Question

Part I— Just Bad Luck? Brrrring! Brrrring! Jane checked the caller ID on her phone. “Sam! Great!” she thought. It was always nice to get a call from her older brother. But a little twinge of worry tugged at her. It was just a couple of weeks ago that he had mentioned making an appointment with his doctor about some abdominal pain he had been having. “Hi Sam! It’s great to hear from you,” Jane answered. “Hi Jane. Well I appreciate that you still pick up, anyway. You know I call just to give you a hard time about something, little sis.” “Very funny. So, how are you planning to pick on me today?” “Honestly, I wish this call was for fun,” Sam said. “But it’s only serious stuff this time. Remember I said that I had made an appointment with my doctor? Well, the news isn’t good. My doctor says I have colon cancer.” “Oh, no, Sam! I remember when Dad died from colon cancer when we were kids.” e words tumbled out all in a rush. Jane felt a lump gathering in her throat. “Hold on,” Sam said. “ is isn’t an early death sentence yet. e doctor says that although they found lots of tumors in my colon, it’s still at an early stage, so treatment is possible. Drastic, though. My doctor is suggesting that the best thing to do is to surgically remove my colon altogether. And Sis, the doctor said that since both Dad and I have the same type of cancer, it would be a good idea for you to have your colon checked, too.” After the phone conversation with her brother, Jane was worried there could be more than just “bad luck” running in her family’s medical history. eir father’s too-early death from colon cancer was still a painful memory. She knew that her grandfather on her father’s side had died of some type of cancer even before she was born, although that was so long ago the family didn’t talk about it much. Had her grandfather died of colon cancer too, Jane wondered. Would it be her turn next? And what was the risk to her young twins, Mark and Caroline?

 Part II—A Visit to the Doctor “Good afternoon, Jane,” Dr. Peters said as she entered the examination room. “I understand that you’re here to talk about some concerns related to cancer in your family.” Jane explained the history of cancer in her family, including her father’s early death from colon cancer and her brother’s recent diagnosis of the same disease, ending with the recommendation from her brother’s doctor to have her own colon checked. “What does that mean, to have my colon ‘checked’?” As she asked the question, Jane was already feeling a little uncomfortable about it. “I know that the idea of having a procedure done to look at your colon is a little off-putting,” Dr. Peters began, “but it really can be one of the most important tests if your family has a history of colon cancer.” She continued to explain: “ e procedure that allows the interior of the colon to be examined is called a colonoscopy. e purpose of such a screening is to look for sites of increased cell growth in the colon, called polyps or adenomas. ese adenomas are small benign tumors that form in the intestinal lining. People who inherit a predisposition to colon cancer are at higher risk to form these adenomas, and at an early age. Although the adenomas are benign, the cells within them are one step closer to becoming malignant. So, colonoscopy screenings don’t prevent cancer, but they do allow sites of altered cell growth to be detected, so that treatment can begin as soon as they appear. By detecting these adenomas early and removing them before they become malignant, we can prevent colon cancer. “So regular colonoscopy screenings, beginning at an early age, are highly recommended for people with a familial predisposition to colon cancer,” Dr. Peters continued. “And even if a person doesn’t have a family history of colon cancer, it’s still recommended to have a colonoscopy screening once a year beginning at age .” “I understand now why it would be important to have my colon checked,” Jane said, “but is there some way I can find out for sure whether I have inherited a predisposition to colon cancer?” “I was just getting to that topic,” Dr. Peters replied. “In some cases, genetic testing can reveal whether you are predisposed to colon cancer. Normally those kinds of genetic tests are done first on family members who are affected. Since your brother lives nearby, I’d suggest you talk with him about making an appointment together with a genetic counselor for more information about testing.”

