- Pre-evaluation of host contamination
- Raw data and analysis result from tailored PDX bioinformatics analysis package
- Cloud-based data storage and delivery system
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.
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.
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.
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.
The recommended service package delivers 12Gb Whole Exome Sequencing data and 10Gb of Transcriptome sequencing data.
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.
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
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
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
We can process fresh frozen tissue, or gDNA and total RNA derived from your PDX models, with the following general requirements:
Fresh frozen tissue
Liquid nitrogen snap frozen tissue ≥ 100mg,
Tumor content >70%
Intact gDNA ≥ 200 ng,
Concentration ≥ 2.5 ng/µl,
Volume ≥ 15ul
Total RNA ≥ 200 ng,
Concentration ≥ 20ng/µl,
RIN ≥ 7, 28S/18S ≥ 1.0