Basic Genetic Testing for Clinical Staff

[INTRO SLIDE]

INTRO TO GENETICS. Helping you understand the science behind your patients' care. Mikayla Jennings, MS, CGC. Presented by [Shriners Children's logo, Greenwood Genetic Center logo]

Mikayla Jennings, Genetic Counselor: Hello, my name is Mikayla Jennings, and I am a clinical genetic counselor at the Greenwood Genetic Center. I am here today to provide you with additional information about Whole Genome Sequencing

First let’s review some background genetics concepts.

[SLIDE 1]

Chromosome to Gene to Protein
A simplified scientific diagram showing how biological information flows from a cell → chromosomes → genes → DNA → proteins.

• On the left is a yellow illustration of a cell, with a nucleus shown as a circular structure containing scribble‑like blue lines representing DNA.
• Next to the cell is a pair of blue chromosomes, each drawn as an X‑shaped structure with banding patterns. A label states that each chromosome is composed of one large, continuous DNA molecule.
• Moving right, text: Gene - a gene is a segment of DNA that encodes a protein product.
• Moving down, a zoom‑in of a DNA double helix shows its twisting structure with colored nucleotide pairs.
• Beneath the DNA are labels for the four nucleotides:
  • Adenine
  • Thymine
  • Guanine
  • Cytosine
• Further to the right, a chain of blue spheres represents a protein molecule. Text: Protein - A protein is a complex organic compound composed of hundreds or or thousands of amino acids.

Mikayla: Our genetic information is packaged into chromosomes within each cell. If we stretch out the chromosomes, we can see the DNA, which is made up of four nucleotides: adenine (A), cytosine (C), guanine (G), and thymine (T). The nucleotides make up thousands of individual instructions called genes.

Genes are specific segments of DNA that code for proteins. This is done through the process of transcription and translation. DNA is transcribed into RNA. The RNA sequence is then translated into an amnio acid sequence that becomes the functional protein product.

[SLIDE 2]

This image compares a normal DNA and protein sequence to an abnormal sequence caused by a single‑base change.

• Top portion:
  • Heading: “Normal Sequence.”
  • DNA sequence: ATG AAG TTT GGC GCA TTG CAA.
  • Protein sequence: Met, Lys, Phe, Gly, Ala, Leu, Gln.
  • The codon GCA, which codes for alanine, is circled.
• A downward red arrow indicates the mutation.
• Bottom portion:
  • Heading: “Abnormal Sequence.”
  • DNA sequence: ATG AAG TTT GGC CCA TTG CAA.
  • Protein sequence: Met, Lys, Phe, Gly, Pro, Leu, Gln.
  • The changed codon CCA is now highlighted, and the amino acid below appears in green as Pro.

This image illustrates a missense mutation, where one DNA base change leads to substitution of one amino acid for another in the resulting protein.

Mikayla: There are different types of genetic changes or variants that can impact a gene, leading to an abnormal or non-functioning protein. A missense variant occurs when a nucleotide change results in the replacement of an amnio acid with another in the protein. This amnio acid change may alter the function of the protein.

[SLIDE 3]

This image compares a normal DNA sequence and the protein it codes for to an abnormal sequence resulting from a deletion.

• Top portion:
  • Heading: “Normal Sequence.”
  • DNA sequence: ATG, AAA, TTT, AAG, GCA, TTG, CAA.
  • The codon AAG has a red “X” over it, indicating deletion of a base.
  • Protein sequence: Met, Lys, Phe, Lys, Ala, Leu, Gln.
• A downward red arrow points to the mutated sequence.
• Bottom portion:
  • Heading: “Abnormal Sequence.”
  • DNA sequence: ATG, AAG, TTT, TAG, GCA, TTG, CAA.
  • Protein sequence: Met, Lys, Phe.
  • A red stop sign icon marks the premature stop codon.

At the bottom, text states: “Stop Codons = TAG, TGA, TAA.”

