340 Fendler and Atwal: Systematic deciphering of cancer genome networks across multiple loci, in the population. led to a massive increase in the number of While predisposition from certain alleles genes one could simultaneously investigate. confer susceptibility to cancer [8], random In the last decade, two types of array tech- somatic mutations throughout the lifetime of nologies played a significant role in our un- the organism without predisposition may derstanding of how cancer cells differ from also lead to similar results. In either case, ge- normal cells — one measuring gene expres- nomic instability, a signature feature of can- sion and the other gene copy number. Ex- cer [6], leads to somatic mutations including pression analysis of cancer cells focus on single nucleotide polymorphisms (SNPs†), gene regulation by measuring under/overex- insertions and deletions of large or small pressed mRNA in a sample tumor, while the segments of DNA, chromosomal transloca- second focuses on genomic structural tions, inversions, and other structural re- changes via copied and deleted regions of arrangements due to broken and rejoined DNA. Both technologies have their respec- DNA, epigenetic modifications (usually tive successes and difficulties. For example, chromatin modifications), and DNA acqui- array comparative genomic hybridization sition from other sources such as infections (aCGH) data, or copy number data, explic- from HPV [9], which all may lead to aber- itly informs which regions of the genome rant expression profiles or altered protein have been altered. However, it is still uncer- function due to amino acid substitution. tain which specific genes within the altered Most acquired mutations throughout the region are aberrantly expressed. Further, ex- lifetime of an individual are likely benign; pression analysis can specify the genes that however, when a mutation alters a gene or are under/overexpressed, but do not inform the expression of a gene that confers growth, about the causal molecular mechanisms un- malignant neoplasms arise. The cells within derlying the gene expression change. the growing tumor are progeny of the origi- In 2005, building upon the concepts of nal cell, whose driver or set of driver genes Sanger sequencing, rather than microarray initiated expansive growth. A malignant hybridization, sequencing DNA of interest tumor mirrors the selective process origi- became the next-generation in genomic dis- nally described by Darwin through a selec- covery technologies [11-15]. Next-genera- tive process, rewarding those that grow and tion sequencing (NGS) is the ability to expand unchecked. In the last decade, an at- sequence DNA samples using a reference li- tempt to understand how these mutations brary in a massive parallel capacity, revolu- lead to cancer was initiated through the de- tionizing sample resolution and the time velopment of many “micro”-techniques. necessary to sequence those samples [12]. These include the use of the microscope, While cost initially prohibited this technol- biochemical and cell biological techniques, ogy for widespread use, now NGS is mod- as well as advanced genomic-based tools, erately more expensive than microarrays with significant focus in the last decade on and in the next 5 months will likely be sim- the latter [10]. ilarly priced [16]. NGS technologies are an Since genes regulate the growth of improvement over microarrays for multiple cells, a natural approach to understanding reasons [17]. First, microarray technology cancer is to identify “what genes have gone requires a priori knowledge of the genes of awry?” At the time this question was posed, interest, introducing probe bias, whereas the technologies to answer these questions NGS technologies do not. Second, microar- were not well developed. Thus, genomic- ray segments may cross-hybridize to incor- based tools grew out of this need. Southern rect probes introducing noise in the signal, blotting, which identifies DNA sequences while NGS technologies rely on sequencing, using oligonucleotide probe hybridization, which counts single nucleotides. As a con- along with the development of the microar- sequence of this single base-pair resolution, ray chip, a chip with thousands of embed- NGS technologies can identify point muta- ded probes corresponding to a specific gene, tions in cancers [18,19]. Finally, nanograms