SNPs

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SNPs

• Human Genome

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SNP Typing

• Allele specific hybridization
• ASO probes usually with the polymorphic base in a
  central position in the probe sequence

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SNP Typing

• minisequencing reaction or single nucleotide
  primer extension where the polymorphic base is
  determined by the addition of the ddNTP
  complementary to the base interrogated by a DNA
  polymerase.
• Secondly there is the allele-specific extension
  where the DNA polymerase amplifies only if the
  primers have a perfect match with the template.

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SNP Typing

• Taqman TaqMan this assay is based in the
  5nuclease activity of Taq polymerase. When the
  probes are intact, the quencher interacts with
  the fluorophore by FRET, quenching their
  fluorescence.
• one probe is complementary to the wild-type
  allele and the other to the variant allele. These
  probes have different fluorescent dyes attached
  to the 5end and a quencher attached to the 3
  end.
• In the extension step, the 5 fluorescent dye is
  cleaved by the 5 nuclease activity of the Taq
  polymerase, leading to an increase influorescence
  of the reporter dye. Mismatch probes are
  displaced without fragmentation.

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ADAM33 Astma

• Linkage analysis performed using multipoint
  linkage LOD score (MLS) of 2.94 near D20S906 and
  a second MLS of 2.94 at D20S482.
• 218 nuclear families, the asthma plus BHR
  phenotype increased the evidence for linkage (MLS
  of 3.93 at D20S482, 35 excess allele sharing)
  and refined the candidate region to the second
  peak
• The region spanned 4.28 centimorgans (cM) (from
  9.08 cM to 13.36 cM, Fig. 1b) within markers
  D20S842 and D20S849. (BAC) clones were sequenced
  to facilitate gene identification

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Identification of 40 genes

• A combination of public data mining,
  complementary DNA (cDNA) library screening,
  direct cDNA selection and polymerase chain
  reaction with reverse transcription (RTPCR) was
  used to characterize 40 genes

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Association Studies

• Unrelated affected offspring from families
  showing evidence for linkage were selected as
  cases.
• Caucasian controls were collected in both the US
  and the UK in order to match the country of
  origin with the cases.
• On average, 130 IBD-affected individuals and 217
  hyper-normal controls were compared for allele
  and genotype frequencies.

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Adam33

• Analyses of 135 nucleotide polymorphisms (SNPs)
  in 23 genes spanning the 90 confidence interval
  revealed that the ADAM33 region showed the most
  significant association signal in the linkage
  region.
• 130 kilobases (kb) to the left of ADAM33 and up
  to 40 kb to the right.

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Adam33

• Within this ,185-kb linkage disequilibrium
  interval, 24 SNPs in three genes were significant
  in either the combined or separate US/UK
  analyses.The majority of these SNPs (14) were in
  ADAM33.

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Linkage Disequilibrium
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Gene Structure and SNPs