James Fasham
@JamesFasham
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🧬👨⚕️Genetics doctor & PhD 💻 💬 Social media: @ESHGsociety @JMG_BMJ and @BritSocGenMed . 🤖 @DiseaseGenes bot creator ( #Genetics #Genomics #RareDisease )
Exeter, England
Joined July 2015
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Pinned Tweet
3 pieces of big news:
✅I have completed my CCT in Clinical Genetics
👨⚕️I have accepted a consultant position in Exeter
🧑🎓
@ExeterBRC
have offered me a fellowship to continue my research at
@UniofExeter
V grateful to everyone who has helped me on this (15 year!) journey.
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My favourite ever explanations of next generation sequencing (NGS) is now available on YouTube 🧬
One to bookmark for teaching🔖
Many thanks Matthew Wakeling
#Genomics
#Genetics
#Bioinformatics
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gnomAD v4 is online 😲
- 5 x bigger (>800k)
- Aligned to GRCh38
- 138k individuals of diverse ancestry
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Want to know about new disease genes as they are published?
I made a bot to do just that.
Please help me improve it and let me know if it's helpful
#Genomics
#Genetics
#RareDisease
Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder
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The poster is up! 🖼️
If you care about rapid identification of new disease gene associations then please visit it at P17.039.C.
Also please follow
@DiseaseGenes
Presenting it on Tuesday.
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Getting ready for
#RareChromoDay
this Thursday 🍪🧬☺️
@Unique_charity
@Unique_charity
provide invaluable support and resources for families affected by rare chromosome and genetic conditions
Show your support on Thursday 13th June by wearing Blue & Yellow, & showing off your baking skills
@eshgsociety
@ExeterGenomes
@swynn_unique
@GeneticAll_UK
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If you perform a 100 gene panel test on "unaffected" individuals from
@uk_biobank
you get a rare missense variant in 1 in 5 people, more frequently with bigger panels
@rnbeaumont1
@carolinefwright
poster
#ESHG2022
@ExeterMed
@UofE_Research
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"Mutations we almost missed" is a sell out in Hall 2!
#ESHG2023
🙍🧑🦰👨🏾🦲👩🏽🦱🧑🦰👨🏾🦳👱
@annnlynch
quoting from
@EllardSian
paper in this slide.
*Definitely* one to catch up on using the
@eshgsociety
platform if you are clinic facing or laboratory
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👏🏻 a round of encouraging applause breaks out as 1st year PhD student Kilian Salomon takes the largest stage at
#eshg2024
#SupportiveScience
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Wow, what an
#ESHG2022
talk!
#CRISPR
-Cas9 causes off target structural variants in zebrafish
NOT detected by short-read sequencing and ARE passed on to offspring.
Huge implications to studies and any possible future therapeutic editing
Paper is here:
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Microtubule minus-end tracking protein CAMSAP1 causes recognizable,
#tubulinopathy
-like, neuronal migration disorder.
Read our work
#OpenAccess
in
@AJHGNews
🧵1/5
#RareDisease
#MedicalGenetics
#Genomics
#Neuroradiology
#MorbidGene
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honoured to have received
@BritSocGenMed
prize for my talk on SCN9A (publication pinned at the top of my tweets) Thank you to my funders
@gw4_cat
/
@wellcometrust
&
@RDExeter
. Thank you to the organisers for the opportunity. I look forward to seeing everyone in 2022
#BSGMACGS2021
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😊Shocked & delighted to be honoured with the Robin Winter Prize
#jointmeeting2022
🏆
I've composed myself would now like to particularly thank Emma Baple & Andrew Crosby (
@RDExeter
), lab colleagues and my supportive funders
@gw4_cat
.
A mini celebration then on to the thesis!
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Do you use Polyphen-2, SIFT, REVEL, GAVIN or ClinPred for interpreting clinical variants? Should you? Are more tools better than one? Some answers in our work using a unique clinically relevant dataset out this week!
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in other news...
☺️ Outcome 6 ✅
Very nearly 15 years postgraduate training complete - CCT in July
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Many thanks to my very talented wife
@FashamJuleen
for the perfect
#genetics
gift - my very own hand-crocheted
#chromosome9
! Hoping to share a big discovery on here with you all later this year
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👀
- includes this useful figure explaining pentrance / expressivity/ pleiotropy
#Genetics
#Genomics
#MedicalGenetics
One more paper out this week - it's been a busy few months
@ExeterMed
! Review of incomplete penetrance and variable expressivity,
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👀60 individuals homozygous for Phe508del (ΔF508) in the new version of gnomAD (v.4.0.0) (~1 in 12,000).
Reminder that individuals with CF exist in UKBB () and pen. estimate in line with Boussaroque et al 2020 () (see graph)
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👇 the end of the clinician scientist?
