Genomics and Biotechnology: Genome Projects, Recombinant DNA, Cloning, GMOs and Gene Therapy

1Overview

In 1990 an international group of researchers set out to read every letter of human DNA, a text of about six billion characters per cell. The sequence was finished in 2003, and the work is still not over: reading DNA has become so fast that, as the National Human Genome Research Institute puts it, the ability to sequence has far outpaced the ability to interpret. This lesson looks at the genome as a whole (genomics) and at the technologies built on it: recombinant DNA, cloning, genetically modified organisms and gene therapy. Each technology also raises questions that science alone cannot answer, so the lesson includes the social and ethical thinking that the Curricular Competencies ask students to practise.

2From genes to genomes

A genome is the complete set of DNA in an organism, and genomics is the study of all of it: identifying and characterizing all the genes and other functional elements and how they interact. The term is often contrasted with genetics, the study of a particular gene or trait. Genomics has grown from basic research into a major part of medicine, agriculture, environmental monitoring, ancestry research and forensics.

Some numbers help build a sense of scale. A human cell holds roughly 6 billion DNA letters (two copies of the genome), and one sequenced genome needs on the order of 200 GB of computer storage, which is why genomics is called a "big data" field. Only a fraction of the genome codes for protein: the human genome contains about 19,900 protein-producing genes, and many other regions regulate genes or produce functional RNAs. Fewer than 1% of the genes differ between people, and the differences range from single-letter changes (SNPs) to larger structural variants. Many are harmless; some contribute to rare disorders, cancer or common diseases.

Major genome projects

Large coordinated projects have shaped the field. Three illustrate different goals.

The microbiome project is a reminder that "the genome" can mean the genes of the microbes a person carries, not only the person's own. A related site article describes this in more detail.

In real life. The Human Genome Project gave medicine a reference sequence. Today a person's genome can be compared with that reference to look for variants that explain an unexplained disease, to guide drug choice, or to understand a tumour. The project also built ethical, legal and social questions into genomics from the beginning: who owns genetic information, and who may see it?

3Personal genomics

Direct-to-consumer (DTC) genetic testing lets a person order a test without going through a health-care provider or insurer. Such tests may report on traits, wellness and lifestyle factors, response to medications, disease risk and ancestry. The evaluation of such services is an important skill.

• Benefits: convenient access to information about oneself and ancestry; some tests may be reimbursable through health spending accounts.
• Limitations: most insurance does not cover them; results generally need confirmation by clinical testing ordered by a provider before they can be used to diagnose a condition or guide care; there are few regulations, so quality varies and a company should be evaluated before testing.
• Privacy and ethics: participants should be told how their data will be used and shared (informed consent). Powerful tools can, in special circumstances, link a de-identified genome back to a person. Shared datasets use graded access (open, registered or controlled) for that reason, and algorithms that interpret DNA can contain unseen bias.

4Recombinant DNA technology

Recombinant DNA technology uses enzymes to cut and paste DNA sequences of interest. A segment of DNA is isolated, joined with DNA from another source (even another species), and placed in a host cell, usually a bacterium or yeast, which copies it along with its own DNA. The technique is used to produce proteins that treat disease, notably insulin and growth hormone.

1. Isolate the gene of interest (for example the human insulin gene) and cut it out with restriction enzymes that recognize specific DNA sequences.
2. Prepare a vector. A bacterial plasmid, a small circle of DNA, is cut with the same enzyme so that the ends match.
3. Join the gene into the plasmid with DNA ligase to form a recombinant plasmid.
4. Introduce the plasmid into host cells and grow large quantities of them.
5. Harvest the copies of the gene or the protein it encodes and purify it for use.

5Cloning

Cloning produces genetically identical copies of a gene, cell, tissue or whole organism. Natural clones occur in some plants and single-celled organisms, and identical twins are natural clones formed when a fertilized egg splits. Three artificial types are distinguished.

