Frequently asked questions

• Access and login:
  • Can I register my colleague for data access?
  • Someone I know is a member of the Research Network, but they haven't received login details yet - why?
• Clinical Research interface:
  • I want to contact one or more clinicians to get more information about a set of participants that I want to collaborate to publish a paper on.
  • A clinical colleague has a patient they would like me to look at more closely to see if I can find any variants that were un-tiered or tier 3 that could have caused their disorder.
  • I reported a diagnosis using the Researcher Identified Potential Diagnosis form, but I have heard nothing. Has it gone back to the doctor? Did they think it was the answer?
  • I want to look at all the participants recruited from my local Genomic Medicine Service (GMS) and see if I can identify new diagnoses.
  • I have found some variants that I think are probably causal but I need DNA/RNA to confirm that they are functional.
  • I want to report a variant that was found to be causal through the NGRL Genomes Project through ClinVar, can I?
  • I want to share a gene using GeneMatcher to see if there are other cases around the world.
  • I am working in a consortium with others treating the same disorder, can I discuss variants and phenotypes with other clinicians to identify diagnoses?
  • I have noticed missing clinical data that would help a lot with research, can I collect and import it into the Research Environment?
  • I am both a clinician and a researcher, can I publish information about my own patients using data from the NGRL?
• Data:
  • How do I identify compound heterozygous mutations within the Genomics England Dataset?
  • How often are the data updated?
  • What is Rare Disease Tiering data?
  • Where can I find information on de novo variants?
  • Why can't I see all the genomes in the 'genomes/by_date' folder?
  • Why do some participants have multiple genomic data on the same reference assembly?
  • How do I know if a pathogenic variant with a high allele frequency is true or a variant calling error?
• Tools:
  • Can I bring in docker/container?
  • Can I install software in the Research Environment?
  • Is it possible to annotate variants within the Research Environment?
  • Is there an R package we can use to interrogate data from LabKey?
  • Problem loading IGV in the research environment
  • Vcf2maf on the HPC
  • LabKey DOCTYPE error
  • Loading R packages when versions are not synchronised
• Research:
  • Creating "lollipops" diagrams in the RE
  • Reference genomes within the Research Environment
  • If I think I have found a variant that I believe is pathogenic, who should I tell?