. This includes any additional conventional staining or FISH tests requested/required. Includes confirmation of array findings, if required, for the proband Chromosome breakage studies, eg FA, or AT D E 7 10 Includes slide making and G-banding and processing steps post DNA extraction. Covers blood and solid tissue referrals G-band analysis appropriate to referral reason and if necessary other conventional staining (eg C band, NOR) to aid interpretation. Sequencing MECP2 by Sanger or NGS DMD linkage AS/PWS if linked markers used Includes SCE prep and analysis for FA, and scanning for chromosome 7 and 14 rearrangements for AT. Transformed/relapse category includes those where a full analysis on the sample is required. Postnatal covers blood and solid tissue referrals Includes long term culture, slide making and G- banding and processing steps post DNA extraction Rapid aneuploidy testing for +13, +18 and +21, X/Y (QF-PCR FISH) Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 18 Band GenU Score General examples F 15 G 25 H 40 Specific examples Diagnostic, transformed or relapsed Haematological (marrow, blood, lymph node, effusion) or tumour whole genome screen by karyotyping or array analysis includes any additional conventional staining or FISH tests requested/required. Haematological FISH only testing 5-19 hybridisations 20-49 amplicons (MLPA to count as 2 amplicons when part of full screen) Prenatal constitutional whole genome screen by karyotyping or array analysis including a rapid aneuploidy pre-screen test. This includes any additional conventional staining or FISH tests requested/required. Includes confirmation of array findings, if required. 50-100 amplicons (MLPA to count as 2 amplicons when part of full screen) Sequencing factor 8 by Sanger or NGS Includes long term culture, slide making and G- banding and processing steps post DNA extraction Rapid aneuploidy testing for +13, +18 and +21, X/Y (QF-PCR FISH) Sequencing FBN1 Sequencing BRCA1+BRCA2 1-50 genes analysed by NGS Over 100 amplicons 51-500 genes analysed by NGS Sequencing 12 genes for Noonan Spectrum Disorders Sequencing a group of genes in parallel that contribute to a single report Sequencing 105 genes for Retinal Degeneration Aug 2006 (revised Sept 2007, revised Oct 2009, revised Oct 2012, revised Jan 2014, revised Jun 2014, revised Mar 2016, revised October 2016) 19