This image illustrates a nonsense mutation, in which deletion of a base alters all subsequent codons, leading to incorrect amino acids and often an early stop codon.

Mikayla: A nonsense variant occurs when a nucleotide change results in a premature stop codon. This stops the gene instructions early and results in a truncated or shortened protein.

[SLIDE 4]

The image shows a comparison between a normal DNA sequence and an abnormal DNA sequence, with each sequence paired to the amino acids it codes for in a protein.

• At the top, the heading reads “Normal Sequence.”
  • The normal DNA sequence shown is: ATG, AAG, TTT, GGC, GCA, TTG, AAA. There is a red "X" through the "G" in "AAG."
  • Beneath the DNA sequence is a row labeled Protein, displaying the corresponding amino acids: Met, Lys, Phe, Gly, Ala, Leu, Lys.
  • The codon AAG in the normal sequence is circled, and a downward red arrow indicates a mutation.
• Below this:
  • The heading reads “Abnormal Sequence.”
  • The abnormal DNA sequence is: ATG, AAT, TTG, GCG, CAT, TGA, AA.
  • The protein line shows the sequence: Met, Lys, Phe (in faded green text: Leu, Ala, His) then a red STOP sign, indicating translation ends prematurely.

This image illustrates a frameshift mutation, where a normal codon changes into a stop codon, halting protein synthesis early.

Mikayla: An insertion or deletion, also called frameshift variants, occur when one or more nucleotides are inserted or deleted from the gene sequence. This can cause the reading frame of the gene sequence to be altered. This may result in a different sequence of amino acids and an abnormal protein product.

[SLIDE 5]

Sequencing Methodologies
A comparison of four genetic sequencing approaches, using a book metaphor to show scope.

• Four side‑by‑side panels, each with a title, sample sentences, and a book illustration in the two right panels.

Single gene sequencing:

• Sample text: “The car was red. The car was rdd.”
• Description: Look for errors in a single sentence in the book.

Targeted gene panel sequencing:

• Sample text includes multiple short sentences (car, boat, train).
• Description: Look for errors in a specific group of sentences in the book.

Exome sequencing:

• Illustration of an open book.
• Description: Look for errors in the most important “chapters” in the book (all protein‑coding regions).

Whole Genome sequencing:

• Illustration of a closed book.
• Description: Look for errors in every single word in the book.

Mikayla: Whole Genome Sequencing is a specific type of test that looks for spelling/nucleotide changes not only in the pieces of genes that code for proteins called exons, but also in the closely surrounding information called introns. These types of changes are known as sequence variants. This test also looks for small, missing or extra pieces of DNA known as deletions and duplications. These types of changes are known as copy number variants.

[SLIDE 6]

This image is a diagram comparing the location of nuclear DNA and mitochondrial DNA inside a cell.

• On the left is a large, rounded cell with a labeled nucleus at its center.
• Inside the nucleus are several blue chromosome‑shaped structures, labeled “Chromosomes (Nuclear DNA).”
• The outer area of the cell contains several purple, bean‑shaped structures labeled “Mitochondria.”
• On the right side, the mitochondria are enlarged for detail.
  • Inside the enlarged mitochondria, small loops of genetic material are labeled “Mitochondrial DNA.”
• Text in the bottom left corner reads “It is up to you whether you would like our lab to report mitochondrial DNA findings.”

This image visually contrasts where DNA is located in a cell: chromosomes in the nucleus versus circular mitochondrial DNA inside mitochondria.

Mikayla: Whole genome sequencing includes the genetic information found in the nuclear genome, but it can also include the mitochondrial genome. This can be included to identify a mitochondrial condition. These conditions can cause a wide range of symptoms, and many body systems can be affected. It is up to you and your patient whether or not you want to include the mitochondrial information with the whole genome sequencing test.

[SLIDE 7]

Secondary Findings
A DNA double helix illustration showing positions of “primary” and “secondary” genetic findings.

