Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians

Coble, Michael D.; Just, Rebecca S.; O’Callaghan, Jennifer; Letmanyi, Ilona H.; Peterson, Christine Tara; Irwin, Jodi A.; Parsons, Thomas J.

doi:10.1007/s00414-004-0427-6

Cited by 198 publications

(188 citation statements)

References 37 publications

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“…Moilanen, personal communication). On the other hand, none of the haplogroup K mtDNA sequences available through extensive population and forensic surveys, including our own 47 samples, have been shown to possess the 7598A mutation (Herrnstadt et al 2002;Coble et al 2004;unpublished data). Therefore, it is unlikely that the 7598A mutation represents a phylogenetically ancient polymorphism in this haplogroup.…”

Section: Discussionmentioning

confidence: 85%

“…In addition, we surveyed more than 1,000 published full mtDNA sequences of Caucasian origin available in GenBank (Torroni et al 1996;Howell et al 2003;Moilanen et al 2003;Achilli et al 2004;Coble et al 2004), those available in the mtSNP Database, published reports of whole genome sequences (Ingman et al 2000;Kivisild et al 2002;Tanaka et al 2004), and a list of unpublished polymorphisms (MITOMAP 2005; http:// www.mitomap.org) for the 7598A/COX2 mutation. We found two mtDNAs of Caucasian origin that also carried this mutation (Fig.…”

Section: Genetic and Phylogenetic Analysismentioning

confidence: 99%

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De novo COX2 mutation in a LHON family of Caucasian origin: implication for the role of mtDNA polymorphism in human pathology

et al. 2006

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Recent studies suggest that certain mutations with phylogeographic importance as haplogroup markers may also influence the phenotypic expression of particular mitochondrial disorders. One such disorder, Leber's hereditary optic neuropathy (LHON), demonstrates a clear expression bias in mtDNAs belonging to haplogroup J, a West Eurasian maternal lineage defined by polymorphic markers that have been called 'secondary' disease mutations. In this report, we present evidence for a de novo heteroplasmic COX2 mutation associated with a LHON clinical phenotype. This particular mutation-at nucleotide position 7,598-occurs in West Eurasian haplogroup H, the most common maternal lineage among individuals of European descent, whereas previous studies have detected this mutation only in East Eurasian haplogroup E. A review of the available mtDNA sequence data indicates that the COX2 7598 mutation occurs as a homoplasic event at the tips of these phylogenetic branches, suggesting that it could be a variant that is rapidly eliminated by selection. This finding points to the potential background influence of polymorphisms on the expression of mild deleterious mutations such as LHON mtDNA defects and further highlights the difficulties in distinguishing deleterious mtDNA changes from neutral polymorphisms and their significance in the development of mitochondriopathies.Keywords Leber's hereditary optic neuropathy AE COX2 AE Haplogroup marker AE mtDNA polymorphism AE Mitochondriopathy

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Section: Discussionmentioning

confidence: 85%

Section: Genetic and Phylogenetic Analysismentioning

confidence: 99%

De novo COX2 mutation in a LHON family of Caucasian origin: implication for the role of mtDNA polymorphism in human pathology

et al. 2006

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“…However, some aspects of this putative pathogenic variation, which has recently been reported in a patient of European descent with muscle weakness, ptosis and cardiomyopathy, 34 should be noted. The variation was initially observed in a European sequence, 35 but later also identified in two African sequences, 36 which resulted in its classification as a polymorphism belonging to the L2a1b haplogroup (Phylotree.org). In concurrence with this, of the five cases in our group where this variation was detected, four clustered to this haplogroup and the other to a subgroup of L0.…”

Section: Non-haplogroup-associated Mtdna Variantsmentioning

confidence: 99%

Characterization of mtDNA variation in a cohort of South African paediatric patients with mitochondrial disease

et al. 2012

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Mitochondrial disease can be attributed to both mitochondrial and nuclear gene mutations. It has a heterogeneous clinical and biochemical profile, which is compounded by the diversity of the genetic background. Disease-based epidemiological information has expanded significantly in recent decades, but little information is known that clarifies the aetiology in African patients. The aim of this study was to investigate mitochondrial DNA variation and pathogenic mutations in the muscle of diagnosed paediatric patients from South Africa. A cohort of 71 South African paediatric patients was included and a high-throughput nucleotide sequencing approach was used to sequence full-length muscle mtDNA. The average coverage of the mtDNA genome was 81 ± 26 per position. After assigning haplogroups, it was determined that although the nature of non-haplogroup-defining variants was similar in African and non-African haplogroup patients, the number of substitutions were significantly higher in African patients. We describe previously reported disease-associated and novel variants in this cohort. We observed a general lack of commonly reported syndrome-associated mutations, which supports clinical observations and confirms general observations in African patients when using single mutation screening strategies based on (predominantly non-African) mtDNA disease-based information. It is finally concluded that this first extensive report on muscle mtDNA sequences in African paediatric patients highlights the need for a full-length mtDNA sequencing strategy, which applies to all populations where specific mutations is not present. This, in addition to nuclear DNA gene mutation and pathogenicity evaluations, will be required to better unravel the aetiology of these disorders in African patients.

