Lab 1 BIOS110 Human Genome Project

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Jan 9, 2024

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BIOS110 WEB Lab 1 Human Genome Project LAB 1: THE HUMAN GENOME PROJECT Learning Objectives: Students will be able to do the following upon completion of this lab handout:  Define the terms genome, genomics, bioinformatics, autosomes, contig, base pairs, haplotype  Describe the historical background, purpose and major findings of the Human Genome Project  Understand the DNA sequencing method strategies used to sequence the human genome  Explain how identifying single nucleotide polymorphisms could lead to pharmacogenomics, a type of personalized medical treatment  Explain some ethical issues related to human genome sequencing and genetics Purpose: To learn about the human genome and the potential applications of DNA sequencing Lab Materials : Computer and internet access Background Reading : Human Genetics, Chapter 1 and Chapter 13 Chromosomes Optional Background Info: National Human Genome Research Institute : L essons Learned from the Human Genome Projec t (video), About Genomics , and YouTube (FYI) Map of the Second Genetic Code , the Epigenome, is Unveiled (article) The Epigenome at Glance (<2 minutes long video; closed captioning is available) I. Introduction: Overview of the Human Genome Project A genome is the entire DNA in an organism. The human genome is found in the nucleus as 23 pairs of chromosomes and is collectively composed of nucleotides made of the DNA base letters: adenine (A), thymine (T), guanine (G), and cytosine (C). Genomics describes the study of the genome and complex diseases, which caused by a combination of environmental factors and individual genes interacting with each other. Both public and private organizations were involved in the race to sequence the human genome. The HGP was coordinated by the government agencies in the United States by the Department of Energy and the National Human Genome Research Institute . The International Human Genome Sequencing Consortium included a global collaboration among 6 countries and 16 labs. Within 24 hours of assembly DNA sequences were submitted to a public database for anyone to view and study in 1996. The Human Genome Project (HGP) formally began in1990; a draft sequence was published in 2000, and was the project was completed in 2003 by sequencing the first human genome. Personalized treatment plans may be available in the future when individual DNA sequences, genetics and non- genetic factors are better understood. 1

BIOS110 WEB Lab 1 Human Genome Project FIGURE 1: Comparing Human Genome Sequence: Past and Present Human Genome Project Current DNA Sequencing Technology Estimated Cost $2.7 billion Under $10,000 Required amount of time 13 years (BAC method) Few days *Lab Activity: Watch this PBS video: Human Genome Project (closed captioning is available) Lab Report Question 1 : According to the video’s opening minutes, “The human genome was compared to a _Symphony___ that has been edited over a billion years.” a. symphony b. poem c. storybook Lab Report Question 2: Which of the following nucleotide base is not found in DNA base pairing? a. uracil (U) b. guanine (G) c. thymine (T) d. cytosine (C) Lab Report Question 3 : How bases are found in the human genome, which represents the instructions for making a human being? a. 1 million b. 3 billion c. 50 trillion Lab Report Question 4 : New computerized DNA sequencing technology allows scientists to sequence a ________ every second, instead of identifying a few hundred bases in a day by hand. a. billion bases b. million bases c. thousand bases *Lab Activity : Learn about the DNA donors for the DNA sequencing efforts of the company Celera Genomics. Lab Report Question 5 . What are the two (2) most interesting facts that you learned about the DNA donors used for human genome sequencing project? Why are these facts interesting to you? One of the most interesting facts that I learned about DNA donors is that they chose specifically 3 females and 2 males. Another fact that I found interesting was the one about how there was 27 million sequences made up from the 5 individuals. Lab Report Question 6 : If all humans share 99.9% of their DNA with each other (that is, 99.9% genetically identical), what questions or concerns do you have about finding disease genes in all people using the DNA database from Celera Genomics? If you have no concerns, briefly explain your answer. 2

