Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism). Advances in genomics have triggered a revolution in discovery-based research to understand even the most complex biological systems such as the brain. The field includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.
National Human Genome Research Institute (2010-11-08). "FAQ About Genetic and Genomic Science". Genome.gov. Retrieved 2011-12-03
Genome analysis
After an organism has been selected, genome projects involve three components: the sequencing of DNA, the assembly of that sequence to create a representation of the original chromosome, and the annotation and analysis of that representation.
1. Sequencing
Historically, sequencing was done in sequencing centers, centralized facilities (ranging from large independent institutions such as Joint Genome Institute which sequence dozens of terabases a year, to local molecular biology core facilities) which contain research laboratories with the costly instrumentation and technical support necessary. As sequencing technology continues to improve, however, a new generation of effective fast turnaround benchtop sequencers has come within reach of the average academic laboratory. On the whole, genome sequencing approaches fall into two broad categories, shotgun and high-throughput (aka next-generation) sequencing.
Pevsner, Jonathan (2009). Bioinformatics and functional genomics (2nd ed.). Hoboken, N.J: Wiley-Blackwell.
2. Assembly
Sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as current DNA sequencing technology cannot read whole genomes as a continuous sequence, but rather reads small pieces of between 20 and 1000 bases, depending on the technology used. Typically the short fragments, called reads, result from shotgun sequencing genomic DNA, or gene transcripts (ESTs).
- Assembly approaches
- Finishing
Pevsner, Jonathan (2009). Bioinformatics and functional genomics (2nd ed.). Hoboken, N.J: Wiley-Blackwell.
3. Annotation
The DNA sequence assembly alone is of little value without additional analysis. Genome annotation is the process of attaching biological information to , and consists of three main steps:
- identifying portions of the genome that do not code for proteins
- identifying elements on the genome, a process called gene prediction, and
- attaching biological information to these elements.
Traditionally, the basic level of annotation is using BLAST for finding similarities, and then annotating genomes based on homolouges. More recently, additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g. Ensembl) rely on both curated data sources as well as a range of software tools in their automated genome annotation pipeline. Structural annotation consists of the identification of genomic elements, primarily ORFs and their localisation, or gene structure. Functional annotation consists of attaching biological information to genomic elements.
Stein, L. (2001). "Genome Annotation: From Sequence to Biology". Nature Reviews Genetics 2 (7): 493–503.
Brent, Michael R (January 2008). "Steady progress and recent breakthroughs in the accuracy of automated genome annotation". Nature reviews. Genetics 9 (1): 62–73.
4. Sequencing pipelines and databases
The need for reproducibility and efficient management of the large amount of data associated with genome projects mean that computational pipelines have important applications in genomics
Keith, Jonathan M, ed. (2008). "Bioinformatics". Methods in Molecular Biology™ 453.
Applications of genomics
Genomics has provided applications in many fields, including medicine, biotechnology, anthropology and other social sciences.
- Genomic medicine
Feero, W. Gregory; Alan E. Guttmacher; Christopher J. O'Donnell; Elizabeth G. Nabel (2011-12-01). "Genomic Medicine: Genomics of Cardiovascular Disease". The New England Journal of Medicine 365 (22): 2098–109.
- Synthetic biology and bioengineering
Church, George M; Edward Regis (2012). Regenesis : how synthetic biology will reinvent nature and ourselves. New York: Basic Books.
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