DNA is the genetic material that provides instructions for what our bodies look like and how they function. DNA is packaged into structures called

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2 DNA is the genetic material that provides instructions for what our bodies look like and how they function. DNA is packaged into structures called chromosomes. We have 23 pairs of chromosomes (for a total of 46 chromosomes) within each cell of our body. Each chromosome contains many genes, and each gene contains hundreds to thousands of DNA bases (A, T, C, and G), which spell out the code for a unique protein. All of the genetic material contained within the 23 pairs of chromosomes is called the genome.

3 Chromosome Cell T A C G A C G T DNA base Gene DNA (Deoxyribonucleic acid)

4 Our genome can be thought of as a biological biography, or a book about us. Our genome is made up of chromosomes (chapters in the book) which house our genes (sentences in the book) that contain all of the information needed to instruct our body how to grow and function.

5 BOOK GENOME CHAPTERS CHROMOSOMES SENTENCE GENE

6 The DNA bases (A, T, C, and G) that form our genes are arranged in a specific order. Changes in the order of these DNA bases can change the sentences in our book, and likewise may change the function of that gene. This is similar to changing a word in a sentence, which then changes the meaning of the sentence. Example: The gray cat ran down the hall. The gray cat ran down the ball.

7 T A T C G A C G T DNA base Gene DNA (Deoxyribonucleic acid) The gray cat ran down the hall. The gray cat ran down the ball. Changes in DNA might change the way a gene works.

8 Types of genetic variants Changes in the DNA bases of our genome are called genetic mutations or variants. Many types of genetic variants can occur. In a missense variant, one DNA base is substituted for another, changing the meaning of our sentence. In some cases, this change can lead to disease. An insertion variant occurs when an additional DNA base or multiple bases are inserted into our genome where they don t belong. This type of variant changes our sentence in a way that may not make sense. In some cases, this change can lead to disease. In a deletion variant, DNA bases are missing. This type of variant takes away information from our sentence, and therefore the sentence may no longer make sense. In some cases, this change can lead to disease. A duplication variant occurs when a number of DNvA bases appear twice in the genome, one after the other. This is similar to writing the same word twice in our sentence. This type of change leads to a sentence that contains grammatical errors. In some cases, this change can lead to disease. In a nonsense variant, changes in the DNA bases tell the code to stop, prematurely inserting a period into the sentence. This premature ending most often produces a sentence that no longer makes sense. In some cases, this change can lead to disease. Other types of changes, which may or may not cause disease, are known as variants of unknown significance. These variants, or changes in DNA bases, may produce an altered sentence with the same meaning as the original sentence. Example: The gray cat ran down the hall. The grey cat ran down the hall.

9 Types of genetic variants The gray cat ran down the hall. The gray cat ran down the ball. The gray green cat ran down the hall. The gray ran down the hall. The gray cat cat ran down the hall. The gray. Original Missense Insertion Deletion Duplication Nonsense

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11 Genomic technologies

12 Chromosome analysis The structures in each cell of our body that house our genes are called chromosomes. Each chromosome contains millions of DNA base pairs that make up our genes. The individual base pairs cannot be seen by a microscope. However, the larger chromosome structure can be seen under a microscope. One common genetic test that analyzes the larger structure of each chromosome is called a karyotype. A karyotype can show when there are extra or missing chromosomes or pieces of chromosomes. Like a chapter in a book, each chromosome is critical in telling the complete story. When a chromosome is missing, or there is an extra chromosome, the book s story changes. This can lead to genetic disorders such as Down Syndrome where there is an entire extra copy of chromosome 21. In addition to an entire missing or extra chromosome, a karyotype can sometimes reveal when part of a chromosome is missing, or rearranged in a way that does not make sense. Chromosome deletions, or missing parts of the books chapter, can lead to genetic disease. Also, rearrangements in the genetic material contained on the chromosome, similar to mixing up the chapters in a book, can lead to genetic disease. However, not all rearrangements lead to disease.

