Novel deep learning-based survival prediction for oral cancer by analyzing tumor-infiltrating lymphocyte profiles through CIBERSORT.

The tumor microenvironment (TME) within mucosal neoplastic tissue in oral cancer (ORCA) is greatly influenced by tumor-infiltrating lymphocytes (TILs). Here, a clustering method was performed using CIBERSORT profiles of ORCA data that were filtered from the publicly accessible data of patients with head and neck cancer in The Cancer Genome Atlas (TCGA) using hierarchical clustering where patients were regrouped into binary risk groups based on the clustering-measuring scores and survival patterns associated with individual groups. Based on this analysis, clinically reasonable differences were identified in 16 out of 22 TIL fractions between groups. A deep neural network classifier was trained using the TIL fraction patterns. This internally validated classifier was used on another individual ORCA dataset from the International Cancer Genome Consortium data portal, and patient survival patterns were precisely predicted. Seven common differentially expressed genes between the two risk groups were obtained. This new approach confirms the importance of TILs in the TME and provides a direction for the use of a novel deep-learning approach for cancer prognosis.

Complete chloroplast genome sequences of Wonwhang (Pyrus pyrifolia) and its phylogenetic analysis.

The complete chloroplast genome of Wonwhang (BioSample SAMN05196235), Pyrus pyrifolia, was assembled and analyzed by de novo assembly using whole-genome sequencing data. The accession NC_015996 was used as a reference sequence in this study. The total chloroplast genome size of the Wonwhang was 159,922 bp in length, including a pair of inverted repeat regions (IRs) of 26,392 bp that are separated by a large single-copy region of 72,023 bp and a small single-copy region of 19,235 bp. A total of 132 genes, including 93 protein-coding genes, 31 tRNA genes and eight rRNA genes, were predicted from the chloroplast genomes. Among them, 18 genes occur in IRs, containing nine protein-coding genes, five tRNA genes and four rRNA genes. The GC content of Wonwhang chloroplast genome is 36.6%. The phylogenetic analysis with nine Rosids species and three other species revealed that Wonwhang was clustered with Malus genus.

The draft genome sequence of European pear (Pyrus communis L. 'Bartlett').

We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus × domestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.