PAMs are maintained in regions of truncal LOH and partially lost in regions of private LOH.
<p>All data shown is from case A38. <b>A)</b> All truncal PAMs on chromosome 18 in all four cell lines have a VAF of 1, and <b>B)</b> All truncal PAMs discovered are present in all four cell lines with a copy number of 1 (haploid). <b>C)</b> A38 cell lines T...
محفوظ في:
| المؤلف الرئيسي: | |
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| مؤلفون آخرون: | , , , , , , , , , , , |
| منشور في: |
2024
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| الموضوعات: | |
| الوسوم: |
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| الملخص: | <p>All data shown is from case A38. <b>A)</b> All truncal PAMs on chromosome 18 in all four cell lines have a VAF of 1, and <b>B)</b> All truncal PAMs discovered are present in all four cell lines with a copy number of 1 (haploid). <b>C)</b> A38 cell lines T2-T4 are at least diploid on chromosome 14 while T1 is haploid based on VAF. <b>D)</b> Truncal PAMs are 50% lost in T1, corresponding to a VAF of 1 and a CN of 1. PAMs are 100% maintained in T2-T4 where the VAF remains 0.5, indicative of heterozygosity. <b>E)</b> Chromosome 6 is at least diploid in all cell lines. Notably, T1 and T2 are triploid as indicated by VAF peaks at 0.35 and 0.7. <b>F)</b> All truncal PAMs are maintained in all four cell lines as heterozygosity is maintained. <b>G)</b> Percent PAM maintenance, average CN, and average VAF plotted by chromosome arm for A38 cell line T1. PAM loss occurs in haploid regions, where the VAF and CN are both 1. <b>H)</b> PAM maintenance, average VAF, and average CN across chromosome arms aggregated for all four A38 cell lines. Notably, areas of LOH common to all cell lines (truncal LOH) present 100% PAM maintenance, while PAM loss is limited to regions of private LOH. Regions of truncal LOH can be identified where CN = 1 in all samples and/or VAF = 1 in all samples. <b>I)</b> Summary data of truncal PAMs in case A38 WGS data. Truncal PAMs are 100% maintained in regions of truncal LOH, 67% maintained in regions of private LOH, and 99% maintained in heterozygous regions. Pairwise comparisons by Kruskal-Wallis test. <b>J)</b> Plot of truncal PAM VAF comparing PAMs maintained in all four cell lines and truncal PAMs lost in at least 1 cell line. Truncal PAMs that are maintained have a significantly higher mean VAF (0.6029) than those susceptible to loss (0.4598) (Mann-Whitney Rank Sum, p = 2.267x10<sup>-16</sup>). Additionally, maintained PAMs are more likely to have a VAF of 1 indicative of their occurrence in regions of LOH. In contrast, PAMs that were lost had a maximum VAF of 0.6483. n = 1080 for maintained PAMs, n = 146 for lost PAMs. All error presented in SEM.</p> |
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