Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region

Wilson, Mark; Allard, Marc W.; Monson, Keith L.; Miller, Kevin W.P.; Budowle, Bruce

doi:10.1016/s0379-0738(02)00206-2

Cited by 56 publications

(60 citation statements)

References 14 publications

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“…This C-stretch has been encountered in other populations [56,59], and, as with the Nairobi samples, the heteroplasmy is almost always so pronounced that it is difficult to determine even a majority length variant (but see the method we adopted). Sequence data from reverse sequencing primers show that the terminal ACA bases of the control region are retained just prior to the beginning of the tRNAphe gene, so we agree with others [18,56,59] in treating this condition as involving C insertions rather than multiple A-C transversions. We chose to designate length variation in this region by counting the number of cytosines present in the majority molecule type and listing those as insertions at 573 (Fig.…”

Section: Resultssupporting

confidence: 86%

“…The highest virtual G peak corresponds to the majority molecule type, and, logically, the C-stretch ends four nucleotides before that majority G peak. We have not observed a simple duplication of six Cs, as previously reported [18].…”

Section: Resultssupporting

confidence: 69%

“…Nucleotides are numbered according to the revised Cambridge Reference Sequence (rCRS [43,44]). The sequences were aligned using Sequencher software (GeneCodes, Ann Arbor, Michigan) according to a series of rules developed for the consistent placement of gaps [18].…”

Section: Dna Samples and Extractionmentioning

confidence: 99%

“…However, published anthropological mtDNA sequences are often too short for forensic purposes, usually restricted to HVI, and lack standardization from study to study in the sequence range that is reported. Some attempts have been made to establish standardization of sequence ranges and quality in forensic science [17,18,19]. However, the typical forensic target range of 16024-16365 for HVI and 73-340 for HVII is also rather arbitrary, and omits adjacent highly variable sites.…”

Section: Introductionmentioning

confidence: 99%

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Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database

et al. 2004

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Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations.

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Section: Resultssupporting

confidence: 86%

Section: Resultssupporting

confidence: 69%

Section: Dna Samples and Extractionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database

et al. 2004

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“…Only high quality sequences lacking background signal were used. Sequences were aligned to the Cambridge reference sequence (Anderson et al 1981) using Sequence Navigator software 1.0.1 and SeqScape software 2.0 (both: Applied Biosystems, Darmstadt) following international guidelines for mtDNA typing (Bär et al 2000;Wilson et al 2002).…”

Section: Methodsmentioning

confidence: 99%

Different methods to determine length heteroplasmy within the mitochondrial control region

et al. 2004

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The first and second hypervariable regions of the human mitochondrial DNA control region contain two homopolymeric stretches of cytosine (nt 16184-16193 and nt303-315, respectively). According to the Cambridge reference sequence these homopolymeric stretches are interrupted by thymine (T), at positions 16189 and 310, respectively. Monotonous runs of the same base have been suggested to be hot spots for mutations, probably caused by replication slippage, resulting in length heteroplasmy. This paper describes a rapid method based on restriction cleavage of labelled PCR products encompassing the homopolymeric tract in HVII to quantify the relative proportions of different length variants present in an individual. To compare the accuracy of this method, cloned PCR products from several heteroplasmic individuals have been additionally sequenced.

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Match statistics for sequence‐based alleles in profiles from forensic PCR‐mps kits

Young¹,

Marciano

Crenshaw

et al. 2021

Electrophoresis

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The first autosomal sequence‐based allele (aka SNP‐STR haplotype) frequency database for forensic massively parallel sequencing (MPS) has been published, thereby removing one of the remaining barriers to implementing MPS in casework. The database was developed using a specific set of flank trim sites. If different trim sites or different kits with different primers are used for casework, then SNP‐STR haplotypes may be detected that do not have frequencies in the database. We describe a procedure to address calculation of match probabilities when casework samples are generated using an MPS kit with different trim sites than those present in the relevant population frequency database. The procedure provides a framework for comparison of any MPS kit or database combination while also accommodating comparison of MPS and CE profiles.

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Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region

Cited by 56 publications

References 14 publications

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database

Different methods to determine length heteroplasmy within the mitochondrial control region

Match statistics for sequence‐based alleles in profiles from forensic PCR‐mps kits

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