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again good morning or good afternoon and welcome to the webinar on detection of copy number variants in next-gen sequencing data and integration with gene expression during the webinar I shall first provide a short overview of the company and then introduce the data set that will be used for today's discussion after that I'm going to guide you through the workflow for analyzing copy number variations from low pass whole genome sequencing and show several examples of copy number variants detected in the webinar data set the variations that you are going to see include whole chromosome deletions in and amplifications as well as smaller changes such as segmental deletions and amplification genes I'm also going to show you how to interpret the copy number variants using pathway analysis and finally discuss tools to integrate gene expression data based on RNA seek with copy number results partic delivers a single platform for next-generation sequencing analysis beginning with alignment and ending with pathway analysis it quickly handles demanding datasets with flexible hardware configurations and allows you to dive deep into data analysis with robust visualizations and statistics to get to the underlying biology with partic data analysis is easy from start to finish the point-and-click interface with sa specific workflows make statistical analysis easier than ever before downstream biological interpretation is a key element putting the statistical results into biological context with path analysis and more and finally our unique integrated genomics workflows allow data integration across essays and technologies for a systems biology view let me start by showing you an exciting new discovery we made by analyzing this data the top panel of the slide focuses on the copy number analysis the heat map presented presented copy number changes in seven breast cancer cell lines listed here on the left hand side the colors of the plot represent copy number status with blue indicating deletion yellow indicating expected euploid copy number of two and red indicating amplification the baseline cell line in this example mcf 10a with the expected copy number of two is at the bottom track of the heat map the amplified the amplification detected in the cancer cell lines effects a genomic region that harbors a gene called an Adele the exon and inference structure of the riddle gene in shown in the annotation track above the heat map this region was automatically flagged by the software because gene expression data based on the same set of samples indicates that the expression levels of an Adele are increased in the cancer cell lines and that increase parallels the copy number amplifications the expression levels are shown by the dot plot on the bottom the normal samples are depicted in white while the cancer samples are in red the connecting lines indicate the same biological sample sequence by paired n in single and chemistry the horizontal axis shows a lock to rpkm expression values this up regulation of gene expression by gene amplification is likely a...