Technical Information

Services

We provide services for high-throughput next-generation sequencing using the Illumina HiSeq 2500 platform. Standard services include: Whole Exome Sequencing (WES), Whole Genome Sequencing (WGS), targeted sequencing, Transcriptome and digital expression profiling (RNA-SEQ), Gene regulation & epigenetic analysis (ChIP-SEQ), Small RNA discovery (smRNA-SEQ), and Multiplex sequencing (multiple samples in one lane).

Pricing for HiSeq 2500 sequencing is based on the length of the sequencing run, data requirement, and whether it is a single read, paired end or multiplex. The current charges for using these services are listed on the Genomics Services Price List.

Sample Submission

Customers should submit ≥6 micrograms of DNA sample at a minimum concentration of 30 ng/microliter for Whole Genome Sequencing, Whole Exome Sequencing and Target Region Sequencing. Customers should submit ≥2 micrograms of total RNA sample at a minimum concentration of 60 ng/microliter for Transcriptome and RNA-Seq.

Data

NGS data processing and analysis are performed using BGI's proprietary pipeline. All of the sequencing data are transferred via FTP or copied to a hard drive as customer requested. There are two reports for a sequencing project, the first is the sample QC report and the second is the sequencing results. Please see Genomics Services Standard Report.

Turnaround Time

This will vary depending on the number of sample and type of sequencing. Typically, the standard turnaround time for WES and WGS is targeted to 6-8 weeks.

Genomics Services Standard Report

BGI@CHOP standard report files

  1. Whole Exome Sequencing (WES)

    1. Sequencing Raw data:
      1. FASTQ files
    2. Alignment QC data:
      1. Summary of effective data
        1. Raw reads
        2. Reads mapped to genome
        3. Mapping rate (%)
        4. Duplication rate (%)
        5. Average read length (bp)
        6. Reads mapped to target region
        7. Reads mapped to flanking region
        8. Capture specificity (%)
        9. Mean depth of target region
        10. Mean depth of flanking region
        11. Mismatch rate in target region (%)
        12. Mismatch rate in all effective sequence (%)
        13. Coverage of target region (%)
        14. Coverage of flanking region (%)
        15. Percentage of target region 10x
        16. Percentage of target region 20x
        17. Percentage of target region 30x
        18. Percentage of target region 40x
        19. Percentage of target region 50x
        20. Percentage of flanking region 10x
        21. Percentage of flanking region 20x
        22. Percentage of flanking region 30x
        23. Percentage of flanking region 40x
        24. Percentage of flanking region 50x
      2. Histogram of depth distribution in target regions
      3. Evenness of target region capture sequencing
  2. II. Whole Genome Sequencing (WGS)
    1. Sequencing Raw data:
      1. FASTQ files
    2. Alignment QC data:
      1. Data summary
        1. Summary of original sequence data
      2. Coverage calculation
        1. Coverage statistic of whole genome for the sample
        2. Coverage statistic of each chromosome for the sample
      3. Depth distribution
        1. Distribution of per base sequencing depth