1. SNP Detection
Congtam Pham
2/24/04
Dr. Marth’s Class

2. Reduced Representation Sequencing
600
500
400
clone
analyze

3. Random Shotgun Reads Aligned to Whole Genome
entire genome
reads

4. Overlapping BAC Clones

5. ESTs may contain multiple exons
whole genome
ESTs
may contain multiple exons
- may be alternative splice variants of a single gene

6. Results: Validations: 1.42 million SNPs throughout the human genome
average density = 1 SNP/ 1.3kb
Validations:
Random samples of SNPs evaluated in independent population samples to
allele frequency
95% - polymorphic
4% - non-polymorphic (false positives)
1% - uniformly heterozygous
Random samples of SNPs studied in different ethnic groups
82% - polymorphic in at least one ethnic group
(>10% allele frequency)
77% - polymorphic in at least one ethnic group
(>20% allele frequency)

7. Heterozygosity (π) of Chromosomes
Chromosome π (x10-4) Y X
remaining avg = 7.65

8. Nucleotide Diversity GC content, heterozygosity
HLA locus on chromosome 6
highly heterozygous

9. SNPs in the public domain: how useful are they?
Allele frequencies of SNPs found in dbSNP
TSC SNPs Overlap SNPs
# STSs that failed / (5.3%) / (14.8%)
PCR and sequencing
Total characterized
SNPs not detecteda / (17.3%) / (16.8%)
Uncommon SNPsb (6.0%) (7.1%)
Common SNPs in ≥1 populationc (76.7%) (76.1%)
Common SNPs in ≥2 populationc (52.4%) (54.3%)
Common SNPs in ≥3 populationc (27.0%) (26.9%)
amonomorphic (only one of the 2 predicted alleles found in all 3 populations
bminor allele frequency <20% in all 3 populations
ca SNP is “common” when minor allele frequency is ≥20%
Marth et al., 2001

10. Conclusions For researchers interested in using the publicly available
candidate SNPs:
66-70% chance that SNPs have <20% minor allele frequency
50% chance that SNPs have ≥20% minor allele frequency
Major Concern:
candidate SNPs may not be true polymorphisms but rather
duplicated regions of the genome with near-identical
sequences

11. Quality and Completeness of
SNP Databases
# SNPs identified %validated by resequencing
All SNPs %
Double-hit SNPs %
12% non-validation rate may be due to:
false-positive SNPs (errors in construction of SNP databases)
rare variants
false-negative SNPs (SNPs missed in resequencing)
population-specific SNPs
Different rates of non-validation reported in other surveys may reflect true SNPs
that were missed or inherent differences between the different sets of genes
Double hits are SNPs for which both alleles have been seen more than once and
therefore, more common and more ideal for the construction of haplotype maps