scholarly journals Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1345
Author(s):  
Jennifer Churchill Cihlar ◽  
Christina Amory ◽  
Robert Lagacé ◽  
Chantal Roth ◽  
Walther Parson ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Validation Studies ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Massively Parallel Sequencing ◽  
Whole Genome ◽  
Developmental Validation ◽  
Average Maximum ◽  
Variant Frequency ◽  
Sensitivity Specificity

For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology—Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge—has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly accurate and reproducible results were generated for a variety of sample qualities and quantities, supporting the reliability of this specific whole genome mitochondrial DNA MPS system for analysis of forensic biological evidence.

scholarly journals Haplocheck: Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies

2020 ◽  
Author(s):  
Hansi Weissensteiner ◽  
Lukas Forer ◽  
Liane Fendt ◽  
Azin Kheirkhah ◽  
Antonio Salas ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Nuclear Dna ◽  
Nuclear Genome ◽  
Whole Genome ◽  
Sequencing Studies ◽  
Project Data ◽  
The Impact

AbstractWithin-species contamination is a major issue in sequencing studies, especially for mitochondrial studies. Contamination can be detected by analysing the nuclear genome or by inspecting the heteroplasmic sites in the mitochondrial genome. Existing methods using the nuclear genome are computationally expensive, and no suitable tool for detecting contamination in large-scale mitochondrial datasets is available. Here we present haplocheck, a tool that requires only the mitochondrial genome to detect contamination in both mitochondrial and whole-genome sequencing studies. Haplocheck is able to distinguish between contaminated and real heteroplasmic sites using the mitochondrial phylogeny. By applying haplocheck to the 1000 Genomes Project data, we show (1) high concordance in contamination estimates between mitochondrial and nuclear DNA and (2) quantify the impact of mitochondrial copy numbers on the mitochondrial based contamination results. Haplocheck complements leading nuclear DNA based contamination tools, and can therefore be used as a proxy tool in nuclear genome studies.Haplocheck is available both as a command-line tool at https://github.com/genepi/haplocheck and as a cloud web-service producing interactive reports that facilitates the navigation through the phylogeny of contaminated samples.

Neanderthals and modern humans

2017 ◽  
Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde
Keyword(s):  
Genetic Differentiation ◽  
Nuclear Dna ◽  
Homo Sapiens ◽  
Whole Genome ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Homo Neanderthalensis ◽  
Modern Mind ◽  
Similarities And Differences ◽  
Mode 3

This chapter deals with the similarities and differences between Homo neanderthalensis and Homo sapiens, by considering genetic, brain, and cognitive evidence. The genetic differentiation emerges from fossil genetic evidence obtained first from mtDNA and later from nuclear DNA. With high throughput whole genome sequencing, sequences have been obtained from the Denisova Cave (Siberia) fossils. Nuclear DNA of a third species (“Denisovans”) has been obtained from the same cave and used to define the phylogenetic relationships among the three species during the Upper Palaeolithic. Archaeological comparisons make it possible to advance a four-mode model of the evolution of symbolism. Neanderthals and modern humans would share a “modern mind” as defined up to Symbolic Mode 3. Whether the Neanderthals reached symbolic Mode 4 remains unsettled.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

scholarly journals Analysis of ancient DNA from a prehistoric Amerindian cemetery

1999 ◽  
Vol 354 (1379) ◽  
pp. 153-159 ◽  
Author(s):  
Anne C. Stone ◽  
Mark Stoneking
Keyword(s):  
Ancient Dna ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Genetic Research ◽  
Hypervariable Region ◽  
Dna Preservation ◽  
European Contact ◽  
Novel Method ◽  
High Level ◽  
Central Illinois

