DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants

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.

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

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.

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

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.

Crack Behavior of Fe-Based Coating by Plasma Cladding

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.

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

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.