The genome of the chicken DT40 bursal lymphoma cell line.
Bottom Line: In a comparison to two domestic chicken genomes and the Gallus gallus reference genome, we found no unique mutational processes shaping the DT40 genome except for a mild increase in insertion and deletion events, particularly deletions at tandem repeats.We mapped coding sequence mutations that are unique to the DT40 genome; mutations inactivating the PIK3R1 and ATRX genes likely contributed to the oncogenic transformation.The sequence data generated by this study, including a searchable de novo genome assembly and annotated lists of mutated genes, will support future research using this cell line.
Affiliation: Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.Show MeSH
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Mentions: Copy number variations (CNV) are apparent from the sequence coverage of individual chromosomes (Figure 2A). The sex chromosomes W and Z are present at 26× and 27× coverage, respectively, confirming their monosomic status and the female origin of the cell line. Chromosomes 2 and 24 show much higher coverage than the expected diploid level. A number of small chromosomes deviate from the mean coverage, indicating that overall sequence coverage is not a reliable measure of ploidy for chromosomes less than approximately 5 Mb in length. It is possible that there is bias against microchromosomes in the sample preparation procedure. We also analyzed CNV using the Sequenza package (Favero et al. 2014), which indicated, based on read depth, that chromosome 2 is trisomic, whereas chromosome 24 is tetrasomic (Figure 2B).
Affiliation: Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.