AMP ISV in Somatic Conditions - Technical Technical Survey Question Title * 1. What is your occupation/role? Pathologist Physician Oncologist Researcher Bioinformatician Laboratory Medical Director Laboratory Supervisor Pathologist Assistant Clinical Laboratory Technologist / Technician Other (please specify) Question Title * 2. What kinds of clinical NGS testing does your lab offer? Please check all that apply. Solid tumor panels Hematological malignancy panels Mixed panels Cancer Exome Cancer Genome Transcriptome Other (please specify) Question Title * 3. What enrichment method does your lab use? Amplicon-based, hot spot Amplicon-based, whole gene Hybrid capture Other (please specify) Question Title * 4. If you perform panel testing, check the number of genes contained within each panel and list the corresponding panel(s) type e.g. 50-100; solid tumor. Please check all that apply and list all corresponding types of panels that you perform. 1 - 10 11 - 25 26 - 50 50 - 100 100 + Question Title * 5. What type of gene sequencing panel is used by your laboratory? Laboratory developed panel Commercial kit If commercial kit, please provide name(s) of kit Question Title * 6. What kinds of alterations are you detecting and reporting using NGS data? Indels CNV SNV Gene fusions Other (please specify) Question Title * 7. NGS technology used in your lab: Life Technology Illumina Other (please specify) Question Title * 8. What is your minimal tumor burden (or neoplastic cellularity) for accepting a specimen for NGS testing? less than 5% 5% 10% 20% 30% 50% or more Other (please specify) Question Title * 9. Do you request submission of a normal specimen along with the tumor specimen? No Yes If Yes, please comment on usage Question Title * 10. What is your sample failure rate for clinical NGS specimens? 1% 5% 10% Other (please specify) Question Title * 11. What is your detection limit (variant allele frequency)? 1% 5% 10% Other (please specify) Question Title * 12. What is your minimum sequencing depth? 50x 100x 500x Other (please specify) Question Title * 13. What is your average sequencing depth? 100x 200x 500x 1000x 2000x 3000x Other (please specify) Question Title * 14. What kind of pipeline do you use to perform data processing from a FASTQ file to VCF file? Select all that are appropriate. Commercial application Custom / in-house solution If commercial, which software do you use? Question Title * 15. What kind of long term storage do you use for clinical data? Locally maintained servers in laboratory space (on-site) Institutional hosted servers in data center(s) (off-site) Public cloud storage services (off-site) Other (please specify) Question Title * 16. What kind of clinical NGS data do you store? Check all that apply. Unprocessed data FASTQ BAM VCF Other (please specify) Question Title * 17. If you report CNVs based on NGS data, what software do you use? Commercial software In-house / custom software If commercial, which software do you use? Question Title * 18. What informatics solution(s) is/are used for somatic variant annotation? Select ALL that apply. Open source software Commercial / third party software Custom developed software Manual annotation If commercial, which software do you use? Question Title * 19. What database(s) is/are used for filtering polymorphic variants based on minor allele frequency (MAF)? Select ALL that apply. 1000genomes NHLBI Exome Sequencing Project (ESP) (Exome Variant Server) dbSNP Custom/In-house database MAF is not used for filtering Other (please specify) Question Title * 20. If MAF is used to filter, what numerical cutoff for MAF has been established by your laboratory for polymorphic variants? 1% 3% 5% Other (please specify %) Question Title * 21. Is ethnicity specific MAF taken into consideration when filtering polymorphic variants? No Yes If Yes, please comment on usage Question Title * 22. What in-silico analysis tool(s) are used for predicting the effect of a sequence variant(s)? Tools for predicting damaging effect of amino acid substitution and/or small Indels (SIFT, PolyPhen, CADD, MutationTaster, others) Phylogenetic information/conservation score-based in-silico prediction tools (e.g PhyloP, phastCons, GREP++, others) Splice site prediction tools (Human Splice Finder (HSF), BDGP, NetGene2, others) Other (please specify application name) Question Title * 23. What variant database(s) is/are used for variant annotation (check more than one if applicable)? Catalogue of Somatic Mutations in Cancer (COSMIC) dbSNP ClinVar My Cancer Genome International Cancer Genome Consortium (ICGC) cBioPortal for cancer genomics Leiden Open Variation Database (LOVD) Online Mendelian Inheritance in Man (OMIM) The Human Gene Mutation Database (HGMD) Custom/In-house developed database Other (please specify) Question Title * 24. If you have an in-house variant database, how do you manage the database? Question Title * 25. Do you perform confirmatory testing for identified variants? Always Never Sometimes If sometimes, please comment under what circumstances confirmatory testing is performed. Question Title * 26. If you perform confirmatory testing, what method(s) do you use? Select ALL that apply. Sanger sequencing Allele specific PCR RT-PCR Melt curve analysis FISH (copy number changes, fusions) Other (please specify) Question Title * 27. Please add any information you feel would be beneficial to provide in this survey. Question Title * 28. (Optional) Please provide your name and email address to enable us to contact you in the future. The information will strictly be used only for the purpose of this survey. Done