Sem_BGI Genomics

Speaker Information   
Name: Chen Chao
Work Experience
2009—present   BGI, Shenzhen, China
Professional skills
Basic bioinformatic analysis skills
Research experience and interests
Chao Chen graduated from Physics major of Ocean University of China at 2010 and then joined BGI, He always focusing on research and application of next-generation sequencing technology of cancer genome, has leaded several Cancer genome project, accumulated abundant experience on bioinformatics.During these years in BGI, he attended or leaded many important projects, including “200 WES and 60 transcriptomes research of Bladder cancer”, “200 WES of Kidney cancer” and “200 WGS of Kidney cancer” etc., Based on experience in bioinformatics analysis of cancer, he attended some important conferences like “International Cancer Genome Consortium Workshop(ICGC 2014)”, “Tokyo university Global COE Workshop (2012)”.
Publications
 Gui, Y., Guo, G., Huang, Y., . . . Chen, C., . . . Cai, Z. (2011). Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nature Genetics, 43(9), 875-878.Guo, G., Gui, Y., Gao, S., . . . Chen, C., . . . Wang, J. (2012). Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nature Genetics, 44(1), 17-19.Guo, G., Sun, X., Chen, C., Wu, S., Huang, P., Li, Z., . . . Cai, Z. (2013). Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nature Genetics, 45(12), 1459-1463.

Wu, S., Huang, P., Li, C., . . . Chen, C., . . . Cai, Z. (2014). Telomerase Reverse Transcriptase Gene Promoter Mutations Help Discern the Origin of Urogenital Tumors: A Genomic and Molecular Study. European Urology, 65(2), 247-277.

 Appendix:

I. BGI Introduction

BGI is a leading genomic center in the world, located in China. We have Multi-Omics platform based on Next-Generation Sequencing (NGS) technology (137 HiSeq 2000 from Illumina, 27 Solid 4 sequencers from ABI, one Roche 454 and over 30 units of ABI 3730 sequencers) with more than 4000 employees, including 1500 bioinformatics scientist for fastest sequencing data generation and analysis.

Based on NGS, BGI is providing ultra-high throughput sequencing service and professional bioinformatics analysis for scientific researches worldwide, including the following services:

DNA level: RNA level: Epigenetic level: Protein level
De novo sequencingWhole genome resequencingMetagenome sequencing

Exome sequencing

Targeted region sequencing

Single cell sequencing

Cell line sequencing

Transcriptome sequencingRNA-seq(Quantification)Small RNA Sequencing Bisulfite SequencingMeDIP SequencingChip Sequecing

RRBS(in human)

Proteomics Mass Spectrometry PlatformLTQ Orbitrap Velos,maxis, QTRAP® 5500

BGI Latest Publication

1)         Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation. Cell, 2012, 151(7): 1431-42. Epub 21 Dec 2012.

2)         An integrated map of genetic variation from 1,092 human genomes.Nature, 491(7422):56–65. Epub 31 Oct 2012.

3)         A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature.2012.Epub 26 Sep 2012.

4)         The oyster genome reveals stress adaptation and complexity of shell formation. Nature,2012,Epub 19 Sep 2012.

5)         Exome sequencing identifies MVK mutations in disseminated superficial actinic porokeratosis. Nature Genetics,2012,Epub 16 Sep 2102.

6)         The draft genome of a diploid cotton Gossypium raimondii. Nature Genetics,2012,Epub 26 Aug 2012.

7)         Genome-wide and Caste-Specific DNA Methylomes of the Ants Camponotus floridanus and Harpegnathos saltator. Current Biology.2012.22(19):1-10

8)         Exome sequencing identifies NMNAT1 mutations as a cause of Leber congenital amaurosis. Nat Genet.2012.,Epub 30 Jul 2012.

9)         Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma. Science.2012.Epub 26 Jul 2012.

10)      Insights into salt tolerance from the genome of Thellungiella salsuginea. PNAS.2012,Epub 9 Jul 2012

11)      The yak genome and adaptation to life at high altitude. Nature Genetics,2012,Epub 1 Jul 2012

12)      Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics. Jun 2012

13)      Comparative population genomics of maize domestication and improvement. Nature Genetics. Jun 2012

14)      The tomato genome sequence provides insights into fleshy fruit evolution. Nature. May 2012

15)      Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nature Genetics. May 2012

16)      An atlas of DNA methylomes in porcine adipose and muscle tissues. Nature Communications. May 2012

17)      Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnology. May 2012.

18)      Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor. Cell. Mar

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