NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome.

BACKGROUND: Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool 'HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets. METHODS: We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a 'quick mode' to identify presence of HPV types and an 'integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html. RESULTS: On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene E7, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71. CONCLUSIONS: HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.

Two male-sterile mutants of Zea Mays (Poaceae) with an extra cell division in the anther wall.

Two recessive male-sterile mutants of maize with similar patterns of pollen abortion were studied. Genetic studies showed that one of the two mutations was allelic with a previously identified male-sterility locus (ms23) and the other mutation was in a newly identified male-sterility locus (ms32). Cytological characterization of homozygous mutants and fertile heterozygous control siblings was performed using brightfield, fluorescence, and electron microscopy. During normal anther development, the final anther wall periclinal division divides the secondary parietal anther wall layer into the middle layer and tapetum, forming an anther with four wall layers. This is followed by differentiation of the tapetal cells into protoplastic binucleate, secretory tissue. In both the ms23 and ms32 mutants, the prospective tapetal layer divided into two layers, termed t1 and t2, forming an anther with five wall layers. Neither the t1 nor the t2 layers differentiated normally into tapetal layers, as determined by examination of cell walls, nucleus number, and cytoplasmic organization. Pollen mother cells aborted after the onset of prophase I of meiosis, suggesting that an early developmental coordination may exist between tapetum and pollen mother cells.