scholarly journals DNA damage is a major cause of sequencing errors, directly confounding variant identification

2016 ◽  
Author(s):  
Lixin Chen ◽  
Pingfang Liu ◽  
Thomas C. Evans ◽  
Laurence M. Ettwiller
Keyword(s):  
Dna Damage ◽  
Deep Sequencing ◽  
False Positive ◽  
Accurate Determination ◽  
Allelic Frequency ◽  
The Cancer Genome Atlas ◽  
Detection Methods ◽  
Accurate Identification ◽  
Sequencing Errors

AbstractPervasive mutations in somatic cells generate a heterogeneous genomic population within an organism and may result in serious medical conditions. While cancer is the most studied disease associated with somatic variations, recent advances in single cell and ultra deep sequencing indicate that a number of phenotypes and pathologies are impacted by cell specific variants. Currently, the accurate identification of low allelic frequency somatic variants relies on a combination of deep sequencing coverage and multiple evidences of the presence of variants. However, in this study we show that false positive variants can account for more than 70% of identified somatic variations, rendering conventional detection methods inadequate for accurate determination of low allelic variants. Interestingly, these false positive variants primarily originate from mutagenic DNA damage which directly confounds determination of genuine somatic mutations. Furthermore, we developed and validated a simple metric to measure mutagenic DNA damage, and demonstrated that mutagenic DNA damage is the leading cause of sequencing errors in widely used resources including the 1000 Genomes Project and The Cancer Genome Atlas.

scholarly journals Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells

2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Joost B. Beltman ◽  
Jos Urbanus ◽  
Arno Velds ◽  
Nienke van Rooij ◽  
Jan C. Rohr ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Accurate Determination ◽  
Dna Barcodes ◽  
Illumina Platform ◽  
Sequencing Errors ◽  
In Cells

scholarly journals Response to Comment on “DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification”

Science ◽  
2018 ◽  
Vol 361 (6409) ◽  
pp. eaat0958 ◽  
Author(s):  
Lixin Chen ◽  
Pingfang Liu ◽  
Thomas C. Evans ◽  
Laurence M. Ettwiller
Keyword(s):  
Dna Damage ◽  
Oxidative Damage ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Sequencing Errors ◽  
Cancer Genome Atlas ◽  
Genome Atlas ◽  
Variant Identification

Following the Comment of Stewart et al., we repeated our analysis on sequencing runs from The Cancer Genome Atlas (TCGA) using their suggested parameters. We found signs of oxidative damage in all sequence contexts and irrespective of the sequencing date, reaffirming that DNA damage affects mutation-calling pipelines in their ability to accurately identify somatic variations.

scholarly journals Feline leukaemia virus infection: A practical approach to diagnosis

2020 ◽  
Vol 22 (9) ◽  
pp. 831-846
Author(s):  
Regina Hofmann-Lehmann ◽  
Katrin Hartmann
Keyword(s):  
Accurate Determination ◽  
Molecular Techniques ◽  
Detection Methods ◽  
Domestic Cats ◽  
Immunological Parameters ◽  
Leukaemia Virus ◽  
Diagnostic Assays ◽  
Feline Leukaemia Virus ◽  
Cat Diseases

Practical relevance: Feline leukaemia virus (FeLV) is a retrovirus of domestic cats worldwide. Cats lacking strong FeLV-specific immunity and undergoing progressive infection commonly develop fatal FeLV-associated disease. Many aspects of FeLV infection pathogenesis have been elucidated, some during more recent years using molecular techniques. It is recommended that the FeLV status of every cat is known, since FeLV infection can influence the prognosis and clinical management of every sick cat. Moreover, knowledge of a cat’s FeLV status is of epidemiological importance to prevent further spread of the infection. Clinical challenges: Diagnosing FeLV infection remains challenging due to different outcomes of infection, which can vary over time depending on the balance between the virus and the host’s immune system. Furthermore, testing for FeLV infection has become more refined over the years and now includes diagnostic assays for different viral and immunological parameters. Knowledge of FeLV infection pathogenesis, as well as the particulars of FeLV detection methods, is an important prerequisite for correct interpretation of any test results and accurate determination of a cat’s FeLV status. Aims: The current review presents recent knowledge on FeLV pathogenesis, key features to be determined in FeLV infection, and frequently used FeLV detection methods, and their characteristics and interpretation. An algorithm for the diagnosis of FeLV infection in a single cat, developed by the European Advisory Board on Cat Diseases, is included, and FeLV testing in specific situations is addressed. As well as increasing awareness of this deadly infection in domestic cats, the aim is to contribute diagnostic expertise to allow veterinarians in practice to improve their recognition, and further reduce the prevalence, of FeLV infection.

