Applications of Biotechnology & Genomics
Biotechnology: "The use of biological systems to create goods & services"
       Clinical :     Diagnosis & Treatment of human genetic diseases
       Forensic :  Data  Evidence in legal proceedings
                          Identification of unknown or questioned material
       Commercial : Production of transgenic products & organisms
                               Improvement of production traits of agricultural species

Genomics: the study of complete gene sets (genomes) of organisms
        Proteomics: study of coordinate protein expression patterns across genomes
                                "There is one genome, there are many proteomes."
        Bioinformatics:  computational analysis of genomic & proteomic data
Restriction Fragment Length Polymorphism (RFLP) Analysis

  Restriction maps vary among individuals & species according to DNA sequence
       SNPs alter restriction sites & produce Restriction Fragment Length Polymorphisms (RFLPs)
       RFLPs inherited in Mendelian co-dominant alleles

  Variation in the pattern of restriction digests identifies point mutations
   RFLPs may indicate point mutations (SNPs) directly
       Ex.: MstII RFLP test differentiates sickle-cell HbS versus HbA alleles [HOMEWORK]
   RFLPS can be genetic markers for specific alleles
       marker: restriction site shows presence / absence of genetically linked trait  [HOMEWORK]
            Markers do not cause the traits!
            Restriction fragment pattern indicates which trait alleles are present          

Allele-Specific Oligonucleotides (ASOs)

   Allelic differences due to single SNPs
        ASOs used as SNP-specific probes
        "Southern Blot" test without electrophoresis, probe "sticks" to only one allele:
            Genetic screen "positive or negative" result
            Ex.: 508-ASO Test for Cystic Fibrosis probes deletion mutation (OMIM219700)
       
    Pre-Natal Screening: the GATACCA model

       Ex.: Mr. & Ms. Mus seek genetic counseling ....
       Ex.: Pre-implantation Genetic Diagnosis (PGD)

[ See also Species-Specific Oligonucleotides (SSOs)
                Quantitative "Real-Time" PCR assays (RT-PCR) ]

DNA Fingerprinting
    Determination of an individual-specific genetic patterns
  
  Variable Number of Tandem Repeat (VNTR) loci

                Minisatellites - 15~100 nucleotide motifs repeated several times

                Microsatellites - di-, tri-, tetra-nucleotide motifs repeated 101s ~ 106s of times
                                              (CACACACACACA versus CACACACA) [IG1 21.02]
                 Origin by slipped-mismatch replication
         Copy number mutates rapidly, even between parents & children
             VNTR loci are highly polymorphic  [HOMEWORK] [IG1 21.03]
                  good marker for within-population studies [IG1 21.05]
                  [Animation of DNA Fingerprinting for forensics ]


        Forensics - use of DNA data as legal evidence [IG1 21.04]
             Positive identification of individuals [HOMEWORK] with high probability [IG1 21.06]
              CODIS Multiplex Fingerprinting [IG1 19.12]

DNA "Chips"
       Oligonucleotide probes ("oligos") immobilized on a glass chip
              randomly-cut genomic DNA is tagged & used to "probe" the chip
              [click here for an animation of DNA microarrays]

      "Variant Detector Arrays (VDAs)" detect specific SNP alleles in genome                                                             

       "GeneChips" perform automated "Northern" analysis:
             specific mRNAs or cDNAs are detected in proteome
            "heat map" indicate levels of gene expression

       DNA "re-sequencing (iterative) arrays" sequence ~500 Kbp in one experiment

Genomics: the genetic analysis of entire genomes    
               The Human Genome Project  (sponsored by HuGO)
               A statement of genetic ethics (Lee et al. 2008)
     3.2 x 109 base pair (3,200 Mbp) genome sequence completed
                10-year project launched 1990,
                    "First draft" announced March 2001,
                         "Finished draft" of euchromatic sequence, October 2004
                    
                Similar projects previously completed in Drosophila & Mus
                    Genome projects underway in multiple species (2014 list)

   'Top Down' Strategy: Move from large-scale  fine-scale map
            Large-scale mapping of chromosomes provides "scaffold"
            Fine-scale mapping of individual genes
            Sequence contigs   complete genome assembled as overlaps

  Insights: ~ 20,050 protein-coding "genes" in human genome [IG1 19 Table02]
                  ~   6,000 have unknown functions [IG1 19.02, 19.03]
                  Functions explored with Expressed Sequence Tags (ESTs)
                       partial sequences of 5' ends of cDNA reverse transcribed from mRNA [IG1 22.12]
                           cDNA   DNA sequence expressed as mRNA  presumptive "gene"
                           Sequences of ESTs with unknown functions from "non-model" species
                               compared with genes of known function from "genome-enabled" species

             >60% of genome without typical genetic function [IG1 19.06]
                       repetitive DNA arranged tandem or dispersed repeats [IG1 19.09]
                       Alu family constitutes 11% of human genome: affect splicing & transcription

              only  ~ 7,000 novel genes in Homo wrt Drosophila [IG1 19.04]
               Comparison of Homo & Chimpanzee (Pan) genomes  98.44% similar : What are the differences? 

      Bioinformatics: extracting biological information from (huge) data sets [e.g., NCBI GenBank resource]
           Example: Analysis of functional differences in Caspase-12 gene of Human versus Chimpanzee :                 
                          Go to NCBI data base: Search for  " Pan + Caspase 12 "
                          Go to  Nucleotide database: Retrieve chimp CASP12 DNA sequence in FASTA format
                          Identify human homolog human CASP12 (variant 2) with BLAST [Basic Local Alignment and Search Tool]                        
                          Find ORFs in chimp & human sequences with ExPASy: What's up with that?

    Proteomics: the total pattern of protein expression in an organism
             DNA Chips to explore life-stage & tissue-specific patterns

All text material ©2016 by Steven M. Carr