Overcoming bias and systematic errors in next generation sequencing data 英文参考文献.docVIP

Taub et al. Genome Medicine 2010,2:87 /content/2/12/87 CO MMENTA RY Overcoming bias and systematic errors in next generation sequencing data Margaret A Taub* , Hector Corrada Bravo and Rafael A Irizarry* 1 2 1 FDA-approved clinical diagnostic tests, including MammaPrint, and Pathwork’s Tissue of Origin test [7,8]. With high-throughput sequencing still in its infancy, many questions remain to be addressed before any hope of achieving approval for clinical applications is warranted. Although a study on the scale of the MAQC analyses for microarrays has yet to be carried out for sequencing (although one is in the works), there is already evidence that similar technical biases are present in sequencing data, and these will need to be understood and adjusted for to enable use of these new technologies in a clinical setting. In this commentary, we present some of these known biases and discuss the current state of solutions aimed at addressing them. Looking ahead to the application of this new technology in the clinical setting, we see both hurdles and promise. Abstract Considerable time and eort has been spent in developing analysis and quality assessment methods to allow the use of microarrays in a clinical setting. As is the case for microarrays and other high-throughput technologies, data from new high-throughput sequencing technologies are subject to technological and biological biases and systematic errors that can impact downstream analyses. Only when these issues can be readily identied and reliably adjusted for will clinical applications of these new technologies be feasible. Although much work remains to be done in this area, we describe consistently observed biases that should be taken into account when analyzing high- throughput sequenci