Gene Expression Profiling

CareDx used modern genomics and bioinformatics technology to develop its AlloMap molecular diagnostic solution based on gene expression patterns in blood cells that provide clinically useful information. Gene expression patterns reflect the activity of genes in the various types of blood cells at the time the sample was taken. Overall gene activity in a blood sample can be affected by drugs, immune activation, inflammation, or by recruitment of new cells from the bone marrow.

Developing novel in vitro diagnostic tools requires analysis of carefully characterized blood samples to find genes that are differentially expressed as markers for disease or other clinical conditions.

Gene expression is initially evaluated using microarrays or RNA-sequencing, which take advantage of the sequence of the entire human genome to assess the expression of most genes in the genome in a single analysis. Using sophisticated bioinformatic tools, candidate marker genes are identified in the microarray or RNA-seq data from among the full set of expressed genes. The most promising candidates are then tested in new sample sets using quantitative real-time PCR (qRT-PCR), which is a highly sensitive and reproducible technique for measuring gene expression, to find markers where differential expression between the two clinical conditions is confirmed. From this list of confirmed marker genes, computer algorithms are used to identify the combination that best discriminates one clinical condition from the other.

The final product of the development process is a list of genes to be assessed, their corresponding qRT-PCR assays, and a mathematical algorithm that combines the resulting expression levels into a score that provides information regarding the clinical condition that existed when the blood sample was collected.

We are also pursuing other areas of transplant surveillance, such as the use of cell-free DNA (cfDNA) as a biomarker for rejection.