Big data cohorts are great, but I agree that we would be so much poorer if clinicians stopped doing basic research
@MasudHusain
argues in
@Brain1878
this is in fact happening driven by an increase in bureaucracy
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People ask "what will happen when all disease genes are discovered?" Answer: we will have BEGUN to understand genetic diseases (phenotypic heterogeneity)
An example in our new
#OpenAccess
paper 🧵1/3
#HereditarySpasticParaplegia
#HSP
#Neurogenetics
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A proud moment when your bot informs you your big paper is now online😊
Proper thread tommorow for those happy to wait
SLC4A10 mutation causes a neurological disorder associated with impaired GABAergic transmission
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Lots of energy & ideas at the 1st meeting of
@eshgsociety
Social Media Commitee this PM
We will be very active during
#ESHG2023
so please give us a follow to find out whats going on
@JdelPicchia
@jorisveltman
@aleenamolbio
@ritabmatos
@NutriGenome
@TeodoraBarbarii
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Fantastic to see
@CSOSue
highlighting progress in monogenic
#diabetes
as an example of
#genomics
progressing patient care - building on work from from the fantastic
@ExeterMed
team 👏
@exeter_lab
@diabetesgenes
@Exeter_Diabetes
@athattersley
@Elisa_EDF
& many others
#FoG2022
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Andrew Parrish &
@RDExeter
🧬
Demonstrating how long reads will enable us to provide more diagnoses for acutely unwell children much faster
@ExeterGenomes
@ExeterMed
@nanopore
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#RareChromoDay
has arrived at Exeter Clinical Genetics ☺️🟡🔵
Keep up the great work
@Unique_charity
!l
It's
#RareChromoDay
! Celebrating anyone living with a rare chromosome or gene condition and their families and carers. Please show your support...
More at
#unique
#RareChromosomeDisorder
#GeneDisorder
#RareDisease
#Genetics
#UniqueButNotAlone
#rarechromo
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Wow that's some missense constraint (new figure from gnomAD v4) 💪
Anyone want to guess the gene?
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Sitting in the UK
#Neurogenetics
meeting 🧠
Fantastic to hear about another rapid diagnosis of a treatable metabolic epilepsy disorder by
@ExeterGenomes
R14 with patient recovery 👍👍👍
#RareDisease
#Genetics
@DrHKRobinson
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Current
#pku
#GeneEditing
talk by Dominque Booke is hot off the press!
Rapid and definitive treatment of phenylketonuria in variant-humanized mice with corrective editing
Published in
@NatureComms
an hour ago! 😮
@NSPKU
@official_espku
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Standing room only for
@lucyjmallin
and
@RDExeter
Speaking at a satellite 🛰️ at
#ESHG2023
re
@ExeterGenomes
Rapid Whole Genomic Sequencing service (R14) for acutely unwell infants and children 👶
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Hugely exciting progress to see these cutting-edge long-read high-throughput sequencing machines in an NHS lab
- where better than in Exeter
👇The next step in getting answers for patients who remain undiagnosed despite modern testing (I have a few in mind already)
#Genomics
Today we have welcomed a PromethION 24 to the Exeter genomics Laboratory - exciting new tech to help us to make more diagnoses for acutely unwell children
@SWGenomics
@NHSgms
@CSOSue
@SWGLH
@Danielle_ONT
@gerald_goh
@nanopore
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Delighted to be joining
@BritSocGenMed
as SM Editor / Comms, working alongside
@mbishop_uk
@GemmaChand
.
Now more than ever we need collaboration between clinical, laboratory and research professionals
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@carolinefwright
Room A8
#eshg2024
Educating us about the penetrance of developmental disorder variants in the general population
1/n 🧵
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Thank you! to
#ESHG2021
organisers for selecting my poster (P09.048.A) as runner-up for the Poster Prize 🍾🍾🍾
Thanks to the families 👪 we work with, my supervisors🧑🏫
@RDExeter
and all of my colleagues , my funders
@gw4_cat
and
@BritSocGenMed
for their generous fellowship
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Many thanks to
@BritSocGenMed
for selecting me for their
@eshgsociety
fellowship this year
I’ll be celebrating in the customary 2021 way ... drinking a whole beer in my own house after the kids have gone to bed. see you all at
#ESHG2021
!
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I'm in the first dysmorphology workshop in
#eshg2024
🧒🏻
Well attended, always a highlight 🌟
🪑
@SofiaDouzgou
@KrawitzPeter
Arjan Bowman
@GestaltMatcher
in action
🏆 new
@Ddysmo
& Jill Clayton-Smith trainee award
🚫 No photos from the talks to respect patients discussed
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Thank you for your kind words ☺️
@ahoischen
,
SM at
#ESHG2024
was very much a team sport 🏅
My thanks to SM co-chair
@aleenamolbio
and the committee,
@jorisveltman
@NutriGenome
,
@ritabmatos
,
@pilarcacheiro
,
@TeodoraBarbarii
,
@b0mb0l0
@mo__wafik
+ ESHG staff &
@agnieszkaml
👏🏼
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In silico predictors confusing?
