Genomics in Healthcare

Genomics in Healthcare

• Personalized and precision medicine involves tailoring medical treatments to an individual's unique genomic information.
• Key terms include: Cytogenetics, Genomics, Epigenomics, Transcriptomics, Proteomics, Pharmacogenomics, Metabolomics, Microbiomics
• The reasons for requesting genetic testing need to be explained.
• Genetic counselors play a key role in the genetic testing process.
• Cytogenetic testing methods include Karyotyping, SKY, and FISH.
• Recognize common abbreviations and nomenclature used for chromosomal alterations.
• Single Nucleotide Polymorphism (SNP) genotyping is important in personalized medicine.
• Genome Wide Association Studies (GWAS) aim to find genes associated with diseases.
• Microarray comparative genomic hybridization (array CGH) explains copy number variations.
• It's important to understand the similarities and differences between whole genome, exome, and targeted next-generation sequencing.
• Microsatellite Polymorphisms or Short Tandem Repeats (STRs) are important in forensics.
• Biomarkers, specifically diagnostic, predictive, and prognostic ones, are important to define and to describe.
• Gene therapy and types of diseases being treated with gene therapy need definition.
• Understanding CRISPR-Cas and its importance in gene editing is crucial.
• CRISPR is used in gene therapy to treat sickle cell disease.

Genomic Medicine

• Emerging medical care that uses an individual’s genomic information in disease prevention and clinical care.
• Precision medicine and personalized medicine, are synonyms

Genetic and Multiomics Testing Overview

• Testing can be done at the DNA, RNA, and protein levels.
• DNA relates to cytogenetics, genomics, and epigenomics.
• RNA relates to transcriptomics (RNA sequencing, microarray, and gene expression).
• Protein relates to proteomics and protein function, as well as antibody production.

Indications for Genetic Testing

• Genetic testing and chromosomal analysis are requested for advanced maternal age in pregnancy.
• Testing also indicated in cases of developmental delay, intellectual disability, and multiple congenital abnormalities in a child or infant.
• Dysmorphic features in an infant or recurrent miscarriages are further indications for genetic testing.
• Infertility, delayed puberty, and biochemical abnormalities might warrant genetic testing.
• Genetic testing can play a role in diagnosis and management of cancer such as leukemia, lymphoma, or solid tumors.

Genetic Counseling

• Genetic counselors or maternal-fetal care specialists can provide information about how a possible genetic condition might influence their family
• The counselor will discuss personal and family history to estimate the risk of a genetic condition.
• Genetic testing is often recommended as part of the counseling process.
• Results from genetic tests are available with counseling, aiding in the interpretation of results and identifying possible interventions and next steps.

Cytogenetics in Detail

• Cytogenetics involves the study of chromosomes and their abnormalities.
• Karyotyping is a method to identify chromosomal banding patterns
• Karyotyping has the lowest resolution, limited to alterations of >4-6 million base pairs.
• Flow Cytometry sorts chromosomes by size and shape.
• Fluorescence in situ hybridization (FISH) has higher resolution, while Spectral karyotyping (SKY) detects spectral changes.
• In Karyotyping, chromosomes get aligned by length, arm ratio, and banding patterns.
• This process allows for the detection of gross chromosomal changes.

Cytogenetic Nomenclature

• cen = centromere
• Single colon (:) represents a break.
• Double colon represents a break and following reunion.
• comma (,) separates chromosome numbers.
• del = deletion
• dup = duplication
• inv = inversion
• ins = insertion
• mat = maternal origin
• minus (-) sign = loss of a chromosome.
• mos = mosaic
• p = short arm
• pat = paternal origin
• plus (+) sign = gain of a chromosome.
• q = long arm
• rcp = reciprocal
• rob = Robertsonian translocation
• slash (/) separates cell lines or clones.
• semicolon (;) separates chromosomes and breakpoints in rearrangements involving more than one chromosome.
• t = translocation
• upd = uniparental disomy
• 48,XX,+18+21 signifies a female with both trisomy 18 and trisomy 21.
• 46,XY,t(9;22)(q34;q11.2) involves A break and reunion at bands 9q34 and 22q11.2, as seen in CML.
• 46,XX,t(3;8)(p10;p10) signifies reciprocal balanced translocation between chromosomes 3 and 8 at bands p10.
• 45,XX,rob(13;14)(q10;q10) signifies Robertsonian translocation involving chromosomes 13 and 14 at bands q10.
• 46,XY,upd(15)pat signifies uniparental disomy of chromosome 15 of paternal origin

Fluorescence In Situ Hybridization (FISH)

• This is a technique used for detecting chromosomal copy number changes.
• FISH can detect amplifications, deletions, and translocations.

Spectral Karyotyping (SKY)

• Spectral karyotyping is a process also refered to painting
• It is usefull to compare normal tissue karyotypes to cancer tissue karyotypes

Polymorphism and SNPs

• Polymorphism in a population represents a genetic change in two or more alleles with a gene frequency >0.01.
• Single Nucleotide Polymorphisms (SNPs) are single-base pair differences at specific positions in the genome
• SNP frequency is <0.01, classifying it as a single nucleotide variant (SNV).

