Chapter 8 Additional DNA Markers: Amelogenin, Y-Chromosome STRs, mtDNA, SNPs, Alu Repeats ©2002 Academic Press.

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Chapter 8 Additional DNA Markers: Amelogenin, Y-Chromosome STRs, mtDNA, SNPs, Alu Repeats ©2002 Academic Press

Amelogenin Sex-Typing Marker 6 bp deletion X = 212 bp Y = 218 bp X = 106 bp Y = 112 bp AmpFlSTR kits PowerPlex 1.1 1:1 Mixture: 3X + 1Y Female: X, X Male: X, Y ©2002 Academic Press

Lineage Markers Mitochondrial DNA (mtDNA) Y chromosome maternally inherited polymorphic control region (D-loop) multiple copies per cell; survives better Y chromosome paternally inherited variety of Y STR and Y SNP markers haplotype rather than genotype ©2002 Academic Press

Human Mitochondrial DNA HV1 HV2 16024 16365 340 73 342 bases 268 bases 1 Control Region ~1100 bp mtDNA 16,569 bp HV1 HV2 ©2002 Academic Press

Maternal Inheritance of mtDNA 1 2 3 5 4 12 11 10 9 6 7 8 18 17 15 16 13 14 MtDNA Haplotype Groups: 2,3,6,8,11,13,15,16 4,9,10 14,17,18 A B C D E F G ©2002 Academic Press

mtDNA Sample Process Flow Performed separately and preferably after evidence is completed Extract mtDNA from evidence (Q) sample Extract mtDNA from reference (K) sample PCR Amplify HV1 and HV2 Regions PCR Amplify HV1 and HV2 Regions Sequence HV1 and HV2 Amplicons (both strands) Sequence HV1 and HV2 Amplicons (both strands) Confirm sequence with forward and reverse strands Confirm sequence with forward and reverse strands Note differences from Anderson (reference) sequence Note differences from Anderson (reference) sequence Compare Q and K sequences ©2002 Academic Press Compare with database to determine haplotype frequency

heteroplasmic sequence mtDNA Heteroplasmy homoplasmic sequence heteroplasmic sequence ©2002 Academic Press position 6371 C/T

Comparison of STR and SNP Markers Occurrence in Human Genome ~1 in every 15 kb ~1 in every 1 kb General Informativeness High Low; only 20-30% as informative as STRs Marker Type di-, tri-, tetranucleotide repeat markers biallelic markers Number of Alleles per Marker typically >5 typically 2 Detection Methods gel/capillary electrophoresis sequence analysis; microchip hybridization Multiplex Capability >10 markers with multiple fluorescent dyes potential of 1000s on microchip Characteristics Short Tandem Repeats (STRs) Single Nucleotide Polymorphisms (SNPs) ©2002 Academic Press

Alu insertion PCR Assay Human Alu Repeat (~300 bp) AluI Two possible alleles 400 bp 100 bp ©2002 Academic Press