Genetics Exam 2 Human Genome Project

Genomics:

Comprehensive study of the genomes from humans and other organisms

CNV's:

Copy Number Variations A large DNA segment that is found a variable number of times in the genome Due to gene deletions and duplications

Discuss potential benefits of the human genome project as related to the field of medicine.

Gene Testing: improve diagnosis of disease, detect genetic predispositions to disease Gene Therapy: treat patients with genes in which they are deficient Pharmacogenomics: design custom drugs based on individual genetic profiles

The Cancer Genome Project:

Goal is to determine the gene expression profiles of normal, pre-cancer, and cancer cells with the hope of developing improved detection, diagnosis, and treatments.

The Road map to Epigenomics:

Goal is to identify regions of DNA methylation, histone modifications, chromatin accessibility, and small RNA transcripts associated with normal cells as well as human disease.

Project proteomics:

Identify individual proteins and protein-protein interactions necessary for critical life processes. Develop gene expression profiles and identify proteins that are markers for diseases (biomarkers). Find proteins that could be targets for the development of drugs to treat genetic disorders and other diseases.

Discuss the purpose and findings of the ENCODE project.

Purpose: to identify all functional elements in the human genome Exciting findings (Sept. 2012): - ~80% of the genome is functional - Many of the "genes" code for RNA, not protein, as the end product - These long noncoding RNAs (lncRNAs) play a role in gene regulation - ~90% of SNPs associated with human disease and other phenotypes fall outside of the protein-coding regions.

1000 genomes project:

Started in January 2008, A study to sequence the genomes of at least 1,000 people around the world, Purpose is to further refine the human genome map by establishing a detailed catalog of genetic variations (SNP's, CNV's), Now planning to sequence genomes of 2500 people from 25 populations worldwide using next generation sequencing.

Proteomics:

Study of all the proteins present in a cell at a given time.

Human Microbiome project:

The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans (the human microbiome). Launched in 2008, it was a five-year project, best characterized as a feasibility study, and had a total budget of $115 million. The ultimate goal of this and similar NIH-sponsored microbiome projects was to test how changes in the human microbiome are associated with human health or disease. This topic is currently not well understood. Important components of the Human Microbiome Project were culture-independent methods of microbial community characterization, such as metagenomics (which provides a broad genetic perspective on a single microbial community), as well as extensive whole genome sequencing (which provides a "deep" genetic perspective on certain aspects of a given microbial community, i.e. of individual bacterial species). The latter served as reference genomic sequences — 3000 such sequences of individual bacterial isolates are currently planned — for comparison purposes during subsequent metagenomic analysis. The microbiology of five body sites was emphasized: oral, skin, vaginal, gut, and nasal/lung. The project also financed deep sequencing of bacterial 16S rRNA sequences amplified by polymerase chain reaction from human subjects.

Discuss some of the facts learned from the project.

The Human genome contains over 3 billion nucleotides and about 21,000 genes. Only about 1% of the human genome is composed of exons. Many human genes share similarities with other organisms, underscoring the unity of life.

Physical map-

shows order and physical distance between genes and genetic markers, measured in bases, kilobases (kb), or megabases (Mb) Based on different strategies Human DNA is cut into fragments by specific enzymes called restriction endonucleases Fragments are cloned in vectors such as bacteria or yeast • Clones are screened for landmarks, e.g. STS = sequence-tagged site Clones with overlapping markers are ordered into a contig map Various clones are selected for DNA sequencing

Cummings, 11th ed., pgs. 342-343, # 1, 4-6, 10, 11, 16,17

textbook questions

Discuss the 6 major goals of the human genome project.

1) To develop a high resolution genetic map of each human chromosome. 2) To develop physical maps of each chromosome. 3) To determine the nucleotide sequence of the entire human genome. Reference sequence of ~ 3 billion base pairs was published in 2003 (99% of gene-containing part of human genome sequenced to 99.9% accuracy) 4) To develop improved methods for DNA sequencing, gene identification, and data collection/analysis. 5) To identify and address the major ethical, legal, and social implications of the Human Genome Project (ELSI). 6) To sequence the genomes of other model organisms to study gene function and evolutionary relationships. Genomic maps of numerous organisms have now been completed: E. coli and many other microorganisms, baker's yeast, fruitfly, roundworm, rat, mouse, and dog

SNP's:

Single Nucleotide Polymorphisms A DNA sequence variation involving a single nucleotide base

Evaluate ethical issues related to the human genome project.

ethics/opinions

Genetic map-

shows the order and relative distance between genes and genetic markers on a chromosome; deduced from studies of genetic linkage.