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UCL Genomics

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UCL Genomics is a collaborative research facility with expertise in state-of-the-art genomic technologies, project design and data analysis. Operational for over 20 years, this cost recovery, not-for-profit core facility uses the most up-to-date equipment to support your genomic research requirements. We are equipped automated systems for optimal high throughput and consistency and can accommodate both small and large scale projects.

Highly experienced application specialists offer full support at every stage from optimal experimental design to data analysis. We support collaborations both nationally and internationally, including those in academia, clinical settings and industry. 

We form part of the Genetics and Genomic Medicine programme at the UCL Great Ormond Street Institute of Child Health. UCL Genomics moved to dedicated laboratory space at the Zayed Centre for Research into Rare Disease in Children (ZCR) in 2019 and merged with UCL Pathogen Genomics Unit in January 2020 to create an expanded facility, pooling both resources and expertise and now forms part of the Genomics Science Technology platform at UCL.

About UCL Genomics

UCL Genomics is housed at the Zayed Centre for Research into Rare Disease in Children (ZCR) with its own bespoke, dedicated laboratories. Our facility offers a number of dedicated genomic streams, including:

1. Nucleic acid extractions
2. Quality Control
3. Genotyping microarrays
4. Methylation microarrays
5. Short/Long read sequencing
6. Pathogen sequencing
7. Single cell sequencing
8. Bioinformatics 
9. Education

 

Technology at UCL Genomics

UCL Genomics is a modern facility with state-of-the-art technologies. Our labs are equipped with a range of QC and microarray equipment, liquid handing automation and sequencers. We have dedicated pre-PCR laboratories, dedicated genomic laboratory workspace and a genomic instrument laboratory. Some technologies are accessible for hire by UCL users following training. Below highlights some of our technologies at UCL Genomics.

A range of liquid handlers:
- Hamilton Nimbus Presto with Kingfisher technology (for high throughput extractions)
- Hamilton STAR and Hamilton STARlet
- Agilent Bravo liquid handler x2
- Opentrons OT-2 liquid handler
- Agilent Magnis (for low sample number, walk-away SureSelect library preparations)

A range of sequencers including:
- MiniSeq, MiSeq x2, NextSeq 500, NextSeq 2000, MinION and GridION

A range of quality control equipment including:
- Qubit fluorometer (2.0 and 3.0), Agilent Bioanalyser 2100, Agilent Tapestation 4200 x2, Nanodrop and an Omega FLUOstar plate reader

A range of equipment for high throughput microarray processing:
- TECAN liquid handler, iScan with autoloader, Hybex and ovens

A range of ancillary equipment including:
- Covaris, Vacuspeed, plate centrifuges, deep well centrifuge

A range of equipment to support single cell technology
- Chromium single cell 10x, Octo dissociator

Bioinformatics support
- Powerful clusters, IPA software

 

Other genomic technologies at UCL

Long Read Sequencing Facility

For access to PacBio and ONT platforms, please visit the Long Read Sequencing Facility at UCL Queen Square Institute of Neurology via this link https://www.ucl.ac.uk/ion/research/research-departments/neuromuscular-diseases/long-read-sequencing-facility

 

iSeq@UCL

The Illumina iSeq is a state-of-the-art, innovative and user-centric sequencing system offering accessible benchtop NGS sequencing that directly engages students and staff in the use of the technology. Experienced users can use the machine for preliminary or proof of concept experiments and students can gain hands-on experience in NGS sequencing coupled with high performance computing as part of their taught programmes of study, which is unparalled in a university. iSeq@UCL is located within the Division of Biosciences. Please contact Prof Andrea Townsend-Nicholson for more information on accessing this instrumentation.

 

Our applications

Select one of the dedicated application streams below for more information

Bioinformatics analysis

Click here for more about bioinformatics at UCL Genomics

 

Education and training

Education at UCLG

Our expert application specialists are on hand to help design your projects, assist with grant applcations, walk you through genomic concepts, explain technologies and data formats. UCL Genomics also offers routine training and access to some of our equipment to allow you to run your own projects (access currently limited due to Covid-19 restrictions as of April 2022). Contact us for more information.

