FAQs

What services do you provide?

We provide a comprehensive service to handle all aspects of next-generation sequencing-based translational research projects, from sample to data. The services include experimental design, library preparation, sequencing, analysis, and interpretation of sequencing data, as well as dissemination of results.

How much data do I need for my project?

A list of common applications and recommended data requirements can be found on our guidelines page.

Which sequencing applications do you support?

We focus our support on a defined set of next-generation sequencing-based approaches, allowing us to maintain streamlined and standardised sample preparation and analysis pipelines ensuring fast turnaround times. We currently support variant and mutation detection from whole-genome and targeted re-sequencing, expression profiling by RNA-seq, protein-DNA interaction screening by ChIP-seq, methylation profiling by MeDIP-siq and bisulphite sequencing, as well as 16s metagenomic profiling. Please refer to our Services page for a full list of supported applications.

Do you support Sanger sequencing?

No, we only provide support for next-generation sequencing projects.

Do you provide informatics support for any sequencing project?

No, we can only provide support for medical genomics projects involving the analysis of samples and/or data derived from human or human pathogen samples. If you are not sure whether your project falls within the remit of our facility, please get in touch with us to discuss your proposal.

At which stage of the project should I get in touch with you?

You should get in touch with us as early as possible, ideally at the planning stage of your project. This allows us to identify any potential problems with the experimental design that could impact on the subsequent bioinformatics analysis and helps to achieve the desired outcome, avoiding disappointment.

Can I track the progress of my project?

We will keep you informed about the progress of your project but please feel free to drop us an email at any time (igf@imperial.ac.uk).

 

How will I receive my results?

We will provide secure access to your data via our web portal.

How much does it cost?

For standard sequencing applications please refer to Pricing (behind login). Support for approaches not offered as part of our portfolio of standard services are considered on a case by case basis and we will either provide a costing or discuss the possibility of a collaboration.

Are you interested in collaborations?

Yes - if your study uses approaches which are not part of our standard portfolio, or you are developing a new approach, we will consider offering our service on a collaborative basis. In this case, we would request co-authorship on publications resulting from the work. The exact authorship arrangements will be discussed during the planning stage of the project.

Who can access your services?

Currently, the service is open to all investigators and clinicians within Imperial College and the Imperial College Healthcare NHS Trust. A service for external customers is in preparation. We encourage those with patient samples where clinical outcomes may be influenced or disease pathogenesis better understood to consider working with us to generate genetic and genomic data from their patient samples. We also generate genome sequences of bacteria and other microbes causing human infectious diseases to help diagnose and track the source of infection outbreaks.

How long will it take until I receive results?

We aim to provide results to the customer within the shortest possible time. However, depending on what services you require from us (from experimental design to data analysis) and the number of samples in the queue, the time frame varies between one week to a few months. Once your samples/data have been received by the facility they will enter the queue and we will provide you with an estimated delivery time for the results.

Why would my sample fail quality control?

An insufficient amount and poor quality of DNA or RNA are among the main reasons for the failure of library preparation or sequencing. For this reason, we use stringent quality control processes on the provided samples in advance to make sure that they are of sufficient quality for library preparation. If the samples do not meet our minimum quality requirements, we will let you know in order to decide whether you would like to proceed further. However, in this case, we can not be held liable for poor quality outcomes of sequencing and data analysis.

How should I acknowledge your facility?

The acknowledgement of our work in publications is very important to assess impact and ensure continued funding of the facility. Please add the following statement in all publications resulting from work supported by our facility:

“The Imperial BRC Genomics Facility has provided resources and support that have contributed to the research results reported within this paper. The Imperial BRC Genomics Facility is supported by NIHR funding to the Imperial Biomedical Research Centre”.

Who should I contact for more information?

Please send an email to igf@imperial.ac.uk with a brief description of your project and the required support. We will then arrange a meeting to discuss your study in more detail.

How do we deal with Index Hopping?

Relatively high levels of index misassignment (commonly known as “index hopping”) have been reported on HiSeq 4000 platform (Sinha et al). Libraries with higher levels of free adaptors will see higher levels of “index hopping”. The free adaptors have the potential to prime and extend library molecules in the same lane during the clustering step. This can result in misassignment of reads through index swapping and causing errors in demultiplexing data, as reads from one sample have the potential to end up in the FASTQ files of a different sample. In our hands, by using best laboratory practice for cleanup and library storage, we have found that less than 1 or 2% of the reads are misassigned.

However, for projects requiring a high level of confidence for rare variants (e.g. cancer sample analysis) we use a custom dual indexing system. This strategy assigns unique barcodes on each end of each library. The barcodes are not shared by any other sample making misassignment virtually impossible.

A few suggested mitigation strategies to reduce index swaps are listed below:

  • Remove free adaptors using an extra bead clean-up of each individual library before pooling.
  • Use dual indexing strategies with unique barcodes on both ends. (Swapping would have to occur at both ends for read misassignment to occur) (unique i5 and i7 indexes)
  • Store libraries individually at -20°C
  • Pool libraries prior to sequencing