Stephen Kingsmore, National Centre for Genome Resources - “Digital Gene Expression (DGE) and Measurement of Alternative Splice Isoforms, eQTLs and cSN
[Starts with apologizing for chewing out a guy from Duke... I have no idea what the back story is on that.]
Developed their own pipeline, with a web interface called Alpheus, which is remotely accessible. They have and Ag biotech focus, which is their niche. Would like to get into personal genome sequencing.
Application 1: Schizophrenia DGE.
pipeline: ends with Anova analysis. Alignment to several references: transcripts and genome. 7% span exon junctions. MRNA-Seq Coverage. Read count gene based expression analysis is as good as or better than arrays or similar tech. Using Principle component analysis. Using mRNA-Seq, you can clearly separate their controls and cases, which they couldn't do with Arrays. It improves diagnosis component of Variance.
Showing “Volcano Plots”.
Many of genes found for schizophrenia converged on a single pathway, known to be involved in neurochemistry.
Have a visualization tool, and showed that you can see junctions and retained introns, and then wanted to do it more high throughput. Started a collaboration to focus on junctions, to quantify alternative transcript isoforms. Working on first map of splicing of transcriptome in human tissues. 94% of human genes have multiple exons. Every one had alternative splicing in at least one of the tissues examined.
92% have biochemically relevant splicing. (minimum 15%?)
8 types of alternative splicing... 63% of alternative splicing is tissue regulated. 30% of splicing occurs between individuals. (So tissue splicing trumps individuals)
[Brief discussion of 454 based experiment... similar results, I think.]
Thus:
1.cost effective,
2.timely
3.biologically relevant
4.identified stuff missed by genome sequencing
Finally, also compared genotypes from individuals looking at cSNPs. Cis-acting SNPS causing allelic imbalance. Used it to find eSNPS (171 found). Finally, you can also Fine Map eQTN within eQTL.
Developed their own pipeline, with a web interface called Alpheus, which is remotely accessible. They have and Ag biotech focus, which is their niche. Would like to get into personal genome sequencing.
Application 1: Schizophrenia DGE.
pipeline: ends with Anova analysis. Alignment to several references: transcripts and genome. 7% span exon junctions. MRNA-Seq Coverage. Read count gene based expression analysis is as good as or better than arrays or similar tech. Using Principle component analysis. Using mRNA-Seq, you can clearly separate their controls and cases, which they couldn't do with Arrays. It improves diagnosis component of Variance.
Showing “Volcano Plots”.
Many of genes found for schizophrenia converged on a single pathway, known to be involved in neurochemistry.
Have a visualization tool, and showed that you can see junctions and retained introns, and then wanted to do it more high throughput. Started a collaboration to focus on junctions, to quantify alternative transcript isoforms. Working on first map of splicing of transcriptome in human tissues. 94% of human genes have multiple exons. Every one had alternative splicing in at least one of the tissues examined.
92% have biochemically relevant splicing. (minimum 15%?)
8 types of alternative splicing... 63% of alternative splicing is tissue regulated. 30% of splicing occurs between individuals. (So tissue splicing trumps individuals)
[Brief discussion of 454 based experiment... similar results, I think.]
Thus:
1.cost effective,
2.timely
3.biologically relevant
4.identified stuff missed by genome sequencing
Finally, also compared genotypes from individuals looking at cSNPs. Cis-acting SNPS causing allelic imbalance. Used it to find eSNPS (171 found). Finally, you can also Fine Map eQTN within eQTL.
Labels: AGBT 2009
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