Genomics

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Genomics
Prof. Arnaldo Ferreira
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15.1 Genomic Sequencing is an Extension of
Genetic Mapping

• Mutant genes are the basis of genetic disorders
• Mapping helps identify genes that cause disease
• The first step in developing diagnostic tests and
  treatments for these disorders

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Mapping Genes by Linkage

• Linkage
• Two or more genes located on the same chromosome
  that do not show independent assortment and tend
  to be inherited together
• When the degree of recombination (crossing-over)
  between linked genes is measured, the distance
  between them can be determined

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Recombination Frequencies are Used to Make
Genetic Maps

• A genetic map is made in two steps
• Finding linkage between two genes
• Measuring how frequently crossing-over takes
  place between them
• Centimorgan (cM)
• Unit of distance between genes on chromosomes
• One centimorgan equals a value of 1
  crossing-over between two genes

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Linked Genes on the Same Chromosome

• Crossover frequencies are used to construct
  genetic maps, giving the order and distance
  between genes on the chromosome

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Linkage and Recombination Can be Measured by Lod
Scores

• Lod method
• A probability technique used to determine whether
  two genes are linked
• Lod score
• The ratio of probabilities that two genes are
  linked to the probability that they are not
  linked, expressed as a log10
• Scores of 3 or more establish linkage

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Recombinant DNA Technology Changes Gene-Mapping

• Positional cloning
• A recombinant DNA-based method of mapping and
  cloning genes with no prior information about the
  gene product or its function
• Inheritance of molecular markers is used to
  follow the inheritance of genetic disorders in
  pedigrees

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15.2 Origins of the Human Genome Project

• Instead of finding and mapping markers and
  disease genes one by one, scientists organized
  the Human Genome Project (HGP) to sequence all
  the DNA in the human genome, identify and map the
  thousands of genes to the 24 human chromosomes,
  and assign a function to all the genes in the
  human genome

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Keep In Mind

• The Human Genome Project grew out of methods
  originally developed for basic research
  recombinant DNA technology and DNA sequencing

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15.3 Genome Projects Have Created New Scientific
Fields

• The size of the human genome required
  development of new technologies, including
  automated methods of DNA sequencing and advances
  in software to collect, analyze, and store the
  information derived from genome sequencing

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New Scientific Fields

• Genomics
• The study of the organization, function, and
  evolution of genomes
• Bioinformatics
• The use of software, computational tools, and
  databases to acquire, store, analyze, and
  visualize the information from genomics

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Methods of Sequencing DNA

• To sequence a small amount of DNA, DNA bases (A,
  T, C, G) are tagged with a radioisotope and
  combined with DNA fragments, which are then
  separated by size onto a gel with four lanes
• To sequence an entire genome, the process is
  automated each base is labeled with a different
  fluorescent dye which can be read in a single
  lane by a scanner linked to a computer

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Bioinformatics Storing and Accessing Genetic
Information

• Genomes are stored in databases the human genome
  contains over 3 billion nucleotides

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Some Fields of Genomics

• Comparative genomics
• Compares genomes of different species for clues
  to the evolutionary history of genes or a species
• Structural genomics
• Derives three-dimensional structures for proteins
• Pharmacogenomics
• Analyzes genes and proteins to identify targets
  for therapeutic drugs

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15.4 Genomics Sequencing, Identifying, and
Mapping Genes

• Geneticists developed two strategies for genome
  sequencing
• The governments genome project used the
  clone-by-clone method
• The privately-funded Celera genome project used
  the shotgun method

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The Clone-by-Clone Method

• Clone-by-clone method
• A method of genome sequencing that begins with
  genetic and physical maps
• Uses clones from a genomic library that have been
  arranged to cover an entire chromosome
• After the order of clones is known, they are
  sequenced

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Shotgun Cloning

• Shotgun sequencing
• A method of genome sequencing that selects clones
  at random from a genomic library
• After the clones are sequenced, assembly software
  organizes them into the genomic sequence

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Completing the Genome

• The bacterium Haemophilus influenzae was the
  first organism to have its genome sequenced
• Drafts of the human genome were published in
  2001and 2003 neither project sequenced the 15
  of the genome in heterochromatic regions

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Keep In Mind

• Genomics relies on interconnected databases and
  software to analyze sequenced genomes and
  identify genes

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Annotation is Used to Find Where Genes Are

• Annotation
• Analysis of genomic nucleotide sequence data to
  identify protein-coding genes, non-protein-coding
  genes, their regulatory sequences and functions
• Only 5 of human DNA encodes genes

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How are Genes Identified in a DNA Sequence?

