Polygenic Risk Scores & Disease Prediction

• Genetic Markers in Disease
• Lecture 9 of COM5081, Fundamentals of Pathology
• Kelsey Reindel, D.O., Assistant Professor, Family Medicine & OPP, Dr. Kiran Patel College of Osteopathic Medicine, Nova Southeastern University.

Genes

• Genes provide the cell with instructions for making a specific protein, which carries out a particular function in the body.
• Humans share the same genes, arranged in roughly the same order.
• More than 99.9% of one person's DNA sequence is identical to any other human.

Genetic Differences

• A human gene may vary by 1-3 nucleotides (letters) from person to person.
• Nucleotide differences can change a protein's shape/function, amount made, when made, or where made.
• Affect traits like eye, hair, and skin color.
• Variations in the genome influence disease risk and medication responses.

DNA

• DNA letters are nucleotides (3.5 billion in humans) of four kinds: A, T, G, and C.
• The order determines genetic information.
• A gene is a DNA fragment that contains thousands to millions of these letters.
• A mutated gene differs from the normal version by one or two letters and can cause a genetic disease.

Genome

• A genome is the entire genetic material of an organism.
• Sequencing a genome means reading the succession of all its letters.

The Human Genome Project (HGP)

• Launched in October 1990.
• April 2003- generating the first sequence of the human genome.
• It accelerated the study of human biology and improved medicine.

HGP milestone announcements

• June 2000: The International Human Genome Sequencing Consortium produced a draft human genome sequence that accounted for 90% of the human genome.
• April 2003: The consortium generated an essentially complete human genome sequence, accounting for 92% and improved from the draft sequence.
• March 2022: The Telomere-to-Telomere (T2T) consortium filled the remaining gaps and produced the first truly complete human genome sequence.

Genetic Variants

• Genetic variants are changes in the DNA sequence that can occur in both coding and non-coding regions.
• Genetic variants include:
  • Single Nucleotide Polymorphisms/Variations (SNP/SNV)
  • Insertions and Deletions (Indels)
  • Copy Number Variations
  • Translocations and Inversions
• Harmful variants can result in damaged, extra, or no protein, with health consequences.

Genetic Disorders

• A genetic disorder is a disease caused by a change in the DNA sequence away from the normal sequence.
• Genetic mutations can be inherited or occur spontaneously.
• Acquired mutations can occur during a person's life.

Types of Genetic Disorders

• Chromosomal: Missing or duplicated chromosome material.
  • Includes conditions like Down Syndrome, Turner Syndrome, Klinefelter Syndrome, Trisomy 18, and Trisomy 13.
• Complex (Multifactorial): Mutations in multiple genes, gene mutations combined with environmental factors, or chromosome damage.
  • Includes Cancers, Diabetes, CAD, Autism Spectrum Disorder, and Alzheimer's Disease.
• Single-Gene (Monogenic): A single gene mutation.
  • Includes CF, DMD, Congenital Deafness, Hemochromatosis, NF1, Sickle Cell Disease, and Tay-Sachs Disease.
• The passing of genetic variants explains why diseases run in families.

Genetic Markers

• Genetic markers are variants in the DNA at a known location on a chromosome, associated with a specific disease phenotype.
• Markers that confer a high probability of disease are useful as diagnostic tools or predictors of prognosis or response to therapy.
• Single nucleotide polymorphisms (SNPs) have been a focus as potential genetic markers, occurring frequently in the human genome and are easy to genotype.

Genetic Testing

• Genetic tests have been developed for thousands of diseases.
• Most tests look at single genes and are used to diagnose rare genetic disorders.
• Tests are being developed to look at multiple genes that may increase or decrease a personal risk of common diseases, such as cancer or diabetes.
• Such tests and other applications of genomic technologies have the potential to help prevent common diseases and improve the health of individuals and populations.

