GENETIC VARIANTS: SIMPLE ENOUGH FOR MY DAUGHTER’S 4TH GRADE CLASS
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Have you attended a recent Accipio from the Variant Classification team hoping to find out about variants, but it went completely over your head? Then this is for you! We’ll discuss what variants are, the types we see and how they relate to cancer. Don’t worry this will be simple enough for my daughter’s 4th grade class. Wendy Sorensen.
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GENETIC VARIANTS: SIMPLE ENOUGH FOR MY DAUGHTER’S 4TH GRADE CLASS
- 1. VARIANTS for my Daughter’s 4th grade class
- 2. Who is this presentation for? 2
- 3. My background • BS Geology SUU • CODIS ABI lab ~ 2 yrs • Data Review ~ 5 yrs • QA ~ 2 yrs • Informatics ~ 5 yrs 3
- 5. Cells
- 6. Cells
- 11. WHAT ARE THE PARTS OF A GENE? 11
- 13. • Book - Genome – Harry Potter and the Prisoner of Azkaban • Chapter - Chromosome – Talons and Tea Leaves • Paragraph - Genes
- 14. She stopped again, and then said, in a very matter-of-fact tone, “You look in excellent health to me, Potter, so you'll excuse me if I don't let you off homework today. I assure you that if you die, you need not hand it in.” ~ Professor McGonagall, Harry Potter and the Prisoner of Azkaban
- 15. • Sentence - Exon • Word - Amino Acid – die • Letter - Base (nucleotide) – d
- 17. DNA is different from a book • Bases (letters) – ATCG • Amino Acids (words) – 21 total • Always 3 bases long (codon) – ATG – methionine – start codon – CTA – leucine – TAA – Stop codon (TAG, TGA)
- 18. Parts of a gene
- 19. Parts of a gene She stopped again, and then said, in a very matter-of-fact tone, “You look in excellent health to me, Potter, so you'll excuse me if I don't let you off homework today. at work must joke if hop last here I assure you that if you die, you need not hand it in.”
- 20. Parts of a gene She stopped again, and then said, in a very matter-of-fact tone, “You look in excellent health to me, Potter, so you'll excuse me if I don't let you off homework today. at work must joke if hop last here I assure you that if you die, you need not hand it in.”
- 22. WHAT IS A VARIANT? 22
- 23. Wild Type • I assure you that if you die, you need not hand it in. • Je vous assure que si vous mourez, vous n'avez pas besoin de vous le remettre.
- 25. Types of Variants • Sequence (Seq) • Large Rearrangement (LR)
- 26. Types of Variants • Sequence (Seq) – SNP (Single Nucleotide Polymorphsim)
- 27. Types of Variants I assure you that if you die you need not hand it in. I assure you that if you dye you need not hand it in. Silent I assure you that if you dig you need not hand it in. Missense I assure you that if you di. Nonsense I assure you that if you din eed noth . Deletion I assure you that if you die xyo unee dno than di ti n. Insertion I assure you that if you cro aky oun eedn oth andi ti n. Indel
- 28. Types of Variants • Large Rearrangement (LR)
- 30. Nomenclature • BIC (Breast Cancer Information Core) • HGVS (Human Genome Variation Society)
- 31. Nomenclature I assure you that if you dig you need not hand it in. • BIC D40I (156E>G) • HGVS c.156E>G (p.Die40Dig) 154 155 156 40
- 32. Nomenclature I assure you that if you din eed noth . • BIC 156del4 • HGVS c.156_159del (p.Die40Dinfs*3) 154 155 156 40
- 33. WHAT IS VARIANT CLASSIFICATION? 33
- 34. Functional Category • Will the protein still function? – Deleterious – Suspected Deleterious – Uncertain – Favor Polymorphism – Polymorphism
- 35. Clinical Category • Should you take action? – High Risk – Elevated Risk – Risk May Be Increased – Clinical Significance Unknown – Special Interpretation – Clinically Insignificant
- 36. HOW DO VARIANTS CAUSE CANCER? 36
- 37. Cancer • Uncontrolled division of abnormal cells.
