Teacher Notes

The Genetics of Cancer

Student Laboratory Kit

Materials Included In Kit

Agarose, powder, electrophoresis grade, 3 g
DNA Sample 1, 80 μL
DNA Sample 2, 80 μL
DNA Sample 3, 80 μL
DNA Sample 4, 80 μL
Methylene blue electrophoresis staining solution, concentrate 10X, 100 mL
TAE electrophoresis buffer, concentrate 50X, 100 mL
Genetics of Cancer Scenario
Pipets, disposable, needle tip, 50
Staining trays, 6

Additional Materials Required

Water, distilled, 1.5 L†
Bag, resealable, quart*
Beakers, 600-mL, 2*
Electrophoresis chamber with power or battery supply*
Erlenmeyer flasks, 500- and 1000-mL†
Graduated cylinders, 50-mL, 2†
Light box or other light source (optional)*
Marker or wax pencil†
Microcentrifuge tube tray*
Microwave or hot plate to melt agarose gel*
Parafilm M® or plastic wrap†
Ruler, metric*
Stirring rods, glass, 2†
*for each lab group
for Prelab Preparation

Prelab Preparation

Preparation of 1X electrophoresis buffer

  1. Measure 20 mL of 50X TAE buffer in a graduated cylinder.
  2. Add the 50X buffer to 980 mL of distilled water in a 1000-mL Erlenmeyer flask.
  3. Mix with a glass stirring rod.
  4. Seal with Parafilm M® or plastic wrap.
  5. Label and store in a refrigerator.
  6. Repeat if necessary.
Note: Prepare enough buffer solution to allow each group to cover the gel in the chamber to a depth of about 2 mm. Depending on the type of electrophoresis units being used, the amount of buffer needed may be as much as 300 mL per chamber. Gel preparation requires an additional 60 mL of buffer to make a 6 x 6 cm gel.

Make fresh buffer weekly.

Preparation of 1X Methylene Blue Electrophoresis Stain
  1. Measure 30 mL of the 10X methylene blue staining solution in a graduated cylinder.
  2. Add the staining solution to 270 mL of warm distilled water in a 500-mL Erlenmeyer flask.
  3. Mix with a glass stirring rod.
  4. Seal with Parafilm M or plastic wrap.
  5. Label and store in a refrigerator.
Note: 40 mL is enough to stain a gel in the staining tray that is provided.

Safety Precautions

Electrical Hazard: Treat the electrophoresis units like any other electrical source—very carefully! Be sure all connecting wires, terminals and work surfaces are dry before using the electrophoresis units. Remind students to never try to open the lid of the electrophoresis unit while the power is on. Exercise extreme caution in handling the methylene blue—it will readily stain clothing and skin. Wearing chemical splash goggles and gloves is strongly recommended. Wash hands thoroughly with soap and water before leaving the laboratory. Please consult current Safety Data Sheets for additional safety, handling and disposal information.


Please consult your current Flinn Scientific Catalog/Reference Manual for general guidelines and specific procedures, and review all federal, state and local regulations that may apply, before proceeding. All solutions used in this lab may be disposed of down the drain using copious amounts of water according to Flinn Suggested Disposal Method #26b. Used gels may be disposed of in the regular trash according to Flinn Suggested Disposal Method #26a. The DNA in this kit is derived from bacteriophage samples. It is not pathogenic to humans and therefore it is not considered a biohazard.

Lab Hints


  • Store DNA samples in the freezer until ready to use. DNA stored at room temperature or warmer may degrade over time. Short periods at room temperature will not affect results.
  • The concentrated methylene blue electrophoresis stain, concentrated electrophoresis buffer and agarose powder may be stored at room temperature.
  • The gel preparation pages have been listed separately so that they may be copied for student use if desired.
  • Gel preparation requires approximately 10–20 minutes plus at least an additional 20 minutes for the gel to solidify (60 minutes is optimal solidification time). Longer solidification times “harden” the gel, minimizing tears and creating more distinctive bands of DNA.
  • When preparing agarose gels using a stirring hot plate, rotate a magnetic stir bar very slowly to diminish the number of bubbles in the agarose solution.
  • Without a balance, prepare all six 0.8% gels simultaneously. Measure 375 mL of electrophoresis buffer in a 500-mL Erlenmeyer flask, add the entire 3 g of agarose to the flask and dissolve as directed.


