Genomics and Proteomics

Molecular Diagnostics

• Molecular diagnostics covers molecular science, techniques, lab operations, and testing applications.
• It is a lab method using tissue, blood, or fluid samples to check for genes, proteins, or molecules indicating disease, like cancer.
• Molecular testing analyzes biological genome and proteome markers, applying molecular biology to medical testing.
• It identifies genetic information sections linked to specific diseases, such as cancer, for accurate patient diagnoses.
• A DNA or RNA sequencing test identifies markers for potential future diseases.
• Molecular diagnostic areas cover infectious diseases, hematopathology, genetics, and solid tumors.
• Tests can determine an individual's resistance to specific drugs.
• Consumer-facing diagnostic tests, like mail-order genetic DNA kits, provide DNA analysis from saliva samples.
• However, according to John Greg Howe, PhD, at Yale, at-home kits lack the detail of places like the Yale Center for Genomic Analysis.
• It is also referred to as MOLECULAR PATHOLOGY and involves analyzing DNA or RNA for red flags signaling the potential of a disease.
• The field has grown rapidly.
• Despite progress since Hippocrates era, the emergence of COVID-19 is notable.
• Precise diagnostic tools are crucial in managing and understanding disease epidemiology as the COVID-19 pandemic evolves.
• Molecular tests have multiple applications in clinical oncology.
• Molecular diagnostic tests have expanded from a few in laboratory medicine departments to most pathology areas since 1992.
• NAAT stands for Nucleic Acid Amplification Test.

Common Molecular Diagnostic Tests

• Tests determine if patients have a gene mutation linked to a specific disease, whether inherited or acquired.
• Inherited diseases can be tested for during prenatal, newborn, and adult stages of life.
• Cystic Fibrosis (CF) is an example of a commonly inherited disease.
• Newborns with two CF-related gene mutations are likely to have the condition.
• Treatment can prolong the life of a child with the disease.
• Molecular tests can be done for common inherited hereditary cancers, such as checking for BRCA1 and BRCA2 gene mutations in breast cancer, which increase the risk.
• Acquired gene mutations are tested for in cases like chronic myeloid leukemia (CML).

Cystic Fibrosis

• Cystic Fibrosis is an inherited condition causing sticky mucus buildup in the lungs and digestive system, leading to frequent infections or breathing difficulties.

Next-Generation Sequencing

• Genome sequencing refers to understanding the order of approximately 3 billion nucleotides in a genome making up a person's complete DNA.
• Following the first sequencing of the human genome, an explosion in DNA sequencing innovation occurred.
• This innovation has spurred the development of next-generation sequencing and more efficient sequencing methods.
• DNA sequencing refers to lab techniques determining the exact nucleotide sequence.

Future of Molecular Diagnostics

• The field is in the early stages of understanding how DNA sequence changes indicate disease and their causes.
• There is more need to figure out how to utilize and apply vast information.
• Research scientists are focusing on understanding various diseases more deeply, by using vast amount of information.

Areas of Molecular Diagnostics

• Infectious Diseases – Microbiology and Virology
• Hematopathology – Hematology, Microbiology, and Clinical microscopy
• Genetics
• Solid Tumor

Notes

• In cancer medicine molecular diagnostic assays are commonly used because:
  • They are routinely used for personal diagnoses
  • They are for personalization
  • and for predictive tests

Genome

• It is a complete genetic information set in an organism, providing all information the organism requires to function

Deoxyribonucleic Acid (DNA)

• DNA carries genetic information for an organism's development and function.
• It resides in the nucleus or nuclei of cells.
• It is made of coiling strands twisting to resemble a double helix.
• DNA bases pair up: Adenine with Thymine, and Cytosine with Guanine.
• Each base is attached to a sugar molecule and phosphate molecule, forming the sugar-phosphate backbone.

Genetic Disorders

• Albinism:
  • Inherited condition causing very light skin, hair, and eyes.
  • It is due to less melanin and a lack of melanocytes, resulting in white hair and blue eyes.
• Down Syndrome:
  • Genetic condition from an extra chromosome.
  • It affects body and brain development.
  • Known as Trisomy 21.

Genes

• Contains info to make protein product
• Other genes code for RNA products
• Is set of DNA or genetic information

Genome

• Overall collection of genetic content of a cell

Genomics

• Study of genomes

Nucleic Acids

• They are Large biomolecules that play essential roles in all cells and viruses
• They involve storage and expression of genomic information

Nucleosides

• Nitrogen base bound to unphosphorylated sugar
• Is a two-subunit molecule in which a pentose sugar is bonded to a nitrogen-containing heterocyclic base
• Adenosine (A), guanosine (G), cytidine (C), and thymidine (T) are nucleosides.
• Hereditary component of all living cells

Nucleotides

• If the ribose sugar is phosphorylated, the molecule is a nucleoside mono-, di-, or triphophosphate or a nucleotide.
• For example, adenosine with one phosphate is adenosine monophosphate (AMP).
• Adenosine with three phosphates is adenosine triphosphate (ATP).
• Nucleotides can be converted to nucleosides through Hydrolysis. If Hydrolysis = Tinatanggalan ng tubig

