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Forensic Biology by Richard Li

Chapter 21: Mitochondrial DNA Profiling. Forensic Biology by Richard Li. mt DNA Basics. DNA found in mitochondria Bacteria-like Circular No recombination Short and “no-nonsense” Main advantages in forensics: More copies in cell; less subject to degradation Hair shaft Bones

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Forensic Biology by Richard Li

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  1. Chapter 21: Mitochondrial DNA Profiling Forensic Biologyby Richard Li

  2. mt DNA Basics • DNA found in mitochondria • Bacteria-like • Circular • No recombination • Short and “no-nonsense” • Main advantages in forensics: • More copies in cell; less subject to degradation • Hair shaft • Bones • Decomposed samples

  3. mt DNA Basics • Main disadvantages in forensics • Low power of discrimination • Maternally inherited • No recombination • Less polymorphic than nuclear DNA • Most common Caucasian type found in 7.1% of all Caucasians • More subject to contamination during analysis than nuclear DNA • More copies per cell – including cells from analyst or other sources

  4. Human Mitochondrial Genome • Mitochondria = Sub-cellular organelles which are generated ATP from breakdown of food

  5. Human Mitochondrial Genome • 16,569 nucleotides (more or less) and 37 genes • 13 genes coding for proteins in ETC • 24 genes coding for tRNA and rRNA • A person’s mtDNA sequence is called a mitotype • 10x higher mutation rate than nuclear genome • Revised Cambridge Reference Sequence • First human mtDNA genome sequenced • Later revised to correct mistakes: rCRS • Used as reference for mitotype nomenclature

  6. mtDNA Polymorphic Regions • Located in control region called D-Loop • No genes in D-loop • Hypervariable regions: • HV1 (16,024-16,365; 342 bp) • HV2 (73-340; 248 bp) • HV3 (438-574; 137 bp) • Most commonly region in forensics: • HV1 • HV2

  7. mtDNA Polymorphic Regions • Mitotype reporting • Reported against rCRS • Sequence polymorphisms • E.g. 16233T; 73A • Length polymorphisms • Insertions or deletions • Insertions: E.g. 524.1A, 524.2C • Deletions: E.g. 16296d • Heteroplasmy • More than one detectable mitotype in a person or some tissues in a person (esp. hair)

  8. Forensic mtDNA Testing • Two methods of detection: • Allele-specific oligonucleotide (ASO) assay • Rapid • Can be used to screen and eliminate suspects prior to DNA sequencing • Targets 18 most common sequence polymorphisms • DNA Sequencing • More labor intensive • Better methods are helping reduce time and labor involved • All polymorphisms can be detected so more informative than ASO

  9. ASO Assay

  10. DNA Sequencing • Current method developed by Sanger • Uses modified nucleotides called ddNTPS • Dideoxynucleotide triphosphates (ddATP, ddGTP, ddTTP, ddCTP)

  11. Reaction contains: • Denatured “template” DNA • Short, synthetic single-stranded DNA primer • Large concentration of dNTPs (normal nucleotide triphosphates) • Small concentration of ddNTPs • Labeled with different fluorescent dyes (e.g. G black, A green, T red, C purple) • DNA polymerase • Salts and buffers

  12. Interpretation of MtDNA Results • Scientific working group on DNA analysis methods (SWGDAM) and International Society of Forensic Genetics (ISFG) • Cannot exclude • Questioned sample has same sequence as reference sample • Exclusion • Two or more nucleotides differences between questioned sample and reference sample • Inconclusive • Questioned and reference sample differ by one nucleotide

  13. Identifying Tsar Nicholas & Family • Russian Tsar Nicholas II and family removed from power and murdered during Bolshevik Revolution in 1918 • Shot by firing squad, doused with sulfuric acid, buried in a shallow pit under a road • Remains went undiscovered until 1991 • Nine skeletons discovered (4 male adults, 2 female adults, and 3 female children) • Unrecognizable by any method other than DNA • Too decomposed for nuclear DNA typing (RFLP)

  14. Identifying Tsar Nicholas & Family • mtDNA extracted from femur of each skeleton • Blood samples obtained from maternally-related descendants • Tsarina Alexandra • Prince Phillip (England) is grand nephew of unbroken maternal descent • His sequence matched that of one adult female skeleton (the Tsarina) and all 3 female children’s skeletons • Tsar • Sequence of adult male skeletons compared to two relatives of unbroken maternal descent to Tsar

  15. Identifying Tsar Nicholas & Family • Single nucleotide difference found at 16,169 • Tsar had heteroplasmy at this site (T and C detected in sequencing reaction) • Putative relatives had only T • Inconclusive • Body of Tsar’s brother exhumed and tested • Tests showed same heteroplasmy as Tsar • Tsar’s identity confirmed • Eye-witness reports indicate that the footman, the family cook, and the family doctor were the other 3males in the grave; the Tsarina’s assistant was the second adult female

  16. Identifying Tsar Nicholas & Family • Tsar had four daughters and one son • One daughter and the son not accounted for • In 2007, two additional bodies found in same area • mtDNA testing confirmed that they belonged to the missing daughter and son

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