◾ Orthogonal Comparison

2015 ◽  
pp. 126-139
Keyword(s):  
Orthogonal Comparison

scholarly journals DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 507
Author(s):  
Bernd Timo Hermann ◽  
Sebastian Pfeil ◽  
Nicole Groenke ◽  
Samuel Schaible ◽  
Robert Kunze ◽  
...  
Keyword(s):  
Cancer Detection ◽  
Genetic Variants ◽  
Liquid Biopsy ◽  
Hot Spot ◽  
Treatment Success ◽  
Low Frequency ◽  
Variant Calling ◽  
Subsequent Treatment ◽  
Precision Oncology ◽  
Orthogonal Comparison

Detection of genetic variants in clinically relevant genomic hot-spot regions has become a promising application of next-generation sequencing technology in precision oncology. Effective personalized diagnostics requires the detection of variants with often very low frequencies. This can be achieved by targeted, short-read sequencing that provides high sequencing depths. However, rare genetic variants can contain crucial information for early cancer detection and subsequent treatment success, an inevitable level of background noise usually limits the accuracy of low frequency variant calling assays. To address this challenge, we developed DEEPGENTM, a variant calling assay intended for the detection of low frequency variants within liquid biopsy samples. We processed reference samples with validated mutations of known frequencies (0%–0.5%) to determine DEEPGENTM’s performance and minimal input requirements. Our findings confirm DEEPGENTM’s effectiveness in discriminating between signal and noise down to 0.09% variant allele frequency and an LOD(90) at 0.18%. A superior sensitivity was also confirmed by orthogonal comparison to a commercially available liquid biopsy-based assay for cancer detection.

scholarly journals INFLUENCE OF `CRIMSON SWEET' WATERMELON WITH VISPORE ROW COVER IN COMBINATION WITH WAVELENGTH SELECTIVE MULCHES

HortScience ◽  
1993 ◽  
Vol 28 (4) ◽  
pp. 270E-270
Author(s):  
Mack A. Wilson ◽  
Victor A. Khan ◽  
Clauzell Stevens
Keyword(s):  
Significant Interaction ◽  
Total Yield ◽  
Marketable Yield ◽  
Row Covers ◽  
Orthogonal Comparison

Several plastic mulches [clear, black, IRT-76 (green), and ALOR (brown)] were used in combination with four row covers [(clear and white slitted), spunbonded polyester and VisPore]. The total numbers and marketable numbers per 1000/ha were highest with the clear and IRT-76 mulches without the use of row covers, respectively. There was a significant orthagonal comparison interaction with the clear & IRT-76 mulches vs. black & ALOR mulches. A significant orthogonal comparison interaction was observed with total yield with row covers vs. no row cover, mulch vs. control, clear and IRT-76 vs. black & ALOR, clear vs. IRT-76, and black vs. ALOR. Marketable yield showed a significant interaction with orthogonal comparison with row covers vs. no row cover and clear & IRT-76 vs. black & ALOR.

scholarly journals GROWTH RESPONSES OF WATERMELON ON WAVELENGTH SELECTIVE MULCHES AND VISPORE ROW COVER IN MISSOURI

HortScience ◽  
1992 ◽  
Vol 27 (11) ◽  
pp. 1177c-1177
Author(s):  
Mack A. Wilson ◽  
Victor A. Kahn
Keyword(s):  
Bare Soil ◽  
Growth And Yield ◽  
Growth Responses ◽  
Orthogonal Comparison

The influence of VisPore row cover and four synthetic mulches on the growth and yield of watermelons were studied. Row cover and synthetic mulch treatments consisted of VisPore row cover, IRT-76 (green), AL-0R (brown), clear and black polyethylene mulches. VisPore was used with a combination of' four mulches and two controls (VisPore alone and bare soil). Significant differences were observed by orthogonal comparison when no row cover (NRC) was compared to row cover (RC) on the number '000/acre of marketable `Crimson Sweet' watermelons. Total, marketable and percent marketable yields were significantly different when orthogonal comparison were performed on NRC vs. RC. Yields were greater when RC vs. NRC treatments were used on `Crimson Sweet' watermelons.

scholarly journals PENGARUH LAMA PERENDAMAN PANGKAL SETEK DALAM LARUTAN NAA (NAPTHALENE ACETIC ACID) PADA PERTUMBUHAN SETEK LADA

2020 ◽  
Vol 8 (2) ◽  
pp. 311
Author(s):  
Syaicha Fachrun Nisa ◽  
Niar Nurmauli ◽  
Akari Edy ◽  
Sugiatno Sugiatno
Keyword(s):  
Acetic Acid ◽  
Dry Weight ◽  
Piper Nigrum ◽  
Naphthalene Acetic Acid ◽  
Stem Cuttings ◽  
Fresh Weight ◽  
Orthogonal Comparison ◽  
Napthaleneacetic Acid ◽  
Α Level ◽  
Total Fresh Weight

