Target Region Sequencing

With the development of molecular biology and bioinformatics technology, scientists have known more about the genetic bases of many complex diseases utilizing various genetic analysis approaches and methods. Some diseases have strong associations with the abnormal of certain chromosomes or mutations in certain genes. Based on this knowledge, researchers could focus on targeted genomic regions that may be related to specific traits way.

Target region capture means enriching specific chromosomes (e.g., Y chromosome), specific regions (e.g., HLA region, MHC region) or specific genes, by microarray hybridization (NimbleGen Sequence Capture Array) or solution hybridization (Agilent Sure-Select™ system) based on probes designed according to the bases sequence of interested genomic regions. Target region capture using microarray hybridization is illustrated briefly in figure below.

Target region capture

Technical Features

  •  Focusing on genetic variants of interest
  •  Deeper investigation on specific regions
  •  Faster turnaround time—faster time to publication & application
  •  Higher throughput—suitable for larger sample size
  •  Lower cost—more cost effective than PCR

Experimental Pipeline

Customers only need to provide qualified DNA samples and the candidate genes list, and BGI will move on all of the following procedures, including probe customization, hybridization, sequencing and bioinformatics analysis (see figure below).

Workflow of Target Region Sequencing

Bioinformatics Analysis

After data filtering includes removing adaptors, contamination and low-quality reads from raw reads, the clean reads were mapped to the reference genome using the SOAPaligner software. Bioinformatics analysis of Target region sequencing data mainly focus on the detection, annotation and statistics of SNPs and InDel (see figure below). Meanwhile BGI also offer QC report of capture and sequencing. We can also perform customized analysis to meet requirements of specific projects.

Bioinformatics pipeline of targeted region sequencing

 Standard Bioinformatics Analysis

  •  Summary of data production
  •  Histogram of depth distribution in target regions
  •  Evenness of target region capture sequencing
  •  Consensus genotypes calling and SNPs detection
  •  Annotation of the resulting SNPs
  •  Detection of insertions and deletions
  •   Annotation of the resulting Indels

Personalized Bioinformatics Analysis

  •  Amino acid substitution prediction
  •  Population SNP calling and allele frequency estimation
  •  Mendelian disorder analysis
  •  NGS-GWAS analysis
  •  Positive signals detection