Low-Coverage Whole Genome Sequencing Using Laser Capture Microscopy with Combined Digital Droplet PCR: An Effective Tool to Study Copy Number and Kras Mutations in Early Lung Adenocarcinoma Development.
Low-Coverage Whole Genome Sequencing Using Laser Capture Microscopy with Combined Digital Droplet PCR: An Effective Tool to Study Copy Number and Kras Mutations in Early Lung Adenocarcinoma Development.
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DOI：
10.3390/ijms222112034
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发表时间：
2021-11-06
影响因子：
5.6
通讯作者：
Sears CR
中科院分区：
文献类型：
--
作者：
Mickler EA;Zhou H;Phang TL;Geraci MW;Stearman RS;Sears CR
定义早期肿瘤进展的详细基因组特征对于将致癌作用中的关键调控因子和途径确定为潜在的药物靶点至关重要。在人类肺癌中，表征早期癌症发展的工作主要集中在鳞状癌，因为最早的病变在气道中更近端，并且通常可以通过重复的支气管镜检查来获得。腺癌通常位于肺的远端，限制了癌前病变和早期阶段活检的可及性。小鼠肺癌模型概括了许多人类基因组特征，并提供了一种肿瘤发生的模型，其中癌前非典型腺瘤性增生和原位腺癌通常在同一动物中同时发生。在这里，我们将激光捕获显微镜（LCM）的组织表征和收集与数字液滴PCR（ddPCR）和低覆盖率全基因组测序（LC-WGS）相结合。ddPCR可用于鉴定Kras（Kirsten大鼠肉瘤病毒癌基因同源物，这里集中于Kras Q61）中的特定错义突变并估计突变优势的百分比。LC-WGS是一种使用低输入DNA推断整个基因组中的局部拷贝数改变（CNA）的具有成本效益的方法。结合这些方法，肺癌的组织学分期可以与Kras突变和CNA的出现相关联。这种方法的实用性适用于人类癌症的其他小鼠模型。
Defining detailed genomic characterization of early tumor progression is critical to identifying key regulators and pathways in carcinogenesis as potentially druggable targets. In human lung cancer, work to characterize early cancer development has mainly focused on squamous cancer, as the earliest lesions are more proximal in the airways and often accessible by repeated bronchoscopy. Adenocarcinomas are typically located distally in the lung, limiting accessibility for biopsy of pre-malignant and early stages. Mouse lung cancer models recapitulate many human genomic features and provide a model for tumorigenesis with pre-malignant atypical adenomatous hyperplasia and in situ adenocarcinomas often developing contemporaneously within the same animal. Here, we combined tissue characterization and collection by laser capture microscopy (LCM) with digital droplet PCR (ddPCR) and low-coverage whole genome sequencing (LC-WGS). ddPCR can be used to identify specific missense mutations in Kras (Kirsten rat sarcoma viral oncogene homolog, here focused on Kras Q61) and estimate the percentage of mutation predominance. LC-WGS is a cost-effective method to infer localized copy number alterations (CNAs) across the genome using low-input DNA. Combining these methods, the histological stage of lung cancer can be correlated with appearance of Kras mutations and CNAs. The utility of this approach is adaptable to other mouse models of human cancer.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
--
作者：
Kellar A;Egan C;Morris D
通讯作者：
Morris D
影响因子：
11.2
作者：
Jakubek, Yasminka;Lang, Wenhua;Kadara, Humam
通讯作者：
Kadara, Humam
DOI：
10.1164/rccm.201806-1178oc
发表时间：
2019-09-15
影响因子：
24.7
作者：
Kadara, Humam;Sivakumar, Smruthy;Scheet, Paul
通讯作者：
Scheet, Paul
影响因子：
4.7
作者：
Zhou, Huaxin;Saliba, Jacob;Sears, Catherine R.
通讯作者：
Sears, Catherine R.