Differences In Nucleoside and Nucleotides

• Nucleosides = Unphosphorylated
• Nucleotides = Phosphorylated

Pyrimidine

• Cytosine
• Thymine
• Uracil

Purine

• Adenine
• Guanine

Types of Nucleic Acids

• DNA
• RNA

Deoxyribonucleic Acid (DNA)

• A nucleotide polymer in which of the monomers contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine.
• This double helical structure of DNA was first described by James Watson and Francis Crick.
• The genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals.
• It is found in the nucleus of eukaryotes and in the chloroplasts and mitochondria.
• Sugar = Deoxyribose

Notes on DNA

• In Prokaryotes, Nucleoid and cytoplasm contains the DNA, DNA is free flowing since there is now envelope
• In Eukaryotes, Complex Historian Portion = Chromatin

Recombination

• Occurs through the molecular process of crossing over or physical exchange between molecules.
• A recombinant molecule or organism is one that holds a new combination of DNA sequences.
• "Nasisira DNA to produce new combination"

Conjugation

Bacteria that participate in conjugation are of two types, or sexes, termed F+ and F- For conjugation to occur, F+ and F- cells must be in contact with each other. Duplex DNA Double Stranded DNA dsDNA ssDNA

Ribonucleic Acid (RNA)

• It differs from DNA in the sugar moieties, having ribose instead of deoxyribose and, in one nitrogen base component, having uracil instead of thymine
• A nucleic acid present in all living cells that has structural similarities to DNA.

Building Blocks of RNA

• Adenine = AMP
• Guanine = GMP
• Cytosine = CMP
• Uracil = UMP

Primase

• A ribonucleic acid (RNA) synthesizing enzyme that lays down short RNA primers required for priming DNA synthesis.
• It must work repeatedly on the lagging strand to prime synthesis of each Okazaki fragment.
• Its is enzyme (6-11 Base Pairs)

Types or Structure of RNA

• Ribosomal RNA = rRNA is an important structural and functional part of the ribosomes, cellular organelles where proteins are synthesized

1. The largest components of cellular RNA
2. One of the most important

• Messenger RNA = mRNA is the initial connection between the information stored in DNA and the translation apparatus that will ultimately produce the protein products responsible for the phenotype dictated by the chromosome.

1. Carries the genetic information to start protein synthesis

• Transfer RNA

Transcription

• Transfer amino acids to match the correct mRNA codon and carries amino acid to ribosome
• The copying of one strand of DNA into RNA by a process similar to that of DNA replication.
• the nucleolus; is the location of ribosomal RNA synthesis
• the polymerization of RNA from a DNA template is catalyzed by RNA polymerase.

Translation

• is the process through which information encoded in mRNA directs the addition of amino acids during protein synthesis

Quality Management System (QMS)

• Defines and establishes an organization's quality policy and objectives -- Note: Quality: Katangian ng specimen to give precise results
• ISO (International Organization for Standardization) [French: Organisation Internationale de Normalisation] -- International standards ensure that the products and services you use daily are safe, reliable, and of high quality. -- Known for its Global standards for trusted goods and services -- Iso Slogan: "MAking lives easier, safer, and better." -- Main goal: --- Helps healthcare workers to give accurate and precise results to patients ---Ensurers that products are safe, reliable, and quality

Three Elements of a Quality Assurance Program

• the directors' qualifications
• on-site laboratory inspection
• interlaboratory comparison and proficiency testing.

Clinical & Laboratory Standards Institute (CLSI)

• An international, interdisciplinary, nonprofit, standards developing, and educational organization that promotes the development and use of voluntary consensus standards and guidelines within the health care community. -- Consensus ---General agreement = unanimity
• Recognized worldwide for the application of unique consensus process in the development of standards and guidelines for patient testing and related health care issues.

###Contamination- Data Accuracy

• It’s important to examine if contamination introduces foreign genetic material into samples, resulting to incorrect and unreliable results.

###Contamination Consideration-Contamination in Nucleic Acid Testing

• Data Accuracy and Reliability
• Contamination can introduce foreign genetic material into samples, leading to inaccurate and unreliable results. Common contaminants: RNAse

Avoiding False Positives and False Negatives

• Contamination can result in false positive or false negative results, leading to incorrect interpretations.

###Ethical Considerations: -Contamination can introduce unintended genetic material into samples, potentially leading to ethical concerns. -For research involving human samples or genetically modified organisms, contamination can result in unintended consequences or misinterpretation of results.

Notes

• Ethical - Right and wrong of conduct

Contamination. . .

• Is the process of making something dirty or poisionous

Explore genomics, the study of genomes, and proteomics, the study of proteins. Understand their roles in molecular diagnostics, DNA sequencing, and personalized medicine, including cancer treatment. Learn about DNA structure, quality assurance, and in vivo testing.