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Nicholas McGranahan Profile
Nicholas McGranahan

@NickyMcGranahan

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Group leader at the CRUK-UCL Lung Cancer Centre of Excellence. Cancer genomics, bioinformatics, and somatic evolution.

London, England
Joined May 2017
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@NickyMcGranahan
Nicholas McGranahan
6 months
CONIPHER, our method for automated reconstruction of tumour subclonal structure and phylogeny that we used in our recently published TRACERx studies, is now out in Nature Protocols! (). Welcome to the CONIPHER TREEtorial, just in time for Christmas! 🌲 1/n
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@NickyMcGranahan
Nicholas McGranahan
5 years
Latest #TRACERx paper out in @nature - exploring how the immune system sculpts lung cancer evolution: . Big team effort @CharlesSwanton @StephanBeck6 @AndyFeber @SwantonLab @squezadd @MariamJHanjani @nbirkbak Blog here:
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@NickyMcGranahan
Nicholas McGranahan
3 years
Very excited to share this review by @jrm_black We explore the importance of both genetic and non-genetic ITH and their role in tumour evolution, and argue for a broad research focus beyond the cancer genome:
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@NickyMcGranahan
Nicholas McGranahan
4 years
Excited to share our latest work investigating why tumours frequently double their genomes and how we can exploit this to identify cancer genes. #TRACERx @Saioa_l @CharlesSwanton @uclcancer @TheCrick
@NatureGenet
Nature Genetics
4 years
Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution (López et al.)
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@NickyMcGranahan
Nicholas McGranahan
4 months
Incredibly honoured that our work has been recognised! Our work is computational, focussing on using data to understand cancer - we are entirely reliant on wonderful collaborators and public data. (& generous funders @wellcometrust @CRUKCOLcentre @CRUKLungCentre @RosetreesT )
@BlavatnikAwards
Blavatnik Awards
4 months
🎉The Blavatnik Awards and @nyasciences are excited to announce the Honourees of the 2024 Blavatnik Awards in the UK! Please join us in congratulating these nine incredible scientists sparking innovations that will transform our future world. Learn more:
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@NickyMcGranahan
Nicholas McGranahan
3 years
Excited to share out latest paper : Do you want to infer T cell infiltrate, but only have bulk DNA-seq? Our tool, T Cell ExTRECT, provides a solution! And here's tweetorial about our serendipitous discovery 👇
@BobbyBentham
Bobby Bentham
3 years
Out now in @nature ! Introducing our new method T cell ExTRECT that uses DNA sequencing data to directly quantify T cell fraction and its application in cancer. A quick thread 🧵 (1/20)
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@NickyMcGranahan
Nicholas McGranahan
7 years
Our new paper exploring allele specific HLA loss and immune evasion in lung cancer is out in Cell: @CharlesSwanton
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@NickyMcGranahan
Nicholas McGranahan
1 year
Extremely proud of @AMIHuebner - passing her viva with flying colours (never in doubt!)...and many thanks to her examiners @markowetzlab @NischalanP @uclcancer @CRUKCOLcentre @CRUKLungCentre #cancerevolution #cancermetastasis
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@NickyMcGranahan
Nicholas McGranahan
7 months
Exciting computational post-doc position available in our lab. Hate cancer? Love research? Enjoy harnessing computational tools to explore the interplay between cancer cell plasticity and cancer genome evolution? This job is made for you.