- 38. Gene functions • Activates enzymes to repair DNA – ATM • DNA Repair – BRCA1/BRCA2 • Instructs cells to stop dividing – TP53
- 40. Gene functions and cancer • Many mutations in lots of different genes cause cancer
- 43. Legacy Reporting
- 44. NGReporting
- 45. NGReporting
- 46. NGReporting
- 49. THANK YOU.
Editor's Notes
- My daughter dressed up as Bellatrix Lestrange for Halloween.
- CODIS- Combine DNA Index System
- Estimated 37 trillion cells in a human body
- Every cell contains nucleus – which holds our DNA DNA (deoxyribonucleic acid) DNA in our cells is identical DNA is in a double helix shape and coils so it can be compact in the cell
- DNA broken into 23 chromosome pairs (46 total) – each one you inherited one from mom and one from dad Instructions to create proteins Proteins have different functions Eye color Red blood cells Resistance to disease What determines the protein? Genes! 30000 genes on 46 chromosomes
- An adult produces 10s of billions new cells each day. Cell division is a process called Mitosis Each daughter cell contains the same DNA as the parent cell
- Homologous pairs crossover to create new combinations of genes on that chromosome. Reproductive cells only contain 23 chromosome
- Does anyone know the context of what’s happening in the story at this point? Harry came from his first divination class where Prof Trelewany told him he had the grim in his tea cup and is predicted to die.
- DNA is copied into all of our cells, just like a book is printed millions of times.
- Each 3 letters is a codon – it “codes” for an amino acid.
- How can you tell the start of a paragraph? How can you tell the end? Start of the gene – promoter (like the indent of a paragraph) End of the gene – terminater (like the hard return at the end of a paragraph)
- How can you tell the start of the sentence? What about the end? Extra words are introns. Sentences are the exons.
- How can you tell the start of the sentence? What about the end? Extra words are introns. Sentences are the exons.
- Introns are spliced out before making a protein. Just like in a finished book we don’t see the edits that the editor made and remove before printing the book.
- Change or a mistake
- Different ethnicities have different wild types – or “normal” DNA To determine wild type for a gene- you need to look at multiple ethinicities to find out the most common sequence of DNA for that gene.
- Error in a book – hard return and an indent. This appears to end the paragraph (gene) early.
- Sequence variants are small changes (one or more base changes) Large Rearrangement variants are large changes (often include whole exons or genes) The different is a fuzzy line, and at Myriad we determine which is which by the technology that can detect them.
- You’ll often hear Sequence variants called SNPs, but this can be incorrect. A SNP involves only one base, but sequence variants can include many.
- c. <DNA change> p. <protein change> D is short hand for Die in this example I is short hand for Dig in this example
- fs – indicates a frameshift (insertion or deletion that does not = 3 bases) * - indicates a premature stop codon 3 tells how many codons away the stop codon occurs
- If a variant is Deleterious or Suspected Deleterious it’s called a mutation The others are referred to as variants
- Which gene the mutation occurs in determines whether it’s high or elevated risk Risk May Be Increased, Clinical Significance Unknown and Special Interpretation are used mostly with Uncertain functional category
- Exposure to carcinogens like tobacco, radiation, viruses, age cause mutations in our DNA. Our bodies have defense mechanisms that protect us against cancer.
- Many genes are involved in regulating cell division. There is duplication, multiple genes that perform these functions. Multiple copies of each gene.
- Mistakes occur that are corrected during replication If they can’t be corrected any daughter cell from that division will also carry the variant
- Many genes are involved in regulating cell division. You need multiples mutations before cancer will form.
- If you inherit a mutation, your risk for cancer will be higher because every cell in your body starts out with a mutation. Germline – inherited in all cells, somatic – acquired in a few cells.
- Risk information imbedded in a paragraph on the report
- HGVS nomeclature
- Risks highlighted on the report and compared to population risk
- NCCN – National Comprehensive Cancer Network – panels for each cancer type meet once a year to review literature and determine risks and management guidelines for these cancers.