Ultrasonic Sector Scanning Method in the Application of the Accurate Determination of the Concrete Bored Pile Defect Position

2012 ◽  
Vol 430-432 ◽  
pp. 1128-1132 ◽  
Author(s):  
De Zhi Liu ◽  
Jian Min Ren ◽  
Yang Yang
Keyword(s):  
Measurement Method ◽  
Accurate Determination ◽  
Detection Methods ◽  
Engineering Practice ◽  
Large Defect ◽  
Scanning Method ◽  
Bored Pile ◽  
Defect Position ◽  
Bored Piles

Based on the detection of cast-in-place concrete defects of bored pile as the research object, the scale of the commonly used method for measuring the determination of the defect position, which can't determine the accurate range is very large defect location of the problem, taking the first measurement method, planing initially determined by fan scanning method to determine the accurate out concrete piles defect position method, and digging pile defect position after the actual situation comparison of verifying test, test results are accurate effect and good. In the concrete bored piles detection, the level measurement method that ultrasonic testing is generally used for measuring the location range of the defects inspects too large range , which brings the inspection people can't determine the accurate defect position , affects the normal construction. Based on the engineering practice of using level measuring method and fan scanning technique combining detection methods to solve the determination on the accurate location of the defects in concrete bored piles.

scholarly journals DNA barcoding reveals the diversity of sharks in Guyana coastal markets

2017 ◽  
Vol 15 (4) ◽  
Author(s):  
Matthew A. Kolmann ◽  
Ahmed A. Elbassiouny ◽  
Elford A. Liverpool ◽  
Nathan R. Lovejoy
Keyword(s):  
Dna Barcoding ◽  
Accurate Determination ◽  
Total Sample ◽  
Artisanal Fishing ◽  
Species Identity ◽  
Sustainable Fisheries ◽  
International Union ◽  
Accurate Identification ◽  
Fundamental Challenge

ABSTRACT A fundamental challenge for both sustainable fisheries and biodiversity protection in the Neotropics is the accurate determination of species identity. The biodiversity of the coastal sharks of Guyana is poorly understood, but these species are subject to both artisanal fishing as well as harvesting by industrialized offshore fleets. To determine what species of sharks are frequently caught and consumed along the coastline of Guyana, we used DNA barcoding to identify market specimens. We sequenced the mitochondrial co1 gene for 132 samples collected from six markets, and compared our sequences to those available in the Barcode of Life Database (BOLD) and GenBank. Nearly 30% of the total sample diversity was represented by two species of Hammerhead Sharks (Sphyrna mokarran and S. lewini), both listed as Endangered by the International Union for Conservation of Nature (IUCN). Other significant portions of the samples included Sharpnose Sharks (23% - Rhizoprionodon spp.), considered Vulnerable in Brazilian waters due to unregulated gillnet fisheries, and the Smalltail Shark (17% - Carcharhinus porosus). We found that barcoding provides efficient and accurate identification of market specimens in Guyana, making this study the first in over thirty years to address Guyana’s coastal shark biodiversity.

scholarly journals A Review of the Melting Curves of Transition Metals at High Pressures Using Static Compression Techniques

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 416
Author(s):  
Paraskevas Parisiades
Keyword(s):  
Transition Metals ◽  
High Pressures ◽  
Accurate Determination ◽  
Detection Methods ◽  
Melting Transition ◽  
Static Compression ◽  
Melting Curves ◽  
Strong Focus ◽  
Diamond Anvil

The accurate determination of melting curves for transition metals is an intense topic within high pressure research, both because of the technical challenges included as well as the controversial data obtained from various experiments. This review presents the main static techniques that are used for melting studies, with a strong focus on the diamond anvil cell; it also explores the state of the art of melting detection methods and analyzes the major reasons for discrepancies in the determination of the melting curves of transition metals. The physics of the melting transition is also discussed.

scholarly journals Headspace Gas–Liquid Chromatographic Determination of Dithiocarbamate Residues in Fruits and Vegetables with Confirmation by Conversion to Ethylenethiourea

1996 ◽  
Vol 79 (6) ◽  
pp. 1417-1422 ◽  
Author(s):  
Nazir Ahmad ◽  
Lin Guo ◽  
Peter Mandarakas ◽  
Viola Farah ◽  
Semeone Appleby ◽  
...  
Keyword(s):  
False Positive ◽  
Fruits And Vegetables ◽  
Accurate Determination ◽  
Internal Standard ◽  
Chromatographic Determination ◽  
Prolonged Treatment ◽  
Improved Method ◽  
Headspace Gas ◽  
Liquid Chromatographic

