The Rapidly Expanding Field of “–Omics” Technologies - Science For Environmental Protection: The Road Ahead - page 203

plement of mRNAs from the genome because alternative splicing 1 is common
and contributes largely to protein and functional diversity in humans and other
higher organisms (Xu et al. 2011). Technologies for measuring mRNA tran-
scripts in all their varieties, including alternatively spliced transcripts and copy-
number variants, have grown rapidly in the last few years. For example, a new
approach called the Glue Grant Human Transcriptome Array completes a com-
prehensive analysis of the human transcriptome using a 6.9 million-feature oli-
gonucleotide array. The array assesses gene-level and exon-level expression by
using high-density tiling of probes that cover a large collection of transcriptome.
It can also detect alternative splicing and can analyze noncoding transcripts and
common variants (such as single nucleotide polymorphisms) of genes (so called
cSNPs) (Xu et al. 2011). This technology was recently used in a multicenter
clinical program that produced high-quality reproducible data (Xu et al. 2011). It
is an example of the rapid change in technologies in the -omics world and will
increasingly provide new approaches to understanding how environmental fac-
tors influence the development of common diseases. Such technologies will also
have many applications in the fields of microbial genomics, evolutionary biol-
ogy, and other areas of interest to EPA.
BOX C-1 Comparison of Sanger and Next-Generation Sequencing (NGS)
 The initial preparation of the DNA sample is more labor intensive for
NGS than for Sanger, but the amount of sequence data obtained per sample
is substantially more.
 The number of sequencing reads from a single instrument per run is of
the order of thousands with Sanger, but millions to billions with NGS; for ex-
ample, a bacterial genome can be sequenced in a single run in days using
NGS, versus months using Sanger sequencing.
 Read lengths from Sanger sequencing are up to 900 [base pairs], but
in NGS vary from 30 to 500 [base pairs] depending on the platform.
 DNA sequencing costs have been driven down by NGS and base pair
per dollar costs show a consistent 19-months doubling time reduction for
Sanger sequencing. For NGS, the equivalent figure is approximately 5-
months doubling time cost reduction.
 NGS can detect somatic mutations at [less than or equal to] 1%,
whereas Sanger sequencing has significantly less sensitivity.
 The greater versatility of NGS is illustrated in generating whole-
genome datasets, such as miRNA and ChIP-Seq; Sanger sequencing lacks
this capability.
Abbreviations: ChIP-Seq, chromatin immunoprecipitation sequencing; miRNA,
micro RNA; NGS, next-generation sequencing. Source: Woollard et al. 2011.
1 Alternative splicing “the process by which individual exons of pre-mRNAs are
spliced to produce different isoforms of mRNA transcripts from the same gene” (Xu et al.
2011).