Difference between revisions of "Forensic epigenetics using a bioinformatics approach"

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(New page: {{Projectproposal |Contact person=Huub Hoefsloot |Contact person2=Dr. P.J. Verschure, SILS, UvA |Contact person3=Dr. Jana Naue |Master areas=Systems Biology, Bioinformatics |Fulfilled=No }...)
 
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Latest revision as of 16:36, 17 December 2015


About Forensic epigenetics using a bioinformatics approach


Description

Background:

The epigenetic composition of the genome exhibits a regulatory layer that determines heritable changes in gene activity that are not encoded by the DNA sequence itself. Chemical modifications of the DNA and chromatin, i.e. DNA methylation, posttranslational histone modifications and chromatin compaction determine the epigenetic composition. During embryonic development the epigenetic composition is established. The epigenetic composition is crucial for cellular identity. However, the epigenome, specifically the DNA’s chemical composition (CpG methylation) is known to change as a result of aging. In the project we are using DNA cytosine CpG methylation detection as a tool for forensic applications to determine the age of potential victims of human trafficking and of unknown perpetrators whose DNA has been found at a crime scene, such as rape cases and violent offences.

Results sofar:

We created a statistical pipeline in R to find markers showing a strong correlation with age. In collaboration with Dr. H. Hoefsloot (Biosystems data analysis, SILS UvA) we used a random forest model analyzing public available data measuring DNA methylation in whole blood from the ‘Marmal-Aid database’.

Present project:

We will use bioinformatic tools to find and better specify already noted markers or other markers focusing on different subquestions:

  1. To compare the DNA methylation age-determination findings regarding the heterogeneous cellular composition of blood
  2. To find DNA methylation age-determination markers in other tissues
  3. To analyze DNA methylation age-determination markers in different age groups and determine overall and group-specific markers
  4. To take the genetic background (population, single nucleotide polymorphism) into consideration

We are looking for a motivated student with background in R including statistical modeling and some knowledge in biology/genetics, preferably with in handling public available epigenetic data (e.g. 450K data of the GEO database)

Contact

The project will be connected to research performed in the team of Dr. P.J. Verschure, SILS, UvA Dr. Jana Naue (postdoc on the Forensic epigenetic project)