EquipmentOpen to all usersTraining requiredCharge for use/access
Illumina NextSeq 2000UCL users YesYes
Illumina NextSeq 500UCL users YesYes
Illumina MiSeqUCL users YesYes
Illumina MiniSeqUCL users YesYes
Omega FLUOstar plate readerUCL users YesYes
Agilent Tapestation 4200UCL users YesYes
Agilent BioanalyserUCL users YesYes
Covaris E220 Focused-ultrasonicatorUCL users YesYes
QuantaBio qPCR machineUCL users YesYes
ONT GridIONUCL users YesYes

 

iSeq@UCL

The Illumina iSeq is a state-of-the-art, innovative and user-centric sequencing system offering accessible benchtop NGS sequencing that directly engages students and staff in the use of the technology. Experienced users can use the machine for preliminary or proof of concept experiments and students can gain hands-on experience in NGS sequencing coupled with high performance computing as part of their taught programmes of study, which is unparalled in a university. iSeq@UCL is located within the Division of Biosciences. Please contact Prof Andrea Townsend-Nicholson for more information on accessing this instrumentation.

 

Short course in Applied Genomics 2022

If you are interested in attending a short course in Applied Genomics, please get in contact with Mark Kristiansen to discuss. *Note that this course is extremely popular, and there may be a long waiting list.

Course dates 2022 - LIMITED

Wednesday 12 October - Tuesday 18 October 2022 - FULL

This module aims to provide students with an up-to-date and broad knowledge of the principles of genomics, genomic technologies, methods of genomic analysis and the application of Genomics in medicine and life sciences.

 

MSc Personalised Medicine and Novel Therapies

The Applied Genomics module is part of the Master's degree in Personalised Medicine and Novel Therapies run from the UCL Great Ormond Street Institute of Child Health. This MSc programme provides an in-depth education in this cutting-edge and rapidly developing field. It is delivered by scientists and clinicians and includes a focussed set of core modules specialising in all aspects of personalised medicine, including genomics, bioinformatics, statistics and the regulatory aspects of novel therapies such as clinical trial design. Optional modules allow you to explore the applications and scope of personalised medicine. You are given opportunities to develop analytic skills during the programme before undertaking your independent research project. For more information, please click here.

Click here for more information about the MSc Personalised Medicine and Novel Therapies programme at UCL.

 

MSc Cell and Gene Therapy

The Applied Genomics module is part of the Master's degree in Cell and Gene Therapy run from the UCL Great Ormond Street Institute of Child Health. This MSc programme provides an in-depth education in this cutting-edge and rapidly developing field. It is delivered by scientists and clinicians researching, developing and testing new treatments for genetically inherited and acquired diseases using gene delivery technology, stem cell manipulation and DNA repair techniques. For information, please click here.

 

Work experience

UCL Genomics prides itself on providing in depth training in genomic technologies to scientists, researchers and clinicians as well as accommodating work experience students and hosting educational programmes as part of the UCL Summer School. Please get in touch for more information.

FAQs

Here you will find answers to some of the most frequently asked questions

What can UCL Genomics do?
We offer a wide range of services including nucleic acid extractions, genotyping and methylation microarrays, DNA/RNA short and long read sequencing, pathogen sequencing and single cell sequencing. For most of our streams, we provide a complete service provision model from project design through to analysis (if required). We are happy to help with small projects and have the automation for larger high-throughput studies. We can also provide training to UCL users to use some of our equipment.

How much will it cost?
UCL Genomics is a collaborative cost recovery core facility and we keep our costs to a minimum. We charge facility fees which cover the day-to-day costs fof operating the facility. These fees are based on the amount of time it will take us to complete your project. Our transparent quotes will clearly separate costs of the consumables and reagents and labware from the facility fee. We are required to apply VAT (at 20%) on all projects from non-UCL users of the facility. if you are an external collaborator to UCL Genomics and you have a collaboration with a UCL principal investigator that can be evidenced through a grant application, please do get in touch to discuss further details.

