Genes, Mutations and Genetic Testing

1. School of Medicine, Health Sciences and Engineering Susquehanna Township High School Lecture Series  Week 6, September 2013 Clinical Relevance of This Week’s Topic Genes, Mutations and Genetic Testing Wen Jie Zhang, MD, PhD

2. Environmental Factors Genetic Factors (Carcinogens) (Mutations) Cancer Substitutions Physical Deletions Chemical Insertions Biological Translocations Lifestyle Carcinogenesis

3. The Human Genome 23 pairs of chromosomes made of 3 billion base pairs • Extragenic DNA • Repetitive sequences • Control regions • Spacer DNA between genes • Function mostly unknown ~35,000 genes 70% 30% ASCO

4. The chemical structure of a four-base fragment of A DNA double helix.

5. Genes

6. Chromosome and Gene

7. Gene StructureTranscription and Translation

8. DNA sequence changes that may or may not alter protein function (common definition) Functional protein Functional protein Polymorphism

9. Disease-Associated Mutations Alter Protein Function Functional protein Nonfunctional or missing protein ASCO

10. Common Mutations • Substitutions (point mutation) In a DNA sequence, a single nucleotide is exchanged for another (A G, C T), leading to missense or nonsense mutation. • Insertions (insertion mutation) The addition of one or more nucleotide base pairs into a DNA sequence. • Deletions (deletion mutation) Part of a chromosome or a sequence (base pairs) of DNA is missing from a DNA sequence.

11. Missense Mutation • Missense Mutation (non-synonymous) is a point mutation in which a single nucleotide change (substitution) results in a codon that codes for a different amino acid • Example Genetic Disease Sickle-cell disease (SCD) or  sickle-cell anemia (SCA) – a hereditary blood disorder, characterized by red blood cells that assume an abnormal, rigid, sickle shape.

12. A Missense Mutation

13. Mutations

14. Missense Mutation (cont’d) • Missense Mutation (non-synonymous) is a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid • Example Genetic Disease Sickle-cell disease (SCD) or  sickle-cell anemia (SCA) – a hereditary blood disorder, characterized by red blood cells that assume an abnormal, rigid, sickle shape.

16. Nonsense Mutations • Nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribedmRNA, and in a truncated, incomplete, and usually nonfunctionalprotein product. • Example Genetic Disease β-Thalassemia– are forms of inherited autosomal recessiveblood disorders that originated in the Mediterranean region. In thalassemia, the disease is caused by the weakening and destruction of red blood cells.

17. Simple Nonsense Mutation

18. Large Insertion Mutation

19. Large Deletion Mutation

20. Chromosomal Translocation

21. Genetic Testing • Genetic testing is “the analysis of, chromosomes (DNA), proteins, and certain metabolites in order to detect heritable disease-related genotypes, mutations, phenotypes, or karyotypesfor clinical purposes.” • There were more than 1,200 clinically applicable genetic tests available. • Genetic tests are performed on a sample of blood, hair, skin, amniotic fluid (the fluid that surrounds a fetus during pregnancy), or other tissue such as semen.

22. Types of Genetic Testing

23. Prenatal Diagnostic Testing • Prenatal testing is used to detect changes in a fetus's genes or chromosomes before birth, offered to couples with an increased risk of having a baby with a genetic or chromosomal disorder. • Sex determination (discernment)

24. Cleft Lip/Palate

25. Newborn Screening Test • Newborn screening is used just after birth to identify genetic disorders that can be treated early in life. The routine testing of infants for certain disorders is the most widespread use of genetic testing • Millions of babies are tested each year in the United States. 

26. Carrier Testing • Carrier testing is used to identify people who carry one copy of a gene mutation that, when present in two copies, causes a genetic disorder.

27. Pre-implantation Genetic Diagnosis • Genetic testing procedures are performed on human embryos prior to the implantation as part of an in vitro fertilization procedure.

28. Predictive and Presymptomatic Testing • Predictive and presymptomatic types of testing are used to detect gene mutations associated with disorders that appear after birth, often later in life. These tests can be helpful to people who have a family member with a genetic disorder, but who have no symptoms of the disorder themselves at the time of testing (BRCA1/2).

29. 92 Breast, dx 45, d. 89 86 Noncarrier Ovary, dx 59 d. 62 Breast, dx 59 73 68 71 BRCA1-mutation carrier Affected with cancer Breast, dx 36 36 BRCA1-Linked Hereditary Breast and Ovarian Cancer ASCO

30. Beth (27) Diana (32) Cindy, 39 Risk Assessment Models Breast cancer at 69 y Risk(%) 19 39 7 Model Gail Claus Normal person First menstrual period: 15 y Prior biopsy: 0 Atypical hyperplasia: Unknown First live birth: No birth Predicted possibility of BRCA1 mutation=8.5% (Couch Model) ASCO

31. Tumor suppressor gene on chromosome 17 • Autosomal dominant transmission • Protein has role in genomic stability • >1,200 different mutations reported Nonsense Missense Splice-site ASCO Breast Cancer Information Core BRCA1

32. Tumor suppressor gene on chromosome 13 • Autosomal dominant transmission • Protein has role in genomic stability • >1,200 different mutations reported Nonsense Missense Splice-site BRCA2 ASCO Breast Cancer Information Core

33. Forensic/Identity Testing • Forensic/identity testing uses DNA sequences to identify an individual for legal purposes.  • Can identify crime or catastrophe victims, rule out or implicate a crime suspect, or establish biological relationships between people (for example, paternity).

34. Testing for Phamacogenomics • A type of genetic testing that determines the influence of genetic variation on drug response.

35. ChromosomeNomenclature &Banding Patterns

36. GeneHuman DiseaseFunction APC Colon cancer Interacts with catenins DCC Colon cancer CAM domains E-cadherin Breast cancer Intracellularly interacts (CDH1) with catenins DPC4 Pancreatic cancer TGF--related signaling BRCA1 Mammary cancer/ DNA damage repair, Ovarian cancer checkpoint control, apoptosis BRCA2Mammary cancer DNA damage repair, genomic stability ATM Ataxia-telangiectasia DNA damage response mutated gene upstream in p53 pathway P53 Mutated in >50% Transcription factor, tumors checkpoint control, apoptosis Tumor Suppressor Genes

37. Coda