文献名：Differential Pathogenesis of Lung Adenocarcinoma Subtypes Involving Sequence Mutations, Copy Number, Chromosomal Instability, and Methylation
Lung adenocarcinoma (LAD)的遗传变异度很大。
这个癌症可以分成三类：The LAD molecular subtypes (Bronchioid, Magnoid, and Squamoid)
然后我们在三个subtypes里面分析了以下四个特征，发现不同subtypes差异非常显著。
1、Gene mutation rates (EGFR, KRAS, STK11, TP53),
2、chromosomal instability,
3、regional copy number
4、genomewide DNA methylation
另外三个临床特征也是很显著。
1、Patient overall survival,
2、cisplatin plus vinorelbine therapy response
3、predicted gefitinib sensitivity
所以，我们的分类非常好，而且对临床非常有帮助。
对LAD的研究数据包括
1，DNA copy number
2，gene sequence mutation
3，DNA methylation
4，gene expression
即使是TP53这样的基因在LAD的突变率也才35%，所以我们的LAD应该更加细分，因为EGFR mutation and KRAS mutation这样的突变对治疗很有指导意义，细分更加有助于临床针对性治疗方案的选择。
我们选取了116个LAD样本的数据，分析了1，genome-wide gene expression,,2，genomewide DNA copy number, 3，genome-wide DNA methylation, 4，selected gene sequence mutations
得到的结论是：LAD molecular subtypes correlate with grossly distinct genomic alterations and patient therapy response
数据来源如下：
Gene expression --> Agilent 44 K microarrays.
DNA copy number --> Affymetrix 250 K Sty and SNP6 microarrays.
DNA methylation --> MSNP microarray assay.
DNA from EGFR, KRAS, STK11 and TP53 exons --> ABI sequencers
我们用的是R语言包 ConsensusClusterPlus根据gene expression 来对我们的LAD进行分类molecular subtypes
分类的基因有506个(the top 25% most variable genes, 3,045, using ConsensusClusterPlus)，A nearest centroid subtype predictor utilizing 506 genes

这三类LAD的过表达基因参与不同的生物功能，
Bronchioid – excretion genes, asthma genes, and surfactants (SFTPB, SFTPC, SFTPD);
Magnoid – DNA repair genes, such as thymine-DNA glycosylase (TDG);
Squamoid – defense response genes, such as chemokine ligand 10 (CXCL10)
而且也对应不同的临床数据
Bronchioid had the most females, nonsmokers, early stage tumors, and low grade tumors, the greatest acinar content, the least necrosis, and the least invasion.
Squamoid had the most high grade tumors, the greatest solid content, and the lowest papillary content.
Magnoid had themost smokers and the heaviest smokers by pack years.
它们的基因突变pattern也有很大区别。
Bronchioid had the greatest EGFR mutation frequency
Magnoid had the greatest mutation frequencies in TP53, KRAS and STK11.
为了研究不同亚型癌症的突变模式的不同（genomewide mutation rates），我们同时又研究了a large set of rarely mutated genes (n = 623) from the Ding et al. cohort

结论：
Bronchioid subtype 更有可能受益于EGFR inhibitory therapy
Magnoid tumors also have severe genomic alterations including the greatest CIN, the most regional CN alterations, DNA hypermethylation, and the greatest genomewide mutation rate.
the Squamoid subtype displayed the fewest distinctive alterations that included only regional CN alterations