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ABSTRACT: A duplex primer set for the amplification of mitochondrial DNA HVI and HVII control regions was evaluated for the optimization of a DNA sequencing protocol suitable for forensic casework. HVI and HVII products, with the absence of non-specific products, could be detected by agarose gel electrophoresis when as little as 0.5 and 0.1pg of DNA were amplified for 34 and 38 cycles, respectively. Because HVI and HVII amplicons are co-synthesized in the duplex PCR, fewer steps are required (lessening the risk of cross contamination events) and more frugal use of precious extracted DNA samples is possible, both desirable features for forensic casework. The ABI Prism BigDyetrade mark version 1.1 chemistry provided high quality sequencing data, with little or no background noise and uniform peak heights, outcomes that favored reliable detection of heteroplasmy, particularly at early sequence reads (<40 bases). Optimal compromise between sensitivity and sequence accuracy in the absence of noise was achieved starting at 150 mitochondrial genome copies. The protocol is effective (no sequence errors) with highly degraded DNA (average detectable template size of 200bp). Dual artificial template mixtures with the minor component at 15% suggests that heteroplasmy should be detected at this level with confidence.
Forensic Science International 11/2005; 154(2-3):137-48. · 2.30 Impact Factor
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ABSTRACT: To detect sequence variation in 105 Croatian individuals by the use of duplex polymerase chain reaction amplification of full-length hypervariable region I and II (HVI/HVII) products and subsequent hybridization to a linear array of 27 immobilized sequence-specific oligonucleotide (SSO) probes, which targets six regions within HVI and HVII, and two additional sites, 189 and 16093.
Chelex-extracted bloodstains were used for amplification of HV regions. In all cases, a single robust amplification was sufficient for immobilized SSO probe typing and subsequent direct sequence analysis for both HVI and HVII. This method, suitable for a range of forensic samples (including shaft portions of single hairs), was also applied to the analysis of 18 skeletal elements recovered from a mass grave. Using a panel of immobilized SSO probes, we have developed a rapid screening approach to mitochondrial DNA (mtDNA) haplotyping before direct sequence analysis.
We established a reference sequence database of mtDNA haplotypes for 105 randomly selected Croatian individuals. Fifty different mitotypes were observed (33 unique). The most frequent mitotypes occurred 18 times or approximately 17.1% [111111 189 (A) 16093 (T)] and 11 times or approximately 10.5% [131111 189 (A) 16093 (T)]; all other mitotypes occurred 5% or less. The corresponding genetic diversity value for this database was approximately 0.952. The usefulness of establishing an mtDNA reference database with immobilized SSO probe testing has been demonstrated by determining the strength of a match comparison obtained for one skeletal element and a corresponding maternal reference from 18 specimens recovered from a mass grave.
The sequence variation detected by the panel of immobilized SSO probes is sufficiently diverse to be used for identification of human skeletal remains from mass graves. The immobilized SSO typing strip targets polymorphic regions within HVI and HVII and is a useful identification tool for mass grave and mass disaster analysis, as well as for criminal casework testing.
Croatian Medical Journal 07/2001; 42(3):328-35. · 1.80 Impact Factor
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ABSTRACT: An immobilized sequence-specific oligonucleotide (SSO) probe system consisting of 16 SSO probes that detect sequence polymorphisms within five regions of the mtDNA control region was used to investigate the frequency of heteroplasmy in human mtDNA. Five regions of hypervariable region II (HVII) of the control region were studied in blood-, muscle-, heart-, and brain-tissue samples collected from 43 individuals during autopsy. An initial search for heteroplasmy was conducted by use of the SSO probe system. Samples in which multiple probe signals were detected within a region were sequenced for the HVII region, to verify the typing-strip results. The frequency of heteroplasmy was 5 of 43 individuals, or 11.6%. The frequency of heteroplasmy differed across tissue types, being higher in muscle tissue. The difference in the frequency of heteroplasmy across different age groups was statistically significant, which suggests that heteroplasmy increases with age. As a test for contamination and to confirm heteroplasmy, the samples were sequenced for the HVI region and were typed by use of a panel of five polymorphic nuclear markers. Portions of the tissues that appeared to be heteroplasmic were extracted at least one additional time; all gave identical results. The results from these tests indicate that the multiple sequences present in individual samples result from heteroplasmy and not from contamination.
The American Journal of Human Genetics 05/2000; 66(4):1384-97. · 10.60 Impact Factor