BIOS110 WEB Lab 1 Human Genome Project Using a DNA database like the one from Celera Genomics, where humans are considered to share 99.9% of their DNA, does present certain challenges and considerations when searching for disease genes. There is one concern that comes to mind and that is Genetic Variation. Because even though humans share 99.9% of their DNA, the remaining 0.1% accounts for significant genetic variation among individuals. This variation can have a profound impact on an individual's susceptibility to diseases. So, the challenge is in identifying the specific genetic variations that contribute to disease susceptibility within this small fraction of genetic differences. Lab Report Question 7 . If the DNA sequencing technology becomes more easily available for each citizen to afford to have done, suggest a reason for (pro) and a reason against (con) for each individual's DNA sequence be included in his/her medical records? a. PRO Argument (In support of) Personalized Medicine: Including an individual's DNA sequence in their medical records can enable personalized medicine. Healthcare providers can tailor treatments and interventions based on a person's genetic profile, increasing the likelihood of successful outcomes and reducing adverse effects. b. CON Argument (Against) Privacy Concerns: Genetic information is highly personal and sensitive. Including DNA sequences in medical records could raise significant privacy concerns. There's a risk of unauthorized access, discrimination, or misuse of this information, potentially leading to insurance or employment discrimination. II. Bioinformatics and DNA Sequencing Methods A new field of research called bioinformatics emerged from the race to sequence the human genome. Bioinformatics is the interface of computer technology being used to manage genomic information – to obtain, store, and analyze DNA to identify molecular targets for new drugs and characterize human diseases. Bioinformatics computer scientists and computational biologists are major contributors to research taking place in pharmaceutical companies, government agencies and many universities. Automation and sequencing technology were common facts in the public and private groups. A variation of the shotgun sequencing technology was used: small DNA fragment were made, sequenced and used to reassemble the final DNA sequence based on sequence overlaps and aligning landmarks within the genome. Two strategies were used to sequence the human genome – 3

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BIOS110 WEB Lab 1 Human Genome Project (1) map based sequencing using bacterial artificial chromosomes (BAC) and (2) whole genome shotgun sequencing. Both methods create a finished DNA sequence by assembling overlapping DNA fragments in sequential order using different landmarks in the genome to align sequences. The Human Genome Project group of collaborating labs followed the “divide-and-conquer” strategy using the BAC method, or map-based sequencing. The BAC method maps the DNA fragments before sequencing - the BAC clones were “mapped” to specific chromosomes first so spatial relationships of shorter, overlapping DNA sequences could be identified. Human DNA was broken up into fragmented pieces, inserted into a vector, and cloned (copied) into bacteria cells that replicate in large numbers very quickly to provide enough DNA to be extracted and analyzed further. Individual BAC clones were sequenced using the shotgun sequencing method. A “BAC “library” of as many 20,000 different clones containing short, overlapping DNA sequences were assembled together to identify the 3 billion base pairs of the human genome. Whole shotgun sequencing was invented for large-scaled DNA sequencing, creating and sequencing random DNA fragments of the entire genome by Eugene Myers worked at Celera Genomics, a private company owned by scientists and entrepreneur Craig Venter. Computer algorithms were created to facilitate DNA sequencing and supercomputers were used to sequence the DNA from five volunteers of various demographic backgrounds; one of the DNA donors included Craig Venter himself. The entire genome was randomly broken apart and pieced back together using overlapping sequences and identifying markers (of repeating elements of non-gene coding sequences ) into the final sequence. Whole genome shotgun sequencing of the whole human genome took only 9 months from (September 1999 to June 2000) to complete using supercomputers composed of 7,000 processers working 1,000 faster than traditional computers at the time. How is DNA sequencing done? The sample is obtained and the DNA is extracted. The DNA in the chromosomes are cut into smaller pieces. A computer is used to determine the DNA sequence and assemble the smaller DNA pieces into correct order *Lab Activity : Watch this video about DNA Sequencing ( closed captioning available) Lab Report Question 8 : The human genome is made of 46 total chromosomes (or 23 pairs of chromosomes) which includes _________ as shown in a karyotype (textbook page 231, Fig 13.3 and karyotype video ) An autosome is a non-sex chromosome, or a body chromosome. a. 46 autosomes; no sex chromosomes b. 45 autosomes; 1 sex chromosome (e.g., Z for females; R for males) c. 44 autosomes; 2 sex chromosomes (e.g., XX for females; XY for males) 4