• A long DNA double helix stretches across the image in multicolored base‑pair segments.
• A square box on the left section highlights a primary finding, described as:
  • “Genetic change related to patient’s current condition.”
• A square box on the right section highlights a secondary finding, described as:
  • “Medically important genetic changes, but not related to the patient’s current condition.”
• Below this are examples:
  • Cancer predisposition
  • Heart conditions
• Text in the bottom left corner reads “It is up to you whether you would like our lab to report secondary findings.”

Mikayla: Whole genome sequencing is a genetic test that can be used to identify a genetic cause for your patient’s symptoms. This test is phenotypically driven, so it is important to include all of the clinical features of your patient when ordering this test. This allows the lab to filter through the genetic data in an informative way. The intention is not to report on all genetic changes an individual has, but rather those that are relevant to your patient’s medical history. This test can also report on what we call secondary findings, which are changes in genes that increase the risk for things like cancer or cardiovascular disease. You will want to discuss with your patient whether or not they would like to include secondary findings. For more information on the option to report secondary findings, please have your patient watch the video on secondary findings.

In addition to your patient’s sample, parental samples can also be included with this test. This testing can be performed as a singleton (with just your patient’s sample), a duo (your patient’s sample and one parent), or as a trio (your patient’s sample and both parents). Parent samples are used for the interpretation of your patient’s results. Parents do not receive their own test reports. If a variant is reported in your patient and parental samples are included, the lab will report on the inheritance of that variant.

[SLIDE 8]

Potential Results of Genetic Testing
A Venn diagram with three overlapping circles describing possible outcomes of genetic testing.

• The left circle is blue, labeled “Normal.”
  • Text: “No clinically significant changes identified.”
• The right circle is red, labeled “Abnormal.”
  • Text: “Disease‑causing change identified.”
• The overlapping center area is purple, labeled “Variant of Uncertain Significance (VUS).”
  • Text: “Change identified but significance is unknown.”

Mikayla: There are three types of results we can get back from genetic testing. The first is a positive result, which means that we found a genetic change that either explains existing symptoms or is likely to impact your patient’s health in another way.

We can also get a negative result from whole genome sequencing. A negative result from this test is reassuring but doesn’t rule out all possible genetic causes for symptoms.

Finally, this testing can identify uncertain results, which we call variants of uncertain significance. This means that the whole genome sequencing found a variant in a gene, but we don’t know if this is changing how the gene functions or not. Over time, especially as this testing is done for more people, we learn more about uncertain results and can better understand if these changes are harmful or not. These changes can be upgraded to pathogenic or downgraded to benign or normal.

Please keep in mind that in genetics we are learning new information over time. Your patient’s genetic information can be reanalyzed at your request in the future or the laboratory may contact you with updated information.

The intention of this testing is to identify the cause for a patient’s concerns. However, we can sometimes uncover unexpected or incidental information that can impact the patient and their family members. For example, the testing may reveal that a patient may develop additional health problems in the future. If parent samples are included, it may reveal that a patient’s parent has the same genetic condition as their child. The testing may reveal consanguinity or that the patient’s parents are related to each other, or even that one of the patient’s parents is not their biological parent.

Whole genome sequences does not detect all types of genetic changes, so it is important to consider if additional testing is needed, following a non-diagnostic result. There are also certain changes that are not typically reported, including carrier status for autosomal recessive genetic conditions, changes that may cause a slight increased risk for common and easily diagnosable conditions such as diabetes and hypertension, changes that can give information about drug metabolism (pharmacogenetics), or variants in genes that cause certain adult onset conditions that cannot be prevented and not related to the patient’s current medical conditions.

We hope this helped you learn more about genetics and genetic testing with whole genome sequencing. Ultimately, our goal with this testing is to identify the cause for a patient’s concerns. If you have additional questions about whole genome sequencing, please contact the laboratory you will be ordering this testing from.

[SLIDE 7]

Brought to you in partnership by [Shriners Children's logo] [Greenwood Genetic Center logo]