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“…Full sequencing of HVI and HVII may be able to subdivide a few more of these samples but regardless many of these samples will likely remain undistinguishable from one another based on HVI and HVII sequences alone (10,21). Expansion of mtDNA sequencing and typing to the full mtDNA genome permits use of polymorphisms that occur outside the control region.…”

Section: Subdividing the Most Common Type With Coding Region Snpsmentioning

confidence: 99%

“…The presence of multiple signals within a probe region resulting from sequence heteroplasmy is described as is the absence of signal within a probe region resulting from failed hybridization of PCR products due to additional destabilizing polymorphisms. In addition, a new coding region single nucleotide polymorphism (SNP) assay was employed to help subdivide 51 individuals possessing the most common Caucasian mtDNA haplotype (10,11).…”

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Mitochondrial DNA Typing Screens with Control Region and Coding Region SNPs

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Redman

et al. 2005

Journal of Forensic Sciences

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Mitochondrial DNA (mtDNA) analysis has found an important niche in forensic DNA typing. It is used with highly degraded samples or low-copy number materials such as might be found from shed hair or bones exposed to severe environmental conditions. The primary advantage of mtDNA is that it is present in high copy number within cells and therefore more likely to be recovered from highly degraded specimens. A major disadvantage to traditional forensic mtDNA analysis is that it is time-consuming and labor-intensive to generate and review the 610 nucleotides of sequence information commonly targeted in hypervariable regions I and II (HVI and HVII) of the control region. In addition, common haplotypes exist in HVI/HVII mtDNA sequences that can reduce the ability to differentiate two unrelated samples. In this report we describe the utility of two newly available screening assays for rapid exclusion of non-matching samples. The LINEAR ARRAY mtDNA HVI/HVII Region-Sequencing Typing Kit (Roche Applied Science, Indianapolis, IN) was used to type 666 individuals from U.S. Caucasian, African American, and Hispanic groups. Processing of the LINEAR ARRAY probe panels "mito strips" was automated on a ProfiBlot workstation. Observable variation in 666 individuals is reported and frequencies of the mitotypes within and between populations are presented. Samples exhibiting the most common Caucasian mitotype were subdivided with a multiplexed amplification and detection assay using eleven single nucleotide polymorphisms in the mitochondrial genome. These types of screening assays should enable more rapid evaluation of forensic casework samples such that only samples not excluded would be subjected to further characterization through full HVI/HVII mtDNA sequence analysis.KEYWORDS: forensic science, DNA typing, mtDNA, SSO probes, mitochondrial DNA coding region, primer extension For the past decade, DNA sequencing of hypervariable regions I (HVI) and II (HVII) in the control region of mitochondrial DNA (mtDNA) has been useful in forensic casework for the analysis of human remains when nuclear DNA systems fail due to low amounts of DNA or highly degraded specimens (1-3). However, considerable effort and expense are required to develop a full HVI and HVII mtDNA sequence (typically positions 16024-16365 and 1 Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899.2 Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, MD 20899.3 Department of Human Genetics, Roche Molecular Systems, Alameda, CA 94501. 4 Comparative Biochemistry Group, University of California, Berkeley, CA. * Contribution of the U.S. National Institute of Standards and Technology. Not subject to copyright. Certain commercial equipment, instruments and materials are identified in order to specify experimental procedures as completely as possible. In no case does such identification imply a recommendation or endorsement by the National Institute of Standards and Technology nor does it...

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Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians

Cited by 198 publications

References 37 publications

De novo COX2 mutation in a LHON family of Caucasian origin: implication for the role of mtDNA polymorphism in human pathology

De novo COX2 mutation in a LHON family of Caucasian origin: implication for the role of mtDNA polymorphism in human pathology

Characterization of mtDNA variation in a cohort of South African paediatric patients with mitochondrial disease

Mitochondrial DNA Typing Screens with Control Region and Coding Region SNPs

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