Oral Presentations: UC 327
Improving Classification of Transposable Elements in the Human Genome
Presentation Type
Presentation
Faculty Mentor’s Full Name
Travis Wheeler
Abstract / Artist's Statement
Transposable elements (TEs) are sequences of DNA that can replicate and reinsert themselves in the genome. Remnants of TEs are annotated and classified into subfamilies based on their DNA sequence. A subfamily represents all the remnant copies generated in a burst of replication by one parent TE. Biologists use subfamilies to study genetic diseases and to figure out evolutionary relationships (e.g. between human sub-populations), so it is important that TE remnants are classified accurately. We evaluated how accurately the current method annotates and classifies TE remnants in the human genome using a database of known segmental duplications. When a segment of genome with a TE remnant is duplicated, the TE remnants in each copy come from the same parent and should be assigned to the same subfamily. We identified the location and subfamily of all TE remnants in all segmental duplications and compared them. We found that a large fraction of TE remnants are assigned to different subfamilies, raising concerns about the quality of current subfamily classification methods.
Category
Life Sciences
Improving Classification of Transposable Elements in the Human Genome
Transposable elements (TEs) are sequences of DNA that can replicate and reinsert themselves in the genome. Remnants of TEs are annotated and classified into subfamilies based on their DNA sequence. A subfamily represents all the remnant copies generated in a burst of replication by one parent TE. Biologists use subfamilies to study genetic diseases and to figure out evolutionary relationships (e.g. between human sub-populations), so it is important that TE remnants are classified accurately. We evaluated how accurately the current method annotates and classifies TE remnants in the human genome using a database of known segmental duplications. When a segment of genome with a TE remnant is duplicated, the TE remnants in each copy come from the same parent and should be assigned to the same subfamily. We identified the location and subfamily of all TE remnants in all segmental duplications and compared them. We found that a large fraction of TE remnants are assigned to different subfamilies, raising concerns about the quality of current subfamily classification methods.