2014 APHL Next Generation Sequencing (NGS) Survey

Transcription

1 APHL would like you to complete the Next Generation Sequencing (NGS) in Public Health Laboratories Survey. The purpose of this survey is to collect information on current capacities for NGS testing and data analysis at state and local public health laboratories. This will provide baseline capacity data at an early stage of CDC s Advanced Molecular Detection initiative and aid in the identification of state and local laboratory needs as the initiative moves forward. We strongly encourage that you work with your staff lead on NGS activities or molecular supervisor to complete this survey. Next Generation Sequencing 1. Does your laboratory have a next generation sequencing (NGS) instrument? Yes (proceed to questions 1a-h) No (proceed to question 2) 1a. What funding source(s) were used to purchase your NGS instrument(s)? CDC Epidemiology Laboratory Capacity (ELC) Cooperative Agreement Funds CDC Public Health Emergency Preparedness Cooperative Agreement (PHEP Funds) FDA Genome Trakr Project State funds Other Grant Funds-please specify grant: Other funding mechanism -please specify: 1b. How many laboratory staff are trained to perform sequencing? Dedicated sequencing staff (enter whole number) Other staff trained to perform sequencing (enter whole number) 1c.Which of the following instruments does your laboratory have? Illumina HiSeq Illumina MiSeq Illumina NexSeq 500 IonTorrent PGM IonTorrent Proton PacBio RS PacBio RS II Other-please specify: 1c.1 Of the instruments selected above, how many of each do you have? 1d. Where in your laboratory is the NGS instrument(s) located? Bacteriology Microbiology Molecular section Newborn Screening Sequencing Core Virology Other-please specify: Page 1

2 1e. Which NGS applications are your laboratory currently using or evaluating? Include those applications that are currently being evaluated. Characterization of antimicrobial drug resistance Characterization of pathogens (e.g. strain typing, genotyping) Characterization of virulence factors or virulence determinants High resolution cluster identification in outbreak investigations Identification of pathogens Monitoring of emerging variants/ clones Newborn screening applications Tracing of transmission chains Other -please specify: None of the above 1f. Please list the top 5 priority pathogens and/or disorders for which NGS applications are currently used or being evaluated: 1g. Which of the following NGS applications will your laboratory implement or evaluate in the coming 12 months? Characterization of antimicrobial drug resistance Characterization of pathogens (e.g. strain typing, genotyping) Characterization of virulence factors or virulence determinants High resolution cluster identification in outbreak investigations Identification of pathogens Monitoring of emerging variants/ clones Newborn screening applications Tracing of transmission chains Other -please specify: None of the above 1h. Please list the top 5 pathogens and/or disorders for which NGS applications may be developed and/or implemented in the next 12 months: Please proceed to question Will your laboratory purchase an NGS instrument in the next 12 months? Yes (proceed to questions 2a-d) No (proceed to question 3) 2a. Which of the following instruments is your laboratory considering? Illumina HiSeq Illumina MiSeq Illumina NexSeq 500 IonTorrent PGM IonTorrent Proton PacBio RS PacBio RS II Other -please specify: Page 2

3 2b. Which of the following NGS applications will your laboratory implement or evaluate? Characterization of antimicrobial drug resistance Characterization of pathogens (e.g. strain typing, genotyping) Characterization of virulence factors or virulence determinants High resolution cluster identification in outbreak investigations Identification of pathogens Monitoring of emerging variants/ clones Newborn screening applications Tracing of transmission chains Other -please specify: Unsure 2c. Please list the top 5 priority pathogens and/or disorders for which NGS applications would be considered once an instrument is available. 2d. What funding sources will you use to purchase the sequencing instrument? CDC ELC Funds CDC PHEP Funds FDA Genome Trakr Project State funds Other Grant Funds -please specify: Other funding mechanism-please specify: Please proceed to question What are the reasons for NOT purchasing a NGS instrument? Don t have sufficient staff to add new methods Have access to NGS through partnership Instruments are too expensive Methodology too expensive No available funding No expertise available to perform bioinformatics No expertise available to perform testing Procurement issues Waiting until NGS applications are more fully developed Other-please specify: None of the above Please proceed to question 9. Data Storage/ Transmission 4. How do you store NGS data generated in or for your laboratory? In-house server Instrument Manufacturer Owned Cloud (e.g. BaseSpace) Other Cloud Service -please specify: Other mechanism -please specify: None of the above Page 3

