PMC:3480879 / 1190-3427
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3480879","sourcedb":"PMC","sourceid":"3480879","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3480879","text":"Introduction\nIn the last decade, numerous genomic studies have addressed the enormous complexity of the cancer genome. Genomic profiling using microarray technology could stratify the tumors into homogeneous subgroups, providing novel clinical insights for the development of diagnostics and therapeutics as well as systematic views on the underlying mechanisms of tumor progression. In addition to the microarray technologies, explosive advances on sequencing technologies have been made recently, which is called \"next generation sequencing (NGS).\" Compared to the previous DNA sequencing of the Sanger method using dideoxynucleotide termination reaction termed as \"first-generation\" sequencing, NGS uses massively parallel sequencing method generating hundreds of millions of short (~200 bp) DNA reads, which can sequence a human genome rapidly with extremely lower cost. The earlier NGS method with the single-end read sequencing inevitably produces the short-read problems, limiting the accuracy of genome alignment. This could be improved by applying a paired-end sequencing method, allowing substantial advances in identifying not only point mutations but also genomic rearrangements, such as deletions, amplifications, inversions, translocations, and gene-fusions [1, 2].\nThe NGS technology is now divided into \"second generation sequencing\" and \"third generation sequencing.\" The second generation sequencing refers to the strategies of short-read alignment, while the rapidly being developed technology of the third generation sequencing refers to the single DNA molecule based sequencing. The third generation method has advantage of less amount of DNA input that allows the emerging field of single cell sequencing [3]. Moreover, there is no step for PCR amplification, therefore, the nucleotide incorporation errors can be handled.\nHowever, all the platforms of NGS technologies still have limitations in accurate base calling and alignment. The errors are likely to be platform-dependent, which increases the complexity of the data analysis. Therefore, the cost for bioinformatic analysis, rather than the sequencing itself continues to grow, which is referred to as \"the $1,000 genomes, the $100,000 analysis\" problem [4].","divisions":[{"label":"Title","span":{"begin":0,"end":12}}],"tracks":[{"project":"2_test","denotations":[{"id":"23105932-21307932-44836615","span":{"begin":1273,"end":1274},"obj":"21307932"},{"id":"23105932-20847746-44836616","span":{"begin":1276,"end":1277},"obj":"20847746"},{"id":"23105932-20858600-44836617","span":{"begin":1728,"end":1729},"obj":"20858600"},{"id":"23105932-21114804-44836618","span":{"begin":2234,"end":2235},"obj":"21114804"}],"attributes":[{"subj":"23105932-21307932-44836615","pred":"source","obj":"2_test"},{"subj":"23105932-20847746-44836616","pred":"source","obj":"2_test"},{"subj":"23105932-20858600-44836617","pred":"source","obj":"2_test"},{"subj":"23105932-21114804-44836618","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93e2ec","default":true}]}]}}