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Forensic Genetics and Medicine > Forensic applications of RNA and methylation > Flashcards

Forensic applications of RNA and methylation Flashcards

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1
Q

Name four different markers that can be used for identification

A
  • STR
  • Mini-STR
  • Y STR
  • mtDNA
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2
Q

What is the plex range of STRs, how many cycles are used in the PCR, how much DNA and from which samples is it commonly done?

A
  • plex range: 15-24
  • PCR cycles: 28-30
  • DNA: 100pg
  • samples: blood, hair roots, saliva with high quality DNA
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3
Q

What is the plex range of mini-STRs, how many cycles are used in the PCR, how much DNA and from which samples is it commonly done?

A
  • plex: 9
  • cycles: 30
  • DNA: 50pg
  • samples: degraded samples - bones
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4
Q

What is the plex range of Y-STRs, how many cycles are used in the PCR, how much DNA and from which samples is it commonly done?

A
  • Plex: 17-23
  • PCR: 30 cycles
  • DNA: 100pg
  • samples: sexual assault mixtures
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5
Q

What is the plex range of mtDNA, how much DNA and from which samples is it commonly done?

A
  • Plex: HV1, HV2, HV3
  • DNA: 1 pg, less than 1 cell, 100-1000 copies
  • samples: hair shafts, bone samples with low copy number
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6
Q

Which areas are invovled in forensic analysis?

A
  • genetics
  • molecular biology
  • proteomics
  • genomics
  • epigenetics
  • population genetics
  • biostatistics
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7
Q

Name two new applications in forensic genetics

A
  • identification of type of biological fluid
  • prediction of an unknown person’s age, physical appearance and ancestry
  • to be used as investigative leads in a crime scene investigation
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8
Q

Which specific genes is used for circulatory blood recognition?

A

Glycoprotein A

is a major protein component of the human erythrocyte membrane

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9
Q

Which specific genes are used for menstrual blood recognition?

A

MMP11, MMP7

Zinc-dependent peptidases that take part in the disassembly of extracellular matrix and are expressed during tissue remodeling such as the female endometrium during the menstrual cycle

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10
Q

Which specific genes are used for semen analysis/the presence of spermatozoa?

A
  • PRM1, PRM2 Protamine
  • arginine rich proteins that help condensing the spermatid chromatin inside the nucleus
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11
Q

Which gene is used for seminal fluid recognition in the absence of spermatozoa?

A

TGM 4 Transglutaminase 4

Catalyses the permanent cross-linking of peptide bound glutamine residues. Specific expression to the prostate

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12
Q

Which genes are used for saliva recognition?

A
  • HIS (histatin) and STATH (Statherin)
  • Histatin: histidine-rich protein that is part of the immune defense of the oral cavity
  • Statherin: stable acidic phosphoprotein of the saliva
  • also: keratin 4 and 13; SPRR2A
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13
Q

Which genes are used for the regonition of vaginal secretions?

A
  • HBD1 human beta defensin
  • MUC4 Mucin 4
  • defensin: antimicrobial protein produced by the neutrophils
  • mucin: found in epithelial tissues of the body and belongs to the family of highly glycosylated proteins
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14
Q

Name some housekeeping genes that can be used to relate tissue specific markers to

A
  • GAPDH
  • ACTB
  • SI5
  • UCE
  • TEF
  • G6PDH
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15
Q

Which is tissue specific mRNA for skin?

A

Corneodesmosin

Loricin

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16
Q

Which are mRNA tests of blood (in general, I guess)

A
  • Hemoglobin
  • leucocyte markers
    • CD93
    • AMICA1
17
Q

What can DNA methylation determine in forensics?

A
  • differentiate monozygotic twins
  • authentication of DNA samples
  • parental origin of alleles
  • identify tissue type/source
  • cause and circumstances of death
  • age of tissue donor
18
Q

Name the two major epigenetic modifications

A
  • histone modifications
  • DNA methylation
    • changes with increasing age
    • contribute to age related disease
19
Q

Name some methods for age estimation

A
  • telomere length
  • t-cell rearrangements
  • RNA-biomarkers determine age based on four gamma globulin transcripts
  • measure increase of a 4977 mtDNA deletion
  • epigenetic changes
20
Q

What is DNA methylation?

A

The addition of a methyl group 5’ position of the cytocine ring at a CpG site

21
Q

Name some pro-aging factors (that induce methylation changes)

A

smoking, stress, alcohol

22
Q

Name some anti-aging factors (that counteract methylation changes)

A

physical activity, antioxidant intake, calorie restriction diet

23
Q

Pyrosequencing for methylation analysis - results at DNA basis

A
  • unmethylated Cytosines appear as thymines (because C will be changed to Uracil)
  • methylated cytosines appear as cytosines
  • the ratio of C and T at a CpG site will give methylation level
24
Q

Forensic age estimation tool

A
  • quick and robust analysis
    • Bisulfite conversion 30min
    • PCR and pyrosequencing 3h
  • high sensitivity
    • 20ng down to 0.25 ng DNA
25
Q

what has still to be done in the forensic age estimation tool?

A
  • find an optimal set of markers - multiplex analysis
  • accuracy in prediction, tissue variation
  • sensitivity and degraded samples
26
Q

How can you fake DNA?

A
  • PCR - separate amplification of 10 loci
  • WGA - multiple displacement amplification
  • cloning
    • amplified individual alleles and cloned them
    • plasmids were purified and genotyped
    • tubes with separate alleles in trillions of copies
    • allele library for all 16 loci in the kit
    • create any profile
27
Q

How can you introduce DNA into blood and saliva?

A
  • red blood cells separeated from white by centrifugation
    • mixed with artificial DNA
    • dripped and dried
  • saliva extract without cells (the top phase after centrifugation)
    • mixed with artifical DNA
    • applied to ski-mask etc
28
Q

What does the DNA autentication assay contain?

A
  • bisulfite treatment
  • sanger sequencing
  • evaluation
    • in vivo material: methylated and unmethylated DNA
    • in vitro material: only unmethylated DNA

Forensic Genetics and Medicine (19 decks)

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