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.

Service Description

Complete solution:&nbsp;Identify germline mutations and predict somatic single nucleotide variations (SNVs) without paired normal human controls. High performance:&nbsp;Highly precise and accurate compared to other methods. Confidence:&nbsp;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:&nbsp;BGl’s certified laboratory quality processes, experience with thousands of PDX samples and robust bioinformatics pipeline.

Why choose BGI for PDX genomics profiling

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.

Project Workflow

How to order

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.

<ul><li>Pre-evaluation of host contamination</li><li>Raw data and analysis result from tailored PDX bioinformatics analysis package</li><li>Cloud-based data storage and delivery system</li></ul>

Service Specification

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



<ul><li>Systematic record and data evaluation</li><li>Host contaminants recognition and analysis</li><li>Detection of Somatic mutations with/without paired normal control</li><li>Cross validation of mutation from WES and Transcriptome sequencing data</li></ul>

PDX bioinformatics analysis , includes

<ul><li>Typical 40 working days from sample QC acceptance to result delivery.</li></ul>

Turn Around Time

<ul><li>Randomization and Systematic Records</li><li>Sample Identity Check</li><li>Mapping to Reference Genomes</li><li>Mouse Contamination Removal</li><li>Examination of Depth, Randomness, and other Intrinsic Information</li><li>Human Variants (SNP, Indel and CNV) Detection and Annotation</li><li>Human SNV Filtering from BGI's In-house Databases</li><li>Mouse SNP and Indel Detection and Annotation</li></ul>

STANDARD ANALYSIS FOR EXOME 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.

Data Analysis

<ul><li>Mouse Contamination Analysis</li><li>Randomization, Distribution and Systematic Records</li><li>Sample Identity Check (For samples with DNA available)</li><li>Mapping to Reference Genomes</li><li>Human SNP detection and cross validation with DNAseq</li><li>Human Gene Expression Analysis</li><li>Human Gene Fusion Detection and Annotation</li><li>Alternative Splicing Analysis</li><li>Novo Transcript Prediction and Annotation</li><li>Mouse Gene Expression Analysis</li><li>Mouse Variants Analysis</li></ul>

STANDARD ANALYSIS FOR TRANSCRIPTOME SEQUENCING DATA

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

PDXomics™ PDX Solution