Applications of Genetics

1. Applications of Genetics • Learning Objectives: • Human genetics • Pedigree Analysis • Genetic Screening • Genetic Counseling • Gene Therapy • Human Genome Project

2. 2. Plant and animal breeding • Artificial Selection • Cloning 3. Recombinant DNA Technology and its applications 4. DNA fingerprinting and its applications 5. Implications of genetic manipulation: the potential benefits, hazards and ethical issues.

3. Human Genetics • Pedigree Analysis • Pedigrees = Family Trees • One of the central tasks of the human geneticist • Pedigree analysis is the construction of family trees • Family history information is often collected at major family gatherings • A pedigree is used to trace inheritance of a trait over several generations.

4. Symbols used in pedigree charts:

5. Inheritance of Haemophilic trait in the Royal Family

6. Three primary patterns of inheritance: • autosomal recessive • autosomal dominant • sex-linked (X-chromosomal)

7. Autosomal Recessive Pedigree • Recessive: neither parent has the characteristic phenotype (disease) displayed by the child • Autosomal: Gene is on one of the autosomes (Chromosomes 1-22). • Phenotype only occurs under homozygous condition

8. Autosomal Dominant Pedigree • Dominant: Affected individuals can appear in every generation • Autosomal: Gene is on one of the autosomes (Chromosomes 1-22). • Phenotype occurs under both homozygous and heterozygous conditions

9. Sex-Linked Pedigree • X-linked: The trait is preferentially seen in males, who are homozygous. Females are heterozygous "carriers" • Most X-linked traits are recessive. • Inheritance of red-green color blindness, an X-linked, recessive trait:

11. Color blind male is father of "carrier" daughters and normal sons. • Carrier daughters have 50% chance to have color blind sons. • Color blind male x carrier female can produce color blind daughters • Can you determine a pedigree for Red-Green Colorblindness?

12. For more information, please refer to the following website: Pedigree analysis problem set available at http://www.biology.arizona.edu/human_bio/problem_sets/color_blindness/intro.html

13. Genetic screening • Diagnosis of inherited diseases before symptoms occur by finding abnormalities in the genes or chromosomes. • Some examples: • sickle cell anaemia • cystic fibrosis • phenylketonuria (PKU) • Down’s Syndrome • Most of these tests performed on cells removed from the fetus (pre-natal diagnosis) and even from a pre-implantation embryo.

14. Ultrasound • One of the simplest and easiest genetics screening tests • Evaluate the physical characteristics of the fetus which may help predict certain abnormalities • Measurements of various body parts can be used to suggest an increased risk of Down Syndrome • look for congenital defects such leaky heart valves, and birth defects such as cleft lip or club foot. • Ultrasound is also used to guide the physician during amniocentesis and chorionic villus sampling (CVS).

15. An example of ultrasound image

16. Amniocentesis • Remove fetal cells from amniotic fluid 14 to 22 weeks after pregnancy. • Culture the cells and look for • chromosome abnormalities (e.g., the three number 21 chromosomes of Down syndrome); • certain enzymatic defects (e.g., an inability to metabolize galactose, hence milk); • the sex of the fetus.

17. Risks: • To the mother: slight discomfort, adverse reaction to medications used, vaginal bleeding or cramping, and infection. • To the foetus: inadvertent puncture is small • To the pregnancy: chance to miscarriage very low (not more than 1/200)

18. Couples who may wish to consider amniocentesis include: • 1. Women 35 years of age and over • 2. Parents who have had a child with Down's syndrome or other chromosome abnormality. • 3. Couples who are known carriers of a chromosome rearrangement • 4. Couples who have had a child with a malformation of the brain or spinal cord

19. Chorionic villus sampling (CVS) • Procedure: • Suck out placental cells by a tube inserted through the abdomen or vagina. • Advantages: • No need to perform cell culture • Can be performed earlier in pregnancy (10-12 weeks) • If an abortion is to be performed, it is a simpler process early in pregnancy

20. Drawbacks: • More risky than amniocentesis • Increase the chance of miscarriage (approximately 0.8%) • Minor complications such as vaginal bleeding or cramping occur more frequently following CVS than amniocentesis • Infection • Transverse limb defects in infants can be resulted • Involve the absence of the distal structures of the limb • May result in the vascular system disruption of the limb • Risk for transverse limb defects following CVS is approximately 0.03%-0.10%