Abstract Ethylene-bis-dithiocarbamate (EBDC) residues were determined as carbon disulfide (CS2) by an improved headspace gas-liquid chromatographic (GLC) procedure. Among 837 samples of 30 agricultural commodities tested, 43% contained residues above the detection limit for the method: 100% of broccoli samples; 80% of cabbage, kiwifruit, and grape samples; and 71% of cucumber samples. Most of the residues in kiwifruit were on or near the skin. Elimination of false-positive detections by the improved method was confirmed with kiwifruit in 2 independent procedures. Whole fruits were washed with 5% EDTA to remove surface residues of EBDC. Analysis of washes for CS2 by the headspace procedure after treatment with acidic stannous chloride and for ethylene thiourea by LC after prolonged treatment at 60°C qualitatively identified the EDTA-soluble residues as EBDC. Although the improved method does not produce false-positive results, peak area responses of CS2 and the internal standard, thiophene, are influenced by chemical composition of the matrix. With matrixes high in sugar or lipids, the apparent CS2 content may be overestimated by 4-fold. Accurate determination of EBDC residues in these sample types requires appropriate adjustments to matrixes.

Morphological and molecular characterisation of two putative Xiphinema americanum-group species, X. parasimile and X. simile (Nematoda: Dorylaimida) from Serbia

Nematology ◽  
2008 ◽  
Vol 10 (1) ◽  
pp. 15-25 ◽  
Author(s):  
László Barsi ◽  
Francesca Luca
Keyword(s):  
Accurate Determination ◽  
Taxonomic Status ◽  
Its Region ◽  
Distinct Species ◽  
Molecular Study ◽  
Accurate Identification ◽  
26S Rdna ◽  
Tail Shape ◽  
Total Dna

Abstract Problems associated with the taxonomic status of Xiphinema parasimile and X. simile are reviewed. Their accurate identification is difficult due to their high morphological and morphometrical similarity. A comparative morphological and molecular study of these species was done to define their specific status and differences. Lip region morphology showed less variability in comparison with tail shape in both species, which was more variable in X. simile. Differences in lip region were constant between these species, but specimens with similar tail shape rarely occurred. Both species showed considerable overlap in all morphometrical data and a polytomous key is inadequate for their practical identification. In practice, the most reliable approach for accurate determination of X. parasimile and X. simile is the use of a combination of morphometrics with morphology of lip and vulval regions and tail shape. Total DNA was isolated from individual nematodes of both species and the ITS region of the 18S and 26S rDNA and D1-D2 expansion segments of the 26S rDNA were amplified and cloned. The ITS-RFLP patterns clearly revealed X. simile and X. parasimile to be distinct species. The restriction profiles of the D1-D2 amplicons also discriminated these species. D1-D2 sequences revealed no intrapopulation variability and their comparison showed 89% of similarity to each other. These data show that both ribosomal regions are useful to differentiate X. parasimile and X. simile as two distinct species despite similar morphology and morphometrics.

scholarly journals Comment on “DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification”

Science ◽  
2018 ◽  
Vol 361 (6409) ◽  
pp. eaas9824 ◽  
Author(s):  
Chip Stewart ◽  
Ignaty Leshchiner ◽  
Julian Hess ◽  
Gad Getz
Keyword(s):  
Dna Damage ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Sample Processing ◽  
Sequencing Errors ◽  
Cancer Genome Atlas ◽  
P 752 ◽  
Genome Atlas ◽  
Variant Identification

Chen et al. (Reports, 17 February 2017, p. 752) highlight an important problem of sequencing artifacts caused by DNA damage at the time of sample processing. However, their manuscript contains several errors that led the authors to incorrect conclusions. Moreover, the same sequencing artifacts were previously described and mitigated in The Cancer Genome Atlas and other published sequencing projects.

A quantitative approach to inner shell losses

1978 ◽  
Vol 36 (1) ◽  
pp. 526-527 ◽  
Author(s):  
R.D. Leapman ◽  
P. Rez ◽  
D.F. Mayers
Keyword(s):  
Energy Transfer ◽  
Cross Section ◽  
Cross Sections ◽  
Accurate Determination ◽  
Background Intensity ◽  
Core Excitation ◽  
Quantitative Basis ◽  
Cross Section Differential ◽  
Bound Electrons

Microanalysis by EELS has been developing rapidly and though the general form of the spectrum is now understood there is a need to put the technique on a more quantitative basis (1,2). Certain aspects important for microanalysis include: (i) accurate determination of the partial cross sections, σx(α,ΔE) for core excitation when scattering lies inside collection angle a and energy range ΔE above the edge, (ii) behavior of the background intensity due to excitation of less strongly bound electrons, necessary for extrapolation beneath the signal of interest, (iii) departures from the simple hydrogenic K-edge seen in L and M losses, effecting σx and complicating microanalysis. Such problems might be approached empirically but here we describe how computation can elucidate the spectrum shape.The inelastic cross section differential with respect to energy transfer E and momentum transfer q for electrons of energy E0 and velocity v can be written as

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