Abstract:
BACKGROUND:The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM's reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting insertions and deletions (indels), which may hinder its utility for clinical genetic testing. RESULTS:Recently, the proprietary analytical workflow for the Ion Torrent sequencer, Torrent Suite (TS), underwent a series of upgrades. We evaluated three major upgrades of TS by calling indels in the BRCA1 and BRCA2 genes. Our analysis revealed that false negative indels could be generated by TS under both default calling parameters and parameters adjusted for maximum sensitivity. However, indel calling with the same data using the open source variant callers, GATK and SAMtools showed that false negatives could be minimised with the use of appropriate bioinformatics analysis. Furthermore, we identified two variant calling measures, Quality-by-Depth (QD) and VARiation of the Width of gaps and inserts (VARW), which substantially reduced false positive indels, including non-homopolymer associated errors without compromising sensitivity. In our best case scenario that involved the TMAP aligner and SAMtools, we achieved 100% sensitivity, 99.99% specificity and 29% False Discovery Rate (FDR) in indel calling from all 23 samples, which is a good performance for mutation screening using PGM. CONCLUSIONS:New versions of TS, BWA and GATK have shown improvements in indel calling sensitivity and specificity over their older counterpart. However, the variant caller of TS exhibits a lower sensitivity than GATK and SAMtools. Our findings demonstrate that although indel calling from PGM sequences may appear to be noisy at first glance, proper computational indel calling analysis is able to maximize both the sensitivity and specificity at the single base level, paving the way for the usage of this technology for future clinical genetic testing.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Yeo ZX,Wong JC,Rozen SG,Lee ASdoi
10.1186/1471-2164-15-516subject
Has Abstractpub_date
2014-06-24 00:00:00pages
516issn
1471-2164pii
1471-2164-15-516journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06784-8
更新日期:2020-06-03 00:00:00
abstract:BACKGROUND:Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. RESULTS:In this study, we identified a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3502-3
更新日期:2017-03-14 00:00:00
abstract:BACKGROUND:Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Sho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-803
更新日期:2014-09-19 00:00:00
abstract:BACKGROUND:The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained. RE...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-718
更新日期:2012-12-22 00:00:00
abstract:UNLABELLED:Little is known, either experimentally or computationally, about the genomic sequence features that regulate malaria genes. A sequence conservation analysis of the malaria species P. falciparum, P. berghei, P. yoelii, and P. chabaudi could significantly advance knowledge of malaria gene regulation. RESULTS:...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-372
更新日期:2007-10-15 00:00:00
abstract:BACKGROUND:Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insight...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3465-9
更新日期:2017-01-13 00:00:00
abstract:BACKGROUND:The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, wh...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-S3-S13
更新日期:2010-12-01 00:00:00
abstract:BACKGROUND:Gibberella ear rot (GER) is one of the most economically important fungal diseases of maize in the temperate zone due to moldy grain contaminated with health threatening mycotoxins. To develop resistant genotypes and control the disease, understanding the host-pathogen interaction is essential. RESULTS:RNA-...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4513-4
更新日期:2018-02-09 00:00:00
abstract:BACKGROUND:The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. Its persistence in the stomach mucosa is facilitated by several mechanisms of immune evasion and immune modulation, but also by an unusual genetic variability which might account for the capability to adapt to chan...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-310
更新日期:2014-04-27 00:00:00
abstract:BACKGROUND:Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3782-7
更新日期:2017-05-22 00:00:00
abstract:BACKGROUND:The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obt...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-26
更新日期:2008-01-22 00:00:00
abstract:BACKGROUND:Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5863-2
更新日期:2019-07-16 00:00:00
abstract:BACKGROUND:High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequenc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-16
更新日期:2014-01-10 00:00:00
abstract:BACKGROUND:Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6002-9
更新日期:2019-08-22 00:00:00
abstract:BACKGROUND:Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that chang...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4519-y
更新日期:2018-02-22 00:00:00
abstract:BACKGROUND:Cells transformed by human adenoviruses (Ad) exhibit differential capacities to induce tumours in immunocompetent rodents; for example, Ad12-transformed rodent cells are oncogenic whereas Ad5-transformed cells are not. The E1A gene determines oncogenic phenotype, is a transcriptional regulator and dysregulat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-67
更新日期:2009-02-06 00:00:00
abstract:BACKGROUND:Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecula...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-182
更新日期:2014-03-09 00:00:00
abstract:BACKGROUND:Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-58
更新日期:2010-01-22 00:00:00
abstract:BACKGROUND:Limited nutrient availability during development is associated with metabolic diseases in adulthood. The molecular cause for these defects is unclear. Here, we investigate if transcriptional changes caused by developmental malnutrition reveal an early response that can be linked to metabolism and metabolic d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1654-6
更新日期:2015-06-04 00:00:00
abstract:BACKGROUND:Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colibacillosis is caused by avian pathogenic E. coli (APEC). APEC strains are extraintestinal pathogenic E. coli and have in gener...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3415-6
更新日期:2017-01-03 00:00:00
abstract:BACKGROUND:Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6391-9
更新日期:2019-12-26 00:00:00
abstract:BACKGROUND:Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering the obvious advantages of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphis...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1046
更新日期:2014-12-01 00:00:00
abstract:BACKGROUND:Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model inference based on such data still manifests significant uncertainty. RE...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5720-3
更新日期:2019-06-13 00:00:00
abstract:BACKGROUND:High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integrat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-514
更新日期:2013-07-29 00:00:00
abstract:BACKGROUND:Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS:To overcome these limitations, we developed a novel RoV capture and genome sequencing method combin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3714-6
更新日期:2017-04-24 00:00:00
abstract:BACKGROUND:Genome research in farm animals will expand our basic knowledge of the genetic control of complex traits, and the results will be applied in the livestock industry to improve meat quality and productivity, as well as to reduce the incidence of disease. A combination of quantitative trait locus mapping and mi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-36
更新日期:2006-02-27 00:00:00
abstract::An amendment to this paper has been published and can be accessed via the original article. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-020-6754-2
更新日期:2020-06-03 00:00:00
abstract:BACKGROUND:Detoxification in the liver involves activation of nuclear receptors, such as the constitutive androstane receptor (CAR), which regulate downstream genes of xenobiotic metabolism. Frequently, the metabolism of endobiotics is also modulated, resulting in potentially harmful effects. We therefore used 1,4-Bis ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-384
更新日期:2009-08-19 00:00:00
abstract:BACKGROUND:Ophiocordyceps sinensis is an important traditional Chinese medicine for its comprehensive active ingredients, such as cordycepin, cordycepic acid, and Cordyceps polysaccharide. O. sinensis zjut, a special strain isolated from O. sinensis, has similar pharmacological functions to wild O. sinensis. Currently,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07298-z
更新日期:2020-12-11 00:00:00
abstract:BACKGROUND:The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species' survival. To better understand the Tasma...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-172
更新日期:2012-05-06 00:00:00