Kaitlin Samocha @ksamocha
Assistant Investigator @CGM_MGH. Focus on human genomics and modeling rare variation. She/her. You can find me on the other place with the same name. samochalab.org Joined August 2014-
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Last chance to register for our online course! All lectures will be online next week (and remain online for several months). You can use a chat to ask questions to lecturers. Only 50€ registration cost - for a world class line-up of speakers. eshg.org/bertinoro0-1
gnomAD 4.1 is now live! This release fixes the AN issue in #gnomAD v4.0 & adds 2 new functionalities: 1) Joint AN across all called sites in exomes and genomes 2) A flag indicating when exomes and genomes frequencies are highly discordant Learn more at broad.io/gnomad_v4-1
Alternative image suggested by Katherine Chao:
We didn’t find strong evidence to support the hypothesis that common cis-eQTL-mediated gene expression modifies penetrance of rare coding variants in NDDs.
We used 3 multi-cis-eQTL models (UTMOST, PrediXcan, JTI), to compare predicted gene expression between transmitting parents and their undiagnosed children. We didn’t see any difference in cortex or blood between transmitting parents + their undiagnosed child.
Our paper “Investigating the role of cis-eQTLs in modifying the penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders” (NDDs) is out in Scientific Reports! Three interesting findings led to this study: nature.com/articles/s4159…
This is an excellent opportunity to work with a great researcher on an important problem!
But finally to highlight that this region, despite being within a highly conserved exon is not covered in ‘whole’ exome sequencing (as it is a non-coding RNA). This is a clear example of the power of genome sequencing to uncover novel diagnoses for patients. 9/9
More on our thoughts on variant recurrence, analysis of RNA-sequencing data (which doesn’t show a clear signature), expression of RNU4-2 in brain through development, and analysis of de novo variants in other snRNAs, are all in the preprint. 8/9
Would you believe me if I told you that a single variant in a non-coding RNA explains ~0.5% of all undiagnosed individuals with neurodevelopmental disorders (NDD) in @GenomicsEngland ??? I didn’t initially either, but here is the story of RNU4-2 🧵1/9
Would you believe me if I told you that a single variant in a non-coding RNA explains ~0.5% of all undiagnosed individuals with neurodevelopmental disorders (NDD) in @GenomicsEngland ??? I didn’t initially either, but here is the story of RNU4-2 🧵1/9
Veera Rajagopal @doctorveera
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10K Followers 3K Following The largest hospital-based #research program in the U.S. Where #science and #medicine converge to improve patient care. Blog: https://t.co/YY6ReDgYhy We ❤️🔬
@IsabellaGhement @mzloteanu @RubinPsyc @camjpatrick My view is that we usually shouldn't need to adjust for for multiple comparisons. annalsthoracicsurgery.org/article/S0003-…
@ksamocha @gnomad_project bang bang bang 💪talk the talk, walk the walk 🤝
Published today, our reasons for optimism that success rates in drug discovery can be improved by picking the right targets using human genetics: nature.com/articles/s4158… I break the key findings down panel by panel in this thread: x.com/cureffi/status…
Is having even more gene-disease associations still useful for picking drug targets? For which types of programs does it matter? Has pharma shifted focus towards genetically validated targets? New paper by me, @mnelsonxy, @DongCoco90417, & @jivecast doi.org/10.1101/2023.0…👇
Huge thanks to my PhD supervisor @hilsomartin, our co-authors, @ksamocha, @RuthEberhardt, @kartikchundru, @HelenVFirth, @carolinefwright, and @mehurles, the families and clinicians who contribute to DDD and @deciphergenomic!
Our paper “Investigating the role of cis-eQTLs in modifying the penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders” (NDDs) is out in Scientific Reports! Three interesting findings led to this study: nature.com/articles/s4159…
We are getting amazing emails from people who have identified individuals with RNU4-2 variants ❤️ If this is you, and your families are interested in meeting others or being part of a community, then please direct them to @Unique_charity (@swynn_unique).
Thrilled to share our latest discovery on a spliceosomal snRNA gene causing neurodevelopmental disorders: medrxiv.org/content/10.110… Thank you to everyone who contributed; it’s been a phenomenal effort to collaborate with clinicians and researchers for what would help many families!
@nickywhiffin @ppgardne @GenomicsEngland right, and the lack of variation in this region in all available genome reference data is pretty compelling that mismapping issues aren't a major driver here. these variants show up in multiple NDD cohorts but not at any appreciable level in multiple large control cohorts.
Secondly, what a testament to @nickywhiffin and the global rare disease community that this was able to go from an observation in @GenomicsEngland to a preprint with over 100 observed cases in just over a month. We truly live in a golden age for disease genetics. (3/3)
We’re super excited to host @jnovembre in person at the @broadinstitute #MPG seminar tomorrow morning. Looking forward to hearing his #PopGen perspectives @CGM_MGH @ksamocha
Infertility affects 1 in 6 couples across the globe, but its cause remains unknown in over 30% of cases 😔 In our latest work with @ceclindgren, we discover rare and common genetic variants associated with infertility in 🇬🇧🇩🇰🇪🇪🇫🇮🇮🇸 medrxiv.org/content/10.110… Thread ⬇️
@ksamocha @genome_gov 🎉🥳 Congratulations Kaitlin! Very much well-deserved and certainly just the first of many to come!!!
@ksamocha @genome_gov That’s amazing and super well deserved! Huge congratulations!
@ksamocha Congratulations!! 🎉
@ksamocha @genome_gov Congratulations!!
Wrapping up a wonderful couple of days in Miami for the Pediatric Nephrology conference and some beach time with @sseegal & my littlest nephron. Thanks to @TheSampsonLab for the onesie 🫘 🧬 and @mdefrei13 for the great conference!
@ksamocha @genome_gov Congratulations!!! The first of many to come, for sure :)
@ksamocha @genome_gov Congrats! Excellent news!