Validated primer set that prevents nuclear DNA sequences of mitochondrial origin co-amplification: A revision based on the New Human Genome Reference Sequence (GRCh37)

2011 ◽  
Vol 32 (6-7) ◽  
pp. 782-783 ◽  
Author(s):  
Amanda Ramos ◽  
Cristina Santos ◽  
Elena Barbena ◽  
Ligia Mateiu ◽  
Luis Alvarez ◽  
...  
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Reference Sequence ◽  
Mitochondrial Origin ◽  
Human Genome Reference Sequence ◽  
Human Genome Reference

A legacy of the “1% program” – The “Chinese Chapter” of the human genome reference sequence

2018 ◽  
Vol 45 (11) ◽  
pp. 565-568
Author(s):  
Wei Dong ◽  
Xiaoling Wang ◽  
Zhi Xia ◽  
Xiuqing Zhang ◽  
Huanming Yang
Keyword(s):  
Human Genome ◽  
Reference Sequence ◽  
Human Genome Reference Sequence ◽  
Human Genome Reference

scholarly journals Envisioning the next human genome reference

2021 ◽  
Vol 14 (12) ◽  
Author(s):  
Monkol Lek ◽  
Elaine R. Mardis
Keyword(s):  
Precision Medicine ◽  
Human Genome ◽  
Reference Sequence ◽  
Ethnic Representation ◽  
Genomic Studies ◽  
Human Genome Reference Sequence ◽  
Human Genome Reference

Summary: We provide an Editorial perspective on approaches to improve ethnic representation in the human genome reference sequence, enabling its widespread use in genomic studies and precision medicine to benefit all peoples.

scholarly journals Linear Assembly of a Human Y Centromere

2017 ◽  
Author(s):  
Miten Jain ◽  
Hugh E. Olsen ◽  
Daniel J. Turner ◽  
David Stoddart ◽  
Kira V. Bulazel ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Centromeric Region ◽  
Reference Sequence ◽  
Nanopore Sequencing ◽  
Linear Assembly ◽  
Sequencing Strategy ◽  
Human Genome Reference Sequence ◽  
Human Y Chromosome ◽  
Human Genome Reference

The human genome reference sequence remains incomplete due to the challenge of assembling long tracts of near-identical tandem repeats-in centromeric regions. To address this, we have implemented a nanopore sequencing strategy to generate high quality reads that span hundreds of kilobases of highly repetitive DNAs. Here, we use this advance to produce a sequence assembly and characterization of the centromeric region of a human Y chromosome.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

scholarly journals Toward a global reference database of COI barcodes for marine zooplankton

2021 ◽  
Vol 168 (6) ◽  
Author(s):  
Ann Bucklin ◽  
Katja T. C. A. Peijnenburg ◽  
Ksenia N. Kosobokova ◽  
Todd D. O’Brien ◽  
Leocadio Blanco-Bercial ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Sequences ◽  
Reference Sequence ◽  
Global Ocean ◽  
Reference Database ◽  
Data Repositories ◽  
Marine Zooplankton ◽  
The North ◽  
Coi Sequences ◽  
Taxonomic Groups

AbstractCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

scholarly journals Phylogenetic relationships of Cranichidinae and Prescottiinae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences

2009 ◽  
Vol 104 (3) ◽  
pp. 403-416 ◽  
Author(s):  
Gerardo A. Salazar ◽  
Lidia I. Cabrera ◽  
Santiago Madriñán ◽  
Mark W. Chase
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna

scholarly journals The association of CYP2D6 gene polymorphisms in the full-length coding region with higher recurrence rate of vivax malaria in Yunnan Province, China

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Herong Huang ◽  
Ying Dong ◽  
Yanchun Xu ◽  
Yan Deng ◽  
Canglin Zhang ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Gene Mutation ◽  
Dna Sequences ◽  
Vivax Malaria ◽  
Yunnan Province ◽  
Reference Sequence ◽  
Radical Cure ◽  
Coding Region ◽  
Cyp2d6 Gene ◽  
Genotype 4

Abstract Background Accumulating evidence suggest that compromised CYP2D6 enzyme activity caused by gene mutation could contribute to primaquine failure for the radical cure of vivax malaria. The current study aims to preliminarily reveal the association between the recurrence of vivax malaria in Yunnan Province and CYP2D6 gene mutation by analysing polymorphisms in the entire coding region of human CYP2D6 gene. Methods Blood samples were collected from patients with vivax malaria, who received "chloroquine and 8-day course of primaquine therapy" in Yunnan Province. The suspected relapsed cases were determined by epidemiological approaches and gene sequence alignment. PCR was conducted to amplify the CYP2D6 gene in the human genome, and the amplified products were then sequenced to compare with the non-mutation “reference” sequence, so as to ensure correct sequencing results and to determine 9 exon regions. Subsequently, the DNA sequences of 9 exons were spliced into the coding DNA sequence (CDS), which, by default, is known as maternal CDS. The paternal CDS was obtained by adjusting the bases according to the sequencing peaks. The mutation loci, haplotypes (star alleles), genotypes and odds ratios (OR) of all the CDSs were analysed. Results Of the119 maternal CDS chains in total with 1491 bp in length, 12 mutation sites in the 238 maternal and paternal CDS chains were detected. The c.408G > C mutation was most frequently detected in both suspected relapsed group (SR) and non-relapsed group (NR), reaching 85.2% (75/88) and 76.0% (114/150), respectively. The c.886C > T mutation was most closely related to the recurrence of vivax malaria (OR = 2.167, 95% CI 1.104–4.252, P < 0.05). Among the 23 haplotypes (Hap_1 ~ Hap_23), Hap_3 was non-mutant, and the sequence structure of Hap_9 was the most complicated one. Five star alleles, including *1, *2, *4, *10 and *39, were confirmed by comparison, and CYP2D6*10 allele accounted for the largest percentage (45.4%, 108/238). The frequency of CYP2D6*2 allele in the SR group was significantly higher than that in the NR group (Χ2 = 16.177, P < 0.05). Of the defined 24 genotypes, 8 genotypes, including *4/*4, *4/*o, *2/*39, *39/*m, *39/*x, *1/*r, *1/*n, and *v/*10, were detected only in the SR group. Conclusion Mutation of CYP2D6*10 allele accounts for the highest proportion of vivax malaria cases in Yunnan Province. The mutations of c. 886C > T and CYP2D6*2 allele, which correspond to impaired PQ metabolizer phenotype, are most closely related to the relapse of vivax malaria. In addition, the genotype *4/*4 with null CYP2D6 enzyme function was only detected in the SR group. These results reveal the risk of defected CYP2D6 enzyme activity that diminishes the therapeutic effect of primaquine on vivax malaria.

Sign in / Sign up

Export Citation Format

Share Document