《会读才会写》之阅读摘要
无论是了解一篇文献是否需要进一步阅读还是已经确定要读的文献，都应该首先从摘要开始。在本书中，作者提出有编码的阅读模式，这里我们了解一下摘要所包含的内容编码。
第一篇文献是Dhruva Biswas等人于2019年在Nature Medicine上发现的文章《A clonal expression biomarker associates with lung cancer mortality》，摘要一共6句包括164词：
(1)An aim of molecular biomarkers is to stratify patients with cancer into disease subtypes predictive of outcome, improving diagnostic precision beyond clinical descriptors such as tumor stage. (2)Transcriptomic intratumor heterogeneity (RNAITH) has been shown to confound existing expression-based biomarkers across multiple cancer types. (3)Here, we analyze multi-region whole-exome and RNA sequencing data for 156 tumor regions from 48 patients enrolled in the TRACERx study to explore and control for RNA-ITH in non-small cell lung cancer. (4)We find that chromosomal instability is a major driver of RNA-ITH, and existing prognostic gene expression signatures are vulnerable to tumor sampling bias. (5)To address this, we identify genes expressed homogeneously within individual tumors that encode expression modules of cancer cell proliferation and are often driven by DNA copy-number gains selected early in tumor evolution. (6)Clonal transcriptomic biomarkers overcome tumor sampling bias, associate with survival independent of clinicopathological risk factors, and may provide a general strategy to refine biomarker design across cancer types.
- 第(1)句描述分子biomarker的目的是为了细化肿瘤的分型，提高精准医疗，这是一句对现有文献的综述（Summary of Previous Literatures）。因此我们可以在这句的右侧标注阅读编码SPL
- 第(2)句描述了转录组异质性在多个癌症中成为已知的biomarker的混杂因素，这句话给出了对之前研究的批评（Critique of Previous Literatures）同时也给出了之前研究的欠缺(Gaps of Previous Literature)，因此我们在这句话右方标注阅读编码：CPL/GAP
- 第(3)句描述了作者针对这个问题做了什么（What They Do），即对48个非小细胞肺癌病人的多区域外显子与RNA测序数据进行研究。因此在这句话右侧标注编码WTD
- 第(4) - (6)句都属于结果发现(Results of Findings)包括转录异质性主要受染色体不稳定性影响等。属于文章中最重要的内容，在右侧标注ROF。当我们判断一篇文献是否与我们的研究内容相关时，主要就是通过ROF内容。
另一个例子是Nicholas McGranahan于2015年在Observational Study发表的文章《Clonal status of actionable driver events and the timing of mutational processes in cancer evolution》的摘要：
(1)Deciphering whether actionable driver mutations are found in all or a subset of tumor cells will likely be required to improve drug development and precision medicine strategies. (2)We analyzed nine cancer types to determine the subclonal frequencies of driver events, to time mutational processes during cancer evolution, and to identify drivers of subclonal expansions. (3)Although mutations in known driver genes typically occurred early in cancer evolution, we also identified later subclonal “actionable” mutations, including BRAF (V600E), IDH1 (R132H), PIK3CA (E545K), EGFR (L858R), and KRAS (G12D), which may compromise the efficacy of targeted therapy approaches. (4)More than 20% of IDH1 mutations in glioblastomas, and 15% of mutations in genes in the PI3K (phosphatidylinositol 3-kinase)–AKT–mTOR (mammalian target of rapamycin) signaling axis across all tumor types were subclonal. (5)Mutations in the RAS–MEK (mitogen-activated protein kinase kinase) signaling axis were less likely to be subclonal than mutations in genes associated with PI3K-AKT-mTOR signaling. (6)Analysis of late mutations revealed a link between APOBEC-mediated mutagenesis and the acquisition of subclonal driver mutations and uncovered putative cancer genes involved in subclonal expansions, including CTNNA2 and ATXN1. (7)Our results provide a pan-cancer census of driver events within the context of intratumor heterogeneity and reveal patterns of tumor evolution across cancers. (8)The frequent presence of subclonal driver mutations suggests the need to stratify targeted therapy response according to the proportion of tumor cells in which the driver is identified.
通过阅读发现：第（1）句是之前文献得到的结论，标注SPL；第（2）句是作者的分析，标注WTD；第（3）句到第（6）句都是结果发现，标注ROF；第（7）句是启发。我们同样将这些编码标注在文章的相应句子的右侧。当阅读别人的摘要的时候，有时CPL等内容是缺失的，因为这些内容可能出现在引言部分。
通过以上的分析，我们很容易掌握一套基本的摘要的写作方式：首先给出一句现有文献综述（SPL），然后对现有的文献作一个批判（CPL），现有文献的缺陷自然也出来了（GPL），接着给出自己的分析过程（WTD），最后给出一两句结果发现（ROF）。这样至少5句话而又逻辑清晰的摘要就出来了。
总的来说，通过标注编码的方式来阅读有如下的好处：
- 降低阅读速度，提高阅读的系统性，思维的条理性与边界感比较清晰；
- 通过将阅读内容组织为重复出现的编码，方便写作的时候进行提取；
- 通过摘要给出的SPL与CPL我们可以识别潜在的GAP，为我们提供研究的合理性（RAT，rational）提供素材。
