Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

The effects of the tylosin and Cd on soil enzyme activity

Soil microbial environment have been affected by different concentration heavy metals Cd (HM) and tylosin (TYL) and combination of TYL and HM interactions. Degradation of TYL was caused certain inhibition due to the addition of HM. The germination index of seed had been inhibited owing to the toxic effects of HM and TYL, but we found that the low concentrations of HM (4 mg/kg), the germination index higher than the soil which unadded HM and TYL in it. The soil enzyme activity was significantly suppressed by the addition of HM and TYL. Actinomycete was inhibited by high concentrations of HM for a long time. The studies demonstrated that the pollution of the soil micro-environment has been serious than only add HM or TYL in the soil

High Capacity HEVC Video Hiding Algorithm Based on EMD Coded PU Partition Modes

Data hiding in videos has been a big concern as their rich redundancy can be used for embedding a lot of secret information. Further, as high efficiency video coding (HEVC) introduces many innovative technologies compared with the previous standard, H.264, it has gradually become the mainstream. Therefore, it is valuable to develop new information hiding algorithms by using novel features of HEVC. A HEVC video data hiding algorithm based on prediction unit (PU) partition modes from inter prediction process is proposed in this paper. Firstly, code units (CUs) in two sizes of 8 &times; 8 and 16 &times; 16 are selected for embedding, then the PU partition modes in these CUs are coded by a spatial coding method. After that, two specific hiding algorithms by modifying coded PU partition modes in CUs of 8 &times; 8 and 16 &times; 16 are proposed, respectively. Experimental results show that the proposed algorithm has achieved excellent performance with high visual quality, and high embedding capacity and low bitrate increase in both high- and low-resolution videos compressed with different quantization parameters (QPs). Compared with the state-of-the-art work, the proposed algorithm achieves a much higher capacity while keeping quite high visual quality with little increase of bitrate

Discussion Groups

Attendees break into 4 discussion groups: teacher discuss the basics of today’s lecture series, choose a small group, share your learning experience or inquiries. Group: Jian Gao Group: Zaohong Li Group: Yuanchao Meng Group: Liya A

Nitric oxide content analysis in the aerial parts and in the roots of ARG-26 and ARG-38 seedlings grown on 1/2 MS medium, 1/2 MS medium with 4×NH4NO3, and 1/2 MS medium lacking nitrogen.

<p>Compared to non-transgenic control plants, the nitric oxide content decreased in the aerial parts and in the roots of ARG-26 and ARG-38 seedlings on all of the various 1/2 MS media compositions. no differences were observed for the aerial parts of the plants. (A) the nitric oxide content in seedlings of transgenic cotton grown on 1/2 MS medium. (B) the nitric oxide content in transgenic cotton seedlings grown on 1/2 MS medium with 4× NH₄NO₃. (C) the nitric oxide content in transgenic cotton seedlings grown on 1/2 MS medium lacking NH₄NO3 and KNO3. ‘FW’ refers to fresh leaf weight. ‘WT’ refers to non-transgenic control plants of wild type cotton. *: P<0.05.</p

Fiber lengths of transgenic cotton are compared with Control.

<p>(A) the fiber length of ARG-26-2 compared with that of the Control. (B) the fiber length of ARG-26-7 compared with that of the Control. (C) the fiber length of ARG-38-8 compared with that of the Control. (D) the fiber length of ARG-38-11 compared with that of the Control. ‘Control’ refers to fiber of non-transgenic wild type plants. Scale bar, 5mm.</p

Quantitative PCR analysis of OsArg expression in the leaves of ARG-26 and ARG-38 transgenic cotton.

<p>The <i>OsARG</i> gene was detected in ARG-26 and ARG-38 leaves but not in non-transgenic control leaves. ‘WT’ refers to non-transgenic control plants of wild type cotton. **: P<0.01</p

Map of the plant expression vector.

<p>Map of the plant expression vector.</p