ICMB @ Geuvadisachievements and contributions

Robert Häsler, functional genomics

2

ICMB achievementsmRNA & miRNA sequencing

mRNA

72 samples sequenced

miRNA

24/72 samples already sequenced

high (rank) similarities of results between sites

3

ICMB potential contributions (I)nTARs workflow (novel transcriptional active region)

covered regions known?mapping no nTaryes

sequence QC

no

discard hitbad

linked to known exon/other nTar?

OK

BLAT of high quality unmapped reads

nodiscard hit

no

RF + start codon

yes

RF no UTR, intron

isoform part

yes

nTar / isoform

yes

duplication? BLAT + unique flag

known elongation?

BLAT blast like alignment toolRF reading frame

ICMB references:Philip et al 2012 Bioinformatics, Klostermeier et al 2011 BMC Genomics

4

ICMB potential contributions (II)detection of splice variation patterns

isoform 1

isoform 2

isoform 3

isoform 4

GYN GYN NAG NAG

GYN GYN NAG NAG

GYN GYN NAG NAG

GYN GYN NAG NAG

expression values by cufflinks

mid

high

low

very low

example scenario

5

ICMB potential contributions (II)detection of splice variation patterns

isoform 1

isoform 2

isoform 3

isoform 4

GYN XYN NAG NAG

GYN XYN NAG NAG

GYN XYN NAG NAG

GYN XYN NAG NAG

expression values by cufflinks

example scenario

none

none

low

very low

variant introduced

ICMB references: Brosch et al 2012 Cell Metab, Häsler et al 2011 Eur J Cell Biol, Kramer et al 2011 Genetics, ElSharawy et al 2009 Human Mutat, Hiller et al 2008 RNA; Szafranski et al 2007 Genome Biol, Hiller et al 2006 Am J Hum Genet, Hiller et al 2004 Nat Genet

6

ICMB potential contributions (III)linking miRNA & miRNA-targets

2% encoding vs. 60-70% non-coding RNA

10-30% of all genes regulated by miRNAs

experimental miR target prediction

expensive, slow

in silico miR target prediction

~3000 targets/miRNA

low/no overlap between different prediction tools

functional effects hard to predict

7

ICMB potential contributions (III)linking miRNA & miRNA-targets

TASSDB (Sinah et al, 2012)tandem splice site data base

how to?

sequence patterndonor/acceptor positionconservationnonsense mediated decay

extract available information:

is there a splice-relevant variant?

is the variant associated to

modified mRNA expression?

expected outcome:

candidates of variants from

the 1000 Genomes project with

potential functional impact

ICMB references: Häsler et al 2012 PLoS One, Keller et al 2011 Nat Methods, Schulte et al 2010 NAR, Sinha et al, 2010 BMC Bioinformatics, Hiller et al 2007 NAR

8

ICMB potential contributionssummary

nTARs

splice variation patterns

linking miRNA to miRNA targets

our position in the analysis pipeline?

team

Philip Rosenstiel

Stefan Schreiber

Robert Häsler

Matthias Barann

Daniela Esser

Markus Schilhabel