The Genome Access Course Sequence Variation

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The Genome Access CourseSequence Variation
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Any two copies of the human genome have 1
difference per each 1000 nt
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Variation Types

• Cytological level
• Chromosome numbers
• Segmental duplications, rearrangements, and
  deletions
• Molecular level
• Transposable Elements
• Short Deletions, Sequence and Tandem Repeats
• Sequence level
• Single Nucleotide Polymorphisms (SNPs)
• Small Nucleotide Insertions and Deletions (Indels)

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Variation is useful

• Identify genetic basis for
• Disease risk
• Reactions to environmental triggers
• Responsiveness to drug treatments
• Forensics
• Genetic and physical mapping
• Evolution

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RFLP
SSR
a
x
y
b
a,a a,b b,b
Radioactive probes
Gel electrophoresis
Human Molecular Genetics (Strachan Read 2004)
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• SSR are not frequent enough for complex disease
  association studies
• SNPs are the most abundant type of polymorphism
  (1 SNP has been discovered every 2000 nt)
• 1 every 300 bases on average in the worlds human
  population
• To be considered a polymorphism, the minor allele
  must have a frequency gt 1
• Coding SNPs are more informative for phenotype
  associations but they are less frequent

GATTTAGATCGCGATAGAG GATTTAGATCTCGATAGAG
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Most common diseases are caused by a combination
of genes and environment
Stroke
Manic-depression
Myocardial Infarction
Breast cancer
Hypertension
Diabetes
High Cholesterol
Obesity
Schizophrenia
Inflammatory Bowel Disease
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The SNP consortium

• Construct high density human SNP map for medical
  and population genetics studies
• Identify 1 M candidate SNPs by shotgun sequencing
  of genomic fragments form 24 individuals

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SNPs in Shotgun Genomic Sequences
HGP reference sequence
Shotgun sequences
SNP
SNP
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The SNP consortium

• Construct high density human SNP map for medical
  and population genetics studies
• Identified 1 M candidate SNPs by shotgun
  sequencing of genomic fragments form 24
  individuals
• An additional 1 M SNPs were identified by the HGP
  in the overlaps between BAC clones

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SNPs in Overlapping Genomic Sequences
Overlapping BACs from library
SNP
50 of overlaps contain polymorphisms
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SNP Map

• 1.42 M non-redundant SNPs
• 95 estimated to be polymorphic in at least one
  population (1500 SNP genotyped)
• 82 percent of the SNPs have a minor allele
  frequency gt10

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Types of SNPs

• Genic, coding SNPs
• Non-synonymous
• Synonymous
• Genic, non-coding SNPs
• Regulatory SNPs
• Intronic SNPs
• Intergenic

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The challenge Genotyping

• Sequence comparison
• Genomic sequences
• ESTs
• BACs
• PCR (TaqMan)
• Microarrays
• SSCP
• DHPLC

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TaqMan
R
C
A
AA genotype Red (shown) CC genotype Green AC
genotype R G
R
R
Sayers et al. In SNP and Micro satellite
Genotyping, Biotechniques Pub., MA 2000
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Microarrays
Oligo matching the A allele
Oligo matching the C allele
Wang et al. Science 1998
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Haplotypes
(4 haplotypes in the population for a 6000 bp
region)
The International HapMap Consortium, Nature 2003
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The International HapMap Project

• Genotype 600,000 SNPs in 270 DNA samples from
  several populations from difference ancestral
  geographic locations
• Genotype additional SNPs in regions where
  associations are weak

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Tag SNP
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Sites for Viewing SNPs

• UCSC Browser (http//genome.ucsc.edu)
• SNP Consortium (http//snp.cshl.org/)
• NCBI dbSNP (http//www.ncbi.nlm.nih.gov/SNP)
• Ensembl (http//www.ensembl.org/)

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