  • Have students practice pipetting 10 μl of tap water into a defective gel while waiting their turn to load the gel. Another alternative would be to prepare practice gels with less expensive agar instead of agarose. The Pipetting Practice Kit, Flinn catalog number FB1649, provides a durable, reusable option that works very well.
  • Run the gel at 5 V/cm. For example, if the electrodes are 25 cm apart then the gel should be run at 125 V. Running the gel at a higher voltage may cause the agarose to melt, hindering its ability to act like a molecular sieve. Run a practice gel to determine the length of time the gel will need to run. 20 to 120 minutes is a reasonable time frame to expect results. In general, longer electrophoresis runs at lower voltages will increase the resolution of the DNA fragments. If necessary, connect the power source to a household automatic timer to end the sample run.
  • The sample data included with the kit were collected after 42 minutes at 125 V using an Edvotek M-12 electrophoresis apparatus.|Gel samples submerged under buffer may be stored in the refrigerator for up to two weeks.
  • The DNA samples contain bacteriophage DNA fragments, bromphenol blue tracking dye, xylene cyanole tracking dye, sucrose and TAE buffer.
  • Sucrose or glycerin is added to each DNA sample to make the sample denser than the TAE buffer. This causes the DNA sample to sink into the sample well in the gel.
  • Bromphenol blue migrates at the same rate as a 200–400 bp DNA fragment, toward the beginning of the sample run.
  • Xylene cyanole migrates at the same rate as a 4000 bp DNA fragment. It helps visualize the middle to end of the sample run.
  • TBE buffer may be used in place of the TAE buffer included with this laboratory kit.
  • A 10-μL micropipet with disposable tips may be used instead of the disposable needle-tip pipets.

Teacher Tips

  • Enough materials are provided in this kit for six groups of students. This laboratory activity can reasonably be completed in two or three 50-minute class periods. If the gels have been prepoured and are ready to use, electrophoresis setup, sample transfer and the start of electrophoresis will take approximately 50 minutes. The electrophoresis of samples will take 20 minutes to 2 hours depending on the voltage and equipment used to run the samples. Staining and sample analysis will require an additional 50-minute period.

  • Extend the lesson by extracting DNA from wheat germ, strawberries or cheek cells (Flinn No. FB1562).

Correlation to Next Generation Science Standards (NGSS)

Science & Engineering Practices

Analyzing and interpreting data
Developing and using models
Constructing explanations and designing solutions

Disciplinary Core Ideas

MS-LS1.B: Growth and Development of Organisms
HS-LS1.B: Growth and Development of Organisms
HS-LS1.A: Structure and Function
HS-LS3.A: Inheritance of Traits

Crosscutting Concepts

Cause and effect
Structure and function

Performance Expectations

MS-LS3-2: Develop and use a model to describe why asexual reproduction results in offspring with identical genetic information and sexual reproduction results in offspring with genetic variation.
HS-LS1-1: Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins, which carry out the essential functions of life through systems of specialized cells.

Sample Data

Observations and Analysis

  1. Measure the migration distance in millimeters for each band and sketch the observed DNA banding pattern on the DNA Banding Worksheet.

    The banding patterns will vary due to differences in the electrophoresis run and the periodic substitution of DNA. All DNA will be between 75 and 24,000 bp.

  2. Complete the Data Table.

    Data Table
    Migration distances will vary due to differences in the electrophoresis run and the periodic substitution of DNA. All DNA will be between 75 and 24,000 bp.


Answers to Questions

  1. Why are germline mutations of particular concern to geneticists?

    Gerline mutations are passed on to the next generation.

  2. Why are colored, tracking dyes used when running the fragments through the gel? 

    Colored tracking dyes are used to visualize the position of the colorless DNA within the gel during electrophoresis.

  3. When analyzing the DNA banding pattern, where would you expect to find the largest fragments produced by the restriction enzyme?

    The largest fragments will have moved the shortest distance.

  4. Read the “Genetics of Cancer Scenario” and evaluate the banding pattern results obtained by electrophoresis of the DNA samples. Do the results suggest that anyone is a carrier of the BRCA1 and BARD1 mutations carried by Mary? Explain your analysis of the results and your conclusion.

    DNA sample 3 (James) and DNA sample 4 (Mary) are a match.

  5. Summarize the steps involved in predictive genetic testing.

    DNA is extracted from the nuclei of cells, mixed with a restriction enzyme, processed using PCR, mixed with tracking dyes, loaded into the wells on a submerged agarose gel inside a gel electrophoresis chamber. Current is applied to the system and the DNA is separated according to fragment length. The electrophoresis is stopped and the samples are stained. The unknown samples are compared to a sample known to contain the mutation.