 Part III—Genetic Testing “Hello Sam and Jane, I’m Diane Meeker, and I’ll be your genetic counselor. I understand that you’re both here to talk about possibly having genetic testing to see whether you inherited a predisposition to colon cancer.” “Yes,” Jane replied, “I’m concerned because our dad died of colon cancer when we were kids, and now Sam has it too—and he’s only !” “Why don’t we start there, then, and review your family history. First, do you know of any other family members that have been diagnosed with cancer?” Ms. Meeker asked. “Well, besides Sam and our dad, I know that our grandpa on our father’s side also had cancer,” Jane replied. “But he died long before either of us was born and I don’t know what kind of cancer it was. No one else in our family has had cancer that I know of.” “Based on what you’ve told me about the medical history of your family, I’ve created a pedigree to diagram your family relationships and which individuals have cancer. e extremely early development of colon cancer in both you, Sam, and your father, and the fact that a direct relative of your father died early from some type of cancer suggests that familial adenomatous polyposis (FAP) may be the cause of hereditary colon cancer in your family,” Ms. Meeker said. “But what exactly is it that is being inherited in our family that causes us to develop colon cancer? It’s something about our DNA, right?” Jane asked. “You’re right,” Ms. Meeker replied, “it does have to do with your DNA. e DNA in your cells contains genes, which are the instructions for making proteins. Proteins in the cell control how that cell grows and develops and divides. A mutation in the DNA sequence of a gene can alter the protein made from that gene, so that the protein no longer functions properly. So, some mutations can cause a change in protein function that allows a cell to grow out of control and become cancerous.” “So maybe there’s a mutation in my DNA,” Sam replied. “But if you do a genetic test, how do you know what to look for in my DNA? Don’t humans have lots of DNA? What exactly would you be testing?” “Finding an inherited mutation in a person’s DNA does sound like looking for a needle in a haystack, doesn’t it?” Ms. Meeker replied. “But we do have some clues to suggest where we can look. For example, from other families with FAP, we already know that this syndrome can be caused by an inherited mutation in the adenomatous polyposis coli (APC) gene.” “I see,” Sam replied. “So you won’t be looking at all of my DNA. You only need to look at that one gene and see if it has a mutation, right?” “You’ve got it,” Ms. Meeker said. “So, by taking some of your blood, isolating your DNA, and then sequencing your APC gene, we can compare your sequence to the known normal APC sequence and look for differences.” “ at sounds so simple. So then if you find a mutation in my APC gene, you could look to see whether or not my sister inherited that mutation too, right?” Sam said. “Colon Cancer” by Anne M. Casper Page  “Yes, because you have been diagnosed with colon cancer, we’ll start by looking for a mutation in your DNA first, Sam,” Ms. Meeker confirmed. “And I wish it was as clear-cut as it sounds, but actually I have to caution you both about this genetic test. e process of searching for mutations can be time-consuming and expensive, because often each FAP family carries a mutation at a unique site in the APC gene—and the APC gene is large! In fact, the gene is so large that we don’t actually sequence the DNA for the gene. Instead, we sequence the mRNA, which is the part of the gene that your body uses to make the APC protein. e mRNA is smaller because it cuts out some parts of the sequence of the gene, called introns. Here, let me show you in a drawing,” Ms. Meeker continued as she began to pull out a piece of paper. In order to sequence the mRNA of a gene, scientists first make a DNA copy of the mRNA. is DNA copy is called a cDNA, and it is more stable and easier to work with than the original mRNA. e cDNA is then sequenced. Let’s compare Sam’s APC cDNA sequence with the known normal APC cDNA sequence. To do this, first go to the main NCBI home page (http://www.ncbi.nlm.nih.gov) and follow the instructions below.

• In the dark blue bar across the top, choose the link to “BLAST.” • On the BLAST page, under the “Basic BLAST” category, click the link to “nucleotide blast.”

• On the next page, in the “Enter Query Sequence” section, click the box next to the option “Blast  sequences.

” • Find the normal sequence of APC cDNA on the NCBI website. Open a new browser window and go to the NCBI home page (http://www.ncbi.nlm.nih.gov/). In the top light blue bar, change the “All Databases” search to a search for “Nucleotide.” en in the search box, enter m (which is the accession number for APC) and click “go.” On the search results page, click on the blue link to m. You will need to scroll down the page to find the normal APC sequence. Copy and paste this sequence into the top box on the BLAST page (the Query sequence box).

• Ask your instructor where to find Sam’s sequence. Copy and paste Sam’s APC cDNA sequence in the bottom box on the BLAST page (the Subject sequence box).

• Click the “BLAST” button at the bottom of the page.

• On the BLAST results page, you can scroll down to see the alignment of normal APC (the Query sequence) with Sam’s APC (the Subject sequence). Note though that this format makes it difficult to see mismatches between these two sequences.

• To change the results format to one that makes it easier to look for mismatches, scroll back to the top of the BLAST results page, and click the blue “Formatting Options” link.

• In the “Alignment View” box, change the view from “Pairwise” to “Pairwise with dots for identities.” en click the “Reformat” button in the upper right corner. On the re-formatted results page, each base of Sam’s APC (the Subject sequence) that matches normal APC (the Query sequence) is shown as a dot. “Colon Cancer” by Anne M. Casper Page

 Questions

1. What did you find when you compared Sam’s APC sequence to the known normal APC sequence in the national database? Look carefully, and scroll all the way down through the comparison! 

2. What are three possible consequences of the mutation you found in Sam’s APC sequence?

Answer 1

Ans1: There is a point mutation at nucleotide 1748 where T wa changed to A.

2: First is the silent mutation because the alter codone could code for the same amino acid because genetic code is degenerate if third nucleotide and codone was changed. Second is the missence mutation which causes the codone to code for the altered amino acid and changes the folding of the protein. Third is the nonsense mutation which makes the altered codone to become the stop codone as a result the polypeptide chain becomes shorter.