HKU Gastric Cancer Genomics study - WGS, DNA genotyping array, expression and methylation profiling

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001000782	Whole-genome sequencing was performed by Illumina Inc (San Diego, CA). Libraries were constructed with ~300bp insert length and paired-end 100bp reads were sequenced on Illumina HiSeq2000.	Illumina HiSeq 2000	190
EGAD00010000528	Illumina HumanHT-12 v4 array		-
EGAD00010000532	Illumina Human Omni1-Quad SNP genotyping array		-
EGAD00010000534	Illumina HumanMethylation450 BeadChip		-

Publications	Citations
Identification of neutral tumor evolution across cancer types. Williams MJ, Werner B, Barnes CP, Graham TA, Sottoriva A. Nat Genet 48: 2016 238-244	461
Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers. Guo YA, Chang MM, Huang W, Ooi WF, Xing M, Tan P, Skanderup AJ. Nat Commun 9: 2018 1520	111
Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers. Jung H, Choi JK, Lee EA. Genome Res 28: 2018 1136-1146	44
Accurate somatic variant detection using weakly supervised deep learning. Krishnamachari K, Lu D, Swift-Scott A, Yeraliyev A, Lee K, Huang W, Leng SN, Skanderup AJ. Nat Commun 13: 2022 4248	18
Oncogenic structural aberration landscape in gastric cancer genomes. Saito-Adachi M, Hama N, Totoki Y, Nakamura H, Arai Y, Hosoda F, Rokutan H, Yachida S, Kato M, Fukagawa A, Shibata T. Nat Commun 14: 2023 3688	10
Double optimal transport for differential gene regulatory network inference with unpaired samples. Li M, Zhu B, Meng C, Fan X. Bioinformatics 41: 2025 btaf352	0