As part of an international exchange of knowledge and ideas, the Institute for Genomic Biology and BGI (formerly known as the Beijing Genomics Institute) are engaging in a series of learning and discussion workshops. The first workshop was held in Shenzhen, China, from January 21st to January 25th, 2013.
Seventeen members of the IGB traveled to BGI for the week-long workshop, arriving in Hong Kong and journeying via bus across the border to China to their destination of the Yantian District of Shenzhen.
Founded in Beijing with a mission to support the development of science and technology, build strong research teams, and promote the development of scientific partnership in genomics, BGI’s headquarters were later relocated to Shenzhen as the first citizen-managed, non-profit research institution in China. BGI engages in large-scale, high-accuracy projects, such as sequencing 1% of the human genome for the International Human Genome Project.
The first day of the workshop began with IGB members meeting with BGI leadership to understand their vision concerning sequencing technologies, and the impact of their pending acquisition of Complete Genomics, a company dedicated to large-scale whole human genome sequencing and bioinformatics analysis. They received a tour of the facilities including the Illumina HiSeq 2000 sequencing system, which along with the other sequencers onsite are capable of producing 6 terabytes of data per day.
Lectures that day from BGI members included the application of genomics in biodiversity analysis from Dr. Guojie Zhang, followed by a talk from Dr. Jing Zhao on the progress and application of sequencing technology, and the capabilities of current next-gen sequencing technologies. The day ended with a discussion from Dr. Ruibang Luo on algorithms for alignment and assembly, and the comparison of different assemblers and second-generation assemblers. The IGB members were avid participants in these discussions, raising many relevant points on algorithm use and strategies for the building of gene models and gene annotations.
The second day featured lectures on technologies and methods in metabolomics by Dr. Hemi Luan, and plant genomics by Xin Liu, which focused mostly on BGI strategies for denovo assembly of plant genomes. These lectures and others were well-matched to the interests and background of the IGB members attending and provided high quality, productive discussions and questions between the two groups.
Day three of the workshop began with a lecture from the director of the China National Genebank-Shenzhen, Dr. Yong Zhang. He discussed how they have created a national biological resource bank to promote biodiversity preservation and genomic research, which is partnered with the Smithsonian museum. Dr. Zhang explained the vision of the China National Genebank-Shenzhen, to become a global biorepository for all types of human, plant, animal and microbial samples.
The afternoon lecture on metagenomics by Dr. Wanting Chen focused on current BGI projects, their role in the sequencing of the human gut microbiome and the methods used for 16s rRNA and metagenomic sample preparation and bioinformatic analysis. This was followed by a visit to the library construction facilities. BGI houses completely separate rooms for sample QC, DNA shearing, blunt-ending/A overhang/adaptor ligation, gel size selection (individual agarose gels for each library), PCR, PCR cleanup and for library QC. Another facility performs RNA extractions, with separate rooms for preparation of RNAseq libraries and exome capture.
The final lecture of the day, from Dr. Xin Zhou, was entitled “From molecules to ecosystems, answering macrobiology questions using DNA and genomics.” Dr. Zhou explained the development of DNA barcoding in insects using mtDNA for population studies, and the i5K project involving sequencing the genomes of 5,000 insects. His project, involving sequencing and assembling the transcriptomes of 1,000 insects, is known as 1KITE. The project is nearly complete and will be initially used for phylogenetic studies.
The final day of lectures included disease analysis using GWAS by Dr. Qibin Li, the topic of cancer genomics by Dr. Guangwu Guo, and single cell analysis by Dr. Hou Yong, followed by some hiking in the hills surrounding the BGI building. The following day consisted of tours of the Da Fen oil painting village, which houses several hundred shops, and the Splendid China Folk Village, a large park featuring miniature replicas of several Chinese provinces, and displays of the architectural styles, cultures, and habits of different Chinese dynasties. The group also had lunch with the president of BGI, Dr. Huanming Yang, who gave his insight into the BGI philosophy and future plans for expansion.
After a 2-hour trip through customs at the border of Hong Kong due to a spring festival taking place, the group boarded their flight the next day for the 13 hour trip back to the states. The members of the workshop expressed their extreme gratitude over the opportunity to visit BGI, and for the efforts that were made to adapt the lectures and schedule to the diverse backgrounds of the attendees. The speakers in the workshop were very impressive in their knowledge and scope of contributions to the scientific community.
BGI aims to develop research collaboration and provide scientific support to scientists all over the world, and to contribute to the advancement of innovative biological and genomic research. The IGB shares these goals and gratefully acknowledges BGI for joining us in this series of workshops. In May of this year, the IGB will welcome a delegation of students from BGI to spend the week at IGB on the Illinois campus, to engage in their own interactions with students and faculty here.