Team leader: Yiran Guo
The major research objective of this group is to understand the relationship between DNA variations and interested phenotypic traits. The susceptible alleles of complex diseases are much harder to locate than those of the monogenic diseases because multiple loci contribute to the predisposition of complex diseases and each locus only accounts for a small proportion of the phenotype. With the data release of HapMap phase II, high-density SNP arrays have been used to scan the whole genome to capture alleles with lower frequency and smaller effects. Furthermore, as the new sequencing technology develops, it is now feasible and affordable to sequence the whole set of exons (exome) of each individual in cases and controls to obtain the whole exome allele patterns. We focus on designing and utilizing bioinformatics tools and statistical methods involved in association studies. Furthermore, we work on establishing bioinformatics pipeline for SNP/SV detection to deal with both genotyping data and re-sequencing data effectively.
International collaboration: Genome-wide studies of complex disorder related alleles detection
We participate in the LUCAMP project, which is a Sino-Danish collaboration aiming to detect the high-risk rare alleles (MAF < 0.5%) with different frequencies between diabetic cases and healthy controls, to validate those alleles experimentally and use them to aid disease prediction and prevention. In the first phase of this study, the goal is to sequence the whole exome of 2,000 cases and 2,000 controls and to detect the top SNPs with the most significantly differences in allele frequencies between these two groups of subjects.
The Ministry of Science and Technology, 863 funding: Identify susceptible sites of type II diabetes (T2D) in Chinese population
We collected 1800 DNA samples from Chinese population, and classified them into three groups: 1) patients with T2D; 2) glucose tolerance; 3) controls which were randomly selected and matched well with cases in age and sex. Employed both genotyping and Solexa sequencing, we're identifying susceptible alleles related to the occurrence of T2D in Chinese population.
The Silkworm Genomic Variation Map
Collected from several geographic regions all around the world, a total of 34 silkworms are being resequenced at ~2X each and genomic variation patterns, mostly SNPs, will be detected. We also aim to screen for evidence of artificial selection and/or domestication between the genomes of domesticated and wild silkworms. This project is the phase II of the Silkworm Genomics Project, and Southwest University in Chongqing, China provides all the silkworm samples. In phase I of the Project, BGI and Southwest University achieved the sequencing and analysis of the genome of domesticated silkworm Bombyx mori and the work has been published in Science.