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 Lec 3.1


Lecture 3.1  Genome Mapping

Now moving from analysis of single loci or sequence comparisons to whole genomes--- more difficult and speculative analysis

Background about Maps

I. Genome maps

   A. Definition-- a graphical representation of the chromosome structure of an organism

   B. Tell us the order and relative positions of genes, markers, other landmarks on the chromosome

   C. Cytogenetic, Genetic, and Physical, plus others...

II. Cytogenetic Maps

III. Genetic Maps

   A. Genetic markers

    1. Genes-- expression of mutant alleles, dominant vs. recessive

    2. RFLPs-- Restriction fragment length polymorphisms (figure), codominant marker

    3. RAPD-- random amplified polymorphic DNA (figure), codominant marker
                         PCR primers of 8-10 nucleotides, essentially random sequence, try in different pairs

    4. STRP-- simple (short) tandem repeat polymorphism (figure), codominant marker, PCR based

            a. SSLP-- simple (short) sequence length polymorphism, an STRP with 2-9 bp repeating unit, sometimes called a microsatellite

            b. minisatellite--  repeating unit of 10-60 bp

   B. Genetic maps are based on recombination frequencies

    1. Review recombination (figures)

    2. LOD scores-- logarithm of odds score, take logarithm of (likelihood that two loci are linked/ likelihood that loci are unlinked)

    3. Limitations-- assumes recombination is equally likely throughout the chromosome, cannot separate or determine order of "close" markers, map may differ from actual physical distance

IV. Physical Maps

Based on actual DNA sequence, assemble sequence of various clones into long contiguous (continuous) sequence (contigs) of chromosome

Example of a YAC clone insert (note: chromosome 1 is ~8500 times larger than this YAC insert of about 29,000 bases)

Relies on Sequence tagged sites (STS), a short (100-300 bp), single-copy segment of DNA that can be amplified with a unique pair of PCR primers.

Need 30,000 such markers for complete, high-resolution map of human genome.  Such sites allow assembly of contigs  (figure)


V. Integrating the maps (figure)  NCBI and Genome Database (GDB) Mapview, Genome Database is at


VI. Transcriptional maps ---ESTs, Expressed sequence tags (similar to STSs only ESTs are made from mRNAs/cDNAs so the regions amplified by PCR are from expressed regions, i.e., genes)


VII. HapMaps-- based on SNPs (single nucleotide polymorphisms). Sites in the genome where the DNA sequences of many individuals differ by a single base. For example, some people may have a chromosome with an A at a particular site where others have a chromosome with a G. Each form is called an allele.





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