13 Chromosome analysis million base pairs X Y

14 Microarray One way to test for missing or extra genetic material is through a technology called microarray. DNA microarrays can be used to measure changes at the chromosome level (for example, deletions or duplications that are too small to be seen with a karyotype), or changes at the gene level (variations in single DNA bases - also called single nucleotide polymorphisms or SNPs). Microarrays can be designed to target specific areas of the genome. For example, if we think of the whole genome as a book, a microarray could be designed to proof-read chapter 4 of the book, and report on any spelling or grammar errors, or duplicated or missing words. Florescent probes attached to strands of DNA are used to create different color combinations, indicating how much DNA is present. Because the results of a microarray analysis are too small to be seen even by a standard microscope, a special machine known as a scanner is used to read the results.

15 Microarray Reference DNA Patient DNA Mix equal amounts Deletion (missing DNA) Duplication (extra DNA) Missing patient DNA No missing or extra patient DNA Extra patient DNA

16 Gene panel testing On a gene panel test, many genes from different locations in the genome are evaluated for changes at the same time. Often, the genes on a gene panel test all relate to a single condition or family of similar conditions. For example, a hereditary breast cancer panel test may look at a dozen genes that, when altered, increase the risk for breast cancer.

17 Gene panel testing Variants in any of these genes cause similar disease

18 Whole genome vs. whole exome Whole genome sequencing is the process of reading every single letter in an individual s genetic code (DNA). Whole genome sequencing includes known genes in the genome, as well as all of the DNA surrounding known genes. Whole genome sequencing is like reading a book cover-to-cover. However, only a small portion of the human genome (about 1-2%) actually encodes the proteins that perform all of the body s functions. This portion is referred to as the exome it represents only the coding regions (exons) of the approximately 20,000 genes in the human genome. Exome sequencing is like reading the abstract of a book, where only the most relevant sentences are combined to create a summary.

19 Whole genome vs. whole exome Genome 100% Exome 1-2%

20 Whole genome sequencing vs. whole exome sequencing Genes are divided up into coding and non-coding regions, which are called exons and introns. Only the exons of a gene provide instructions for the body to make a protein. Whole genome sequencing reads every letter of the genetic code, including all introns and exons within genes, and the large spaces of DNA that lie between genes. In whole exome sequencing, only the regions of genes that code for protein (exons) are sequenced.

21 Whole genome sequencing vs. whole exome sequencing Whole Genome Sequencing GENE Exon Intron Exon Intron Exon Intron SEQUENCING AATCGATGGACTAGCAAGTAATTACCGTTCCTAGATCGTA Whole Exome Sequencing GENE Exon Intron Exon Intron Exon Intron Exon Exon Exon SEQUENCING GGACTAGCAAGTAATTACCGT

22 Genomic testing to find cause of rare disease The human genome contains 3 billion base pairs, and each individual carries hundreds of thousands of DNA variants. Most of these variants are silent and do not have any effect on biological function. Many variants code for unique traits between individuals, and are responsible for differences in how our bodies look and function. Only a small handful of variants within each individual may be associated with disease. After performing genome or exome sequencing, it can be very difficult to sort through all the variants identified in an individual and determine which one might be associated with that individual s disease symptoms. It is analogous to looking for a needle in a haystack.

23 Genomic testing to find cause of rare disease

24 Family testing informative Searching for rare, disease-causing genetic variants can be difficult. When only one person in a family has a disease, it can be helpful to perform genetic testing or sequencing in multiple members of the family, to compare the DNA from the sick family member with the DNA of his or her healthy relatives. In this family tree, we see that the sick individual (represented by the color purple) carries a unique genetic variant (mutation) that none of his close relatives have. Therefore, it is possible that the variant he carries is associated with his disease symptoms.

25 Family testing informative

26 Family testing NOT informative However, in this family tree, we see that the sick individual (represented by the color purple) carries a genetic variation (mutation) that some of his healthy relatives also carry. Therefore, in this case, the genetic variation identified in the family is not likely to be the cause of the disease in the sick individual.

