Polymorphism in mtDNA control region of Mizo-Mongloid Breast Cancer samples as revealed by PCR-RFLP analysis

Ghatak, Souvik; Lallawmzuali, Doris; Mukherjee, Subhajit; Mawia, Lal; Pautu, Jeremy L.; Kumar, Nachimuthu Senthil

doi:10.3109/19401736.2014.982627

Cited by 5 publications

(4 citation statements)

References 10 publications

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“…Apart from the general advantages of mitochondrial markers in animal phylogenetic studies, namely their maternal inheritance, lack of recombination, and fast rate of evolution [ 9 , 10 ], several unique qualities make the CR a favoured marker sequence for genetic diversity analyses, in particular, its exceptionally fast evolutionary rate (even in comparison to the rest of the mitochondrial genome [ 11 , 12 ]), polymorphic nature [ 13 ] and presumed selective neutrality as a non-coding region (but see [ 14 , 15 ]). Consequently, this region has been widely used as a genetic marker in phylogenetic studies of various animals including vertebrate classes such as fish (e.g., [ 16 , 17 ]), amphibians [ 18 ], reptiles [ 19 ], birds [ 20 ] and mammals [ 21 , 22 ] as well as numerous invertebrate taxa (e.g., [ 23 – 26 ].…”

Section: Introductionmentioning

confidence: 99%

Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids

2018

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BackgroundIn Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription.While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region.ResultsHere we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids.ConclusionsOur target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1198-x) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids

2018

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“…PCR-RFLP analysis is a simple and robust technique that can be used as a potential tool for early detection of biomarkers in the study of tobacco specific carcinogens induced stomach cancer [15]. The PCR-RFLP results have shown a significant level of heteroplasmy and polymorphic patterns at the D-loop region of mtDNA in Mizo population among the following groups: tuibur consumer, healthy (control) volunteer and stomach cancer patient.…”

Section: Discussionmentioning

confidence: 99%

“…PCR products were digested with AluI, HaeIII, MspI and KpnI (Fermentas, Thermo Scientific) in a total volume of 10 μl (2 μl PCR products, 1 μl enzyme buffers, 1 U enzymes) and placed in the incubator at 37ºC for 4 h. The restriction products were analyzed by electrophoresis (Bio-Rad) on a 10% polyacrylamide gel and the molecular weight of restricted fragments was analyzed by gel documentation system (G-Box; Syngene) after ethidium bromide (Himedia) staining [15].…”

Section: Restriction Digestion Of the Pcr Productmentioning

confidence: 99%

Mutation Profiling in Mitochondrial D-Loop Associated with Stomach Cancer and Tobacco Consumers

Lalmuanpuii¹,

Pautu²,

Bose³

et al. 2015

J Clin Med Genom

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Within North East India, the people of Mizoram are mongoloid in origin and Cancer is a major disease condition among this tribal populace. A peculiar habit of consuming ''tuibur'' (tobacco smoke-infused aqueous solution) has been practiced in Mizoram. Blood and oral swab samples were collected from stomach cancer patients, tuibur consumers and healthy people. DNA was extracted followed by PCR amplification of the D-loop region of mtDNA. Restriction enzyme digestion of 1050 bp of the hyper variable control region of mtDNA was performed in order to gain an insight into the phylogenetic relationship of populace of Mizoram besides the genetic variations among tuibur consumers. The phylogram based on restriction enzyme analysis (AluI, HaeIII, MspI and KpnI) of the D-loop region subsumed within same mtDNA haplogroups and the markers resulted in a similar clustering of the population. The polymorphic samples were sequenced, analyzed and compared with the MITOMAP database. In the hypervariable control region, 292A>AA and 316C>CC are novel microsatellites instability as they have been reported for the first time as it has not been found in the mitochondrial database. 292A>AA position of MT-HV II region is a locus for the mtTF1 binding site Y. Due to the microsatellite instability of this position, the binding of mtTF1 may be altered. 316C>CC is present at the conserved sequence block II in MT-HV II region of human mitochondrial control region. The present study revealed a variety of mtDNA D-loop region mutations and polymorphisms among tuibur consumer besides stomach cancer patients of Mizoram, some of which might be involved in the development of carcinogenesis in stomach for the tuibur consumer.

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“…Conventionally, an assay is usually performed by gel electrophoresis and autoradiography, both of which are time-consuming and technically challenging. 7 In recent years, many other technologies have been developed for allele-specic discrimination, such as allele-specic probe hybridization, 8 allele-specic primer extension via the PCR, 9 enzymatic cleavage 10,11 and oligonucleotide ligation. 12 Among these assays, the ligation detection reaction (LDR) is popular for use in the discrimination of point mutations because of its high speci-city, low cost, and ease of operation.…”

Section: Introductionmentioning

confidence: 99%

Melting temperature of molecular beacons as an indicator of the ligase detection reaction for multiplex detection of point mutations

et al. 2015

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Polymorphism in mtDNA control region of Mizo-Mongloid Breast Cancer samples as revealed by PCR-RFLP analysis

Cited by 5 publications

References 10 publications

Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids

Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids

Mutation Profiling in Mitochondrial D-Loop Associated with Stomach Cancer and Tobacco Consumers

Melting temperature of molecular beacons as an indicator of the ligase detection reaction for multiplex detection of point mutations

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