tuberculosis is homogenous and antibiotic resistances can arise through deletion, insertion or nucleotide substitution (Achtman, 2008 Ilyas, 2017). NGS also helps in analysing of the genetic changes that result in antibiotic resistances and, therefore, enable clinicians to prescribe effective antibiotics. In those cases, WGS is the preferred detection method. Additionally, less than 2% of bacteria are cultivable in laboratory conditions, which could complicate testing even more (Wade, 2002). But for slow growing strains, like Mycobacterium tuberculosis, phenotypic testing could take weeks. Isolation, correct species identification and susceptibility testing of bacteria may take 1 to 2 days. Thus far, PCR-based genetic tests have usually been performed for viral infections but not for bacteria. It enables the diagnosis of rare disease that, when combined, affect more than 300 million people worldwide (Liu et al., 2019 Marshall et al., 2020).Īs additional routine procedure in research laboratories, WGS is used to analyse infectious agents such as bacteria and viruses (Ilyas, 2017). WGS enables the identification of novel gene mutations including complex mutations such as chromosomal translocations and copy number variations (CNVs). It also cut the costs for the diagnosis to a fraction of the other option of whole genome sequencing (WGS).Īs the name indicates, WGS includes sequencing the coding (exons), non-coding (introns) and regulatory regions. The WES strategy opted for by Lifton was sheer brilliance and the decisive factor in finding the correct diagnosis, as around 85% of the disease-causing mutations are present in the exome. In this and other cases, conventional genotyping methods such as karyotyping, fluorescent in-situ hybridisation (FISH) and restriction fragment length polymorphism analysis (RFLP) failed to properly diagnose the disease. The symptoms of both diseases are similar: intestinal problems and dehydration. However, the results of WES revealed the presence of a mutation that resulted in congenital chloride diarrhoea (Choi et al., 2009). The patient, a five months old infant, was suspected to have Bartter’s syndrome. For instance, in 2009 Richard Lifton and colleagues at Yale University diagnosed the clinical condition of a patient using whole exome sequencing (WES) (exome = protein coding regions). These diseases include autism, connective tissue disorders, cardiomyopathies (disease of the heart muscle that impedes blood pumping), and disorders of sex development (Di Resta et al., 2018). For the diagnosis of complex diseases that involve multiple genes, NGS is the most suitable option.
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