DNA Polymorphisms: DNA markers a useful tool in biotechnology

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DNA Polymorphisms DNA markers a useful tool in
biotechnology

• Any section of DNA that varies among individuals
  in a population many forms.
• Examples include SNPs RFLPs STRPs and AFLPs
• RFLPs include VNTRs and STRPs
• microsatellites (STRs) SSLPs STRPs SSRs
• Useful for finding mapping genes involved in
  disease and
• Individual identification epidemiology
  anthropology population/ecology studies
  taxonomy.

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SNPs
Single nucleotide polymorphisms regions of DNA
where one base pair is different. Occur evenly
spread over all the DNA. 1/ 1000-3000
bp Detected by sequencing. If SNP occurs in a
restriction enzyme site it generates an
RFLP. Could be in coding or non-coding
regions. Over 300000 human SNPs known and are
being mapped.
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SNP
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RFLPs

• Restriction fragment length polymorphism.
• Any difference in the DNA that results in a
  restriction enzyme producing a different sized
  piece.
• Mutation at a restriction site prevents
  recognition cutting.
• Results in one band of larger DNA instead of 2
  smaller ones.
• Different numbers of repeats between restriction
  recognition sites also generates an RFLP

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RFLPs
www.ncbi.nlm.nih.gov/.../doc/TechRFLP.shtml
DNA marker may be associated with genetic
condition.
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VNTRs and STRPs as RFLPs Minisatellites and
Microsatellites

• These are RFLPs because they are defined by or
  visible following restriction enzyme cuts.
• Variable Number Tandem Repeats
• Groups (10-100) of nucleotides repeated 2 100
  times (depending on individual and locus).
• Restriction sites on both sides of repeated DNA
• The more repeats the longer the fragment.
• Simple Tandem Repeat Polymorphisms
• Shorter 2-9 nucleotides repeated
• Small enough number for PCR amplification
• Also called STRs SSLPs etc.

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Use of VNTRs
Restriction sites are on either side fragment
length depends on number of repeats in between
sites.
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STRPs
Primers for both sides of repeated region allow
PCR amplification of DNA generates PCR products
that differ in length depending on number of
repeats. Becoming the standard method for DNA
testing in forensics labs. Cheaper easier more
sensitive.
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Hardy-Weinberg meets Gil Grissom

• Simple tandem repeats
• 13 have been chosen for use in forensic work
• The 13 independently assort meaning they are on
  different chromosomes or far apart on the same.
• Product law can be used
• Each of the 13 have a number of different alleles
• Alleles differ by number of repeats
• Repeats vary from 3 to 5. vWA is a
  tetranucleotide.
• Allele frequencies p1 p2 etc. for each allele
• Humans are diploid have 2 alleles for each locus

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STRs in forensics

• Locus vWA
• 14 0.081
• 15 0.107
• 15.2 0.179
• 16 0.306
• 17 0.192
• 18 0.089
• 19 0.047

Alleles in different ethnic and racial groups
examined used as database. Panel of 13
different STRs are used. Because the odds of a
particular combination of the 13 is product of
the frequencies numbers like 1 in 10 billion can
be generated. Hardy-Weinberg 2pq
Band frequency
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THE 13 CODIS STRs and probabilities of Identity
http//expertpages.com/news/dna.htm
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Allele frequencies for D1S80 among US population
groups
Chance of a white person being heterozygous for
alleles 19 and 20 2 x 0.003 x 0.018 (One in
9259)
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RAPD using PCR to find polymorphisms

• Random amplified polymorphic DNA
• Screen DNA from individuals by doing PCR with
  random short primers. (about 8-12 nucleotides)
• By random chance primers will amplify many
  different sections of DNA.
• Look for bands on gel that are not present in
  each individual tested.

avery.rutgers.edu/.../ archives/onions/rapd.html
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RAPD using PCR to find polymorphisms-2