How do I get a quote?
We will prepare a detailed quote for you based on your project needs. Please get in touch with the us to discuss your QC, extraction, microarray, RNA/DNA and single cell sequencing requirements. As we are a TRAC-listed facility, we will initially ask you to complete a Project Registration Form so that we can accurately quote for your project based on your funding source.

How do I pay for the project?
You will first need to return a signed and dated quote. For UCL users, we will arrange for the funds to be transferred from your UCL account through IDJ/IDT. For external users, you will need to provide a purchase order (PO) with the quote and we will then invoice you for the work. Additional information may be required if you have not worked with UCL previously.

What are the sample requirements for sequencing projects?
The sample requirements depend on the type of project.  As a guide, our website has provided information about the recommended input amounts for the kits we use most frequently. The team will advise on the specific sample requirements when you are ready.

How long will it take to process my samples? 
For sequencing projects, it is difficult to give accurate turnaround times for some projects as this depends on the methodology used and how busy we are with other projects.  Although we aim to start processing your samples as soon as possible (and usually within four weeks of submission), sometimes there are external factors that are beyond our control (delivery delays, consumable shoratges). We will keep you informed if such a delay is foreseeable. In all cases, do let us know if you have an urgent deadline for project completion. For samples submitted to the methylation clinic, we aim to deliver data within four working days.
 

What if I only want my samples QC’d?
This option is available to UCL users only.  Please get in touch with us and we will send you a request form.
As a general guide, we need 2µL sample for both the Tapestation and Qubit.

 

How will my data for sequencing projects be returned to me?
Internal UCL researchers will be provided with log-in details for a secure FTP site which allows them to access and download their data. Researcher external to UCL will receive access to a Globus Endpoint. This requires the install of a free plug-in which creates a secure connection to our servers. Data transfer can be optionally encrypted whilst transferring using OpenSSL AES256-SHA.

For anonymised microarray data, UCL dropbox is the preferred choice of data transfer.


What sequencing data formats do you provide?
All data produced from your project belongs to you. For sequencing projects, we normally return demultiplexed FASTQ data. If you wish to perform your own demultiplexing, we can also provide Illumina BCL files or Nanopore FAST5. If we are also analysing data, we will supply you with QC reports, all aligned data and any final results, but this can vary depending on the analysis stream.
 

What bioinformatic analysis can you provide for sequencing projects
We can provide analysis ranging from demutiplexing to custom analysis by our bioinformatician. We also have standardised pipelines for alignment and differential gene expression analysis which we can run your data on and send you the results for interpretation. For more in-depth and custom analysis, we will put you in touch with our bioinformatician to discuss your requirements.  It’s best to do this before the project starts to make sure that the project design is suitable for the research question being asked.
 

How long will you store data for?
We are unable to store data long term but will hold on to your data for three months after we have sent the raw or analysed data to you. After this time, this data will be deleted, so please ensure you have at least a back up copy oif your data.

How do I acknowledge UCL Genomics in my publication?
It is really important for the facility that our work is acknowledged in all publications. For projects where we have worked with you on a collaborative basis (such as for custom analysis or use of in-house designed pathogen capture probes), we would expect to be co-authors on publications

News and events

15/06/2022

UCL Genomics attend conference! 

UCL Genomics attend the 9th Pharmacogenetics and Stratified Medicine Network Open Meeting at the Royal College of Physicians, London today along with all the students of the MSc Personalised Medicine and Novel Therapies programme.

 

08/06/2022

NovaSeq6000 arrives at UCL Genomics! 

UCL Genomics have taken delivery of a NovaSeq6000 today! Installation and training are underway! The facility wishes to thank all our collaborators who supported our application!

 

05/06/2022

Education contribution from UCL Genomics! 