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@NickyMcGranahan
Nicholas McGranahan
1 year
Instead of watching match of the day tonight, why not read our latest work exploring how RNAseq can be harnessed to discover cancer drivers? Thread👇
@jrm_black
James Black
1 year
📢Our preprint ‘RNA allelic frequencies of somatic mutations encode substantial functional information in cancers’ is out today. Excited to tell you all about it, and our new tool, RVdriver: (1/8)
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@NickyMcGranahan
Nicholas McGranahan
4 years
Excited to share our views on #cancer #evolution and #metastasis . With @nbirkbak
@Cancer_Cell
Cancer Cell
4 years
Cancer Genome Evolutionary Trajectories in Metastasis
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@NickyMcGranahan
Nicholas McGranahan
4 years
Are there rules to cancer evolution and chromosomal instability? Very excited to have contributed to work with @tbkwatkins @LimEmilia @rfschwarz @CharlesSwanton @Samuel_Bakhoum published in @Nature Paper 👉👈 Thread👇
@CharlesSwanton
Charles Swanton
4 years
1/24 - Can we decipher order from cancer genomes? Our new paper “Pervasive chromosomal instability and karyotype order in tumour evolution” comes out in Nature today: @BCRFcure @TheCrick @CRUKresearch @RosetreesT @uclcancer @SwantonLab @royalsociety
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@NickyMcGranahan
Nicholas McGranahan
2 years
Interested in cancer evolution? Want to work with an amazing team and incredible collaborators? Post-doc position available in our group! 👇 @CharlesSwanton @MariamJHanjani @ZaccaSimo @kevlitchfield @uclcancer
@uclcancer
UCL Cancer Institute
2 years
New position available to join @NickyMcGranahan Lab at UCL. Seeking collaborative and self-motivated Research Fellow to work on cancer evolution - deciphering impact of treatment on acquisition of somatic alterations and immune microenvironment. ℹ️
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@NickyMcGranahan
Nicholas McGranahan
2 years
Fantastic talk by @Michi_Dii on altered replication timing in cancer…and lots of interesting discussion #AACR22 #proudPI #cancerevolution
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@NickyMcGranahan
Nicholas McGranahan
5 years
Interested in #cancer #evolution and the interplay between the cancer cell and the immune microenvironment ( #TME )? Two computational post-doc positions are available in my lab: Message me for more info. @CRUKresearch @uclcancer @wellcometrust
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@NickyMcGranahan
Nicholas McGranahan
5 years
Excited by exploring tumour evolution and how cancers evade the immune system? There’s still time to apply for a computational post doc position in our lab...
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@NickyMcGranahan
Nicholas McGranahan
5 years
New computational post-doc positions available in my lab: Interested in genome evolution and the interplay between the cancer cell and the immune microenvironment? working on large datasets? Please RT #TRACERx #CancerEvolution #UCL
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@NickyMcGranahan
Nicholas McGranahan
1 year
Can ctDNA can be harnessed to identify ongoing karyotype evolution and heterogeneity in pancreatic cancer? Great work from @jrm_black @AMIHuebner …thread👇
@jrm_black
James Black
1 year
📢Our paper ‘ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA’ is out in @GenomeMedicine . Led by @AMIHuebner and myself, supervised by @NickyMcGranahan & a collaboration with Rodrigo Toledo & @DrMhidalgo . 🧵(1/9)
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@NickyMcGranahan
Nicholas McGranahan
3 years
Very excited to share this work which we were fortunate to be involved with.... The effect of age on the acquisition and selection of cancer driver mu...
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@NickyMcGranahan
Nicholas McGranahan
2 years
Excited to be speaking in this session today! Very much looking forward to learn about novel technologies to understand cancer development and the immune microenvironment at single cell resolution. #AACR2022
@obenaufa
Anna Obenauf
2 years
Join us as #AACR2022 on Tuesday for an exciting session on new #technologies to understand #cancer at #singlecell resolution. I am honoured to present along @IdoAmitLab and @NickyMcGranahan we'll be covering #immunology #barcoding #scRNAseq #genomics #TME #evolution #resistance
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@NickyMcGranahan
Nicholas McGranahan
6 years
Are you excited by the prospect of working on evolution and cancer? In a cutting edge biomedical research facility? On one of the largest datasets available? This jobs for you....
@CharlesSwanton
Charles Swanton
6 years
TRACERx Bioinformatics positions available to work on lung cancer evolution and the immune microenvironment in our lab ⁦ @TheCrick ⁩ please retweet or apply (or both!)
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@NickyMcGranahan
Nicholas McGranahan
3 years
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@NickyMcGranahan
Nicholas McGranahan
4 years
Very proud to have contributed a very small amount to this exciting manuscript. worth reading.
@VanLooLab
Peter Van Loo
4 years
CAMDAC - Copy number Aware Methylation Deconvolution Analysis of Cancer now in preprint at ! Addressing methylation confounders copy number and purity, CAMDAC reveals (epi)genetic heterogeneity in TRACERx lung cancer, allele-specific methylation and more.
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@NickyMcGranahan
Nicholas McGranahan
5 months
Such an honour to be invited! Exciting science, wonderful scientists, and the food wasn’t bad either!