27 Family testing NOT informative

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29 Cancer genomics

30 Cancer development Germline DNA represents the genetic code that is present in our germ cells (eggs and sperm). It is the genetic code that we are born with and that we pass on to our children. Most cells in our bodies have DNA that is nearly identical to our germline DNA. However, cancer can develop through the process of accumulated DNA mutations in a single cell. As this cell with acquired DNA mutations divides and multiplies, it continues to accumulate genetic mutations. At some point, the mutations affect the cell and it loses the signal to stop growing and dividing. This leads to unregulated growth of mutated cells, eventually forming cancer (or a tumor). Because tumor cells acquire so many genetic mutations along the way, the sequence of DNA isolated from a person s tumor can be very different from that individual s germline DNA.

31 Cancer development Germline DNA Tumor DNA Tumor Normal cell DNA mutation(s)

32 Genomic testing for targeted therapies Some DNA mutations that lead to cancer also make the cancer cells susceptible to the effects of certain drugs. These drugs are called targeted therapies, because they target the genetic changes in the cancer cells as a way of fighting the cancer. Genomic molecular testing of the cancer tissue (also called tumor profiling) can sometimes reveal targeted therapies that are most likely to kill the cancer cells.

33 Genomic testing for targeted therapies Tumor cell Target drug

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35 Pharmacogenomics

36 Predicting drug response with genomic testing Our genetic make-up helps to determine how our body will respond to and process (metabolize) medications and drugs. How effective a medication will be can be predicted in part by evaluating an individual s genetic variation in metabolism genes. This type of testing and evaluation is called pharmacogenomics. Through pharmacogenomic testing, the predicted individual response to a medication can be lumped into one of four categories. The best scenario is shown in green, when an individual experiences benefit from a drug with no toxicity or side effects this drug is an ideal treatment for this individual. A scenario in which a drug may be avoided is shown in red, when, based on an individual s genetic profile, a drug is expected to be toxic and not have any benefit. Some drugs may be beneficial, but may also have a high risk for side effects (yellow). Many chemotherapy drugs fall into this category.

37 Predicting drug response with genomic testing H TOXICITY Drug TOXIC and NOT beneficial Drug NOT toxic and NOT beneficial Drug TOXIC but beneficial Drug NOT toxic and beneficial L EFFECTIVENESS H

38 Many factors affect drug response There are many factors that affect our response to medications. Some of these are intrinsic, meaning that they are factors that are inherently part of us or controlled by our body. Examples of these are age, gender, race and genetics. Some factors that affect our response to drugs are extrinsic, meaning that they come from outside of our body. Examples of these are diet, nicotine or alcohol use, and other drugs that we take.

39 Many factors affect drug response Extrinsic Drug-drug interactions Smoking Environment Intrinsic Age Gender Race Genetics Organ dysfunction Disease Pregnancy Alcohol use Diet Others

40 Prodrug, ultra metabolizer Drugs can enter the body in different forms. A prodrug enters the body in an inactive form and must be converted to an active form by enzymes in the body (often from the CYP450 family of enzymes in the liver). Some genetic variants can increase or decrease the amount of enzyme the body makes. If an individual has an excess of the enzyme that converts the drug to its active form, the conversion happens more quickly than expected, and he/she is called an ultra metabolizer of that drug. This can cause very high levels of drug circulating through the bloodstream, and may result in an increase in side effects or drug toxicity.

41 Prodrug, ultra metabolizer Enzymes Prodrug X X Enzymes X X Time passing High levels of active drug = risk for toxicity and side effects

42 Prodrug, poor metabolizer On the other hand, if an individual has a genetic variant that decreases the amount of enzyme he/she produces, or completely eliminates this enzyme, that person will be a poor metabolizer of a prodrug. The drug will enter the body in an inactive form, but the body will not produce enough enzyme to convert all of the drug to its active form. The person will end up will low levels of active drug in their system, which may result in reduced effectiveness of the drug.

