Long Fragment Read Whole Genome Sequencing

Description
Specification
Resources

Long Fragment Read Whole Genome Sequencing Service Description

Current short-read based Whole Genome Sequencing (WGS) is the most widely used method for identifying genome-wide aberrations such as point mutations with read length typically less than several hundred base pairs. This short-read based WGS approach is proven to be highly informative in terms of detection of point mutations, indels and copy number alterations. However, short-read sequencing often results in sequences with scaffolding gaps, bias due to high GC content, repeat sequences and mis-aligned sequences. To interrogate the human genome at a higher resolution with better quality, the standard NGS workflow is challenged, especially for complex Structural Variation (SV) discovery, due to insufficient read coverage at breakpoints and loss of long-range genomic contiguity.

Technology

BGI’s innovative Single Tube Long Fragment Read (stLFR) technology produces long range information with accurate short-read sequencing, uniform coverage and superior SV detection capability, while maintaining reproducibility and consistency. With a small amount of input HMW genomic DNA (as low as 1 ng, approximately 300 genomic equivalents), added to a single tube containing 30 million barcoded beads, where the gDNA molecules are barcoded and subjected to random priming and polymerase amplification. Co-barcoded DNA fragments are then released followed by a modified library preparation process. The resulting libraries undergo DNA Nanoball (DNB™) generation and DNBSEQ sequencing. BGI’s proprietary computational algorithm uses the barcodes to assemble sequencing reads to the original HMW DNA molecule, enabling the construction of contiguous segments of phased variants.

Long Fragment Read WGS for Superior SV Detection

Compared with conventional WGS services, stLFR-based Long Fragment Read WGS (lfrWGS) delivers less bias, higher cover- age, higher reproducibility and near-complete genomic information. It significantly improves structural variants detection while maintaining the same excellent sensitivity for SNP, Indel and CNV detection.

DNBSEQ™ Sequencing Technology

BGI Human Whole Genome Sequencing services are typically executed with DNBSEQ™ NGS technology platform, for great sequencing data at the competitive pricing in the industry.

This system is powered by combinatorial Probe-Anchor Synthesis (cPAS), linear isothermal Rolling-Circle Replication and DNA Nanoballs (DNB™) technology, followed by high-resolution digital imaging.



Publications

1.Wang, O., et al., Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Res, 2019. 29(5): p. 798-808.
2.Peters, B.A., J. Liu, and R. Drmanac, Co-barcoded sequence reads from long DNA fragments: a cost-effective solution for “perfect genome” sequencing. Front Genet, 2014. 5: p. 466.

Applications

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 PREPARATION
    Sample QC
  • WGS LIBRARY PREPARATION
    Library QC
  • SEQUENCING
    Data QC
  • RAW DATA OUTPUT
    Delivery QC
  • BIOINFORMATICS ANALYSIS

Sequencing Service Specification

BGI Human Whole Genome Sequencing services are executed with the DNBSEQ™ NGS technology platform with the benefit of lower cost and turn-around-times compared to other platforms.

  • Sequencing Quality Standard

    • Co-barcoded LFR library preparation
    • PE100 DNBSEQ™ sequencing
    • Guaranteed ≥80% of bases with quality score of ≥Q30
    • CAP/CLIA laboratory services available
    • Standard and customized bioinformatics analysis available
    • Available data storage and bioinformatics applications

  • Turn Around Time

    • 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, whole blood, fresh frozen tissue and cell pellets, with the following general requirements:

Data Analysis

In addition to raw data output, BGI offers a range of standard and customized bioinformatics pipelines for your whole genome sequencing project.
STANDARD ANALYSIS
  • Filtering
  • Alignment
  • SNP calling and annotation
  • SNP validation and comparison
  • SNP functionality and conservation prediction
  • SNP statistics per functional element
  • InDel calling and annotation
  • InDel validation and comparison
  • InDel statistics per functional element
  • CNV calling and annotation
  • SV calling and annotation
  • Phasing
CUSTOMIZED ANALYSIS

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

Application Example

This figure below shows a case study in which lfrWGS (upper panels) successfully sequenced and identified the culprit of the SMN1 gene (left panels) whose mutations are responsible for the genetic disorder Spinal Muscular Astrophy (SMA). The highly homologous counterpart SMN2 gene (right panels) often interferes with the result from regular WGS (lower panels) by mis-representing the sequencing and mapping results, making this case impossible to resolve. lfrWGS enables analysis of genomic areas that are inaccessible by regular WGS.

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