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SUMMARY:EPFL BioE Talks SERIES  "High-Throughput Differentiation of hIPSCs
  From Hundreds of Individuals to Study Genetic Influences on Gene Expressi
 on"
DTSTART:20201130T160000
DTEND:20201130T170000
DTSTAMP:20260405T164535Z
UID:4d0fe4ee93a9a8fb0082e2dbdaee067193111c6530d0750475fdbf84
CATEGORIES:Conferences - Seminars
DESCRIPTION:Prof. Daniel Gaffney\, Wellcome Sanger Institute\, Hinxton\, C
 ambridge (UK)\nWEEKLY EPFL BIOE TALKS SERIES\n\nAbstract:\nThe majority of
  common human trait associated genetic variation appears to alter gene exp
 ression rather than protein structure. Despite substantial progress in map
 ping expression quantitative trait loci (eQTLs)\, there are significant ga
 ps in our resources to interrogate the function of human noncoding genetic
  variation. For example\, studying genetic variants that change expression
  only in activated cell states\, or those whose function varies across d
 evelopmental stages remains challenging. I will present two related piece
 s of work from our group that address some of these challenges using a mod
 el system based on human induced pluripotent stem cells (hIPSCs). In the 
 first project\, I will discuss using hIPSCs from hundreds of individuals 
 differentiated to macrophages to map "response eQTLs" across scores of 
 stimulated cell states. We show that\, even within a single cell type\, ex
 tensive disease relevant regulatory variation remains undiscovered. In th
 e second project\, I will discuss using “pooled” designs\, where cell
  lines from multiple individuals are grown together and profiled using sin
 gle cell RNA-seq. Here\, we profile IPSCs differentiated to using an estab
 lished dopaminergic protocol\, and discover hundreds of disease relevant-a
 ssociations that are not well captured by existing eQTL data bases\, su
 ch as GTEx. I will also discuss some of the limitations of this system\, s
 uch as extensive variation between lines in differentiation outcomes.\n\nB
 io:\nDaniel Gaffney earned his PhD in evolutionary genetics from Edinburgh
  University in 2006 under the supervision of Dr Peter Keightley. His gradu
 ate research used computational methods to study variation in the mutation
  rate and natural selection in noncoding DNA. From 2006 to 2008 he pursued
  a postdoc with Dr Jacek Majewski in McGill University and Genome Quebec G
 enome Centre\, where he worked on the evolution of transcriptional regulat
 ion and alternative splicing in mammals. From 2008 until 2011 he worked on
  population genetic variation in gene expression and regulation with Dr Jo
 nathan Pritchard at the University of Chicago.\nIn July 2011 Daniel Gaffne
 y started as a Career Development Fellowship Group Leader at the Wellcome 
 Sanger Institute and was promoted to Group Leader in October 2015. The lon
 g-term goal of the group is to understand the molecular and cellular conse
 quences of genetic changes in gene regulatory regions. His research combin
 es statistical genetics with high-throughput experimental techniques in hu
 man cells to address these questions. Much of the group’s recent researc
 h has been focussed on using human induced pluripotent stem cells (hIPSCs)
  and cells derived from hIPSCs as model systems to map and characterise hu
 man noncoding genetic changes.\n\n\n\n\n\nZoom link (with registration) fo
 r attending remotely: https://go.epfl.ch/EPFLBioETalks\n\n\nIMPORTANT NOTI
 CE: due to restrictions resulting from the ongoing Covid-19 situation\, th
 is seminar can be followed via Zoom web-streaming only\, following prior o
 ne-time registration through the link above.
LOCATION:via Zoom web-streaming only\, due to Covid-19 situation https://g
 o.epfl.ch/EPFLBioETalks https://go.epfl.ch/EPFLBioETalks
STATUS:CONFIRMED
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