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Whole-genome reconstruction and mutational signatures in gastric cancer

Niranjan Nagarajan1*, Denis Bertrand1, Axel M Hillmer2, Zhi Jiang Zang34, Fei Yao25, Pierre-Étienne Jacques1, Audrey SM Teo2, Ioana Cutcutache6, Zhenshui Zhang2, Wah Heng Lee1, Yee Yen Sia2, Song Gao7, Pramila N Ariyaratne1, Andrea Ho2, Xing Yi Woo1, Lavanya Veeravali8, Choon Kiat Ong9, Niantao Deng10, Kartiki V Desai11, Chiea Chuen Khor124, Martin L Hibberd124, Atif Shahab8, Jaideepraj Rao13, Mengchu Wu14, Ming Teh15, Feng Zhu16, Sze Yung Chin15, Brendan Pang1415, Jimmy BY So17, Guillaume Bourque1819, Richie Soong1415, Wing-Kin Sung1, Bin Tean Teh9, Steven Rozen6, Xiaoan Ruan2, Khay Guan Yeoh16, Patrick BO Tan101214* and Yijun Ruan220*

Author Affiliations

1 Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore

2 Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore

3 Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore

4 Cancer and Stem Cell Biology Program, Duke-National University of Singapore (NUS) Graduate Medical School, Singapore 169857, Singapore

5 Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore

6 Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore

7 NUS Graduate School of Integrative Sciences and Engineering, Centre for Life Sciences, Singapore 117456, Singapore

8 Research Computing, Genome Institute of Singapore, Singapore 138672, Singapore

9 NCCS-VARI Translational Research Laboratory, National Cancer Centre, Singapore 169610, Singapore

10 Genomic Oncology, Duke-NUS Graduate Medical School, Singapore 169857, Singapore

11 National Institute of Biomedical Genomics, 2nd Floor Netaji Subash Sanatorium, Kalyani 741251 West Bengal, India

12 Infectious Diseases, Genome Institute of Singapore, Singapore 138672, Singapore

13 Department of Surgery, Tan Tock Seng Hospital, Singapore 308433, Singapore

14 Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore

15 Department of Pathology, National University Health System, National University of Singapore, Singapore 119074, Singapore

16 Department of Medicine, National University Health System, National University of Singapore, Singapore 119074, Singapore

17 Department of Surgery, National University Health System, National University of Singapore, Singapore 119074, Singapore

18 Department of Human Genetics, McGill University, Montréal H3A 1B, Canada

19 McGill University and Genome Quebec Innovation Center, Montréal H3A 1A4, Canada

20 Department of Biochemistry, National University of Singapore, Singapore 119074, Singapore

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Genome Biology 2012, 13:R115  doi:10.1186/gb-2012-13-12-r115

Published: 13 December 2012

Additional files

Additional file 1:

Supplementary Methods, Tables and Figures.

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Additional file 2:

Table S6. Details of somatic SVs identified by DNA-PET in gastric tumors NGCII082 and NGCII092.

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Additional file 6:

Table S14. Enriched bases and motifs in the neighbourhood of C > A mutations.

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Additional file 3:

Table S9. Genes recurrently mutated by non-synonymous SNVs or indels in four or more patients out of 40 GC exomes.

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Additional file 4:

Table S10. Enriched functions and pathways in Gastric Cancer.

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Additional file 5:

Table S12. Screen for recurrent mutations in 94 GC tumor/normal pairs by Sanger sequencing.

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