21. Couples who may wish to consider CVS include: • Women 35 years of age and older • Parents who have had a child with Down's syndrome or other chromosome abnormality • Couples who are known carriers of a chromosome rearrangement • Couples who have a family history of a genetic condition for which testing is available

22. Common genetic diseases diagnosed by CVS • Chromosomal abnormalities such as Down’s, Klinefelter’s and Turner’s syndromes can be identified by karyotype analysis. • The cells can be cultured for DNA analysis that helps diagnosis of • 1. Cystic fibrosis • 2. Huntington’s chorea • 3. Thalassemia

24. Genetic Counseling • Genetic counselors are trained persons who help individual and family to • comprehend the medical facts, including the diagnosis, probable course of the disorder, and the available management; • appreciate the way heredity contributes to the disorder, and the risk of recurrence in specified relatives • understand the alternatives for dealing with the risk of occurrence • choose the course of action which seems to them appropriate in view of their risk, their family goals, and their ethical and religious standards, to act in accordance with that decision • make the best possible adjustment to the disorder in an affected family member and/or the risk of recurrence of that disorder.

25. Who Should be Referred? • Families in which one or more members have a serious birth defect or genetic disease. • Families who have a child with multiple congenital anomalies, serious developmental delay, or an unexplained abnormality of growth. • Families in which more than one close relative has the same disease, e.g., mental retardation, deafness, blindness, cancer, early heart attacks, or schizophrenia. • Couples who have had repeated stillbirths or a stillborn baby with birth defects. • Couples who are close blood relatives, e.g., first cousins.

26. Common issues discussed during genetic counseling • Making a diagnosis • Investigate the family history for previous cases of genetic diseases through pedigree analysis • calculate and explain the risk of having affected children • explain the cause of the disease • Quality of life • The quality and likely length of an affected child’s life will be discussed • Availability of treatment, support groups and financial help will also be discussed. • Effects on other family members will be discussed

27. Options: • These include contraception, sterilization, adoption, artificial insemination to avoid the husband’s genes being passed on or IVF using a donor egg if the problem lies with the woman. • Prenatal diagnosis is an option if the couple are willing to consider abortion of an affected fetus. • CVS, amniocentesis and abortion must be discussed. • The reliability of tests such as DNA analysis, ultra-sound scanning must be explained. • Possibility of IVF and gene therapy

28. Ethical issues in genetic counseling • During postnatal counsel • Risk evaluation, preventive options, gene therapy, testing of all family members, confidentiality within the couple • During prenatal counsel • Option of pregnancy termination, selective implantation, sex selection • Problems of Eugenics (The birth of designer baby)

29. Gene Therapy A new method for treating genetic diseases by replacing faulty genes with normal genes or adding normal genes if they are absent. Two types of gene therapy: Somatic cell gene therapy - the insertion of genes into body cells which function only in the treated person and are not passed on to the offspring. Germline gene therapy - the insertion of genes into cells that are involved in reproduction which can be passed on to the future offspring.

30. Diagrammatic Illustration of Gene Therapy

31. General Procedure of Gene Therapy: • Isolate and clone the normal gene. • Introduce it into the chosen human cells with the help of a safe and efficient vector. • The cells may have to be isolated from the body first, corrected and then replaced. • Easier for blood diseases such as sickle cell anaemia because the cells that make blood cells can easily be removed from bone marrow and replaced. • The final problem is to make sure that the gene is expressed normally.

32. Common Vectors Used: • Viruses (e.g. Retrovirus) carrying the required gene • Liposomes containing the cDNA clone • Microinjection and electroporation- Direct injection of donor DNA into the cell

33. Applications of Gene Therapy • e.g. Cystic fibrosis • Cystic fibrosis affects the epithelial cells of the body, but the life-threatening problems mainly affect the lungs. • Lung and trachea epithelial cells are therefore the initial targets for gene therapy. The aim is to get the gene into the cells so that it can make the normal protein, known as CFTR • The cDNA clone is enclosed in a specially designed vector. • Adenovirus infecting the respiratory tract is currently used as the vector for the CFTR gene • The vector does not insert its DNA into the host DNA. If the cell divides, the new DNA is not replaced at the same time so it eventually becomes diluted. • The treatment may only be effective for a few weeks until the epithelial cells die, but it will be easy to repeat the treatment at regular intervals.

34. Advantages and Disadvantages of Gene Therapy

35. Ethical issues of gene therapy • Germline therapy is controversial because it opens up the whole field of eugenics. • The same technique can be used to add genes for desired characteristics. (For example, the American public has demonstrated a desire for enhanced growth of normal children with demands for human growth hormone) • Germline therapy is controversial because the change can be passed on to the children of the treated person and all subsequent generations. • Do we have the right to alter the genome of the future generation?

