Chapter 20: Single-nucleotide Polymorphism Profiling

Chapter 20: Single-nucleotide Polymorphism Profiling

Variations in the human genomeSingle-base pair change originating

from spontaneous mutationsMajority of human DNA

polymorphisms1.4 million identifiedMost are bi-allelic

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Advantages: SNPs are abundant and can be used as

markers SNP amplicon sizes are smaller than STR▪ 50-100 bp in length

Low mutation rates▪ Good for paternity

Many methods available ▪ Multiplex systems

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Disadvantages: SNPs are not as polymorphic Difficult to resolve mixed profiles Majority of DNA databases contain STR

profiles instead of SNP

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First use was with sequence polymorphisms at the HLA-DQA1 locus

Commercial kits: DQα AmpliType Kit AmpliType PM PCR amplification and

Typing kit

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Allele-specific oligonucleotide hybridization assays Analyzes single nucleotide variations at

a given locus ASO probes hybridize to its

complementary DNA sequences in question to distinguish known polymorphic alleles

PCR based

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Forensic identification Paternity Ethnic origin

Phenotyping Nonsynonymous SNPs Can reveal physical characteristics (e.g.

eye color)

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Victim identification & Sexual assault cases

Amelogenin (AMEL) marker usedAMELX & AMELYAMELY null mutations

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