43 Prodrug, poor metabolizer Prodrug Little to no enzyme Enzymes Time passing Low levels of active drug = less effectiveness

44 Active drug, ultra metabolizer An active drug enters the body in an active form, and must eventually be converted into an inactive form in order to be excreted, or eliminated, from the body. If an individual is an ultrametabolizer, meaning he or she has a genetic variant that increases the amount of enzyme the body produces, that person will convert the drug to its inactive form too quickly. This will results in low levels of active drug in the bloodstream, which may make the drug less effective. If the drug is meant to treat symptoms like pain, the drug may appear to only work for a shorter than expected amount of time, or be ineffective all together.

45 Active drug, ultra metabolizer Enzymes X X Enzymes X X Time passing Low levels of active drug = less effectiveness

46 Active drug, poor metabolizer If someone is a poor metabolizer for an active drug, their body will not convert enough of the drug to its inactive form, or will do so very slowly. This will result in very high levels of the active drug in the system, which can increase the risk for side effects and drug toxicity.

47 Active drug, poor metabolizer Little to no enzyme Enzymes Time passing High levels of active drug = risk for toxicity and side effects

48

49 Multifactorial disease

50 Components of multifactorial disease Multifactorial diseases, such as heart disease, cancer, or adult-onset diabetes, are caused by a combination of genetic, environmental and lifestyle factors. Often, several pieces of the puzzle combine to create an increased risk of disease. Breast cancer as an example: Lifestyle factors such as diet, alcohol consumption, and being overweight all contribute to the risk for breast cancer. Environmental factors or factors not under the individual s control, such as age, gender, and age at menses/menopause, also factor into the risk for breast cancer. Family history can be an indicator of risk either due to shared environment among members of a family, or due to low impact (low penetrance) genetic markers being passed from generation to generation. Finally, highly impactful (penetrant) gene variants that are known to cause familial or hereditary cancer syndromes can greatly increase the risk for breast cancer. Heart disease as an example: Lifestyle factors, such as smoking, level of exercise, diet, and stress all contribute to the risk for heart disease. Environmental factors or factors not under the individual s control, such as age, gender, and ethnicity also factor into the risk for heart disease. Family history can be an indicator of risk either due to shared environment among members of a family (for example, a shared diet high in fats), or due to low impact (low penetrance) genetic markers being passed from generation to generation. Finally, highly impactful (penetrant) gene variants that are known to cause familial hypercholesterolemia or familial cardiomyopathy can greatly increase the risk for cardiac disease.

51 Components of multifactorial disease Lifestyle Genes Environment Family History

52 Balancing risk factors Genetic variants, lifestyle, and environmental factors combine to create an individual s risk for any given disease. In scenario 1, gene variant A is the risk variant, meaning that individuals who carry an A at that location in the genome will have an increased risk for disease X, while individuals who carry variant T at that same place in the genome do not have an increased risk for disease X. Good or bad lifestyle choices can also increase or decrease an individual s risk for disease X. In scenario 2, an individual with gene variant A (increased disease risk) who also makes poor lifestyle choices such as bad diet and/or smoking, increases his/her risk for disease X even further. In this same scenario, an individual with gene variant T (no increased disease risk) can further decrease his/ her risk of developing disease X through good lifestyle choices such as healthy diet and exercising. Scenario 3 demonstrates how lifestyle and genetic factors act independently on an individual s risk for disease, thereby allowing increased and decreased risk factors to balance each other out. In essence, good lifestyle choices can sometimes counter-balance genetic risk. In contrast, poor lifestyle choices can lead to an increased risk for disease even in individuals with no genetic predisposition.

53 Balancing risk factors High risk High risk High risk Variant A Variant T Variant A Variant T Variant A Variant T Low risk Low risk Low risk Scenario 1 Scenario 2 Scenario 3

54

55 This project was made possible through the National Society of Genetic Counselors and a grant from the Audrey Heimler Special Project Award. Thank you to the following contributors: Kiley Johnson Shannon Kieran Sara Riordan Bryan Dunn Kelly Nixon Thank you to the many others who made this project a success.

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