Types of Genetic Testing

• FISH
  • Used to find small deletions or duplications in chromosomes.
  • Recommended for suspected genetic syndromes, aneuploidy, and sex chromosomes.
  • Limitations include being limited to the specific disease or chromosome being studied and inability to detect point mutations.
• $300-$350.
• Karyotype
  • Used to examine chromosome structure.
  • Recommended to rule out chromosomal abnormalities, including aneuploidy, larger deletions/duplications, and translocations.
  • Limited to detecting small deletions, duplications or single-gene diseases
  • $600-$1,200
• Chromosomal Microarray
  • Used to quantify individual's amount of genetic material.
  • Recommended to identify causes of autism, developmental delay, intellectual disability, and abnormal prenatal ultrasound findings.
  • Cannot detect balanced chromosomal rearrangements; Also has a 5% of uncertain results.
• Targeted mutation analysis
  • Used to examine a single gene for mutations.
  • Used when a specific familial mutation is known that is more commonly seen.
  • Limited if there are multiple specimens to be tested.
  • $250 - $600

Gene Sequencing (1st-3rd Generation)

• Large investment have been made in improving DNA sequencing making them; cheaper, faster, and more accurate. The following terms are used to distinguish the sequencing methodologies.
• There are 3 main types of methodologies that exist in gene sequencing. 1. Sanger Sequencing/1st Generation, 2. Next Generation Sequencing/2nd Generation, 3. Third Generation Sequencing***

Types of Genetic Testing(cont.)

• Sanger Sequencing/Single Gene Sequencing

  • Used to examine single gene's entire sequence.
  • Used for suspecting a specific genetic syndrome.
  • Has risks of both uncertain results, and not being able to detect deletions or duplications.

• Next Generation Sequencing/Multiple Gene Sequencing Panel

  • Used to examine the sequence of several genes. -Used for when there are several genes that cause similar symptoms .
  • Has risks of both uncertain results, and not being able to detect deletions or duplications.
  • $2,000 - $6,000

• Whole Exome Sequencing

  • DNA sequencing of all the exons, coding within all of the genes.
  • Used in patients with a underlining genetic cause for their symptoms, typically when other gentic testing has not identified the symptoms. -Results in large amount of possibly uncertain results.
  • Results could show patients also have multiple different types of genetic diseases that are potentially not related to the initial test.

• Whole Genome Sequencing -DNA sequencing of a individuals entire genome (coding and non-coding regions)

  • Used in patients with a underlining genetic cause for their symptoms, typically when other gentic testing has not identified the symptoms. Is also used purely for research purposes. Results in large amount of possibly uncertain results.
  • Results could show patients also have multiple different types of genetic diseases that are potentially not related to the initial test.

Sanger Sequencing

• It was developed by Dr. Frederick Sanger which has existed for over 40 years
• It has the ability to sequence short DNA regions (~300-1000bp's) of interest -This method is the highest standard method of sequencing existing due to its high accuracy -The designing of primers for chromosomes is not viable for high throughput, large sequencing projects.

Single Gene Sequencing-Sanger

• Good for monogenic diseases( caused by defects in one disease).
• For more common diseases, identifying genetic markers has become more difficult due to most common diseases being polygenic.

Next Generation Sequencing/2nd Generation

• First discovered in 2000 by the companies which would later become known as illumina.
• Whole genomes can be sequenced in less time then ever .
• Genome, exome, transcriptomics and proteomics tolls give researchers insights into all level biology.

Next Gen. cont...

• NGS is used to find a library within chromosomes 1-22,X/Y , after DNA is extracted and cut the NGS "matches" the amplified bp segments.

Exome Sequencing

• It represents 1.5 to 2.0 percent of the genome.
• Over 85% of known disease-causing mutations are found in exons.
• Not testing the introns in dna testing is main disadvantage.

Whole Genome Sequencing

• Is costlier due to the whole genome being roughly 3.3 x 109 bases.
• Whole genome sequencing may become preferable due to more information about the role of non-coding DNA.

Targeted Gene Panels

• It offers sequence data for a limited subset of genes( Typically 10 to 200 genes).
• Appropriate to sequence many genes for proper diagnosis
• May be beneficial to genome/exome sequencing, but more costly.
• Is now available for cancers, lung disease,inherited cancer syndromes and other disorders.

Accuracy

• Sanger sequencing remains the gold standard ( >99.99 % accuracy).
• Clinical laboratories are starting to challenge the necessity of using Sanger sequencing.

Genetic Markers in Cancer Screening and Management

• Are increasing especially for people where more than one genetic variant is responsible.
• Panel approaches are becoming more efficient and cost effective with NGS technology getting increasing indications for genetic testing.

