Cancer genome sequencing: a review

Abstract

A genomic era of cancer studies is developing rapidly, fueled by the emergence of next-generation sequencing technologies that provide exquisite sensitivity and resolution. This article discusses several areas within cancer genomics that are being transformed by the application of new technology, and in the process are dramatically expanding our understanding of this disease. Although, we anticipate that there will be many exciting discoveries in the near future, the ultimate success of these endeavors rests on our ability to translate what is learned into better diagnosis, treatment and prevention of cancer.

Figure 1.

Summary of readcount data obtained for ten somatic mutations and two validated SNPs in the AML primary tumor, AML relapse tumor and normal skin specimens. As described in the text, all heterozygous mutations were determined by readcount data to be present at around 50% prevalence in the tumor cells with the exception of the FLT3 internal tandem duplication mutant. The variant alleles in the primary and relapse tumor samples are statistically different from that of the skin sample for all mutations. Note that the normal skin sample was contaminated with leukemic cells containing the somatic mutations, as the patient's white blood cell count was 105 000 when the skin punch biopsy was obtained.

Figure 2.

Kaplan–Meier survival analysis of AML patients. Overall survival is shown for patients with (blue) or without (IDH1) mutations. (A) Entire AML cohort. (B) AML patients with normal cytogenetics. (C) AML patients with normal cytogenetics and non-mutated NPM1. (D) AML patients with normal cytogenetics, non-mutated NPM1 and non-mutated FLT3. Differences were assessed by Log rank analysis.