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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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Regions of copy-neutral loss of heterozygosity. LOH regions were scored in 100-kb sequence blocks according to criteria detailed in the main text. (A) Size distribution of LOH regions in the DT40, L2, and Silkie genomes. (B) The distribution of LOH regions on chromosome (Chr) 5 of the DT40, L2, and Silkie genomes as illustrated by the ratio of heterozygous to homozygous SNVs in 100-kb sequence blocks. A ratio less than 0.1 was used to define LOH.
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fig3: Regions of copy-neutral loss of heterozygosity. LOH regions were scored in 100-kb sequence blocks according to criteria detailed in the main text. (A) Size distribution of LOH regions in the DT40, L2, and Silkie genomes. (B) The distribution of LOH regions on chromosome (Chr) 5 of the DT40, L2, and Silkie genomes as illustrated by the ratio of heterozygous to homozygous SNVs in 100-kb sequence blocks. A ratio less than 0.1 was used to define LOH.

Mentions: The SNP array shows multiple genomic regions that lack heterozygous SNPs, most notably a large part of chromosome 2 (Figure 2B). The genome sequence allows a more detailed view of regions of copy number neutral LOH (referred to simply as LOH). We calculated the ratio of heterozygous to homozygous SNVs in 100-kb sequence blocks along each chromosome and detected an average of 322 homozygous and 306 heterozygous SNVs per 100 kb; 26% of the sequence blocks have a heterozygous-to-homozygous (het/hom) ratio less than 0.1, which we classified as LOH. A further 8% contained fewer than 50 homozygous SNVs and were not used for LOH classification. In the L2 and Silkie breed samples, we classified 33% and 30% of the genome as LOH regions, respectively, indicating that there is no overall DT40-specific process resulting in large-scale LOH. The size distribution of the LOH regions is also similar between DT40 and the two domestic breeds (Figure 3A), although there is a greater incidence of short LOH regions (100–200 kb), possibly indicating higher homologous recombination activity in DT40. The size distribution suggests the presence of a larger number of LOH regions below the 100 kb size, but the SNV density does not allow a reliable detection of smaller regions. The position of the LOH regions is mostly unique in the three investigated samples, as illustrated on a selected chromosome (Figure 3B). The two largest LOH regions in the DT40 genome on chromosomes 2 and 20 were confirmed by the Sequenza analysis (Figure 2B). A table of the LOH regions in the DT40 genome at 100-kb resolution is presented as supplementary information (Table S2).


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)

Regions of copy-neutral loss of heterozygosity. LOH regions were scored in 100-kb sequence blocks according to criteria detailed in the main text. (A) Size distribution of LOH regions in the DT40, L2, and Silkie genomes. (B) The distribution of LOH regions on chromosome (Chr) 5 of the DT40, L2, and Silkie genomes as illustrated by the ratio of heterozygous to homozygous SNVs in 100-kb sequence blocks. A ratio less than 0.1 was used to define LOH.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4232548&req=5

fig3: Regions of copy-neutral loss of heterozygosity. LOH regions were scored in 100-kb sequence blocks according to criteria detailed in the main text. (A) Size distribution of LOH regions in the DT40, L2, and Silkie genomes. (B) The distribution of LOH regions on chromosome (Chr) 5 of the DT40, L2, and Silkie genomes as illustrated by the ratio of heterozygous to homozygous SNVs in 100-kb sequence blocks. A ratio less than 0.1 was used to define LOH.
Mentions: The SNP array shows multiple genomic regions that lack heterozygous SNPs, most notably a large part of chromosome 2 (Figure 2B). The genome sequence allows a more detailed view of regions of copy number neutral LOH (referred to simply as LOH). We calculated the ratio of heterozygous to homozygous SNVs in 100-kb sequence blocks along each chromosome and detected an average of 322 homozygous and 306 heterozygous SNVs per 100 kb; 26% of the sequence blocks have a heterozygous-to-homozygous (het/hom) ratio less than 0.1, which we classified as LOH. A further 8% contained fewer than 50 homozygous SNVs and were not used for LOH classification. In the L2 and Silkie breed samples, we classified 33% and 30% of the genome as LOH regions, respectively, indicating that there is no overall DT40-specific process resulting in large-scale LOH. The size distribution of the LOH regions is also similar between DT40 and the two domestic breeds (Figure 3A), although there is a greater incidence of short LOH regions (100–200 kb), possibly indicating higher homologous recombination activity in DT40. The size distribution suggests the presence of a larger number of LOH regions below the 100 kb size, but the SNV density does not allow a reliable detection of smaller regions. The position of the LOH regions is mostly unique in the three investigated samples, as illustrated on a selected chromosome (Figure 3B). The two largest LOH regions in the DT40 genome on chromosomes 2 and 20 were confirmed by the Sequenza analysis (Figure 2B). A table of the LOH regions in the DT40 genome at 100-kb resolution is presented as supplementary information (Table S2).

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