Genetic analysis of patients and molecular analysis of patient tissue samples are often the first steps for identifying disease genes. Southern blotting, for example, can be used to identify a DNA sequence using a similar sequence as a probe while quantitative real-time PCR and Northern blotting can be used to quantify RNA levels. These analyses can identify alterations at the cellular level which may impact the pathology.

For example, changes in gene expression or difference in RNA half-life can alter the RNA levels, leading to disease. Several mutations that alter protein functions also affect pathology and can be identified using classical genetics techniques or next generation sequencing. Antibodies are invaluable tools in such research because they facilitate the quantification of protein levels in a Western blot assay. Once identified, the genes that are altered in a disorder can be changed, induced, and removed in cells grown in vitro. Such studies inform us about the specific functions of these proteins and their contribution to the disease.

A molecular pathologist is interested in studying a disease characterized by gradual loss of T cells in patients. Using microarray analysis of tissue samples, she identifies 129 genes with increased expression compared to control samples and 86 genes expressed at reduced levels. Expression of one of the genes, DAG1, was found to be completely absent in the patient cells while mRNA of DAG2, a mitochondrial protein known to function in cell death, was found to be highly upregulated.

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