Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics

Leggett, Richard M.; Ramírez-González, Ricardo H.; Clavijo, Bernardo; Waite, Darren; Davey, Robert P.

doi:10.3389/fgene.2013.00288

Cited by 162 publications

(109 citation statements)

References 12 publications

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“…A sister relationship between P. juniperinum and P. strictum received high support (pP = 1). Furthermore, these species were grouped with T. pellucida, indicating Polytrichum as an apparent basal lineage; thus, the grouping characterizes the nematodontous mosses [8,36], supported by a pP of 1. This positioning is corroborated by other studies [37][38][39][40][41].…”

Section: Phylogenetic Analysis: Chloroplast and Mitochondriamentioning

confidence: 98%

“…This species has the mitochondrial nad7 as a pseudogene; Anthoceros formosae Steph [29] has maturase K and rps15 as pseudogenes, characterizing these two pseudogenes in cpDNA of Anthocerotophyta [30]. In addition, nad7 from T. pellucida is considered a pseudogene [8]. The mosses share practically the same lack of gene among their representatives; only T. pellucida shows a lack of rps10 and ORF187 in the mtDNA.…”

Section: Figure 1 Blast Ring Image Generator Output Image Of the Chlmentioning

confidence: 99%

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Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

et al. 2018

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Abstract:In this study, the organelle genomes of Polytrichum juniperinum Hedw. and Polytrichum strictum Menzies ex Brid. (Polytrichaceae, Bryophyta) from Antarctica were sequenced and compared with the plastomes of the model moss species Physcomitrella patens Brid. The sizes of the cpDNA in P. juniperinum and P. strictum were estimated to be 55,168 and 20,183 bp, respectively; the sizes of the mtDNA were 88,021 and 58,896 bp, respectively. The genomes are very similar to each other, with the possible loss of petN in the cpDNA, which also showed some gene inversions when compared with the cpDNAs of P. patens Brid. In the mtDNA, it is possible that rps10 was lost. In contrast, Antarctic Polytrichaceae species have nad7 and orf187, without the occurrence of rearrangement events. Phylogenomic analyses of the plastid and mitochondria revealed that the majority-rule tree suggests some differences in the plastids ancestry, however, P. juniperinum and P. strictum were grouped in the same clade in chloroplast, but in mitochondria P. strictum was grouped with Atrichum angustatum (Brid.) Bruch & Schimp. This study helped us understand the evolution of plastomes and chondriosomes in the family Polytrichaceae, and suggest a hybridization event with relation to the mitochondrial data.

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Section: Phylogenetic Analysis: Chloroplast and Mitochondriamentioning

confidence: 98%

Section: Figure 1 Blast Ring Image Generator Output Image Of the Chlmentioning

confidence: 99%

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

et al. 2018

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“…The major technical advantage of WGS is that the speciicity is theoretically 100% (average 95-98% in practice, practically without gaps) with a uniform coverage in the regions of interest (ROIs) throughout the input material. Thus, the chance of losing disease-causing variants due to technical errors is much lower with WGS [57][58][59]. The major challenge in applying this tool on a medical routine is the great costs, the complex pipeline for data analysis and data interpretation.…”

Section: Whole-genome and Whole-exome Sequencingmentioning

confidence: 99%

Application of Next-Generation Sequencing in the Era of Precision Medicine

Pereira¹,

Malta²,

Freire³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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Next-generation sequencing (NGS) technologies represented the next step in the evolution of DNA sequencing, through the generation of thousands to millions of DNA sequences in a short time. The relatively fast emergence and success of NGS in research revolutionized the ield of genomics and medical diagnosis. The traditional medicine model of diagnosis has changed to one precision medicine model, leading to a more accurate diagnosis of human diseases and allowing the selection of molecular target drugs for individual treatment. This chapter atempts to review the main features of NGS technique (concepts, data analysis, applications, advances and challenges), starting with a brief history of DNA sequencing followed by a comprehensive description of most used NGS platforms. Further topics will highlight the application of NGS towards routine practice, including variant detection, whole-exome sequencing (WES), whole-genome sequencing (WGS), custom panels (multi-gene), RNA-seq and epigenetic. The potential use of NGS in precision medicine is vast and a beter knowledge of this technique is necessary for an eicacious implementation in the clinical workplace. A centralized chapter describing the main NGS aspects in the clinic could help beginners, scientists, researchers and health care professionals, as they will be responsible for translating genomic data into genomic medicine.

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“…Studies often identify several "promising" marker candidates that may have a superior performance when combined with each other. Further, NGS approaches require sophisticated biostatistics to interpret the pattern of suspicious findings [22,23]. …”

Section: Multimarker Approachesmentioning

confidence: 99%

CNAPS in Therapy Monitoring

Holdenrieder

2014

Advances in Predictive, Preventive and Personalised Medicine

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Monitoring of disease state and of therapy response is highly relevant for efficient patient management. Monitoring tools comprise observation of clinical signs and performing specific examinations such as imaging or blood analyses. This review focusses on the relevance of blood-based biomarker monitoring by circulating nucleic acids for diverse indications that is exemplified on patients who develop or suffer from cancer disease. These indications include (i) screening of patient groups who have a risk to develop a disease, (ii) monitoring response to local or systemic therapies in patients with a defined diagnosis and (iii) early detection of disease recurrence after the primary therapy has ended. Useful biomarkers have to fulfill the highest methodical, pre-analytical and clinical quality criteria and have to be implemented in standardized patient management procedures. The current situation of circulating nucleic acids is summarized on the levels of genetic, epigenetic, transcript, non-coding RNA and nucleosome markers and an outlook is presented as to how these markers can be integrated into a future strategy that enables a personalized management of the patients.

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Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics

Cited by 162 publications

References 12 publications

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

Application of Next-Generation Sequencing in the Era of Precision Medicine

CNAPS in Therapy Monitoring

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