Dr Rachel Williams and Miss Charlotte Williams (both UCL Genomics) have become educators for the 4th COG-Train course, an international educational initiative providing open-access learning in SARS-CoV-2 genomics.  Learn more about the COG-UK consortium here.

 

01/06/2022

Leysa Forrest and Teodoros Xenakis start their PhDs! 

UCL Genomics' very own application specialist Leysa Forrest starts her PhD (part time) today investigating the role of microbial imbalance (dysbiosis) in the development of preeclampsia under the supervision of Dr Sara Hillman (Maternal and Fetal Medicine Institute for Women's Health), Prof Sergi Castellano and Dr Mark Kristiansen (UCL Great Ormond Street Institute of Child Health). Good luck Leysa!

Teodoros (Dorian) Xenakis, a research fellow in single cell genomics, also starts his PhD today investigating the maternal-fetal cellular communiation in health and disease under the supervision of Dr Sara Hillman (Maternal and Fetal Medicine Institute for Women's Health), Prof Sergi Castellano and Dr Mark Kristiansen (UCL Great Ormond Street Institute of Child Health). Good luck Dorian!

 

11/04/2022

UCL Genomics submits UCL LEAF application for Bronze award!

Kerra Pearce has led on UCL Genomics' application for Bronze status in UCL LEAF (Laboratory Efficiency Assessment Framework). Fantastic effort!

 

01/04/2022

Marius Cotic, UCL Genomics' application specialist, starts his PhD!

UCL Genomics' very own application specialist starts his PhD (part time) today investigating an integrated genomic and environmental approach into identifying biomarkers of schizophrenia and bipolar disorders under the supervision of Prof Elvira Bramon, UCL Division of Psychiatry and Dr Mark Kristiansen, UCL Great Ormond Street Institute of Child Health. Good luck Marius!

 

26/02/2022

NovaSeq6000 is coming to UCL Genomics in summer 2022!

UCL Genomics is pleased to announce that an Illumina NovaSeq6000 will be housed at ZCR in the summer 2022! The facility would like to thank all the support from our collabroators and the fantastic facility team in their successful application to CEF4!

 

11/02/2022

UCL Genomics announces key collaboration with Biotax

UCL Genomics is pleased to annouce an ongoing research collaboration with innovative biotechnology company BiotaX (www.biotax.co)!

 

10/05/2021

Postgraduate study at UCL Great Ormond Street Institute of Child Health

Interested in postgraduate study at the UCL Great Ormond Street Institute of Child Health? You can hear about our programmes in:

  • Paediatrics and Child Health
  • Physiotherapy (Cardiorespiratory, Musculoskeletal, Neurological and Paediatrics)
  • Cell and Gene Therapy
  • Personalised Medicine and Novel Therapies
  • Infancy and Early Childhood Development
  • Child and Adolescent Mental Health
  • Applied and Clinical Neuropsychology

You will meet the programme directors and teaching staff, hear the experiences of students and have lots of opportunity to ask questions. If you already have an offer of a place, are thinking about applying this year or next year, this is the event for you!

Please register through this Eventbrite page on the url link below

https://www.eventbrite.co.uk/e/graduate-open-evening-ucl-great-ormond-st...

 

29 April 2021
UCL Genomics Power Webinar
UCL Genomics Power Webinar event introducing the new mouse methylation content array and other methylation array advancements from Illumina! Join us to hear more about the new Illumina Infinium Mouse Methylation array soon to be available at UCL Genomics. In addition, find out about what other exciting advancements to Illumina methylation arrays are soon to arrive at our internationally recognised Methylation Clinic at the UCL Genomics core facility.

 

19 October 2019
UCL Genomics is now housed at the Zayed Centre for Research into Rare Disease in Children
UCL Genomics would like to thank everyone involved in helping a smooth transition to its fantastic new premises in the Zayed Centre for Research into Rare Disease in Children. UCL Genomics would also like to thank our collaborators for their patience during the move, and we are please to announce that we are now fully operational.