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

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

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

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

5. Genes

6. Chromosome and Gene

7. Gene Structure Transcription and Translation

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

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

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 acidpoint mutationcodonamino 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.blood disorderred blood cellssickle

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 acidpoint mutationcodonamino 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.blood disorderred blood cellssickle

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 transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product.point mutationsequenceDNAstop codontranscribedmRNA  Example Genetic Disease β-Thalassemia – are forms of inherited autosomal recessive blood disorders that originated in the Mediterranean region. In thalassemia, the disease is caused by the weakening and destruction of red blood cells.autosomal recessiveblood disorders Mediterranean region

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 karyotypes for clinical purposes.”chromosomesmetabolitesgenotypes mutationsphenotypeskaryotypes 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. bloodhairskinamniotic fluid

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.fetus 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.human embryosin vitro fertilization

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. ASCO BRCA1-Linked Hereditary Breast and Ovarian Cancer Noncarrier BRCA1-mutation carrier Affected with cancer Breast, dx 45, d. 89 9286 7368 Ovary, dx 59 d. 62 Breast, dx 59 71 Breast, dx 36 36

30. ASCO First menstrual period: 15 y Prior biopsy: 0 Atypical hyperplasia: Unknown First live birth: No birth Risk Assessment Models Beth(27) Cindy, 39 Diana(32) ModelGailClaus Normal person Breast cancer at 69 y Risk (%) 19397 Predicted possibility of BRCA1 mutation=8.5% (Couch Model)

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

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

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. Chromosome Nomenclature & Banding Patterns

36. Tumor Suppressor Genes GeneHuman DiseaseFunction APCColon cancerInteracts with catenins DCCColon cancerCAM domains E-cadherinBreast cancerIntracellularly interacts (CDH1)with catenins DPC4Pancreatic cancerTGF-  -related signaling BRCA1Mammary cancer/DNA damage repair, Ovarian cancercheckpoint control, apoptosis BRCA2Mammary cancerDNA damage repair, genomic stability ATMAtaxia-telangiectasiaDNA damage response mutated geneupstream in p53 pathway P53Mutated in >50%Transcription factor, tumorscheckpoint control, apoptosis

37. Coda