Genomics and Genetic Testing

Genomics and Genetic Testing

DOI: 10.4018/978-1-5225-8066-9.ch012

Abstract

This chapter focuses on the Human Genome Project (HGP), which determined that humans have between 20,000 to 25,000 protein-coding genes and only about 1.5% of the genome codes for proteins, rRNA, and tRNA. The remainder once referred as “junk DNA” is today known to be crucial to survival of the species. Research indicates that genes are not contiguous, and some genes occur within the introns of other genes; some genes can overlap with each other either on the same or on different DNA strands with shared coding and/or regulatory elements; plus, the vast majority of human genes undergo alternative splicing leading to different proteins being encoded by the same gene. Advances in genomics and gene sequencing technologies have created exceptional opportunities for the delivery of personalized medical care. Clinical genetic testing has been helpful in identifying gene variants associated with risks for a number of diseases and health conditions.
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Chapter Outline

  • 12.1 The Human Genome Project

  • 12.2 Genomic Research, Precision Medicine and Pharmacogenetics

  • 12.3 Gene Name and Cytogenetic Location

  • 12.4 Genetic Testing Technology and Methods

  • 12.4.1 Cytogenetic Testing

  • 12.4.2 Biochemical Testing

  • 12.4.3 Molecular Testing

  • 12.5 Genomics, Genetic Testing and Society

  • Chapter Summary

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Learning Outcomes

  • Explain the work of the Human Genome Project and its research and health implications

  • Outline the role of genomics in precision medicine and pharmacogenetics

  • Illustrate with examples how genes are named

  • Differentiate between the various genetic testing methods currently in use

  • Summarize the implications of genomic data and gene testing in society

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12.1 The Human Genome Project

The Human Genome Project (HGP) was an international research effort whose primary goal was to determine the sequence of the human genome and identify the genes it contains (introduced in chapter 8, section 8.1). Funded largely by the US Government through the National Institutes of Health and the Department of Energy and involving collaboration between researchers in the US and other countries, the effort started in 1990 and was completed in 2003. It is now known that humans have between 20,000 to 25,000 protein-coding genes which makes only about 1.5% of the genome coding for proteins, rRNA, and tRNA. The rest of the genome once known as “junk DNA” is today known to be crucial to survival of the species. This non-coding DNA consists of repetitive DNA (59%); introns and regulatory sequences (24%); and other non-coding DNA sequences (15.5%).

According to Naidoo et al. (2011), the HGP provided the raw DNA sequence that helped generate several secondary studies which have greatly improved our knowledge of the architecture and function of the genome. New insights have been gained in gene number and density, non-protein-coding RNA genes, pervasive transcription, high copy number repeat sequences and, evolutionary conservation (Naidoo et al., 2011). For example, genome-wide association studies have gradually increased in the last 15 years exploring complex human diseases and traits, and gene sequencing technologies have become more advanced. The advent of next-generation sequencing technologies has dramatically changed studies in structural and functional genomics. For instance, several microarray-based methods have been replaced by sequencing-based approaches such as ChIP-Seq, RNA-Seq, Methyl-Seq and CNV-Seq (Werner, 2010; Naidoo et al., 2011).

Other progress made from the reference genome generated by the HGP are several large-scale international projects which have contributed substantially to our understanding and knowledge of human genetics and genomics. Examples of such projects include the International HapMap Project; the Encyclopaedia of DNA Elements (ENCODE) Project, the 1000 Genomes Project, the International Cancer Genome Consortium, the National Institute of Health (NIH) Roadmap Epigenomics Program, and the Human Microbiome Project.

Key Terms in this Chapter

National Institute of Health (NIH) Roadmap Epigenomics Program: An international consortium with the goal of creating accessible human epigenomic data that can be used to further integrate and expand on current research in the scientific community.

1000 Genomes Project: An international research effort launched between 2008 and 2015 that was responsible for generating the largest public catalogue of genetic variation and genotypic data.

Encyclopaedia of DNA Elements (ENCODE) Project: A public research association that started in 2003 with a main goal of identifying all functional elements in the genomes of humans and mice.

Personalized Medicine: The application of genomic advances and gene sequencing knowledge towards the delivery of personalized medical care to improve health outcome and reduce patient mortality and morbidity.

International Cancer Genome Consortium: An international association established in 2007 with the aim of identifying, defining, and understanding the genomic changes of 25,000 untreated cancer cases.

International HapMap Project: An international project created in 2002 that contributed to the development of a haplotype map of the human genome.

Pharmacogenomics: A sector within biomedicine and biotechnology that aims to revolutionize modern medicine by advancing pharmaceutical development in vaccines, therapies, and biological molecules.

Human Genome Project: An international project created in 1990 with the goal of sequencing and identifying the entire human genome.

Human Microbiome Project: A research initiative established in 2008 under the United States National Institutes of Health that enabled the study of human microbiota and its role in the development of human health and disease.

Hugo Gene Nomenclature Committee: A committee that sets the official standard for human genome nomenclature and associated genomic information. It aims to assign a unique yet meaningful name or symbol for each known human gene.

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