We published last year showing that, with clinically relevant data, REVEL performed best
Other authors, using functionally validated data, agree REVEL is good, also Meta-SNP.
#VariantInterpretation
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🚨Abstracts close soon!🚨
#ESHG2024
is in
#Berlin
A green city of history at the heart of European
#genetics
&
#genomics
Submit abstracts here:
See the programme here:
3 more weeks until the abstract submission deadline for
#eshg2024
#hybridconference
! The Scientific Programme Committee invites you to submit an abstract for inclusion in the programme. All information can be found on our website
#genetics
#genomics
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Thanks for the scientific programme committee
#ESHG2023
@SerenaNikZainal
@RDExeter
@GemmaChand
@zkutalik
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Why not bookmark these gene-specific DNA variant interpretation guides?
-
#BRCA1
/
#BRCA2
- Mismatch repair (MMR) (
#Lynch
) - New Jan 2022
Both here:
@CanGeneCanVar
#Cancer
#CancerGenetics
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Huge turnout from
@UniofExeter
@ExeterMed
and
@ExeterGenomes
at
#ESHG2023
☺️
Join me on *Saturday 11:00* to learn about how to use social media to increase your papers impact and find my poster highlighting discoveries made using
@DiseaseGenes
🤖
#Genomics
#Genetics
🗣️11 talks and 12 posters by
@ExeterMed
colleagues at this weekend's
@eshgsociety
🧬 meeting in Glasgow
Very excited for the science and networking... less so the 7.5hr train! 🚆
#ESHG
#ESHG23
#ESHG2023
#genetics
#science
#health
@uniofexeHLS
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📢Academic Trainees
👩⚕️in Clinical Genetics
🧬Come to Exeter!
Applications for
@NIHRresearch
ACF & ACL posts open now on Oriel for July / Aug 2024 start
Applications close Tues 23rd April
(See following tweet for application links)
I did an ACF and PhD here, happy for DMs
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⏩“Our fastest time to [whole genome] diagnosis was 7h 18m.” 🏅
seriously impressive
(informatics alone!)
acute genetic testing for acutely unwell patients
- is
#ClinicalGenetics
ready?
A nod to the NHS R14 service
@ExeterExomes
, trailblazing this here in the UK)
Excited to share some new work from us today on ultra-rapid genome sequencing for the diagnosis of critically ill children and adults.
In critical care settings, genetic diagnosis can shorten stays, direct precision therapy, save money, and help with family planning. 1/
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Jenny Lord highlighting that for most developmental disease genes there *is* sufficient RNA in blood (>5TPM) for transcriptional analysis
#ESHG2023
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Its an honour, with
@RDExeter
& Olivia Wenger to be published in GeneReviews - As a clinical geneticist I use this expert resource daily👇
We hope that others will find our summary of this condition helpful
#Genetics
#ClinicalGenetics
#MedicalGenetics
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Fantastic work by Exeter colleagues highlighting a successful search for a non-coding cause of a Mendelian disorder.
Imagine we'll be seeing lots of similar findings as we better understand the non-coding genome
@Exeter_Diabetes
@flanagan_se
@EllardSian
@mnweedon
@Kash_A_Patel
Non-coding variants disrupting a tissue-specific regulatory element in HK1 cause congenital hyperinsulinism
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Poster from Kevin Savage
#ESHG2022
Diagnoses are limited by known gene-disease association data and accurate mode of inheritance
@RDExeter
@GenomicsEngland
@RDExeter
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Maybe a niche tweet,
During the pandemic and for the last few years a small group of us shared
#DessertsofESHG
🍰
You are all welcome to join us by sharing the best desserts from the venue, Berlin and at home
(don't worry, serious science tweeting will resume soon)
#eshg2024
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De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders
#MorbidGene
#eshg2024
Paper 1:
Paper 2:
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👀Eye opening findings from
@mesotronium
#ESHG2021
Only 28% of people know a man with a
#BRCA
alteration can pass it to his children, when given a standard genetic report.
A great case for the new report templates and user focused research
#GCchat
#CancerGenetics
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C08
#ESHG2022
Juliette Coursimault
Cornelia de Lange syndrome:
111 unsolved cases following gene panel
Trio
#genome
+ UTRannotator, Splice etc
Result:
2 x 5'UTR variants
3 x outside panel (SPEN, POU3F3 TAF1)
2 x deep splice variants
@nickywhiffin
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Congratulations to the 22 incoming Clinical Geneticists 🙂 🧬
Medical training fill rates by specialty - some good 100% fills but some very concerning vacancies too.
