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Systematic discovery of complex insertions and deletions in human cancers

Abstract

Complex insertions and deletions (indels) are formed by simultaneously deleting and inserting DNA fragments of different sizes at a common genomic location. Here we present a systematic analysis of somatic complex indels in the coding sequences of samples from over 8,000 cancer cases using Pindel-C. We discovered 285 complex indels in cancer-associated genes (such as PIK3R1, TP53, ARID1A, GATA3 and KMT2D) in approximately 3.5% of cases analyzed; nearly all instances of complex indels were overlooked (81.1%) or misannotated (17.6%) in previous reports of 2,199 samples. In-frame complex indels are enriched in PIK3R1 and EGFR, whereas frameshifts are prevalent in VHL, GATA3, TP53, ARID1A, PTEN and ATRX. Furthermore, complex indels display strong tissue specificity (such as VHL in kidney cancer samples and GATA3 in breast cancer samples). Finally, structural analyses support findings of previously missed, but potentially druggable, mutations in the EGFR, MET and KIT oncogenes. This study indicates the critical importance of improving complex indel discovery and interpretation in medical research.

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Figure 1: Workflow and algorithm testing for somatic complex indel detection and filtering.
Figure 2: The exome-wide landscape and characteristics of somatic complex indels across 20 cancer types.
Figure 3: Schematics showing the configurations of simple and complex indels.
Figure 4: Abundance of somatic complex indels in key cancer genes.
Figure 5: Druggability of somatic complex indels in EGFR and KIT.

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Acknowledgements

This work was supported by the National Cancer Institute grant R01CA180006 (L.D.), the National Human Genome Research Institute grant U01HG006517 (L.D.), the Department of Defense grant W81XWH-14-1-0458 (F.C.) and the National Institute of Diabetes and Digestive and Kidney Diseases grant R01DK087960 (F.C.). Additional support came from the National Institute of General Medical Sciences Cell and Molecular Biology training grant GM 007067 (R.J.) and the National Human Genome Research Institute Genome Analysis Training Program grant T32 HG000045 (M.X.). We acknowledge The Cancer Genome Atlas (http://cancergenome.nih.gov) as the source of primary data, and we thank M. Wyczalkowski for technical assistance and members of TCGA Research Network for helpful discussions.

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Authors and Affiliations

Authors

Contributions

L.D. designed and supervised research. L.D. and K.Y. led data analysis and K.Y., J.W., M.D.M., M.X., R.J., S.C., A.S., V.Y., K.H., K.J.J. and M.C.W. performed data analysis. K.Y. led methods development and E.-W.L., M.M., B.N. and P.E.S. contributed code to Pindel-C. K.Y., R.J., S.C. and S.F. developed the QC code. J.F.M., K.Y. and L.D. prepared figures and tables. F.C. and J.N. performed experimental validation. K.Y., M.C.W. and L.D. wrote the manuscript.

Corresponding author

Correspondence to Li Ding.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 and Supplementary Notes 1-4 (PDF 35613 kb)

Supplementary Table 1

In total 1,128 complex indels on Venter chr1 were spiked in (XLSX 126 kb)

Supplementary Table 2

The complex indels reported by Pindel-C taking the bam file with spiked in Venter complex indels as input (XLSX 98 kb)

Supplementary Table 3

Somatic and germline complex indel validation result in COLO829 cell lines (XLSX 46 kb)

Supplementary Table 4

Exome-wide complex indels (XLSX 451 kb)

Supplementary Table 5

MUSIC correlation analysis (XLSX 894 kb)

Supplementary Table 6

A list of 624 cancer-associated genes compiled from literature (XLSX 41 kb)

Supplementary Table 7

A list of complex indels in cancer-associated genes (XLSX 94 kb)

Supplementary Table 8

Validation of somatic complex indels discovered in exome data using whole genome sequence data (XLSX 53 kb)

Supplementary Table 9

Complex indel variant allele fraction and VAF of simple variants (XLSX 61 kb)

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Ye, K., Wang, J., Jayasinghe, R. et al. Systematic discovery of complex insertions and deletions in human cancers. Nat Med 22, 97–104 (2016). https://doi.org/10.1038/nm.4002

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