Plant and Animal Target Region Sequencing

Plant and Animal Target Region Sequencing

Service Description

With target region sequencing, a subset of genes or regions of a genome are isolated and sequenced. Targeted approaches using next-generation sequencing (NGS) allow researchers to focus analysis on specific areas of interest.

Compared to broader approaches, such whole genome sequencing, targeted sequencing enables researchers to focus on regions that are most likely to be involved in the phenotype under study, conserving resources and generating a smaller, more manageable data set. Targeted approaches can also deliver much higher coverage levels, allowing identification of variants that are rare and more expensive with whole-genome or Sanger sequencing.

Targeted analysis can include the exome, specific genes of interest or targets within genes.

Mouse Exome Sequencing for Pharmaceutical Research:

BGI has particular experience and expertise providing mouse exome sequencing. Our solution utilizes Agilent SureSelect XT Mouse All Exon Kit, whose 50 Mb capture covers the complete mouse exome and spans over 221,784 exons and 24,306 genes. The content was developed based on the current UCSC mm9 mouse genome build. A BED file with the exon and gene annotation is available on the Agilent Array website. Combined with BGI’s powerful next-generation sequencing platform and bioinformatics analysis capability, we have become one of the most important centers for mouse genome research.

Benefits:

  • Highly effective: Designed towards specific species; more effective for capturing the mouse exons
  • Wide detection range: Capture both common and rare variants
  • Highly cost-effective: Focus on ~1% of the genome where most disease- or trait-related variations are located.

Plant and Animal Targeted Sequencing for Agrigenomics:

The discovery of genomic signatures of evolution and the improvement of plants and animals for agricultural purposes have relied on the identification of SNPs, which are associated with phenotypic differences. In order to identify the genes underlying specific phenotypes, the regions containing the informative SNPs must be fine-mapped. Often, these regions are very large and may contain structural variations that are hard to identify with existing technologies.

BGI offers Single Molecule, Real-Time (SMRT) Sequencing on Pacbio’s Sequel System, which offers a flexible solution for targeting regions of interest, regardless of size, and delivers a comprehensive view of the associated genes. It also delivers the read length and accuracy needed to improve fine mapping and simplify the assembly of large regions.

SMRT Sequencing gives you the ability to:

  • Efficiently multiplex large amplicons for rapid screening and identification of variants
  • Discover haplotype-specific markers for improved breeding of polyploids
  • Accurately reassemble entire multi-megabase regions for the study of gene linkage
  • Confirm insertion sites of transgenes and validate gene editing events
  • Study informative regions to determine evolutionary or domestication history
  • Capture complete genes of varying size for flexible and efficient experimental design in gene surveys

Project Workflow

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

  • Sample QC
  • Library QC
  • Data QC
  • Sample preparation
  • library construction
  • sequencing
  • raw data output
  • bioinformatics analysis

How to order

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

Request a Quote

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Sequencing Service Specification

BGI offers targeted sequencing on the industry’s latest platforms, including Illumina’s HiSeq4000 and Pacbio’s Sequel System.

Sequencing service specifications vary according to platform and sample type. For more detailed information, please get in touch with details regarding your project.

HiSeq 4000:

  • Sample Preparation and Services

    Sample Preparation and Services

    • 100bp and 150bp paired-end sequencing options available
    • Agilent SureSelect, NimbleGen SeqCap kits for library construction and enrichment.
    • Cloud-based data storage and delivery system
    • Advanced and custom bioinformatics data analysis available
    • Raw data and bioinformatics analysis data delivery in standard file formats
  • Sequencing Quality Standard

    Sequencing Quality Standard

    • Guaranteed ≥ 80% of bases with quality score of ≥Q30
    • Standard sequencing coverage ≥100X; ≥300X is recommended for cancer samples
  • Turn Around Time

    Turn Around Time

    • Contact your local BGI specialist about lead times for custom capture kits
    • Typical 40 working days from sample QC acceptance to filtered raw data availability
    • Expedited services are available, contact your local BGI specialist for details

Sample Requirements

We can process your gDNA, Cell line, Fresh frozen tissue, FFPE samples from plants and animals, with the following general requirements:

DNA Mass and Concentration

Minimum Sample Volume

Regular Samples

Intact genomic DNA ≥ 2µg, Concentration ≥ 20 ng/ µl

15 μl

Low Input Samples

Intact genomic DNA ≥ 200 ng, Concentration ≥ 2.5 ng/ µl

15 μl

Data Analysis

Besides raw data output, BGI offers a range of standard and customized bioinformatics pipelines for your Target Region Sequencing project. Reports and output data files are delivered in industry standard file formats: FASTQ, BAM, VCF, CNS and Excel

Standard Analysis

  • Filtering

  • Alignment

  • SNP calling and annotation

  • SNP validation and comparison

  • SNP functionality and conservation prediction

  • SNP statistics per functional element

Customized analysis

Further customization of Bioinformatics analysis to suit your unique project is available: please contact your BGI technical representative

Target Region Sequencing Resources

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.