The Norris Farms No. 36 cemetery in central Illinois has been the subject of considerable archaeological and genetic research. Both mitochondrial DNA (mtDNA) and nuclear DNA have been examined in this 700–year–old population. DNA preservation at the site was good, with about 70% of the samples producing mtDNA results and approximately 15% yielding nuclear DNA data. All four of the major Amerindian mtDNA haplogroups were found, in addition to a fifth haplogroup. Sequences of the first hypervariable region of the mtDNA control region revealed a high level of diversity in the Norris Farms population and confirmed that the fifth haplogroup associates with Mongolian sequences and hence is probably authentic. Other than a possible reduction in the number of rare mtDNA lineages in many populations, it does not appear as if European contact significantly altered patterns of Amerindian mtDNA variation, despite the large decrease in population size that occurred. For nuclear DNA analysis, a novel method for DNA–based sex identification that uses nucleotide differences between the X and Y copies of the amelogenin gene was developed and applied successfully in approximately 20 individuals. Despite the well–known problems of poor DNA preservation and the ever–present possibility of contamination with modern DNA, genetic analysis of the Norris Farms No. 36 population demonstrates that ancient DNA can be a fruitful source of new insights into prehistoric populations.

Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing

2010 ◽  
Vol 42 (11) ◽  
pp. 931-936 ◽  
Author(s):  
Akihiro Fujimoto ◽  
Hidewaki Nakagawa ◽  
Naoya Hosono ◽  
Kaoru Nakano ◽  
Tetsuo Abe ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Whole Genome ◽  
Parallel Sequencing ◽  
Variant Analysis ◽  
Japanese Individual

scholarly journals Discordance between Mitochondrial and Nuclear DNA Genes Suggests the Possibility of Hybridization of Indian and Southeast Asian Types of Oecophylla smaragdina (Fabricius) (Hymenoptera, Formicidae) in Bangladesh

2020 ◽  
Author(s):  
M. M. Rahman ◽  
S. Hosoishi ◽  
K. Ogata
Keyword(s):  
Dna Analysis ◽  
Nuclear Dna ◽  
Nuclear Gene ◽  
Southeast Asian ◽  
Phylogenetic Study ◽  
Tropical Islands ◽  
Oecophylla Smaragdina ◽  
Mtdna Sequences ◽  
Mitochondrial Dna Analysis ◽  
Shed Light

Background: Oecophylla smaragdina is distributed from India, SE Asia and Australia including many tropical Islands. A recent phylogenetic study based on mitochondrial DNA analysis reveals that Bangladesh is the overlapping zone of both Indian and Southeast Asian type of O. smaragdina. These two different lineages of Indian and SE Asian type have the opportunities of creating the zone of contacts, but no such data was found. In this study, shed light was given to reveal the chance of hybridized colony of O. smaragdina in Bangladesh. Methods: To asses the hybridization scenario, 28 O. smaragdina colony from 27 localities in Bangladesh were analyzed using Longwave length Rhodopsin (LWRh) nuclear gene sequences and was compared with the mtDNA sequences, which was collected from the same localities and deposited into NCBI GenBank. Results: The inconsistency between mitochondrial and nuclear gene types was observed from two colonies of the overlapped zone of contact. These two colonies were identified as SE Asian type by mtDNA analysis however, by nuclear DNA analysis; it was identified as Indian type. These significant discrepancies within the colony suggested the possibility of hybridization of weaver ant in Bangladesh.

scholarly journals Micro-Spectrophotometric Nuclear DNA Analysis of Aspirated Cells from Thyroid Tumor

1981 ◽  
Vol 20 (1) ◽  
pp. 8-14
Author(s):  
Shosaku ABE ◽  
Shoichi INOUE ◽  
Yutaka OHSAKI ◽  
Makoto MURAO ◽  
Mikio ARAKAWA ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Nuclear Dna ◽  
Thyroid Tumor

scholarly journals Underlying Data for Sequencing the Mitochondrial Genome with the Massively Parallel Sequencing Platform Ion Torrent™ PGM™

BMC Genomics ◽  
2015 ◽  
Vol 16 (Suppl 1) ◽  
pp. S4 ◽  
Author(s):  
Seung Bum Seo ◽  
Xiangpei Zeng ◽  
Jonathan L King ◽  
Bobby L Larue ◽  
Mourad Assidi ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Ion Torrent ◽  
Parallel Sequencing ◽  
Sequencing Platform
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