@mramalg
Maria Ramal Garcia
5 months
It was a pleasure to share some thoughts and science with @NickyMcGranahan ! Meeting passionate young leaders who are doing amazing research is very inspiring
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@NickyMcGranahan
Nicholas McGranahan
5 years
Paper led by Rachel Rosenthal who needs #twitter . Also with @JavierHerrero7 @BennyChain @drmaiseb @crispinhiley and many more...
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@NickyMcGranahan
Nicholas McGranahan
6 years
Non-random mis-segregation of human chromosomes - a foundation for work exploring which copy number events are positively selected in cancer...
@McclellandLab
McClelland Lab
6 years
A huge milestone for our lab, first paper out today. Thank you so much to my lab for all the hard work and fantastic to collaborate with ⁦ @Foijer_lab ⁩ and ⁦ @ElinaVladimirou
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@NickyMcGranahan
Nicholas McGranahan
4 years
And here’s a blog explaining the work...
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@NickyMcGranahan
Nicholas McGranahan
1 year
Thank you very much @SafiaDanovi for coming to talk to us!
@CRUKCOLcentre
CRUKCOLcentre
1 year
A very informative talk by @SafiaDanovi at the @uclcancer : how to publish in Nature
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@NickyMcGranahan
Nicholas McGranahan
7 months
Exciting opportunity within the #CRUK City of London Centre. See below...
@CRUKCOLcentre
CRUKCOLcentre
7 months
📢We are hiring 2 Research IT Engineers! Exciting opportunities to support core #HPC cluster facility and and join us at the City of London Centre - world class hub for cancer biotherapeutics! Please share and apply by 5 Dec👇
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@NickyMcGranahan
Nicholas McGranahan
2 years
@CRUKresearch @CharlesSwanton Perhaps a great example of fantastic mentorship. And the value of being lucky- joining the right lab at the right time! Talking of which, currently plenty of post-doc positions available in TRACERx team!
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@NickyMcGranahan
Nicholas McGranahan
4 years
At the end of the day, you’ve got take each conference as it comes. And just make sure to give 110%.
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@NickyMcGranahan
Nicholas McGranahan
7 years
Great line-up of speakers and sessions for the @CRUKLungCentre conference in Manchester in December!
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@NickyMcGranahan
Nicholas McGranahan
6 months
CONIPHER is a user-friendly package and can be installed through conda (). An example wrapper script to run from command line (). See the protocol for a full description of the method and how to run it! (). 11/n
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@NickyMcGranahan
Nicholas McGranahan
1 year
Excited to travel to Galway for the #ICBG2022 . Looks like an interesting and diverse schedule!
@VIBE_ICBG2024
VIBE/ICBG Conference 2024
2 years
📢With just over 1 week to go until #ICBG2022 we are delighted to share our schedule featuring a fantastic line-up of keynote speakers, contributed talks and poster presentations.
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@NickyMcGranahan
Nicholas McGranahan
1 year
In conclusion, to understand a cancer’s evolution and trajectory we need to consider both genetic and non-genetic diversity. Lots more to enjoy in the paper so please read! Code is available here and the data is on EGA 8/9
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@NickyMcGranahan
Nicholas McGranahan
6 months
@cbailey_58 @jrm_black You wood not believe it!
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@NickyMcGranahan
Nicholas McGranahan
3 years
This work wouldn't have been possible without the amazing resource that is @CR_UK funded TRACERx study @CRUKCOLcentre @CRUKLungCentre @uclcancer !
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@NickyMcGranahan
Nicholas McGranahan
4 years
The future of UK medical research is at risk, including pioneering projects that I work on for @CRUK_Policy . @stellacreasy as my MP, please sign this letter to show your support and help us continue to make progress for patients #ResearchAtRisk @uclcancer
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@NickyMcGranahan
Nicholas McGranahan
6 years
Hugo Aerts begins his talk on AI in radiobiology with a philosophical Q will AI reach the conclusion humans are parasites? #cruklungconf
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@NickyMcGranahan
Nicholas McGranahan
6 months
To address these TREEmendous challenges and help in analysing the large TRACERx cohort we developed CONIPHER, a tool to automate tumour phylogenetic reconstruction while dealing with various sources of noise and errors, and scaling to large numbers of samples and mutations. 3/n
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@NickyMcGranahan
Nicholas McGranahan
6 years
@SafiaDanovi @imartincorena Critical question (or hope it is, as we’re devoting a lot of time to it). WGD may increase evolutionary potential of tumour - allowing elevated mutation rate and copy number changes. @sal_dewhurst may have answer!