These figures are also artificial and don't reflect wider vacancies at consultant level nor do they fit with demand trusts see:
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Genetics doesn't stop at 5pm today!🌙
👏 Excellent attendance at
@ExeterBRC
and
@Unique_charity
film viewing and discussion on newborn genome sequencing pilot 🧬
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#ESHG2022
poster
Absence of Corpus Callosum (aCC) 🧠
- >40% diagnostic rare with ID
- <10% diagnostic rare with normal IQ
- Heterogenous genetic causes
- ARID1B >> all others
shared with consent
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We have moved beyond conference live tweeting, welcome to the era of live sketching ✍️😍
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Congratulations to Lettie Rawlins
Winner of
#ESHG2023
Isabelle Oberlé award🏅for her talk about KPTN-related disorders
@KPTNalliance
@ExeterMed
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🗣️UK Clinical Genetics Trainees
Going to
#BSGM2022
- 8th Nov?
Before you book your train... 🚄
How about a meet-up afterwards (18:15-20:15) for a bit of a catch-up and some networking? ☕️🍷🍲
Please share, DM me if you're keen - I'll book some tables
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@sarabiz86
in Hall 2
#ESHG2023
Neurons tend to accumulate somatic mutations in regions active in the brain - TRANSCIPTION is the main driver of mutation
Opposite for oligodendrocytes
- DIVISION is the main driver
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Fantastic to hear
#ESHG2020
vocally supporting
#blacklivesmatter
in the current difficult time - we have a role as geneticists to lead against racial prejudice, which has no basis in science
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Alone we are rare
Together we are common -
Value every one
#RareDiseaseDay
#HaikuChallenge
Welcome to
#RareDiseaseDay
, Europe! 🎉
There are over 300 million people who live with a rare disease in Europe.
With events taking place all over the continent, there's plenty to get involved in today!
How are you getting involved in
#RareDiseaseDay
in Europe?👇👇👇
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Presentation prize!🥳
Thanks to
@ExeterMed
for the kind words at
#ExeterAnnualResearchEvent2021
, my supervisors
@RDExeter
& funders
@gw4_cat
.
I continue to be humbled by how message from
#SCN9A
has been received
Correct gene-disease curation matters!
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Thank you for sharing and the opportunity to speak 🙂
If anyone is interested in the work of the 🤖 it's here ➡️
@DiseaseGenes
James Fasham from University of Exeter speaking on- Rapid translation of novel disease-gene discoveries into new diagnoses
#BSGM2022
@BritSocGenMed
@UKCGG
@theAGNC
@acgs_news
@UniofExeter
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Useful new features have arrived on Decipher
👩⚕️ClinGen Clinical Actionability advice
🫀Cardiac variant case-cohort data
🧬Consequence filters added to the protein browser
📜gene/disease associations improved
More coming soon
(COI - I am part of the Decipher development panel)
DECIPHER version 11.16 has been released. See the new features at
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Decipher is back up, ahead of schedule ☺️
DECIPHER will be unavailable 4-5 July whilst is moves from the Wellcome Sanger Institute to the European Bioinformatics Institute.
The transition will not involve any changes to the address (URL), the appearance, or the functionality of DECIPHER.
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📅Save the date!
✅Feb 3-5 2025
🧬Fundamentals
🧬of Variant Interpretation
🧬in Clinical Practice
📌Hinxton, nr Cambridge
A cutting-edge update on evolving topics for experienced geneticists as well as a foundation for those new to the subject.
DM for further information
1
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Did you know that many of the award lectures from previous years are available online?
#ESHG2023
ESHG
Mendel
ELPAG
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#MDC23
- Claire Salter
Biallelic PI4KA variants cause neurological, intestinal and immunological disease
a condition with neurological, gastrointestinal and immune phenotypes
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P14.022.B
#ESHG2023
Rachel Moore
@GenomicsEngland
Individuals recruited to 100k for AR disorder with missing second hit
8/31 solved, mostly CFTR intronic variants, also LINE insertions
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Finishing today in strong form!
Fascinating talks
@brinda_341
@meg_elley
@Jess_Oloughlin
@GregWheildon
@Josiaharvey
@lamiciayine
@gunningac
@AJNiwaha
Balanced chairing
@Partridge2019
@TIHewat
+ many
Especially thankful
@ngmorgan1
@SarahIBEx
@Isteefer
prompting lively debate
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Julia Fordham in Hall 5
#ESHG2023
Showcasing the roles of
@emblebi
(eg VEP) and
@decipher_wtsi
in international efforts for gene curation and interpretation of all forms of variation 🧬💻
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