BIOS110 WEB Lab 1 Human Genome Project Lab Report Question 9: Which DNA sequencing method was developed first? a. whole genome shotgun sequencing b. map-base sequencing Lab Report Question 10 : Overlapping DNA sequences were identified then a contiguous series of clones (called a “contig”) which were analyzed to create a physical map of the DNA genome a. True b. False Lab Report Question 11 : Physical map distances (of the size of a gene or genome) are measured in base pairs because DNA is usually double stranded. Counting the total number of base pairs present in the DNA sequence usually equals the number of nucleotides in a single strand. A kilobase (kb) corresponds to ______________ or 1,000 base pairs. A megabase (mb) corresponds to ______________ or 1,000,000 base pairs. a. hundred; thousand b. million; billion c . thousand; million 5

BIOS110 WEB Lab 1 Human Genome Project Lab Report Question 12 : The whole genome shotgun sequencing method is _________ and was developed by Craig Venter’s research team at Celera Genomics. a. more time consuming and required more map-based sequencing work b. less time consuming and required new software to assemble overlapping sequences of different sized DNA fragments of the entire genome FIGURE 2: Major discoveries and consequences of sequencing the human genome  Humans are estimated to have 20,000 genes within the 3 billion base pairs of the genome.  More than 1,800 disease genes have been identified  More than 2,000 genetics have been developed  More than 350 biotechnology products are being tested in clinical trials  Technology and tools used to sequence the human genome are now being used to study the genome of other organisms (e.g., fruit fly, mouse, etc)  The Ethical, Legal and Social Implications research program was developed  Longest human chromosome: Chromosome 1 is made of 249 million nucleotide base pairs  Shortest human chromosome: Chromosome 21 is made of 48 million nucleotide base pairs  Human chromosome with most genes: Chromosome 1 has ~3,168 genes  Human chromosome with the fewest genes: Male Y chromosome has ~344 genes  To learn more facts: The Human Genome Project Completion: Frequently Asked Questions III. Human Genome Size and Single Nucleotide Polymorphisms (SNPs) in the DNA If the all of the DNA letter bases were typed in 12 size font, the human genome would stretch from New York City to Los Angeles. It has been said it would take 50 years to type the 3 billion base pairs at the rate of typing 8 hours a day. However, a typical cell takes only 8 hours to copy the entire genome with minimal replication errors. 6

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BIOS110 WEB Lab 1 Human Genome Project The 46 total chromosomes are actually the 23 pairs of chromosomes – a set of 23 chromosomes inherited from each biological parent. Humans are 99.9% are like based on their similar DNA sequences. Differences in nucleotide sequences are called polymorphisms. As many as 10 -11 million single nucleotide polymorphisms (SNPs; pronounced as “snips”) have been identified and located. Mapping out and identifying SNPs have forensic applications for potentially identifying families and individuals. A SNP in only one DNA strand would also have SNP mutations in their second complementary DNA strand as shown in Figure 7.9 on textbook page 134. *Lab Activity : Click on the following hyperlink to Making SNPs (“snips”) Make Sense Lab Report Question 13 . Each combination of SNPs in a specific DNA region is called a ___________. Different percentages of these SNP combinations may exist in a large population of people. Each person inherits a ______ pair (one copy from dad and one copy from mom), which can be the same or different combination that can be regarded as a person’s SNP profile. a. genotype b. haplotype c. phenotype d. typo Lab Report Question 14. People with different SNP profiles may respond differently to albuterol, an asthma medication. Looking for common SNP profiles in 3,000 bases of the ______ gene in asthmatics may help better predict which persons will respond well to the albuterol, or if another medication is needed. (Recall that genes provide the DNA instructions to make proteins.) View the “Applying SNP Profiles to Drug Choices” menu tab of the above SNP website and use the arrows. a. HIV receptor gene b. Insulin gene c. hemoglobin gene d.ADRB2 gene IV. The Future of Pharmacogenomics People are known to respond to and metabolize drugs differently, such as seen with cancer treatments. One probable reason is due to genetic variations found in individuals, which has led to a new field of research called pharmacogenomics – a combination of the study of traditional pharmaceutical sciences and the genome’s DNA variations found in people. Single nucleotide polymorphisms (SNPs) are the most common DNA variations, which are often linked to an individual’s response to a drug and susceptibility to certain diseases. The gene products, or proteins, are responsible for processing and metabolizing the drugs so accurate genetic testing is an important research focus. As a form of personalized medicine, pharmacogenomics can lead to better choices about treatment options and drug dosage based on an individual’s genomic variations. The economic value of pharmacogenomics studies is in reducing the number of failed drug trials, adverse drug reactions, and side effects with directed treatments. 7

