CPHx: Martin Kerick, Max Plank Inst. – (Epi-)Genomics in prostate cancer: Mutations, Copy Numbers & Methylation

(Epi-)Genomics in prostate cancer: Mutations, Copy Numbers & Methylation
Martin Kerick, Max Plank Inst.

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Focus on Prostate cancer.  DNA-Seq, MeDIP-seq, RNA-seq.

They have a polonator, but not in use.. If anyone wants it, send them an email.

Sequence enrichment, mainly using in solution hybridization.  Works well for them.

Prostate cancers are multifocal. unsettled if that’s clonal or multi-events.

ERG under the control of an Androgen promotor – found in 50% of cases, indicator of poor prognosis, but again, subject of debate.  Commonly observed in TMPRSS2/ERG fusion.

Methylation studied by MeDIP, Mutations/CNV by targeted sequencing.

  • Mutations: 32 patients, tumour and adjacent non-affected tissue.
  • Methylation: 51 tumour patients/53 non-tumour subjects

Somatic SNV profiles: you get about 8000 variants per patient, but only 0-2 somatic non-synonymous mutations per patients.

Had to step back to look at non-coding somatic mutations.

Some patients show differences in transition/transversion status from usual. Associated with (TMPRSS2/ERG), Ratio is higher for cancers with fusion, lower where fusion is missing.

Focussed specifically on fusion events.  Fusions per aligned reds higher in patients with TMPRSS2/ERG fusions.

CNV:  one can do CNV analysis with targeted sequencing.  Demonstrate by showing the same data from exome-seq and whole genome sequencing.  At macro level, the data looks the same, though perhaps noisier with targeted exome.

Applied this to 32 patient to get CNV analysis for targeted genes.  Focussing specifically on cancer gene census genes, you can see nearly all patients (all but 5) show CNV changes for 1-14 genes.

Methylation profiling.

Looked at GSTP1 methylation, show hyper-methylation in 49/51 of tumour patients, but not in normals.  Methylation profiling shown as well [ nice pictures, but can’t replicate it].

Promotor methylation is also significant for cancer gene census genes.

Can also do some tumour classification using methylation status of 7 tumour specific markers.  Clustering shows a clear division between normal division.  Accuracy is 100% for separating tumours and normals.

Summary:

  1. Low somatic variation rate in prostate cancer
  2. transition/transversion  ratio is associated to TMPRSS2/ERG fusion
  3. Chromosomal fusion rate tied to TMPRSS2/ERG fusion status
  4. CNV can be detected with targeted sequencing
  5. CNVs vary among patiens
  6. Hypermethylation can be used to classify tissue samples
  7. hypomethylation in intergenic regions
  8. Hypermethylation is found in promotor/CGI regions

 

3 thoughts on “CPHx: Martin Kerick, Max Plank Inst. – (Epi-)Genomics in prostate cancer: Mutations, Copy Numbers & Methylation

  1. Pingback: Copenhagenomics » Recap of Day 2 at CPHx

  2. Picking an appropriate panel of methylation markers will almost always separate tumor from normals. Methylation anticipates changes in gene expression. What is less clear is whether the anticipated event can be stopped — i.e. treatment response, etc. Harder…

    • Absolutely agree, by the way. Methyation research is still a young field, and has made great strides since massively parallel sequencing has become available, but we still have a ways to go to bring this to the clinic at any level beyond crude inhibition of methylation enzymes.

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