Effect of soaking duration on base stem cuttings in NAA solution (Naphthalene Acetic Acid) on the growth of pepper The need for pepper is increasing along with the development of the food industry with the basic ingredients of pepper. The determining factor of the quality of pepper produced comes from the seeds used. This study aims to determine the effect of soaking DURATION on pepper cuttings (Piper nigrum L.) in the Napthaleneacetic Acid (NAA) solution. The study was conducted in October 2018 until February 2019 in the greenhouse and Plant Science Laboratory of the Faculty of Agriculture, University of Lampung, Bandar Lampung. This study uses a completely randomized group design (RKTS). The treatment of immersion base cuttings in NAA (N) solution concentrates 500 ppm consisting of : without NAA (n0), immersion 0 minutes (n1), soaked 15 minutes (n2), soaked 30 minutes (n3), soaked 60 minutes (n4), and soaked 120 minutes (n5). Homogeneity of variability between treatments was tested by Bartlet Test and data additivity was tested by Tukey test, then continued with Variance Analysis (ANARA). Comparison of the middle value with the orthogonal comparison test at α level of 5%. The results showed that: (1) giving NAA affected the number of roots in the book, the fresh weight of the roots in the book, the dry weight of the roots in the book, the total number of roots, and the total fresh weight of the roots; (2) administration of NAA by immersion is better than dipping in the number of roots in the book, the fresh weight of the roots in the book, the dry weight of the roots in the book, the total number of roots, and the total fresh weight of the roots; and (3) length of soaking cuttings in NAA solution has no effect on the growth of pepper cuttings.

Crack Behavior of Fe-Based Coating by Plasma Cladding

2011 ◽  
Vol 109 ◽  
pp. 145-149
Author(s):  
Jun Bo Liu ◽  
Li Mei Wang ◽  
Bao Xin Huang
Keyword(s):  
Surface State ◽  
Processing Parameter ◽  
Orthogonal Comparison ◽  
Crack Behavior ◽  
Plasma Cladding ◽  
State Processing

On the base of orthogonal comparison tests, influences of many kinds of factors on plasma cladding crack sensibility were studied. The results indicate that substrate and its surface state, processing parameter and components of plasma cladding coating have great effects on crack sensibility of plasma cladding coating. Through changing these factors, it is possible to reduce cracks and expand ranges of applications of this technology.

scholarly journals Orthogonal Comparison of Four Plasma NGS Tests With Tumor Suggests Technical Factors are a Major Source of Assay Discordance

2019 ◽  
pp. 1-9 ◽  
Author(s):  
Daniel Stetson ◽  
Ambar Ahmed ◽  
Xing Xu ◽  
Barrett R.B. Nuttall ◽  
Tristan J. Lubinski ◽  
...  
Keyword(s):  
Tumor Heterogeneity ◽  
False Negative ◽  
Variant Calling ◽  
Circulating Tumor Dna ◽  
Orthogonal Comparison ◽  
Novel Variants ◽  
Technical Factors ◽  
Next Generation Sequencing Ngs ◽  
Biologic Factors ◽  
Generation Sequencing

PURPOSE Discordance between plasma and tumor variant calling has been attributed primarily to tumor heterogeneity, whereas technical variables remain largely unexplored. MATERIALS AND METHODS To measure these variables, we tested four next-generation sequencing (NGS) gene panel assays for mutations in circulating tumor DNA (ctDNA) using replicate sets of 24 plasma samples and compared the results with matched tumor-normal tissue pairs. RESULTS Our orthogonal approach identified false-negative (FN) and false-positive (FP) variants with high confidence and revealed substantial variability among the ctDNA assays, with a range of sensitivity (38% to 89%) and positive predictive value (36% to 80%). Most discordance in our cross-vendor study was observed below 1% variant allele frequency. FP variants displayed mutational biases and tended to be novel variants not found in somatic databases. Of the 56 unique variants called by all four ctDNA assays, 41 (68%) resulted from technical discordance. CONCLUSION These findings suggest that most NGS assay discordance is a result of technical variations and, to a lesser extent, biologic factors such as clonal hematopoiesis of indeterminate potential and tumor heterogeneity.

scholarly journals Orthogonal Comparison of GC–MS and1H NMR Spectroscopy for Short Chain Fatty Acid Quantitation

2017 ◽  
Vol 89 (15) ◽  
pp. 7900-7906 ◽  
Author(s):  
Jingwei Cai ◽  
Jingtao Zhang ◽  
Yuan Tian ◽  
Limin Zhang ◽  
Emmanuel Hatzakis ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Nmr Spectroscopy ◽  
Short Chain Fatty Acid ◽  
Chain Fatty Acid ◽  
Short Chain ◽  
Orthogonal Comparison
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