DNA Typing Systems

Question 1

What are the strengths of DNA testing?

Answer 1

1. Discriminatory potential
2. Great sensitivity
3. DNA is stable in comparison to proteins

Question 2

What are the advantages of short tandem repeats?

Answer 2

1. Can be used w/ degraded samples
2. Small amount of DNA
3. Number of loci is large
4. Multiplexing and automation

Question 3

What are the limitations of short tandem repeats?

Answer 3

1. Possibility of contamination is increased
2. Equipment expensive
3. Micro-variants (differ by less than one repeat)

Question 4

What is the difference between VNTR (minisatellite) & STR (microsatellite)?

Answer 4

1. VNTR → short nucleotide sequence unit
   STR → highly repetitive DNa
2. VNTRs are larger than STRs
3. VNTR → repeating unit consists of 10-100 nucleotides
   STR → repeating unit consists of 2-13 nucleotides

Question 5

What are single nucleotide polymorphisms?

Answer 5

Alterations at a single nucleotide position
Occurs once every 300 nucleotide base pair

Question 6

What are the advantages of SNP?

Answer 6

1. Very numerous in mammalian genomes
2. Single base changes → very short amplicons can be employed
3. Whole genome SNPs microarrays → powerful for biogeographic identification

Question 7

What are the limitations of SNP?

Answer 7

1. Bi-allelic → 3/4 alleles
2. Less informative than multi-allelic STRs → complicates analysis of mixed samples
3. Whole-genome SNPs microarrays → substantial amount of DNA

Question 8

What are some limitations of systems w/ sex-specific transmission used for human identification?

Answer 8

1. High mutation rate
2. Heteroplasmy
   → more than one mtDNA genotype occurs in one individual
   → levels of heteroplasmy may not always be the same in various tissues
   → 1 mtDNA type in 1 tissue & different type in different tissue
3. Lack of recombination

Question 9

What is the advantages of using mtDNA?

Answer 9

1. Small amounts of DNA can be informative
2. Not degraded as fast as nuclear DNA
3. Useful marker for tracing family lineages
4. Discriminatory power is larger than a single nuclear locus

Question 10

What are the limitations of using mtDNA?

Answer 10

1. Cannot distinguish among maternal relatives
2. Heteroplasmy can complicate the analysis
3. MITOMAP → discrimation power limited by the database size

Question 11

When are Y chromosome markers useful in the forensic field?

Answer 11

1. Excluding males in crime cases
2. Kindship testing
3. Disaster victims investigations

Question 12

What is the NGS HLA typign workflow?

Answer 12

1. Sample prep
2. HLA PCR
3. Library construction
4. NGS Seq
5. Raw data
6. Bioinformatics Analysis
7. High resolution HLA results

Question 13

What are the benefits of NGS vs. Sanger Sequencing?

Answer 13

1. Higher sensitivity to detect low-frequency variants
2. Faster turnaround time for high sample volumes
3. Comprehensive genomic coverage
4. Higher throughput with sample multiplexing
5. Ability to sequence hundred to thousands of genes or gene regions simultaneously