Molecular Diagnostics Lecture 1 (1) PDF

Molecular Diagnostics 4TH YEAR STUDENTS BIOTECHNOLOGY PROGRAM  BIOT 401 – Molecular Diagnostics Applied Biotechnology Program u Lectures: 2 hrs/ week…………50 marks u Practical: 2hrs/ week…………45 marks u Mid term exam + others………50 marks u Oral exam………………...….....5 marks...

Molecular Diagnostics 4TH YEAR STUDENTS BIOTECHNOLOGY PROGRAM  BIOT 401 – Molecular Diagnostics Applied Biotechnology Program u Lectures: 2 hrs/ week…………50 marks u Practical: 2hrs/ week…………45 marks u Mid term exam + others………50 marks u Oral exam………………...….....5 marks 150 marks  Overall aim of the course u Distinguish the molecular diagnostic techniques used to detect microorganisms, inherited diseases, DNA polymorphisms, mutations, neoplastic process and DNA- based tissue typing. u Outline the modern molecular diagnostic technologies and the concepts that underpin molecular testing in human diseases. u Learn the principles and main steps of clinical molecular diagnostics.  References Molecular diagnostics: Anthony Warford and Nadège Presneau (2019). Molecular diagnostics: George P. Patrinos, 3rd edition (2017). Genetic Testing  What is genetic testing? uType of medical test that identifies changes in genes, chromosomes, or proteins.  Types of genetic testing 1. Cytogenetic Testing 2. Biochemical Testing 3. Molecular Testing 1. Cytogenetic Testing u It involves the examination of whole chromosomes for abnormalities. u White blood cells, specifically T lymphocytes, are the most readily accessible cells for cytogenetic analysis. Cells from other tissues such as bone marrow (for leukemia), amniotic fluid (prenatal diagnosis), and other tissue biopsies can also be cultured for cytogenetic analysis. 2. Biochemical Testing u Several classes of proteins exist to fulfill the multiple functions, such as enzymes, transporters, structural proteins, regulatory proteins, receptors, and hormones. A mutation in any type of protein can result in disease. Types of Protein Changes Resulting in Altered Function No protein made Too much or too little protein made Misfolded protein made Altered active site or other critical region Incorrectly modified protein Incorrectly localized protein (buildup of protein) Incorrectly assembled protein Clinical testing for a biochemical disease utilizes techniques that examine the protein activity (enzymes), level of metabolites (indirect measurement of protein activity), and the size or quantity of protein (structural proteins) These tests require a tissue sample in which the protein is present, typically blood, urine, amniotic fluid, or cerebrospinal fluid. Because proteins are more unstable than DNA and can degrade quickly, the sample must be collected and stored properly and shipped promptly according to the laboratory’s specifications. 3. Molecular Testing u For small DNA mutations. u It can be performed on any tissue sample and require very small amounts of sample. u For some genetic diseases, many different mutations can occur in the same gene and result in the disease, making molecular testing challenging.  Molecular testing Ø It looks for changes in one or more genes. Ø DNA sequencing Ø These tests can vary in scope: Targeted single variant Single gene Gene Panel Whole exome sequencing Targeted single variant u It looks for a specific variant in one gene. u The selected variant is known to cause a disorder (for example, the specific variant in the HBB gene that causes sickle cell disease). u This type of test is often used to test family members of someone who is known to have a particular variant, to determine whether they have a familial condition. Single gene u It look for any genetic changes in one gene. u These tests are typically used to confirm (or rule out) a specific diagnosis, particularly when there are many variants in the gene that can cause the suspected condition. Gene panel u Panel tests look for variants in more than one gene. u It is often used to pinpoint a diagnosis when a person has symptoms that may fit a wide array of conditions, or when the suspected condition can be caused by variants in many genes. E.g., there are hundreds of genetic causes of epilepsy. Whole exome (genome) sequencing u Analyze the bulk of an individual’s DNA to find genetic variations. u Typically used when single gene or panel testing has not provided a diagnosis, or when the suspected condition or genetic cause is unclear. u It is often more cost- and time-effective than performing multiple single gene or panel tests.  Uses of genetic testing u Newborn screening u Diagnostic testing u Carrier testing u Prenatal testing u Preimplantation testing u Predictive and presymptomatic testing u Forensic testing  Benefits of genetic testing u Genetic testing has potential benefits whether the results are positive or negative for a gene mutation. u A negative result can eliminate the need for unnecessary checkups and screening tests in some cases. u A positive result can direct a person toward available prevention, monitoring, and treatment options. u Some test results can also help people make decisions about having children. u Newborn screening can identify genetic disorders early in life so treatment can be started as early as possible.  Results of genetic testing u Genetic testing should be valid and useful. u A genetic test is valid if it provides an accurate result. u Two main measures of accuracy apply to genetic tests: analytical validity and clinical validity. u Analytical validity refers to how well the test predicts the presence or absence of a particular gene or genetic change. i.e., can the test accurately detect whether a specific genetic variant is present or absent? u Clinical validity refers to how well the genetic variant being analyzed is related to the presence, absence, or risk of a specific disease.  Results of genetic testing u Another measure of the quality of a genetic test is its usefulness, or clinical utility. u Clinical utility refers to whether the test can provide helpful information about diagnosis, treatment, management, or prevention of a disease. u Genetic tests should be specific and sensitive