PDXomics™ PDX Solution

PDXomics™ PDX Solution

Service Description

Patient-derived xenografts (PDX) have been used widely to assess drug efficacy in pre-clinical development. Tumors can be maintained by serial xenografting in nude or SCID mice.
However, nearly 13% of the human genome has similar sequences to those in the mouse genome. This contamination complicates bioinformatics analysis of NGS data generated from PDX tumor samples. The application of xenografts is also challenged by technical issues such as lack of qualified paired controls for somatic mutation detection and host genetic factors in the xenograft.
BGI has developed PDXomics™ to mitigate these challenges: Based on many years of research experience in cancer genomics, we offer a complete solution based on NGS and advanced bioinformatics to support your PDX studies.

 

Why choose BGI for PDX genomics profiling

Complete solution: Identify germline mutations and predict somatic single nucleotide variations (SNVs) without paired normal human controls.

High performance: Highly precise and accurate compared to other methods.

Confidence: Cross-validation and auto correction of genetic variants with integrated public databases and in-house cancer genome database.
Saves Time and Cost: More precise understanding of drug efficacy, resistance and toxicity.

Peace of Mind: BGl’s certified laboratory quality processes, experience with thousands of PDX samples and robust bioinformatics pipeline.

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
  • Sequencing QC
  • Data QC
  • Sample Preparation
  • Library Preparation
  • Sequencing
  • Raw Data Output
  • Bioinformatics Analysis

Service Specification

BGI provides end-to-end services for your PDX model genomics profiling, from library preparation and sequencing to integrative analyses of the cancer transcriptome through state-of-the-art bioinformatics solutions for PDX research.

    • Pre-evaluation of host contamination
    • Raw data and analysis result from tailored PDX bioinformatics analysis package
    • Cloud-based data storage and delivery system

The recommended service package delivers 12Gb Whole Exome Sequencing data and 10Gb of Transcriptome sequencing data.

  • PDX bioinformatics analysis , includes

    PDX bioinformatics analysis , includes

    • Systematic record and data evaluation
    • Host contaminants recognition and analysis
    • Detection of Somatic mutations with/without paired normal control
    • Cross validation of mutation from WES and Transcriptome sequencing data
  • Turn Around Time

    Turn Around Time

    • Typical 40 working days from sample QC acceptance to result delivery.

Data Analysis

In addition to raw data output, BGI offers a comprehensive analysis package tailored to support your PDX studies.
Reports and output data files are delivered in industry standard file formats: FASTQ, BAM, VCF, CNS and Excel.

Standard Analysis for Exome Sequencing Data

  • Randomization and Systematic Records

  • Sample Identity Check

  • Mapping to Reference Genomes

  • Mouse Contamination Removal

  • Examination of Depth, Randomness, and other Intrinsic Information

  • Human Variants (SNP, Indel and CNV) Detection and Annotation

  • Human SNV Filtering from BGI's In-house Databases

  • Mouse SNP and Indel Detection and Annotation

Standard Analysis for Transcriptome Sequencing Data

  • Mouse Contamination Analysis

  • Randomization, Distribution and Systematic Records

  • Sample Identity Check (For samples with DNA available)

  • Mapping to Reference Genomes

  • Human SNP detection and cross validation with DNAseq

  • Human Gene Expression Analysis

  • Human Gene Fusion Detection and Annotation

  • Alternative Splicing Analysis

  • Novo Transcript Prediction and Annotation

  • Mouse Gene Expression Analysis

  • Mouse Variants Analysis

Customized Analysis

Further customization of Bioinformatics analysis to suit your unique project is available, including Filtering of viral and fungal reads Please contact your BGI technical representative

Sample Requirements

We can process fresh frozen tissue, or gDNA and total RNA derived from your PDX models, with the following general requirements:

Sample Type

Requirement

Fresh frozen tissue

Liquid nitrogen snap frozen tissue ≥ 100mg,
Tumor content >70%

gDNA

Intact gDNA ≥ 200 ng,
Concentration ≥ 2.5 ng/µl,
Volume ≥ 15ul

Total RNA

Total RNA ≥ 200 ng,
Concentration ≥ 20ng/µl,
RIN ≥ 7, 28S/18S ≥ 1.0