Y Chromosome

The Y chromosome is useful to trace relationships among males and to evaluate multiple males in a rape case and in male-female mixtures (see Chapter 9). There are at least 246 Y-chromosome SNP markers (Y-SNPs) and at least 227 Y-chromosome STR markers (Y-STRs) described (Butler, 2003). Another author reports that there are at least 219 STR sites on the Y chromosome (Kayser et al., 2004). The STR approach is the usual method utilized for DNA analysis of the Y chromosome.

Mitochondrial DNA (mtDNA)

Mitochondrial DNA is more durable and plentiful than nuclear DNA (see Chapter 8). However, it is less discriminating than nuclear DNA because it is transmitted only from mother to children, and has less variation between individuals than nuclear DNA. It is usually used when the nuclear DNA is degraded, such as when only hair, bone or teeth are present. There is a report of finding suitable mtDNA in guts of maggots (fly larvae) that have fed on human tissue and been collected in death investigations (Wells et al., 2001). There are many more copies of mtDNA than there are copies of nuclear DNA. There are usually 200-1700 copies of mtDNA per cell (Holland and Parsons, 1999). Hetero-plasmy is a special attribute of mtDNA. Heteroplasmy is when a person has two or more different mtDNA sequences present. Human mitochondria have 16 569 base pairs that comprise 37 genes. A region called the discrimination loop, or 'D-loop' is a non-coding control region that has a fair amount of variation, and so is used for DNA testing of SNPs (Butler, 2001). The mtDNA D-loop region has two hypervariable areas called HV1 and HV2. The HV2 area has a region of length heteroplasmy identified as the homopolymeric cytosine stretch (C-stretch).

Investigations of the mtDNA coding region using an SNP method to increase forensic discrimination has been recently described (Coble et al., 2006). Statistical analysis of mtDNA is typically a 'counting method'. Thus instead of calculating the match probability, which will typically be in the range of 0.0050.025 (Budowle et al., 1999), a match is based on how many times a specific sequence is found in a population database (Monson et al., 2002; Parson et al., 2004).

Guidelines for reporting mtDNA analysis (Scientific Working Group on DNA Analysis Methods, SWGDAM, 2003) list three options as outcomes. These

1. Exclusion - the known and unknown samples have two or more nucleotide differences, thus the samples can be excluded as being from the same person or maternal lineage.

2. Inconclusive - one nucleotide difference between unknown sample and the known sample.

3. Cannot Exclude - sequences from known and unknown samples have a common base at each location or a common length variant in the HV2 C-stretch, thus the samples cannot be excluded as being from the same person or maternal lineage.

Messenger ribonucleic acid (RNA)

Messenger RNA (mRNA) appears to have a role in the identification of body fluids such as blood, saliva and semen (Juusola and Ballantyne, 2003). This approach may be utilized more in the future as a replacement for serological and protein analysis.

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