Biohistory Flashcards
Which techniques have a slow speed of analyis and a high power of discrimination?
- RFLP mutli locus probes
- RFLP single locus probes
Solutions for mixtures
- Y-chromosome STRs
- Y-chromosome SNPs
NGS promises the simultaneous analysis of:
- whole exomes
- complete genomes
- whole transcriptomes
- whole methylomes
- many selected targets
Handling inhibition in bones
- removal during extraction
- silica or BTA purification is efficient
- additional clean up by Microcon etc if needed
- counteract in PCR
- addition of BSA
- extra enzyme
- choosing a different enzyme
- dilution of samples
- inhibitors can be monitored by real-time PCR
What is the most common mtDNA haplogroup in Europeans?
H (40-50%)
Decoding procedure
- e.g. cash in transit case
- sequence send to UK
- decoded in UK
- code connected to batch in belgium
- Belgium provides information about who got the cash
What is the use of forensic DNA testing in forensic cases?
- analyse evidence samples at a crime scene
- exonerate innocently accused or convicted
- match traces with DNA profiles in database with convicted/suspects
How can DNA damage be repaired?
With UNG treatment
UNG: Uracil N-glycosylase
At high degree of damage, positions with C/T mixtures seen in mtDNA sequence analysis
- C–> T changes via U, introduced by deamination
- UNG treatment can reduce the number of damaged molecules reducing the C/T mixtures
- UNG removes deaminated C-residues
How is mtDNA assigned into haplogroups?
Defined by certain SNPS in the hypervariabe and coding region
Name reasons why analysis of skeletal remains may be very challenging
- low template amounts
- highly degraded DNA
- damaged DNA
- contaminated
- precious samples - limited availability
–> optimal protocol for all steps is thus highly important
Strategies to overcome inhibition
- counteract inhibitors
- dilution of the DNA extract
- addition of BSA or betaine
- addition of extra enzyme
- use of an inhibitor resistant enzyme
- performing a more efficient removal through the extraction procedure
- making sure that EDA is removed
- inhibitors are smaller molecules than DNA –> filter
- inhibitors may bind to dsDNA –> denature by NaOH treatment
Which techniques are fast in analysis, but have a low power of discrimination?
- poly marker
- D1S80 single STR
- DQalpha
- ABO blood groups
Can solvents, ageing, bleaching or UV radiation wash-out DNA tags ?
no
Which techniques have a slow speed of analysis and a low power of discrimination?
- mtDNA
Name some causes for DNA damage and degradation
Generally occurs with time, but may be facilitated by:
- high humidity
- high temperature
- UV-radiation
- chemicals
- microorganisms
What affects DNA decay?
- release of cellular enzymes
- bacteria
- free radicals
How many SNPs are predicted in the HIrisPlex and from how many genes? What does it predict with high accuracy?
- 24 SNPs from 13 genes
- red and black hair
- blue and brown eyes
Which techniques have a fast speed of analyis and a high power of discrimination?
- SNPs
- mini STRs
- multiplex STRs (highest power)
How does the DNA tagging system work?
One example (there are different systems)
- unique signature between primer regions
- billions of available codes - 20nt unique region wtih 4 possible variants in each position
- totally invisible solution
- tags are unknown to the user
- the sequence of tags are easily read by pyrosequencing analysis
Which markers can be analysed with NGS?
- STRs
- SNPs
- X- and Y-chromosome markers
- the mt genome
at the same time in one shot!!
Name some famous persons where DNA analysis was used
- Josef Mengele
- The Romanovs and the missing children
- Jesse James
- The Evangelist Luke
- Carin Göring
- Kopernikus
Name causes of PRC inhibition
- co-purified compounds in bones or from soil
- humic compounds
- chemically altered carbohydrates
- heavy metals (iron, copper, cadmium and lead)
- collagen and chondroitin
- many other compounds/cheicals for other types of samples
- heme, polysaccharides, proteinases, melanin
NGS analysis is suitable for
- high quality samples
- small amounts/degraded samples
- mixed samples
Security marking with DNA - give examples of what can be DNA tagged
- security ink for bank notes
- label lega documents
- label oil in order to detect spill
- brand protection, e.g. clothes, perfume
- poperty marking, e.g. jewelry, valuables
- museum collection protection
- personal protection