BIOS110 WEB Lab 1 Human Genome Project Lab Report Question 15 : Although the beneficial impact of using pharmacogenomics is promising, what are 2 limitations or potential problems that pharmaceutical companies, scientists and doctors may face in helping making patients recover more effectively? *Lab Activity : Click on the following hyperlink to Your Doctor’s New Genetic Tools video. Closed captioning (cc) is available. Then answer the lab questions. 8

BIOS110 WEB Lab 1 Human Genome Project Lab Report Question 16: What condition is the patient Latrice being treated for in this website? a. malaria b . leukemia (cancer of the white blood cells) c. Crohn’s disease d. asthma Lab Report Question 17: The toxic chemotherapy drug Purinethol works by incorporating itself into the rapidly dividing cancer cells causing cell death. It was discovered that people had different enzyme activity of TMPT, which inactivates and breaks down Purinethol. No or very low levels of TMPT enzyme activity could be _____to the leukemia patient. a. fatal causing death and severe side effects b. beneficial causing healthy effects Lab Report Question 18 . The patient Latrice has her DNA sample tested for the DNA variant for TMPT enzyme activity based on SNP profiling. Her DNA test results indicate that she has the genetic variant for _____ TMPT enzyme activity so she is given _____ of the Purinethol to treat her cancer. a. high; large dose b. high; small dose c. partial; small dose Applications of Genetic Knowledge *Lab Activity: Explore some of the policy, legal and ethical concerned are described on the website Policy Issues in Genetics , sponsored by the National Human Genome Research Institute. Lab Report Question 19 : According to the National Human Genome Research Institute website link, what are two (2) examples of genetic issues you did not know about before and briefly explain why do you think these issues deserve further discussion and debate? * Lab Activity – Read the following May 2015 article by clicking on this hyperlink Pint-sized DNA sequencer impresses first users Lab Report Question 20 : What are the two (2) important facts that you learned from reading about the “pint sized DNA sequencer” article? And would you recommend more research dollars be spent on similar DNA technology? Why and why not? One important fact I learned about was the Minion and I think if the money is going to efficient technology, I definitely think it would be worth it if done properly. Bonus Points: Lab Report Question 21 . A criminal investigator has learned about SNP profiles and different drug responses. Now he/she wants to use SNP profiles to identify suspects involved in a crime with DNA evidence. How would using SNP profiles be useful and what additional evidence 9

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BIOS110 WEB Lab 1 Human Genome Project might be needed to verify identity? Using SNP (Single Nucleotide Polymorphism) profiles in criminal investigations can be a valuable tool for identifying suspects involved in a crime with DNA evidence. SNP profiles offer several advantages: Increased Discrimination: SNP profiling can provide a higher level of discrimination compared to traditional DNA profiling methods like STR (Short Tandem Repeat) analysis. This means that SNP profiles can distinguish between individuals more effectively, reducing the likelihood of false positives or matches with unrelated individuals. Ancestry Information: SNP profiles can also provide information about an individual's ancestry, which can be useful in narrowing down potential suspects based on their ethnic or geographical background. However, using SNP profiles alone may not be sufficient to establish a suspect's identity definitively. To verify identity, additional evidence and steps should be considered: Link to the Crime Scene: SNP profiles alone can establish a genetic profile, but they do not link a person to a specific crime scene. To establish a suspect's involvement in a crime, there should be other forms of evidence such as eyewitness testimonies, surveillance footage, or physical evidence connecting the suspect to the crime scene. Chain of Custody: It is crucial to maintain a strict chain of custody for all DNA samples and evidence to ensure that the samples have not been tampered with or contaminated during collection, transportation, and analysis. 10

Lab 1 BIOS110 Human Genome Project

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