4 5. Do you share any NGS data generated in your laboratory with other entities as part of a network or other partnership? Yes (proceed to question 5a-5c) No (proceed to question 5d) 5a. Which data sharing networks do you currently participate in? Only include networks that share sequencing data. 100,000 Genome Project CDC Listeria Project/Next Generation PulseNet FDA Genome Traker Partnership with industry or academic institution (please include list of partners, data that is shared, and mechanism for sharing data) Partnership with another state or local public health laboratory(s) (Please include list of partners, data that is shared, and mechanism for sharing data) Partnership with other CDC Programs/ Surveillance Systems (please describe) Sequences shared on GenBank but not part of larger initiative Other-please specify: 5b. Do you share metadata with network partners? Yes No Not applicable 5c. Which data fields do you/ would you be willing to share with network partners? Age category Collection year Commodity type (e.g. meat, produce, seafood) Country of origin (USA) Environmental Source (e.g. water, soil, air) Geographic location (HHS Region of patient residence) Geographic location (state) Geographic location (zip code) ID for laboratory submitting DNA sequence (e.g., CDC) Organism genus and species (e.g., Listeria monocytogenes) Organism serotype (if applicable and available) Organism source (e.g., clinical, food, environment) Site of isolation (e.g., blood, cerebral spinal fluid, stool) Unique sample ID (WGS_ID) None of the above Proceed to question 6. 5d. What are the reasons for not sharing any NGS laboratory generated data with other entities? Please check all that apply. Data sharing agreements won t allow my laboratory to share data There are no relevant partners for the data generated in my laboratory There is no mechanism in place to share data securely/ easily Other reason -please specify Page 4

5 Data Analysis/ Bioinformatics 6. Which of the following sources of bioinformatics expertise do you have access to? Please check all that apply. Bioinformaticians on staff (proceed to question 6a-b) Other staff trained to perform bioinformatics analysis (proceed to question 6c-d) Access to bioinformaticians through external partnership (proceed to question 6e) No access to bioinformaticians (proceed to question 9) 6a. How many bioinformaticians does your laboratory have on staff? Please enter whole number. 6b. Please describe nature of data analysis performed by bioinformaticians. 6c. How many other staff in your laboratory are trained in bioinformatics? Please enter whole number. 6d. Please describe the nature of data analysis performed by trained staff. 6e. What is the nature of your external bioinformatics partnership(s)? My laboratory collaborates with CDC for bioinformatics expertise My laboratory collaborates with NCBI for bioinformatics expertise My laboratory is affiliated with a university or institution that has bioinformatics expertise My laboratory partners with a university or institution that has bioinformatics expertise Other -please specify: 7. Which of the following characterizes your primary use of bioinformatics software? Please select only one. Only use commercially available software packages Only use software developed in-house Only use software provided with the instrument or by manufacturer Only use open-source software Primarily develop software in-house but use some commercially developed software Primarily use commercially developed software but develop some in-house Training and Capacity Needs 8. In which of the following areas does your laboratory require training or information? Bioinformatics Terminology CDC NGS Activities and Plans Data Analysis Data Standards Library Preparation and Performance of Sequencing Assays NGS Platform Selection NGS Terminology/ NGS 101 Potential Public Health Applications of NGS Other-please specify: None of the above 9. Has anyone in your laboratory attended training in NGS or bioinformatics? Yes (proceed to question 9a-b) No (proceed to question 10) Page 5

6 9a. Please name the training course(s) attended? 9b. How many individuals have received training in these areas? Please enter whole number. 10. If funding was available for NGS activities, how would you prioritize the spending? Please rank them in order of priority (1 highest, 6 lowest) Additional Personnel Equipment/ service contracts IT infrastructure Reagents/ Supplies Software Training 11. Please provide the name and address for your laboratory s primary NGS point of contact. Name: Please provide any additional comments: Thank you for completing the survey! Page 6