Breast Cancer and Genetic Testing.

• Breast cancer is the second most common in women, and each year roughly 200, 000 diagnosis of breast cancer is discovered.
• Starting at 40, it is typically recommended to have annual screening mammograms.
• The HCP will consider personal facts, family history, genetic background and/or any factors to consider in a high risk.

Genetic Testing Information and Guide Treatment in Breast Cancer.

• A healthcare provider may recommend you to have a mastectomy instead of a lumpectomy.
• Consider contralateral (opposite side) prophylactic mastectomy if you have: BRCA1, BRCA2, CDH1, PALB2, PTEN, STK11, TP53
• Genetic testing is also leading to treatments that are more productive and help reduce chance of relapse or any drug resistance.

Examples of Effective Ways of Genetic Testing:

• PARP : an enzyme that repairs damage of DNA

• PARP Inhibitors: Prevent Cancer cell mutations from repairing the damaged DNA

• BRCA1/2 : causes people be more depedant on PARP in repairing tumors by therapy/ chemotherapy

• Treatment of HER2- neagtitive early breast cancer is performed by those in the BRCA1/2(BRCA1/2) inherited gene mutations.

• HER2 (HUMAN EPIDERMAL GROWHT FACTOR 2): provides cell with proliferative and anti-apoptotic signals

• Knowing the tumors helps it to make the cancer more treatable and allows a more targeted approach.

• Hormone Therapy:

Oncotype DX

• Test on tumor samples with 21 genes
• Oncotype dx is the most common tumor pofiling in US
• Help to inform decisions about what will be help best regarding chemo and other cancers.
• Cancer /reference genes from studies: Estrogen, Inavasion, Reference,Her2
• Low risks : 18
• In Risky :> to 18 and !0.34 * ER Group score + 0.47 * HER2 Group Score +1.04 * Proliferation Group score + 0.10* Invasion Group Score.
• Invasions in regards to genes can trigger cancer.
• Cathepsin L2 and Stromoslysin3 may lead to tumors.

Ovarian Cancer

• Is most popular from unknown events, genetic is one in 6
• Genetics include BRCA 1 and BRCA2
• With gene mutation in Ovrian help determine treatment plans.

Prostate Cancer:

• prostate cancer is the most common in males, typically due to high age ethnicity inherited genetic factors
• testing is used to fine mutations: BRCA1, BRCA2, ATM, CHEK2, MLH1, MSH2, MSH6, PALB2, PMS2, and others. Some mutations can put you at risk for more than one type of cancer.

Markers include

• BRCA2-high risk of prostate cancer
• NCCN : for anyone with a high risk screening as early as age 40 to find at a lethal state before 65 years old.

Genetic Testing Info. (Prostate Cancers)

• the BRCA2 of gene can provide the basis for future treatment.
• NCCN Guidelines recommends (Biopsy, PSA (High levels))

Colorectal Cancer

• The factors of: Sporadic, Familial, Inherited, and the mode of presentation affect presentation.
• sporadic- No family history roughly over 70%
• Familly- 25% of cases, patient has history but not consistant and not heridity syndrome explained
• There are diseases with polyposis that cause the inherited factor include: - familial adenomatous polyposis (FAP), MUTYH-associated polyposis (MAP), and the hamartomatous polyposis syndromes (eg, Peutz-Jeghers, juvenile polyposis). Also here hereditary nonpolyposis CRC (HNPCC; Lynch syndrome).

Biomarker Testing in CRC

• It includes a type of cancer called the Lynch Syndrome caused caused by inherited mutations. -This is called a micro satellite Instability Recommendations: MLH1, MSH2, MSH6, PMS2, and EPCAM and testing for MMR gene mutations

Biomarker Testing

• RAS mutated in approx 40 percent of CRC cases.

Update for testing

• Drug use and addiction is a huge public health crisis that 40- 60% result form genetic.
• 19 significant SNP's significantly associated with the general addiction risk

Explore polygenic risk scores, their data sources, and advantages in disease risk assessment. Understand how they combine with other risk factors and their role in clinical practice. Learn about the implications of 'DNA is not your destiny'.