36. Human Genome Project (HGP) • The goals of the project are to: • identify all the approximately 30,000 genes in human DNA • determine the sequences of the 3 billion chemical bases that make up human DNA • store this information in databases • develop faster, more efficient sequencing technologies • develop tools for data analysis, and • address the ethical, legal, and social issues (ELSI) that may arise from the project.

37. Applications of HGP • Molecular Medicine • Improved diagnosis of disease • Earlier detection of genetic predispositions to disease • Rational drug design • Gene therapy and control systems for drugs • Pharmacogenomics "custom drugs"

38. 2. Microbial Genomics • New energy sources (biofuels) • Environmental monitoring to detect pollutants • Protection from biological and chemical warfare • Safe, efficient toxic waste cleanup • Understanding disease vulnerabilities and revealing drug targets

39. 3. Risk Assessment • Assess health damage and risks caused by radiation exposure, including low-dose exposures • Assess health damage and risks caused by exposure to mutagenic chemicals and cancer-causing toxins • Reduce the likelihood of heritable mutations

40. 4. Bioarchaeology, Anthropology, Evolution, and Human Migration • study evolution through germline mutations in lineages • study migration of different population groups based on female genetic inheritance • study mutations on the Y chromosome to trace lineage and migration of males • compare breakpoints in the evolution of mutations with ages of populations and historical events

41. 5. DNA Forensics (Identification) • Identify potential suspects whose DNA may match evidence left at crime scenes • Exonerate persons wrongly accused of crimes • Identify crime and catastrophe victims • Establish paternity and other family relationships • Identify endangered and protected species as an aid to wildlife officials (could be used for prosecuting poachers) • Detect bacteria and other organisms that may pollute air, water, soil, and food • Match organ donors with recipients in transplant programs • Determine pedigree for seed or livestock breeds • Authenticate consumables such as caviar and wine

42. 6. Agriculture, Livestock Breeding, and Bioprocessing • Disease-, insect-, and drought-resistant crops • Healthier, more productive, disease-resistant farm animals • More nutritious produce • Biopesticides • Edible vaccines incorporated into food products (Biopharming) • New environmental cleanup uses for plants like tobacco

43. Ethnical problems • Fairness in the use of genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others. • Who should have access to personal genetic information, and how will it be used? • Privacy and confidentiality of genetic information. • Who owns and controls genetic information? • Psychological impact and stigmatization due to an individual's genetic differences. • How does personal genetic information affect an individual and society's perceptions of that individual?

44. More information on HGP is available at Dolan DNA learning center (2002), Gene Almanac, [Online] Available at http://www.dnalc.org/resources/resources.html http://www.web-and-flow.com/members/efitzger1/genetics/webquest.htm (The Human Genome WebQuest)

45. Selective Breeding of Animals and Plants • Aims: • To select desirable traits and remove undesirable traits of plants and animals through artificial selection • Two types of breeding involved in artificial selection: • Inbreeding • Outbreeding

46. Inbreeding– mating of closely related individuals Advantages: Create pure line over time Better adapted to steady environment. For example Parental genotypes: Ffgg x Ffgg Gametes: Fg , fg Fg , fg F1: FFgg Ffgg Ffgg ffgg (pure breeding)

47. Disadvantages of inbreeding • Increasing the chance for recessive genes to be homozygous • Most recessive genes are undesirable traits • Leads to a high frequency of defects present at birth • Reduce the genetic variability vigour and fertility of a population.

48. Outbreeding - mating of individuals that are unrelated • Advantages: • Progeny (offspring) are heterozygous and the bad recessive genes are masked by normal dominant alleles. • Hybrid vigour – Progeny are tougher, more fertile and have a greater chance of survival • Produces variation/heterozygosity; on which natural selection can act. • Disadvantage: • No more pure line exists

49. Examples The cross of larger, non-sweet-tasted tomato with small, sweet-tasted tomato. The cross of high-resistant to pest and disease crop with higher-yield crop. Parental genotypes: FFgghhIIjj x FFGGHHiiJJ Gametes: FghIj FGHiJ F1: FfGgHhIiJj Higher chance of heterozygosity in F1 Result in hybrid vigour

50. female parent hybrid male parent The hybrids are stronger and bigger in size than their parents