  6. List three errors that could affect the outcome of any gel electrophoresis procedure.
    1. Not placing the sample deep enough into the well or not placing enough sample into the well.
    2. Puncturing the well with the pipet tip, causing the dye to actually run below the gel.
    3. Connecting the wires to the power supply or chamber incorrectly.
    4. Contaminating pure samples by using the same pipet tip in different samples.
    5. Not recording which sample went into which well.

Teacher Handouts


Student Pages

The Genetics of Cancer


Cancer is a disease of cells that divide indefinitely. Genes that control cell replication become faulty, allowing the cell to reproduce uncontrollably and gradually overwhelm adjacent cells. All cancers are caused by damaged genes and can therefore be deemed genetic. Only a small proportion of cancers, however, are inherited. Most cancers develop from chance gene mutations that occur to the cell’s DNA due to environmental factors.


  • DNA fingerprinting
  • Polymerase chain reaction (PCR)
  • Gel electrophoresis
  • Restriction fragment length polymorphism (RFLP)
  • Genes
  • Variable number of tandem repeats (VNTR)


A genetic mutation signals a cell to produce an abnormal protein. This abnormal protein may be beneficial or harmful, or it may have no effect on the cell. There are two basic kinds of genetic mutations. They are called germline mutations and acquired mutations.

A germline mutation is inherited—passed from parent to child. Since it is inherited, a germline mutation is present in every cell of the body, including the reproductive cells. Consequently, it may be passed from generation to generation. Germline mutations produce what are termed familial cancers, which are responsible for less than 15% of all cancer cases.

Most cancer cases are caused by a series of genetic mutations that develop during a person’s lifetime. These mutations are acquired, not inherited, and are therefore called acquired mutations. Acquired mutations are caused by environmental factors, such as exposure to toxins or radiation, or by damage to the gene through aging. Acquired mutations produce what are termed sporadic cancers because they occur intermittently in the population.

There are two main types of genes that mutate and potentially cause cancer, tumor suppressor genes and oncogenes. Tumor suppressor genes code for three types of proteins. When behaving normally, these proteins have a dampening effect on the regulation of the cell cycle, promote apoptosis (cell death) or act in repairing mismatched DNA. When a tumor suppressor gene is altered, either by mutation or deletion of base pair(s), an abnormal protein is created. The abnormal protein is unable to repair damaged DNA, halt mitosis or cause the cell to die so that eventually a tumor of cells is allowed to form. Many tumor suppressor genes have already been identified, including BRCA1, BRCA2, p53 and BARD1, all of which contribute to inherited forms of early onset breast cancer (breast cancer prior to the age of 45) in both men and women. Most cancers caused by tumor suppressor gene are autosomal recessive, meaning two mutated forms of the gene must be inherited before any increase in incidence of cancer occurs. However, BRCA1, BRCA2 and p53 are autosomal dominant. One copy of the mutated genes raises the chance of breast cancer by 40%. BARD1 acts in conjunction with BRCA1 and BRCA2, if a person carries both a BARD1 and a BRCA1 or BRCA2 mutation, the likelihood of developing breast cancer increases to nearly 100%.

Oncogenes are the other type of abnormal genes that cause cancer. Oncogenes are mutated versions of genes called proto-oncogenes. Proto-oncogenes code for proteins that regulate cell growth and differentiation. Oncogenes code for abnormal proteins that produce hyperactive cell growth and eventually lead to tumor formation. The first oncogene was discovered in 1970 and was termed SRC (pronounced SARK). Since then many other oncogenes have been and continue to be discovered and mapped on the human genome.

Scientists have developed genetic tests for a few types of cancer. These tests are designed to identify individuals who have germline mutations that may eventually cause cancer. This type of genetic test is called predictive testing, which means the test can help predict the probability that an individual will develop cancer. A positive test result only signifies that a person has inherited a known gene mutation and therefore has an increased risk of developing cancer. Not everyone with a positive genetic test for a cancer-related gene will develop cancer. It is imperative to remember that many, but not all, people who inherit a mutated gene will develop cancer. Consequently, anyone who is determined to carry a mutated gene (and therefore a predisposed risk to cancer) may take precautions, such as reducing environmental exposure to cancer-causing agents and also to undergo regular screening for precancerous cells.

