![]() The fundamental premise of cancer genomics is that cancer is caused by somatically acquired mutations, and consequently it is a disease of the genome. The only limitations reside in regions which sequence poorly or map erroneously due to extreme guanine/cytosine (GC) content or repeat architecture, for example, the repeat expansions underlying Fragile X syndrome, or Huntington's disease. However, these data can also be derived from NGS sequencing data directly, obviating the need for dedicated assays while harvesting the full spectrum of genomic variation in a single experiment. For the remaining mutations dedicated assays are frequently performed, such as fluorescence in situ hybridisation (FISH) for conventional karyotyping, or comparative genomic hybridisation (CGH) microarrays to detect submicroscopic chromosomal copy number changes such as microdeletions. Traditional Sanger sequencing is restricted to the discovery of substitutions and small insertions and deletions. The spectrum of DNA variation in a human genome comprises small base changes (substitutions), insertions and deletions of DNA, large genomic deletions of exons or whole genes and rearrangements such as inversions and translocations. NGS captures a broader spectrum of mutations than Sanger sequencing
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