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@NickyMcGranahan
Nicholas McGranahan
6 months
We would like to thank the patients and families, and our funders, without whom this research would not be possible @RosetreesT @wellcometrust @CRUKresearch @CR_UK @CRUKLungCentre @CRUKCOLcentre @uclcancer @TheCrick 12/n
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@NickyMcGranahan
Nicholas McGranahan
6 years
Fascinating. Naked mole rats defy the law of aging.
@kakape
Kai Kupferschmidt
6 years
Are naked mole rats the only mammals that don’t age? A new study in @eLife suggests they are. Unlike other animals their risk of dying does not increase over time.
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@NickyMcGranahan
Nicholas McGranahan
2 years
Highly recommend 👇
@CRUKLungCentre
CRUK Lung Centre
2 years
The @CRUKLungCentre Conference is back this year! We're bringing together leading experts to discuss some of the most thought provoking topics in lung cancer research. Register now for early-bird discount and join us in Manchester this November:
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@NickyMcGranahan
Nicholas McGranahan
6 months
Finally, thanks to co-authors @KristianaGrigo4 @AMIHuebner @abi_bunkum @ColliverEmma @AFrankell for working on the method and manuscript and @CharlesSwanton @ZaccaSimo for co-supervising. We hope that CONIPHER can be a useful tool for the community! 13/13
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@NickyMcGranahan
Nicholas McGranahan
1 year
Finally, we used genomic and transcriptomic features to predict which region of the primary would go on to seed metastasis. Both genomic (especially relating to recent subclonal expansions) and transcriptional features were predictive. 7/9
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@NickyMcGranahan
Nicholas McGranahan
7 years
First tweet...any post-doc looking for a position in a new lab, exploring cancer evolution and anti-tumor immunity?
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@NickyMcGranahan
Nicholas McGranahan
6 months
CONIPHER enabled us to identify expanded subclones dominating an entire sample. Recent subclonal expansions were found to be associated with poor outcome in primary tumours, and subclones seeding metastasis were found to dominate several regions of the primary tumour. 10/n
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@NickyMcGranahan
Nicholas McGranahan
6 months
We used CONIPHER to reconstruct phylogenies for the full TRACERx421 primary () and paired primary-metastasis cohort (). A full wiki for exploring the data (using either R or Python) is publicly available (). 9/n
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@NickyMcGranahan
Nicholas McGranahan
1 year
Genetic diversity and its role in shaping how tumours evolve has been well studied. However, we don’t have a full picture of how non-genetic variation affects tumour evolution. 2/9
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@NickyMcGranahan
Nicholas McGranahan
4 years
In case you can't access the link above:
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@NickyMcGranahan
Nicholas McGranahan
1 year
Second, we looked at allele-specific expression. By controlling for the influence of copy-number, ASE could be used as a window into the methylome, revealing expression that was influenced by non-genetic means, and which genes when mutated have global effects on transcription 5/9
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@NickyMcGranahan
Nicholas McGranahan
7 years
Cancer-genome study challenges mouse 'avatars' : Nature News & Comment
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@NickyMcGranahan
Nicholas McGranahan
7 months
@cancerCCR @JulianeScience Thanks very much for having me. Wonderful to hear about all the exciting science going on!
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@NickyMcGranahan
Nicholas McGranahan
3 years
@landau_lab @jrm_black Thanks Dan! Hopefully it complements your fantastic single cell review
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@NickyMcGranahan
Nicholas McGranahan
1 year
Next - we focussed on RNA variants not found in DNA. We identified five RNA variant signatures, including two underpinned by the activity of known editing enzymes - ADAR and APOBEC3A. Activity of these two signatures was preserved from primary to metastatic disease 6/9
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@NickyMcGranahan
Nicholas McGranahan
1 year
@jrm_black @AMIHuebner The accidental additional ‘can’ provides a clue as to whether it can or not…
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@NickyMcGranahan
Nicholas McGranahan
7 years
Is the staggeringly profitable business of scientific publishing bad for science?
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@NickyMcGranahan
Nicholas McGranahan
6 years
Is forcing cyclists to wear helmets a good idea? Worth watching ....
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@NickyMcGranahan
Nicholas McGranahan
6 months
Stage 1: CONIPHER aims to cluster mutations to identify tumour subclones, which reflect the different branches of the tumour’s phylogeny. Critically, CONIPHER takes into account that the frequency of a mutation may reflect its copy number state. 4/n
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@NickyMcGranahan
Nicholas McGranahan
6 years
@markowetzlab @rfschwarz Definitely keen to combine forces for systematic characterisation!