Genome-Wide Association Studies (GWAS)

• GWAS studies the relationship between genotype and phenotype in a population.
• GWAS identifies multiple gene loci with an effect as risk factors for diseases.

Epigenomics

• Epigenomics studies epigenetic modifications to the DNA of a cell.
• Epigenetic changes occur during development and throughout one's lifespan in response to endogenous and environmental factors.
• Epigenetic regulation of genes controls whether genes are transcribed.

Transcriptomics

• Transcriptomics examines all RNA molecules in a cell, comprising the transcriptome.
• The transcriptome is dynamic and can change as development occurs and in response to endogenous and exogenous factors.

Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR)

• Used for gene expression
• Used for validation of RNA sequence

Proteomics

• This includes the quantitative expression analysis of all proteins or some proteins under specific conditions.
• Mass Spectrometry is a tool often used for proteomic studies

Pharmacogenomics

• This is a field of precision medicine.
• Genetic polymorphisms may influence drug effectiviness.
• Expression of drug receptors, drug uptake, drug breakdown may be influenced by genetics, for certain drugs.
• Polymorphisms for the Cytochrome P450 CYP2D6 gene, may result in reduced metabolism of 25% of clinical drugs.
• Certain alleles of the CYP3A gene, are responsible for metabolizing cholesterol medications, and decreased gene function.

Cancer Pharmacogenomics

• Breast cancer tumors positive for Estrogen Receptor (ER+) can be treated effectively with hormone therapy, like tamoxifen.

Other Omics

• Metabolomics studies the entire range of unique metabolites present in an organism.
• Microbiomics studies the microbiome in a specific environment.
  • The gut microbiome involves trillions of bacteria, fungi and other microbes playing roles in health.
  • The mouth microbiome can contribute to tooth carries, circulatory problems, and type 2 diabetes.

Biomarkers

• Biomarkers objectively measure indicators of normal or pathological biological processes.
• Measurable and reproducible
• Can be early warning systems
• Genes, proteins, or other substances that can be tested to reveal details about cancer.

Prognostic Biomarkers

• Indicate the likelihood of disease recurrence or progression.
• Prostate Specific Antigen (PSA)

Diagnostic Biomarkers

• Detect or confirm the presence of a disease.
• A1C

Susceptibility Biomarkers

• Indicate the possibility of developing a disease for a healthy individual.
• Prostate Specific Antigen (PSA)

Diagnostic Testing for Head, Neck, and Oral Cancers

• Physical exam, removal of tissue (biopsy), and imaging.
• Commercial testing panels?
• NeoTYPE Head & Neck Tumor Profile analyzes 34 biomarkers, including NGS.

Ethics of Genetic Testing

• Requires consideration of privacy
• Must make sure genomic is not miss used by insurace companies
• Equal access must be ensured
• Accuracy of tests must be proven
• Complication of incidental findings

Genetic Testing Results

• Can can help make treatment decisions
• Assist in prevention and screening

Gene Therapy

• This involves the transfer of normal genes into cells to replace missing or defective genes.
• Aims to correct genetic disorders or diseases.
  • Benefits: Prevention, treatment, or cure.
  • Risks: Potential cancer, immune reactions, or damage to organs.
  • Challenges: High cost, limited accessibility, and transient effects.
• For Gene Transfer a vector is required, such as viruses.
• Genome Editing needs a vector to transfer components required for editing.

Leber Congenital Amaurosis as Example

• A rare inherited eye condition due to a RPE65 mutation, which can lead to blindness.
• It can be treated via Subretinal injection of the normal RPE65 gene.
• This therapy is approved by the FDA.

Gene Editing with CRISPR-Cas9

• Precise genome editing aims to remove or add DNA sequences.
  • Used to correct mutations, Knock out or knock in genes, and turn on or turn off genes
• This involved modifying genes in cells in the body (in vivo) or collect, treat corrected cells outside the body, and then return (ex vivo)
• CRISPR comes from a genome editing system that uses engineered nucleases.
  • It is found in bacteria acting as an immune system
  • Uses the Streptococcus Pyogenes protien
  • The enzyme Cas9 specializing in cutting DNA, with two active cutting sites, one for each strand of DNA.
• Cas9 has nuclease domains
• Can uses Ruvc of HNH nudeases that ship DNA, but some requires a short shout DNA sequence near the snipping site

Transthyretin (ATTR) Amyloidosis as Example

• Progressive accumulation of misfolded transthyretin (TTR) protein in tissues.
• Includes the nerves and heart.
• Mutation occur in TTR Autosomal dominant
• It is treated via reduceing in-vivo CRISPR
• Aims to reduce misfolded TTR in serum by knocking out the TTR gene

Sickle Cell Disease treatment with Gene Therapy

• Result of inharitance of two mutated HBB genes
• A treatment is to do CRISPR ex-vivo
  • Needs to correct the cells by transfering them
  • Has a low success in gene editting, because it is tough, and off-target effecs are common.
  • High Malignancy, high cost, viral vector needed.