• Gene (DNA) cloning: a gene is inserted into a vector such as a plasmid, bacterium, yeast or virus, which multiplies to give many copies. This is the most common type in research and is the same technique as recombinant DNA above.
• Reproductive cloning: a whole animal is copied. The nucleus of a body (somatic) cell is transferred into an egg whose own nucleus has been removed, and the egg develops into an early embryo that is implanted in a female.
• Therapeutic cloning: a cloned embryo is made to obtain embryonic stem cells that match the donor's DNA, for research or to grow replacement tissue. The stem cells are harvested at the blastocyst stage, which destroys the embryo.

Dolly the sheep, born in 1996 in Scotland after hundreds of attempts, was the first mammal cloned from a mature somatic cell (an udder cell of a six-year-old sheep). She had shorter-than-normal chromosome ends (telomeres) and died at six, about half the typical lifespan. Cloned mammals have shown larger birth size, organ defects, premature aging and immune problems, and most cloned embryos fail to develop. Clones are also not always identical in appearance: the first cloned cat, Cc, is a calico that differs from her mother because X-chromosome inactivation is random.

The ethical debate differs by type. Reproductive cloning raises concerns about human dignity, identity and autonomy; therapeutic cloning raises objections because it requires destroying embryos. Cloning of livestock has also been assessed for food safety and explored in conservation, although some experts worry about the low genetic variability of cloned populations.

6Genetically modified organisms (GMOs)

A genetically modified organism is a plant, animal or microorganism whose DNA has been altered in ways that do not occur through natural mating or recombination. Genes can be moved between organisms, even unrelated species, using recombinant DNA methods. Most GM crops aim to protect the plant: insect resistance (using a gene for a toxin from the bacterium Bacillus thuringiensis), virus resistance and herbicide tolerance. Others are being developed for higher nutrient content or for drought tolerance.

The World Health Organization notes that it is not possible to make general statements on the safety of all GM foods: each product is assessed case by case, typically for toxicity, allergenicity, nutritional change and unintended effects, and regulation differs between countries. Products on the international market have passed such assessments, and no health effects have been shown in populations where they are approved. Environmental risks vary with local conditions.

7Gene therapy

Gene therapy aims to treat or prevent disease by correcting the underlying genetic problem rather than using drugs or surgery. Two main approaches exist.

• Gene transfer (gene addition): the earliest method adds a working copy of a gene to cells to replace or supplement a faulty one, or adds a new gene to help fight disease.
• Genome editing: a newer approach, for example CRISPR-Cas9, changes the DNA already in a cell. Goals include fixing a variant so the gene works, turning on a gene that helps fight disease, turning off a malfunctioning gene, or removing a DNA segment that impairs function.

Gene therapies are in use for a small number of diseases, including Leber congenital amaurosis (an eye disorder) and spinal muscular atrophy (a muscle disorder), and many more are in research to establish safety and effectiveness. Genome editing is described as promising for future patients. Questions that accompany it include safety and unintended effects, cost and fair access, and the difference between treating the cells of one person and changing DNA that could be inherited.

In real life. A person studying a news story about a "gene-editing cure" can ask structured questions. Which disease and which cells? Gene addition or editing? What does the evidence show about safety and how long the effect lasts? Who can afford it? These questions mirror the evaluation skills the course asks students to build.

8Comparing the technologies

The five technologies are easy to confuse because all of them involve altering or copying DNA. They differ in what is changed, in which cells and for what purpose.

Evaluating the social and ethical implications

Every technology above allows something that was previously impossible, and each has benefits, risks and uncertainty. A useful framework asks the same questions of each case.

Genomics and biotechnology connect the molecular lessons that preceded this one to the organ-system lessons that follow. Insulin made by recombinant methods treats the endocrine disorder in Lesson 7, gene therapy targets diseases of the eye and muscle, and the immune response in Lesson 9 is one reason that cloned or foreign cells can be rejected. The genome is the shared text; the organ systems are the many ways it is read.

?Quick check

Try each question first, then reveal the answer.