Sequencing is a powerful tool for known and novel SNP detection. For known SNPs, genotyping offers a cost-effective way to validate and screen a large number of samples. The BeadArray technology and high density BeadChips of Illumina are used at BGI for genotyping, for their high throughput and short turnaround time. Furthermore, we combine genotyping and next generation sequencing technology to identify both common and rare variants by the next generation GWAS strategy.

Whole genome wide genotyping BeadChips can be used for genome wide discovery of variant. Also cytogenetics analysis can be performed with these chips. Custom genotyping BeadChips can meet the customers‘ needs. The loci researchers focus on can be designed flexibly on a BeadChips and then be genotyped.

MassARRAY verification system is a moderate-throughput SNP genotyping technology, with flexible experimental design and high accuracy. It‘s suitable for verifying whole genome sequencing results and the possible existence of SNP sites. Use of MassARRAY system, which is ideal for analyzing tens to hundreds of SNPs in mass samples, offers a quick and cost-effective approach to drug target validation.

In addition, many types of plant, and animal genotyping chips are available such as porcine, bovine, ovine, canine, equine, and maize. Moreover, customized chips can be designed upon request.

Diabetes-Associated Genes and Variations Study

This Sino-Danish diabetes-associated genes and variations study was launched in 2008 at BGI-Shenzhen. The LuCAMP consortium comprising ten research organizations from Europe and China was formed to carry out this project.

20,000 SNPs were selected for large scale genotyping in 17,000 samples using Illumina iSelect® Genotyping Platform

Bioinformatics:

 

Standard Bioinformatics Analysis:

1. Data production and SNP calling
2. Sample level QC: Sample call rate, sample mix, gender identification
3. SNP level QC: SNP call rate, signal quality test, Hardy Weinberg equilibrium test

Complex Disease Advanced Analysis:

1. Imputation
2. Population structure analysis: Population stratification, Sample kinship check
3. Association analysis
4. Point-wise association test, multiple test correction
5. Annotation analysis
6. Disease association, Genetic risk calculation and SNP annotation

Cancer Advanced Analysis:

1. Imputation
2. Population structure analysis
3. Population stratification
4. Association analysis
5. Point-wise association test, multiple test correction
6. Genetic risk calculation and SNP annotation

Population Advanced Analysis:

1. Population structure analysis
2. Population stratification
3. Association analysis Point-wise association test, multiple test correction
4. Annotation analysis Genetic risk calculation and SNP annotation

Sample Requirements:

1. Purity:OD260/280=1.8-2.0
2. Concentration: ≥50 ng/μl
3. DNA amount: single library preparation starts from at least 1μg. DNA quantity demanded for multiple libraries (built N times) 0.5X(N+1)μg.

Technologies