One of the biggest weaknesses of mtDNA analysis is that some haplotypes are rather common in various population groups. For example, in the FBI mtDNA Population Database of 1655 Caucasians there are 15 individuals that match at 263G, 315.1C and 153 additional profiles that have only a single difference. Thus, 168 out of 1655 (10.2%) of the Caucasian database would not be able to be excluded if a sample was observed with this common mtDNA type! As will be discussed later in the chapter, efforts are underway to gather additional sequence information from polymorphic sites around the entire mtGenome in order to better resolve these most common types (Parsons and Coble 2001, Coble et al. 2004).
Due to the effort both in terms of time and labor required to obtain full sequence information from mtDNA sequencing, screening approaches and rapid low-resolution typing assays can and have been used to eliminate the need for full analysis of samples that can be easily excluded from one another. Many times physical screening methods can put samples into context without having to indiscriminately perform mtDNA sequencing on all samples. For example, microscopic examinations of hair can help eliminate as many questioned hairs as possible leaving the mtDNA laboratory to concentrate their efforts on only key hairs (Houck and Budowle 2001). Likewise anthropological evaluations of bones or teeth can be important first screens prior to making the effort to analyze the mtDNA sequence (see Edson et al. 2004).
With the expense and effort required to obtain full mtDNA sequences across HV1 and HV2, the ability to rapidly screen out samples that do not match can be advantageous to overworked, understaffed, and poorly funded crime laboratories. Several assays have been developed and even validated for use in screening forensic casework (Table 10.5).
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