To develop predictive tests, scientists typically start looking for “mutations” in the DNA by analyzing DNA samples from members of families in which numerous relatives, over several generations, have developed the same cancer. Scientists then look for easily identifiable segments of DNA, known as genetic markers, which are consistently inherited by family members with the disease but are not found in relatives who are cancer free.

One type of predictive testing involves the analysis of DNA by PCR/RFLP and gel electrophoresis. Polymerase Chain Reaction (PCR) is the copying of specific regions of DNA, typically 150–3,000 base pairs long. In order to copy the fragments of DNA, cells containing DNA must first be collected, and the DNA must then be extracted from the cells and fragmented using special enzymes called restriction enzymes. Geneticists prefer to collect samples of buccal (internal cheek) cells or blood. The long strands of DNA are extracted from the nuclei of the cells and cut into fragments using one of many different restriction enzymes. Each restriction enzyme recognizes a specific sequence of base pairs on the strand of DNA and cuts the DNA strand at or near that particular sequence. The specific base pair sequence may be five to sixteen base pairs long. Since the average human DNA sequence is over 3.2 billion base-pairs long (approximately 30,000 genes), there may be as many as 750,000 fragments of DNA after a restriction enzyme completes the fragmentation of DNA. The process of using restriction enzymes to cut the long strands of DNA is called restriction fragment length polymorphism (RFLP pronounced “riflip”). With the exception of identical twins, all individuals have a unique RFLP sequence or DNA fingerprint.

The RFLP fragments generated by the restriction enzyme are loaded into wells made in an agarose gel. Agarose is a refined form of agar. The agarose gel is positioned between two electrodes in an electrophoresis chamber, with the wells adjacent to the cathode (negative electrode). When a voltage is applied to the electrodes, the negatively charged DNA fragments move toward the anode (positive electrode) (see Figure 1). The electrophoresis chamber is filled with a buffer solution, bathing the gel in a liquid that shields the system from changes in pH. The gel acts like a molecular sieve, creating a maze which the fragments must move through on their way toward the anode. Smaller fragments move faster through the holes or pores in the gel while larger fragments move slower because of their size.

The DNA fragments are white to colorless and are invisible in the gel. Molecular biologists add colored tracking dyes so they can visualize the DNA fragments moving through the gel. Typically, two dyes are added—one that migrates at a rate similar to the smallest DNA fragments, and one that migrates at a rate similar to the largest DNA fragments. After the first dye has migrated to within 1 cm of the end of the gel, the power is shut off to the electrophoresis chamber. All DNA fragments stop migrating because the electromotive force stops.

The agarose gel is then carefully removed from the electrophoresis chamber and transferred into a staining tray. The stain binds to the DNA fragments revealing a characteristic banding pattern. Geneticists use a radioactive stain and X-ray film to visualize DNA bands. In this laboratory, a colored dye that may be viewed with white light is used. The resulting banding pattern is compared to a DNA sample have a known genetic mutation. A similar banding pattern would indicate a probable genetic predisposition to that particular form of cancer.

Experiment Overview

This laboratory focuses on the technique of gel electrophoresis used to determine a germline mutation for cancer.


Agarose gel
DNA Sample 1
DNA Sample 2
DNA Sample 3
DNA Sample 4
Methylene blue electrophoresis staining solution, 50 mL
TAE electrophoresis buffer, 200 mL
Water, tap, 100 mL
Beakers, 600-mL, 2
Electrophoresis unit with power or battery supply
Genetics of Cancer Scenario
Light box or other light source (optional)
Paper, white
Paper towels
Pipets, disposable, needle-tip, 8
Resealable bag
Ruler, metric
Staining tray

Safety Precautions

Electrical Hazard: Treat the electrophoresis unit like any other electrical source—very carefully! Be sure all connecting wires, terminals and work surfaces are dry before using the electrophoresis units. Do not open the lid of the electrophoresis unit while the power is on. Use heat protective gloves and wear eye protection when handling hot liquids. Methylene blue will stain skin and clothing. Wear chemical splash goggles, chemical-resistant gloves and a chemical-resistant apron. Wash hands thoroughly with soap and water before leaving the laboratory.


Read the Genetics of Cancer Scenario.

