Different Tumor Types Share a Common Nuclear Map of Chromosome Territories.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Cancer Informatics Pub Date : 2023-01-01 DOI:10.1177/11769351221148592
Fritz F Parl
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Abstract

Different tumor types are characterized by unique histopathological patterns including distinctive nuclear architectures. I hypothesized that the difference in nuclear appearance is reflected in different nuclear maps of chromosome territories, the discrete regions occupied by individual chromosomes in the interphase nucleus. To test this hypothesis, I used interchromosomal translocations (ITLs) as an analytical tool to map chromosome territories in 11 different tumor types from the TCGA PanCancer database encompassing 6003 tumors with 5295 ITLs. For each chromosome I determined the number and percentage of all ITLs for any given tumor type. Chromosomes were ranked according to the frequency and percentage of ITLs per chromosome. The ranking showed similar patterns for all tumor types. Chromosomes 1, 8, 11, 17, and 19 were ranked in the top quarter, accounting for 35.2% of 5295 ITLs, whereas chromosomes 13, 15, 18, 21, and X were in the bottom quarter, accounting for only 10.5% ITLs. The correlation between the chromosome ranking in the total group of 6003 tumors and the ranking in individual tumor types was significant, ranging from P < .0001 to .0033. Thus, contrary to my hypothesis, different tumor types share a common nuclear map of chromosome territories. Based on the large number of ITLs in 11 different types of malignancy one can discern a shared pattern of chromosome territories in cancer and propose a probabilistic model of chromosomes 1, 8, 11, 17, 19 in the center of the nucleus and chromosomes 13, 15, 18, 21, X at the periphery.

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不同类型的肿瘤共享一个共同的染色体区域核图谱。
不同的肿瘤类型具有独特的组织病理学模式,包括独特的核结构。我假设细胞核外观的差异反映在染色体区域的不同核图上,染色体区域是间期细胞核中单个染色体所占据的离散区域。为了验证这一假设,我使用染色体间易位(ITLs)作为分析工具,从TCGA PanCancer数据库中绘制了11种不同肿瘤类型的染色体区域图,该数据库包含6003个具有5295个ITLs的肿瘤。对于每条染色体,我确定了任何给定肿瘤类型的所有itl的数量和百分比。根据每条染色体出现itl的频率和百分比对染色体进行排序。排名显示所有肿瘤类型的模式相似。染色体1、8、11、17和19位于前1 / 4,占5295个itl的35.2%,而染色体13、15、18、21和X位于后1 / 4,仅占10.5%的itl。在6003个肿瘤的总组中,染色体排名与单个肿瘤类型的排名之间存在显著的相关性,从P
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来源期刊
Cancer Informatics
Cancer Informatics Medicine-Oncology
CiteScore
3.00
自引率
5.00%
发文量
30
审稿时长
8 weeks
期刊介绍: The field of cancer research relies on advances in many other disciplines, including omics technology, mass spectrometry, radio imaging, computer science, and biostatistics. Cancer Informatics provides open access to peer-reviewed high-quality manuscripts reporting bioinformatics analysis of molecular genetics and/or clinical data pertaining to cancer, emphasizing the use of machine learning, artificial intelligence, statistical algorithms, advanced imaging techniques, data visualization, and high-throughput technologies. As the leading journal dedicated exclusively to the report of the use of computational methods in cancer research and practice, Cancer Informatics leverages methodological improvements in systems biology, genomics, proteomics, metabolomics, and molecular biochemistry into the fields of cancer detection, treatment, classification, risk-prediction, prevention, outcome, and modeling.
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