Genes, Mutations and Genetic Testing

Wen Jie Zhang, MD, PhD

School of Medicine, Health Sciences and EngineeringSusquehanna Township High School

Lecture Series Week 6, September 2013

Clinical Relevance of This Week’s Topic

CarcinogenesisEnvironmental Factors Genetic Factors

Physical

Chemical

Biological

(Mutations)

Substitutions

Deletions

Insertions

Lifestyle

Cancer(Carcinogens)

Translocations

ASCO

The Human Genome

23 pairs of chromosomes made of 3 billion base pairs

30%70%

~35,000 genesExtragenic

DNARepetitive

sequencesControl regionsSpacer DNA

between genesFunction mostly

unknown

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

Genes

Chromosome and Gene

Gene StructureTranscription and Translation

Polymorphism

DNA sequence changes that may or may not alter protein function (common definition)

Functional protein Functional protein

ASCO

Disease-Associated Mutations Alter Protein Function

Functional protein Nonfunctional or missing protein

Common MutationsSubstitutions (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.

Missense MutationMissense 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.

A Missense Mutation

Mutations

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.

Nonsense MutationsNonsense 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.

Example Genetic Diseaseβ-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.

Simple Nonsense Mutation

Large Insertion Mutation

Large Deletion Mutation

Chromosomal Translocation

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.”

• 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.

Types of Genetic Testing

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)

Cleft Lip/Palate

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.

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.

Pre-implantation Genetic Diagnosis

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

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).

ASCO

BRCA1-Linked Hereditary Breast and Ovarian Cancer

Noncarrier

BRCA1-mutation carrierAffected with cancer

Breast,dx 45, d. 89

92 86

73 68 Ovary, dx 59d. 62

Breast, dx 59

71

Breast, dx 36

36

ASCO

First menstrual period: 15 yPrior biopsy: 0Atypical hyperplasia: UnknownFirst live birth: No birth

Risk Assessment Models

Beth(27)

Cindy, 39

Diana(32)

ModelGailClausNormal person

Breast cancer at 69 yRisk (%)

19397

Predicted possibility of BRCA1 mutation=8.5% (Couch Model)

BRCA1

ASCO

Tumor suppressor gene on chromosome 17 Autosomal dominant transmission Protein has role in genomic stability >1,200 different mutations reported

Breast Cancer Information Core

Nonsense Missense Splice-site

ASCO

BRCA2

Breast Cancer Information Core

Tumor suppressor gene on chromosome 13 Autosomal dominant transmission Protein has role in genomic stability >1,200 different mutations reported

Nonsense Missense Splice-site

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).

Testing for Phamacogenomics

• A type of genetic testing that determines the influence of genetic variation on drug response.

ChromosomeNomenclature &Banding Patterns

Tumor Suppressor GenesGene Human Disease Function

APC Colon cancer Interacts with cateninsDCC Colon cancer CAM domainsE-cadherin Breast cancer Intracellularly interacts(CDH1) with cateninsDPC4 Pancreatic cancer TGF--related signalingBRCA1 Mammary cancer/ DNA damage repair,

Ovarian cancer checkpoint control, apoptosisBRCA2 Mammary cancer DNA damage repair, genomic

stabilityATM Ataxia-telangiectasia DNA damage response

mutated gene upstream in p53 pathwayP53 Mutated in >50% Transcription factor,

tumors checkpoint control, apoptosis

Coda