Genomics

Dataset Information

0

Ena-DATASET-DUKE-NUS-05-12-2017-07:28:25:856-358 - samples

ABSTRACT: This dataset contains whole genome sequencing FASTQ data for 12 cholangiocarcinoma tumor samples, and their matched normal samples. These 12 samples are in addition to 59 samples available in dataset EGAD00001001988, and consist of patients from Thailand, Romania, and Singapore. Paired-end sequencing data was generated by Illumina Hiseq 2000 and 2500, with insert sizes of 170 and 350.

PROVIDER: EGAD00001003834 | EGA |

REPOSITORIES: EGA

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Publications

Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.

Jusakul Apinya A   Cutcutache Ioana I   Yong Chern Han CH   Lim Jing Quan JQ   Huang Mi Ni MN   Padmanabhan Nisha N   Nellore Vishwa V   Kongpetch Sarinya S   Ng Alvin Wei Tian AWT   Ng Ley Moy LM   Choo Su Pin SP   Myint Swe Swe SS   Thanan Raynoo R   Nagarajan Sanjanaa S   Lim Weng Khong WK   Ng Cedric Chuan Young CCY   Boot Arnoud A   Liu Mo M   Ong Choon Kiat CK   Rajasegaran Vikneswari V   Lie Stefanus S   Lim Alvin Soon Tiong AST   Lim Tse Hui TH   Tan Jing J   Loh Jia Liang JL   McPherson John R JR   Khuntikeo Narong N   Bhudhisawasdi Vajaraphongsa V   Yongvanit Puangrat P   Wongkham Sopit S   Totoki Yasushi Y   Nakamura Hiromi H   Arai Yasuhito Y   Yamasaki Satoshi S   Chow Pierce Kah-Hoe PK   Chung Alexander Yaw Fui AYF   Ooi London Lucien Peng Jin LLPJ   Lim Kiat Hon KH   Dima Simona S   Duda Dan G DG   Popescu Irinel I   Broet Philippe P   Hsieh Sen-Yung SY   Yu Ming-Chin MC   Scarpa Aldo A   Lai Jiaming J   Luo Di-Xian DX   Carvalho André Lopes AL   Vettore André Luiz AL   Rhee Hyungjin H   Park Young Nyun YN   Alexandrov Ludmil B LB   Gordân Raluca R   Rozen Steven G SG   Shibata Tatsuhiro T   Pairojkul Chawalit C   Teh Bin Tean BT   Tan Patrick P  

Cancer discovery 20170630 10

Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined 4 CCA clusters-fluke-positive CCAs (clusters 1/2) are enriched in <i>ERBB2</i> amplifications and <i>TP53</i> mutations; conversely, fluke-negative CCAs (clusters 3/4) exhibit high copy  ...[more]

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