Interrogation of polyguaninine nucleotide repeat variability in human T-cells by whole genome sequencing of single cells
(English)Manuscript (preprint) (Other academic)
Polyguanine nucleotide repeats exhibit a greater degree of variation than the average for the genome as a whole. This is partly due to polymerase slippage that causes insertions or deletions in these repeat sequence. The high variability of these repeats makes them useful for tracking the differentiation and fate of cells within tissues and organs. However, the same factors that create this variability also give rise to technical difficulties in DNA amplification and massively parallel DNA sequencing. In the study reported herein, we investigated shotgun sequence data from a standard multi-cell sample as well as sequence data for four single cells from the same individual. This was used to assess sequence quality in whole genome amplified single cell material and to investigate variability in homopolymeric regions between individual T-cells. In a more focused study, a selected set of polyG loci in single cells for which the phylogenetic relationship was known, were amplified and sequence determined. Based on the length differences in polyG repeats between the eight cells a phylogenetic tree was constructed, that was very similar to the known tree.
DNA sequencing, whole genome amplification, single cell, whole genome sequencing, homopolymer, HiSeq2000, massively parallel sequencing, NGS
IdentifiersURN: urn:nbn:se:kth:diva-45659OAI: oai:DiVA.org:kth-45659DiVA: diva2:452769
QS 20112011-10-312011-10-312011-10-31Bibliographically approved