a comparison of single molecule and amplification based sequencing of cancer transcriptomes比较基于单分子和放大的转录组测序的癌症.pdfVIP

A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes 1,2,3 4 4 1,5,6 4 4 Lee T. Sam , Doron Lipson , Tal Raz , Xuhong Cao , John Thompson , Patrice M. Milos , Dan Robinson1,5, Arul M. Chinnaiyan1,5,6,7,8*, Chandan Kumar-Sinha1,5*, Christopher A. Maher1,2,5* 1 Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, United States of America, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan, United States of America, 3 Bioinformatics Program, University of Michigan, Ann Arbor, Michigan, United States of America, 4 Helicos BioSciences Corporation, Cambridge, Massachusetts, United States of America, 5 Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America, 6 Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America, 7 Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America, 8 Department of Urology, University of Michigan, Ann Arbor, Michigan, United States of America Abstract The second wave of next generation sequencing technologies, referred to as single-molecule sequencing (SMS), carries the promise of profiling samples directly without employing polymerase chain reaction steps used by amplification-based sequencing (AS) methods. To examine the merits of both technologies, we examine mRNA sequencing results from single- molecule and amplification-based sequencing in a set of human cancer cell lines and tissues. We observe a characteristic coverage bias towards high abundance transcripts in amplification-based sequencing. A larger fraction of AS reads cover highly expressed genes, such as those