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The genome of the chicken DT40 bursal lymphoma cell line.

Molnár J, Póti Á, Pipek O, Krzystanek M, Kanu N, Swanton C, Tusnády GE, Szallasi Z, Csabai I, Szüts D - G3 (Bethesda) (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.

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Whole chromosome copy number variation. (A) Sequence coverage of chromosomes (Chr) 1–28, 32, W, and Z. A line at 53× coverage indicates the mean coverage of larger disomic chromosomes 1, 3–10. (B) CNV and LOH analysis of the sequencing data using the Sequenza package. The plot shows the mean depth ratio and B allele frequency (BAF) of 1-Mb-sized bins overlapping every 0.5 Mb (black). The blue area represents the interquartile range of the binned data, whereas the red line indicates segments generated from 10 neighboring bins. Chromosomes 1–28, 32, W, and Z are lined-up on the X axis. The copy number scale is set according to the best fit of Sequenza’s probability model, in which the ploidy for DT40 sample was estimated to be 2.2 n. The LOH regions on chromosome 2 and 20 and whole copy number changes of chromosome 24 and 2 are visible. (C) SNP array hybridization analysis of the sequenced sample. The 60,000 SNPs are lined-up on the x axis in order of genomic occurrence. Chromosome boundaries are marked by dashed lines, and chromosome numbers are shown between the two panels. SNPs in genomic regions unassigned to chromosomes are omitted. Top panel shows signal intensity (LogR ratio, LogR); the increased copy number of chromosomes 2 and 24 is apparent. Bottom panel shows B allele frequency (BAF). Large regions of LOH are marked with arrows.
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fig2: Whole chromosome copy number variation. (A) Sequence coverage of chromosomes (Chr) 1–28, 32, W, and Z. A line at 53× coverage indicates the mean coverage of larger disomic chromosomes 1, 3–10. (B) CNV and LOH analysis of the sequencing data using the Sequenza package. The plot shows the mean depth ratio and B allele frequency (BAF) of 1-Mb-sized bins overlapping every 0.5 Mb (black). The blue area represents the interquartile range of the binned data, whereas the red line indicates segments generated from 10 neighboring bins. Chromosomes 1–28, 32, W, and Z are lined-up on the X axis. The copy number scale is set according to the best fit of Sequenza’s probability model, in which the ploidy for DT40 sample was estimated to be 2.2 n. The LOH regions on chromosome 2 and 20 and whole copy number changes of chromosome 24 and 2 are visible. (C) SNP array hybridization analysis of the sequenced sample. The 60,000 SNPs are lined-up on the x axis in order of genomic occurrence. Chromosome boundaries are marked by dashed lines, and chromosome numbers are shown between the two panels. SNPs in genomic regions unassigned to chromosomes are omitted. Top panel shows signal intensity (LogR ratio, LogR); the increased copy number of chromosomes 2 and 24 is apparent. Bottom panel shows B allele frequency (BAF). Large regions of LOH are marked with arrows.

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).


The genome of the chicken DT40 bursal lymphoma cell line.

Molnár J, Póti Á, Pipek O, Krzystanek M, Kanu N, Swanton C, Tusnády GE, Szallasi Z, Csabai I, Szüts D - G3 (Bethesda) (2014)

Whole chromosome copy number variation. (A) Sequence coverage of chromosomes (Chr) 1–28, 32, W, and Z. A line at 53× coverage indicates the mean coverage of larger disomic chromosomes 1, 3–10. (B) CNV and LOH analysis of the sequencing data using the Sequenza package. The plot shows the mean depth ratio and B allele frequency (BAF) of 1-Mb-sized bins overlapping every 0.5 Mb (black). The blue area represents the interquartile range of the binned data, whereas the red line indicates segments generated from 10 neighboring bins. Chromosomes 1–28, 32, W, and Z are lined-up on the X axis. The copy number scale is set according to the best fit of Sequenza’s probability model, in which the ploidy for DT40 sample was estimated to be 2.2 n. The LOH regions on chromosome 2 and 20 and whole copy number changes of chromosome 24 and 2 are visible. (C) SNP array hybridization analysis of the sequenced sample. The 60,000 SNPs are lined-up on the x axis in order of genomic occurrence. Chromosome boundaries are marked by dashed lines, and chromosome numbers are shown between the two panels. SNPs in genomic regions unassigned to chromosomes are omitted. Top panel shows signal intensity (LogR ratio, LogR); the increased copy number of chromosomes 2 and 24 is apparent. Bottom panel shows B allele frequency (BAF). Large regions of LOH are marked with arrows.
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fig2: Whole chromosome copy number variation. (A) Sequence coverage of chromosomes (Chr) 1–28, 32, W, and Z. A line at 53× coverage indicates the mean coverage of larger disomic chromosomes 1, 3–10. (B) CNV and LOH analysis of the sequencing data using the Sequenza package. The plot shows the mean depth ratio and B allele frequency (BAF) of 1-Mb-sized bins overlapping every 0.5 Mb (black). The blue area represents the interquartile range of the binned data, whereas the red line indicates segments generated from 10 neighboring bins. Chromosomes 1–28, 32, W, and Z are lined-up on the X axis. The copy number scale is set according to the best fit of Sequenza’s probability model, in which the ploidy for DT40 sample was estimated to be 2.2 n. The LOH regions on chromosome 2 and 20 and whole copy number changes of chromosome 24 and 2 are visible. (C) SNP array hybridization analysis of the sequenced sample. The 60,000 SNPs are lined-up on the x axis in order of genomic occurrence. Chromosome boundaries are marked by dashed lines, and chromosome numbers are shown between the two panels. SNPs in genomic regions unassigned to chromosomes are omitted. Top panel shows signal intensity (LogR ratio, LogR); the increased copy number of chromosomes 2 and 24 is apparent. Bottom panel shows B allele frequency (BAF). Large regions of LOH are marked with arrows.
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).

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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.

Show MeSH
Related in: MedlinePlus