Mutation analysis is the process of finding known and unknown mutations in DNA and RNA, and PCR (polymerase chain reaction) is used as part of the method.



In the clinic, mutation analysis can be used to detect known mutations for disease diagnosis or select the patients who are most likely to respond in personalised medicine. This can improve the efficacy and outcomes of treatment and reduce the chance of patients getting drugs that are either ineffective, or will cause more severe side effects.

In research, mutation analysis can be used to find unknown mutations through genome-wide analysis, work out how germline mutations can affect an individual’s risk of disease, or help people to understand how accumulations of somatic mutations drive the development of diseases such as cancer. These findings could help researchers and biopharma companies to find new biomarkers, targets and pathways that could lead to new drugs or diagnostics.

Disease-causing mutations on germline or somatic DNA include mis-sense and nonsense mutations, SNPs (single nucleotide polymorphisms) deletions and insertions. These can occur in the coding or non-coding regions of the genome and can be detected using a range of different forms of real-time PCR, for example:

  • ACB (allele-specific competitive blocker ) PCR
  • Blocker PCR
  • Real-time genotyping with locked nucleic acids
  • Restriction enzymes in conjunction with real-time PCR
  • Allele-specific kinetic PCR in conjunction with modified polymerases
  • ARMS (amplification refractory mutation system) PCR
  • TaqMAMA (TaqMan mismatch amplification mutation assay)
  • FLAG (fluorescent amplicon generation) PCR

An example of the use of PCR technique published in PLoS One uses allele-specific PCR with a blocking reagent (ASB-PCR). This uses allele-specific PCR, where the primers are created to anneal to specific sequences, with a blocker that suppresses the non-specific amplification of the wild type allele, and reagent rules to create selective assays for single point substitutions, insertions and deletions. The process can be carried out simultaneously with gene expression analysis.

In cancer diagnosis, mutation analysis often requires surgical biopsy of tissue samples. However, this may change in the future. According to research published in Clinical Chemistry in January 2013, tumour-derived DNA can also be found in the plasma. This could make testing for diagnosis and selection of the most effective therapy much less invasive for patients, and less time consuming and lower cost for healthcare providers.

Suzanne Elvidge is a freelance science, biopharma, business and health writer with more than 20 years of experience. She has written for a range of online and print publications including FierceBiomarkers, FierceDrugDelivery, European Life Science, the Journal of Life Sciences (now the Burrill Report), In Vivo, Life Science Leader, Nature Biotechnology, New Scientist, PR Week and Start-Up. She specialises in writing on pharmaceuticals, biotechnology, healthcare, science, lifestyle and green living, but can write on any topic given enough tea and chocolate biscuits. She lives just beyond the neck end of nowhere in the Peak District with her second-hand bookseller husband and two second-hand cats.