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@NickyMcGranahan
Nicholas McGranahan
6 months
Stage 4: using the final subclones identified, CONIPHER can then enumerate all possible phylogenies, and rank which trees have the lowest error. CONIPHER also automatically outputs clone proportions in each sample. 7/n
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@NickyMcGranahan
Nicholas McGranahan
6 months
Stage 3: CONIPHER uses inferred evolutionary relationships between clones to create a tree. It removes erroneous clones leading to tree cycles and those breaking the pigeonhole principle & crossing rules, resulting in a phylogeny maximising no. mutations retained on the tree. 6/n
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@NickyMcGranahan
Nicholas McGranahan
5 years
@Samuel_Bakhoum @BakalLabICR @CharlesSwanton Thanks @Samuel_Bakhoum - our preliminary work suggests that a benefit of WGD is that it reduces impact of deleterious mutations...
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@NickyMcGranahan
Nicholas McGranahan
6 months
@crispinhiley We hope it will be poplar!
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@NickyMcGranahan
Nicholas McGranahan
6 months
Based on simulations, we find CONIPHER performs well for a high number of samples, correctly classifies truncal and subclonal mutations and correctly identifies erroneous clusters to remove. 8/n
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@NickyMcGranahan
Nicholas McGranahan
1 year
@alitimumab @myESMO @IASLC Thank you very much - should have included this on the slide!
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@NickyMcGranahan
Nicholas McGranahan
6 years
Very interesting read and commentary on lancet paper - what’s the absolute risk of moderate drinking?
@d_spiegel
David Spiegelhalter
6 years
shocking that alcohol paper broke Lancet guidelines in only reporting relative risks: needed fine press office to extract absolute risks from them
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@NickyMcGranahan
Nicholas McGranahan
6 months
Tumours are heterogeneous mixtures of distinct tumour clones as a result of a complex evolutionary process. Reconstructing tumour phylogenies from many samples, affected by complex structural alterations, and with variable levels of noise remains difficult. 2/n
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@NickyMcGranahan
Nicholas McGranahan
1 year
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@NickyMcGranahan
Nicholas McGranahan
3 years
@manojit_ms @JSheltzer @BarryTaylorLab Really cool paper @JSheltzer ! Sex for cancer! We certainly see elevated losses following WGD, indicating ongoing instability. But, little evidence so far of repeated to and fro in many cases.
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@NickyMcGranahan
Nicholas McGranahan
6 months
Stage 2: CONIPHER enumerates the all evolutionary plausible ancestral/descendent relationships between subclones. In this stage, false subclones likely driven by missed copy number events are removed. 5/n
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@NickyMcGranahan
Nicholas McGranahan
7 years
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@NickyMcGranahan
Nicholas McGranahan
2 years
If only this was a parody..,
@rafaelbehr
Rafael Behr
2 years
A more succinct account of the exact opposite of what has happened is hard to find.
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@NickyMcGranahan
Nicholas McGranahan
4 months
@AndreaSottoriva @wellcometrust @CRUKCOLcentre @CRUKLungCentre @RosetreesT Thanks very much Andrea! Look forward to discussing science sometime soon!
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@NickyMcGranahan
Nicholas McGranahan
1 year
@CampKatiee @SwantonLab @CharlesSwanton @Nature Thanks very much Katie - congrats on your recent paper! We haven't really touched upon the immune side here.
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@NickyMcGranahan
Nicholas McGranahan
1 year
First up, we looked at whether patterns of gene expression within tumours (intratumour heterogeneity, ITH) can tell us about the forces shaping evolution prior to sampling. By focussing on highly expressed, low ITH non-cancer genes, we saw signals of weak negative selection 4/9
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@NickyMcGranahan
Nicholas McGranahan
3 years
@markowetzlab Thanks Florian!
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@NickyMcGranahan
Nicholas McGranahan
3 years
Work led by the fantastic @BHFHeptathlon
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@NickyMcGranahan
Nicholas McGranahan
1 year
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@NickyMcGranahan
Nicholas McGranahan
1 year
We investigated this in the #TRACERx cohort of non-small cell lung cancers: 947 tumour regions from 354 patients- all with paired DNA and RNA sequencing data - as well as 96 paired normal tissue samples 3/9
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