• If a DNA sequence encodes a protein, its
  nucleotide sequence is an open reading frame
• Open reading frame (ORF)
• Codons in a gene that encode the amino acids of
  the gene product
• Control sequences (CAAT, CCAAT) at the beginning
  of genes splice sites between exons and introns
  poly-A tail at the end

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Genetic Sequence from Hemoglobin

• Splice junctions between introns and exons
  (blue) site where transcription begins (green)

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Geneticists Discover Gene Functions and Products

• After a gene has been identified by annotation,
  its amino acid sequence is derived and compared
  with sequences already in protein databases
• So far, functions have been assigned to about 60
  of known genes

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Amino Acid Sequence From Hemoglobin

• Derived from the DNA sequence

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15.5 What Have We Learned So Far About the Human
Genome?

• Only about 5 of our 3 billion nucleotides of DNA
  encode genetic information
• Genes are distributed unequally on chromosomes
• Clusters are separated by gene-poor bands
• Humans have 20,000 to 25,000 genes
• Far fewer than the predicted 80,000 to 100,000

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What Have We Learned So Far about the Human
Genome?

• There are more proteins in the body than genes
• mRNAs are processed in many ways so 20,000 to
  25,000 genes can produce 300,000 proteins
• Genomes of humans and other higher organisms are
  similar
• We share half our genes with the fruit fly and
  more than 90 with mice

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Keep In Mind

• The human genome has a surprisingly small number
  of genes and produces a surprisingly large number
  of proteins using a number of different mechanisms

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15.6 Using Genomics and Bioinformatics to Study
a Human Genetic Disorder

• Where is the gene located?
• What is the normal function of the protein
  encoded by this gene?
• How does the mutant gene or protein produce the
  disease phenotype?

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Mapping Genes and Gene Function

• The cystic fibrosis gene was easy to map, convert
  to amino-acid sequence, and determine its
  function, but more than half of identified genes
  have no known function

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Friedreich Ataxia

• Determining the mechanisms of Friedreich ataxia
  is more difficult
• Friedreich ataxia
• A progressive and fatal neurodegenerative
  disorder inherited as an autosomal recessive
  trait
• Symptoms appear between puberty and age 25

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Studying Friedreich Ataxia

• Using positional cloning, the FRDA gene was
  mapped to chromosome 9, then isolated, cloned and
  sequenced
• Parts of the frataxin protein matched sequences
  found in bacteria related to mitochondria
• Researchers found frataxin in mitochondria and
  determined its structure, but its specific
  function is still unknown

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15.7 Proteomics is an Extension of Genomics

• Proteomics is the study of the structure and
  function of proteins, which is important in
  development of new diagnostic tests and drugs
• Proteomics
• Study of expressed proteins in a cell at a
  specific time under a particular set of
  circumstances

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Role of Proteomics

• Understanding gene function and its changing role
  in development and aging
• Identifying proteins that are biomarkers for
  diseases used to develop diagnostic tests
• Finding proteins for development of drugs to
  treat diseases and genetic disorders

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Proteins Expressed in a Cell

• Separated by size and electric charge and
  displayed on a gel

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15.8 Ethical Concerns about Human Genomics

• To deal with the impact of genomic information on
  society, the HGP set up the ELSI (Ethical, Legal,
  and Social Implications) program to ensure that
  genetic information would be safeguarded, not
  used in discriminatory ways
• ELSI works to develop policy guidelines for the
  use of genomic information

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15.9 Looking Beyond the Genome Project What the
Future Holds

• In 2003, scientists of the Human Genome Project
  published a paper describing the impact of
  genomics, organized around 3 major themes
  Research in biology, health care, and society
• Each theme poses challenges

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The Future of Genomics Research

• Six fields were targeted for development as
  genomic and genetic information grows
• Resources Genome sequences and libraries
• Technology such as new sequencing methods
• Software for computational biology
• Training professionals in interdisciplinary
  skills
• Ethical, legal, and social implications
• Education of health professionals and public

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Genetics in SocietyWho Owns Your Genome?

• When John Moore had his spleen removed due to a
  rare form of cancer, his doctor patented a cell
  line and products derived from the spleen
• When Moore sued to share in the profits, the
  court ruled that patients had no property rights
  over tissues removed from their bodies

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Keep In Mind

• Genomics is affecting basic research in biology
  and generating new methods of diagnosis and
  treatment of disease

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New Methods of DNA Sequencing

• With current methods, it costs about 5 million
  to sequence a human genome
• A prize of 10 million has been offered for
  development of a method to reduce the cost and
  increase the speed of genome sequencing