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Forensic Genetics and Medicine > Biohistory > Flashcards

Biohistory Flashcards

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1
Q

Which techniques have a slow speed of analyis and a high power of discrimination?

A
  • RFLP mutli locus probes
  • RFLP single locus probes
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2
Q

Solutions for mixtures

A
  • Y-chromosome STRs
  • Y-chromosome SNPs
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3
Q

NGS promises the simultaneous analysis of:

A
  • whole exomes
  • complete genomes
  • whole transcriptomes
  • whole methylomes
  • many selected targets
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4
Q

Handling inhibition in bones

A
  • 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
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5
Q

What is the most common mtDNA haplogroup in Europeans?

A

H (40-50%)

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6
Q

Decoding procedure

A
  • 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
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7
Q

What is the use of forensic DNA testing in forensic cases?

A
  • analyse evidence samples at a crime scene
  • exonerate innocently accused or convicted
  • match traces with DNA profiles in database with convicted/suspects
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8
Q

How can DNA damage be repaired?

A

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
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9
Q

How is mtDNA assigned into haplogroups?

A

Defined by certain SNPS in the hypervariabe and coding region

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10
Q

Name reasons why analysis of skeletal remains may be very challenging

A
  • low template amounts
  • highly degraded DNA
  • damaged DNA
  • contaminated
  • precious samples - limited availability

–> optimal protocol for all steps is thus highly important

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11
Q

Strategies to overcome inhibition

A
  • 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
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12
Q

Which techniques are fast in analysis, but have a low power of discrimination?

A
  • poly marker
  • D1S80 single STR
  • DQalpha
  • ABO blood groups
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13
Q

Can solvents, ageing, bleaching or UV radiation wash-out DNA tags ?

A

no

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14
Q

Which techniques have a slow speed of analysis and a low power of discrimination?

A
  • mtDNA
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15
Q

Name some causes for DNA damage and degradation

A

Generally occurs with time, but may be facilitated by:

  • high humidity
  • high temperature
  • UV-radiation
  • chemicals
  • microorganisms
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16
Q

What affects DNA decay?

A
  • release of cellular enzymes
  • bacteria
  • free radicals
17
Q

How many SNPs are predicted in the HIrisPlex and from how many genes? What does it predict with high accuracy?

A
  • 24 SNPs from 13 genes
  • red and black hair
  • blue and brown eyes
18
Q

Which techniques have a fast speed of analyis and a high power of discrimination?

A
  • SNPs
  • mini STRs
  • multiplex STRs (highest power)
19
Q

How does the DNA tagging system work?

A

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
20
Q

Which markers can be analysed with NGS?

A
  • STRs
  • SNPs
  • X- and Y-chromosome markers
  • the mt genome

at the same time in one shot!!

21
Q

Name some famous persons where DNA analysis was used

A
  • Josef Mengele
  • The Romanovs and the missing children
  • Jesse James
  • The Evangelist Luke
  • Carin Göring
  • Kopernikus
22
Q

Name causes of PRC inhibition

A
  • 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
23
Q

NGS analysis is suitable for

A
  • high quality samples
  • small amounts/degraded samples
  • mixed samples
24
Q

Security marking with DNA - give examples of what can be DNA tagged

A
  • 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
25
Q

Describe the DNA analysis process of DNA labeled security ink

A
  1. Cut banknote to extract it in water
  2. simple extraction, washing
  3. PCR
  4. binding of ssDNA to magnetic beads
  5. pyrosequencing with cyclic dispensation
26
Q

Give three examples for DNA damage/degradation

A
  • double strand breaks
  • oxidative damage
  • hydrolytic damage
27
Q

Dilution may reduce the inhibitor concentration and increase DNA yield

Addition of BSA may increase DNA yield

A
28
Q

Solutions for degraded DNA and small amounts of DNA

A
  • miniSTRs
  • SNPs - shorter fragments
  • mtDNA - more copies
  • real-time quantification
29
Q

Which are the most susceptible bases for breakage of glycosidic base sugar bonds that lead to base loss and single stranded nicks at the basic site?

A

Guanine, followed by thymine

Forensic Genetics and Medicine (19 decks)

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