Part A. Loading a Gel

  1. Assemble the electrophoresis unit according to the teacher’s instructions.
  2. Place the electrophoresis unit in a horizontal position on top of a piece of white paper on a level table or countertop. Do not move the unit after loading the samples.
  3. Gently slide a gel from a resealable bag into the casting tray with the wells adjacent to the cathode (–) end of the gel tray.
  4. Carefully position the gel and tray into the electrophoresis chamber with the wells toward the cathode end of the unit (see Figure 1). Caution: Be careful not to break or crack the gel. If the gel is damaged it should not be used since the breaks and cracks will affect the results. Notify the teacher immediately.
  5. Pour enough electrophoresis buffer into the unit to submerge the entire gel surface to a depth of 2–5 mm. If the gel begins to float away, reposition it on the tray.
  6. By convention, DNA gels are read from left to right, with the wells located at the top of the gel. With the gel lined up in the electrophoresis chamber and the wells to the left, load the contents of DNA Sample 1 into the well closest to you. Consequently, when the gel is turned so that the wells are at the top, “1” will be in the upper left corner. If there will be empty wells in the gel, leave the outside (end) wells empty, since they are most likely to give aberrant results.
  7. Place the DNA Banding Worksheet on the counter in the same orientation as the electrophoresis unit. The small rectangles on the paper correspond to the wells in the gel (see Figure 1).
  8. Shake the microcentrifuge tubes containing the DNA samples and lightly tap the bottom of each tube on the tabletop to return the contents to the bottom of the tube.
  9. Withdraw 10 μL of DNA Sample 1 from the microcentrifuge tube by filling only the needle tip of a clean pipet. Note: Fill the tip by squeezing the pipet just above the tip, not the bulb. Be careful not to draw the sample further up the pipette (see Figure 2)
  10. Dispense the sample into the first well by holding the pipet tip just inside the well. The sample will sink to the bottom of the well. Caution: Do not puncture the bottom or sides of the well. Do not draw liquid back into the pipet after dispensing the sample (see Figure 3).
  11. Record the DNA sample number on the DNA Banding Worksheet in the appropriate well box.
  12. Using a fresh pipet, withdraw 10 μL of DNA Sample 2 and load it into well 2, adjacent to DNA Sample 1.
  13. Record the DNA sample number on the DNA Banding Worksheet in the appropriate well box.
  14. Repeat steps 12 and 13 for the remaining DNA samples. Use a clean pipet for each sample. Load each sample into the adjacent well. Each student group will load four wells.

 Part B. Running a Gel

  1. Place the lid on the electrophoresis chamber and connect the unit to the power supply according to your teacher’s instructions.
  2. Run the gel as directed by your teacher. Note: Bubbles should form along the electrodes in the chamber while the sample is running. The bubbles are the result of the electrolytic decomposition of water; hydrogen is produced at the cathode and oxygen at the anode.
  3. Turn off the apparatus to stop the gel when the first tracking dye is 1 cm from the positive end of the gel. (This may take 30 minutes to 2 hours. The time necessary to run a gel depends on the type of electrophoresis apparatus and the applied voltage.)
  4. When the power is off, remove the cover and carefully remove the gel tray from the chamber. Place the gel tray on a piece of paper towel. Note: Be careful not to break or crack the gel.

Part C. Staining the DNA
For best results, stain the gel immediately, and place in a refrigerator overnight with water to destain.

  1. Slide the gel off the tray and into the staining tray. Note: Do not stain the gel tray.
  2. Gently pour 40 mL of the methylene blue electrophoresis staining solution into the staining tray.
  3. Allow the gel to stain for 5–10 minutes.
  4. Pour off the stain into a glass beaker. The stain may be reused. Be careful not to damage the gel.
  5. To destain the gel, gently pour room temperature tap water into the staining tray. Do not pour directly onto the gel to avoid damaging the gel. Note: Do not exceed 37 °C—warmer water may soften the gel.
  6. Occasionally agitate the water for 10 minutes.
  7. Pour off the water into a waste beaker.
  8. Repeat steps 5–7 until the DNA bands are distinctly visible.
  9. If the bands are too faint to be observed, repeat steps 2–8.
  10. Complete the DNA Banding Worksheet.

Part D. Storing the Gel
Stained gels may be stored in a laboratory refrigerator for several weeks.

  1. Label a resealable bag with the group name and the date.
  2. Place the stained gel into the resealable bag.
  3. Add 2 mL electrophoresis buffer and 3 drops of methylene blue electrophoresis staining solution to bag.
  4. Place the sealed bag in a refrigerator as directed by your teacher.
  5. Consult your instructor for appropriate disposal procedures.

Student Worksheet PDF


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