Whole genomes redefine the mutational landscape of pancreatic cancer

Corresponding author: Sean M. Grimmond
Director, University of Melbourne Centre for Cancer Research at University of Melbourne

Samples and Methods

样本来源：
Australian Pancreatic Cancer Genome Initiative (APGI; http://www.pancreaticcancer.net.au) as part of the International Cancer Genome Consortium (ICGC; http://www.icgc.org)
方法：
Array-based CNV分析：GAP
Tumour cellularity 分析： qPure
Mutations检测：qSNP和GATK
indels检测：Pindel and GATK.
测序：
100 primary PDACs with an epithelial cellularity of ≥ 40% (n = 75)
cell lines derived from APGI participants (n = 25) to an average depth of 65×
compared to the germline (average depth 38×)

Point mutations and structural variation in PDAC

突变数概览：A total of 857,971 somatic point mutations and small insertions and deletions were detected in the cohort: 7,888 were non-silent mutations in 5,424 genes
突变负荷：the average mutational burden across the cohort was 2.64 per Mb (range 0.65–28.2 per Mb)
结构变异：In total, 11,868 somatic structural variants were detected at an average of 119 per individual (range 15–558) ，主要分类intra-chromosomal rearrangements (5,860), deletions (1,393), duplications (128), tandem duplications (179), inversions (1,629), fold-back inversions (579) and amplified inversions (346)。A total of 6,908 rearrangements directly disrupted gene sequences （大概有一半了） and 1,220 genes contained a breakpoint in 2 or more patients
基因融合：1,236 structural variants led to the joining of two gene loci, however, only 183 of these events were fused in an orientation and frame that was capable of expressing a product 只有183个融合可能导致基因产物改变，而且都只发生一次

Genes affected by mutation and structural variation

Mutations in key genes and pathways in pancreatic cancer

用Mutsig方法分析SMG，除了TP53、SMAD4、CDKN2A 等胰腺癌常见高突变基因外，还有KDM6A和PREX2等等。

Subtyping using structural rearrangements

Subtypes of pancreatic cancer.

Stable subtype
20% of all samples
These tumour genomes contained ≤ 50 structural variation events and often exhibited widespread aneuploidy非整倍体 suggesting defects in cell cycle/mitosis 细胞周期/有丝分裂存在缺陷
KRAS和SMAD4的点突变率与其他人群相似，TP53突变的患病率仅略低(61%，而所有样本的平均值为70%)。此外，与其他亚组相比，端粒长度无明显差异。
Locally rearranged subtype
30% of all samples
This subtype exhibited a significant focal event on one or two chromosomes.
大约有1/3的样本有copy number gain that harboured known oncogenes，包括常见的KRAS, SOX9 and GATA6，其余的有breakage–fusion–bridge (BFB, n = 9) or chromothripsis (n = 15)。
Scattered subtype
36% of all samples
Tumours in this class exhibited a moderate range of non-random chromosomal damage and less than 200 structural variation events.
Unstable subtype
14% of all samples
The tumours exhibited a large number of structural variation events (>200; maximum of 558)

Genomic markers of defective DNA maintenance

The majority of unstable tumours (10 of 14) fell within the top quintile of the BRCA signature when ranked by prevalence per Mb。方法见Signatures of mutational processes in human cancer.

Defective DNA repair without BRCA pathway mutations

BRCA通路基因突变约占具有高BRCA突变特征和/或不稳定基因组的一半。在某些乳腺癌和卵巢癌中，超甲基化在沉默BRCA1、BRCA2和PALB2中发挥作用，然而，该基因组的高密度甲基化组阵列分析使我们排除了这一作用机制。
一例双等位基因失活的体细胞突变被观察到，已知的两个基因在失活时诱导基因组不稳定性和化学敏感性；我们还在基因组不稳定或具有BRCA突变特征的肿瘤中检测到ATM、FANCM、XRCC4和XRCC6等参与DNA维持的其他基因突变；然而因果关系还不清楚。

Putative genotypes of platinum responsiveness 铂类化疗反应

on-genotype tumours (with unstable genomes and/or a high BRCA mutational signature burden) were associated with response to platinum-based therapy.

Conclusion

本研究提供了迄今为止最全面的关于胰腺癌基因组事件的描述，并证明结构变异是胰腺癌基因组损伤的重要机制。它强调了KRAS、TP53、SMAD4、CDKN2A和ARID1A基因突变的重要性，此外还有许多低发生率的基因突变。KDM6A中发现的反复突变进一步强调了染色质修饰的作用，而抑癌基因(如ROBO1、ROBO2、SLIT2和RNF43)相对频繁的失活与WNT信号异常的更广泛作用有关。
结构变异分析将PDAC分为四种亚型，具有潜在的临床意义。