Fluorescent SSCP of overlapping fragments (FSSCP-OF): a highly sensitive method for the screening of mitochondrial DNA variation

Salas, Antonio; Rasmussen, Erik Michael; Lareu, M.V.; Morling, Niels; Carracedo, Ángel

doi:10.1016/s0379-0738(01)00574-6

Cited by 15 publications

(8 citation statements)

References 16 publications

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“…Similarly, polymorphisms of the mitochondrial DNA genome has been reported as useful for identity testing and, in general, for the analysis of degraded material or samples containing little or no genomic DNA (i.e. skeletal remains and hair shafts) [7][8][9][10][11][12]. However, the two routinely analyzed mtDNA hypervariable regions (HVS-I/II) provide limited power of discrimination in a forensic context and in many cases, provide Forensic Science International 140 (2004) 251-257 scant information in evolutionary studies.…”

Section: Introductionmentioning

confidence: 99%

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing

Quintáns

Álvarez-Iglesias

Salas

et al. 2004

Forensic Science International

164

140

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Section: Introductionmentioning

confidence: 99%

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing

Quintáns

Álvarez-Iglesias

Salas

et al. 2004

Forensic Science International

164

140

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“…In HVS-II, the degree of length heteroplasmy is known to be variable between individuals, making it difficult to determine the total number of samples heteroplasmic for HVS-II [42]. Sequencing of the H-strand can be used to resolve some possible artifacts [43]. Heteroplasmy often arises after the insertion of cytosines between positions 303 and 309.…”

Section: Resultsmentioning

confidence: 99%

Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: An expanded Korean population database

Jin

Kwak

Hong

et al. 2006

Forensic Science International

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“…Analysis of restriction fragment length polymorphism (RFLP) sites and screening procedures such as heteroduplex analysis (HD) and single strand conformation polymorphisms (SSCP) have been extensively used in the past and are still used by many laboratories [2], [20], [21]. Since the mid-1990s, sequencing the HVS-I (and sporadically the HVS-II), coupled with the analysis of selected RFLP sites, has been the most common strategy for analysing mtDNA variation.…”

Section: Introductionmentioning

confidence: 99%

A Reduced Number of mtSNPs Saturates Mitochondrial DNA Haplotype Diversity of Worldwide Population Groups

Salas

Amigo

2010

PLoS ONE

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BackgroundThe high levels of variation characterising the mitochondrial DNA (mtDNA) molecule are due ultimately to its high average mutation rate; moreover, mtDNA variation is deeply structured in different populations and ethnic groups. There is growing interest in selecting a reduced number of mtDNA single nucleotide polymorphisms (mtSNPs) that account for the maximum level of discrimination power in a given population. Applications of the selected mtSNP panel range from anthropologic and medical studies to forensic genetic casework.Methodology/Principal FindingsThis study proposes a new simulation-based method that explores the ability of different mtSNP panels to yield the maximum levels of discrimination power. The method explores subsets of mtSNPs of different sizes randomly chosen from a preselected panel of mtSNPs based on frequency. More than 2,000 complete genomes representing three main continental human population groups (Africa, Europe, and Asia) and two admixed populations (“African-Americans” and “Hispanics”) were collected from GenBank and the literature, and were used as training sets. Haplotype diversity was measured for each combination of mtSNP and compared with existing mtSNP panels available in the literature. The data indicates that only a reduced number of mtSNPs ranging from six to 22 are needed to account for 95% of the maximum haplotype diversity of a given population sample. However, only a small proportion of the best mtSNPs are shared between populations, indicating that there is not a perfect set of “universal” mtSNPs suitable for all population contexts. The discrimination power provided by these mtSNPs is much higher than the power of the mtSNP panels proposed in the literature to date. Some mtSNP combinations also yield high diversity values in admixed populations.Conclusions/SignificanceThe proposed computational approach for exploring combinations of mtSNPs that optimise the discrimination power of a given set of mtSNPs is more efficient than previous empirical approaches. In contrast to precedent findings, the results seem to indicate that only few mtSNPs are needed to reach high levels of discrimination power in a population, independently of its ancestral background.

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Fluorescent SSCP of overlapping fragments (FSSCP-OF): a highly sensitive method for the screening of mitochondrial DNA variation

Cited by 15 publications

References 16 publications

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing

Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: An expanded Korean population database

A Reduced Number of mtSNPs Saturates Mitochondrial DNA Haplotype Diversity of Worldwide Population Groups

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