Identification of genetic variants using bar-coded multiplexed sequencing
| Autor: | Margot Redman, Nils Homer, Trisha Laub, Szabolcs Szelinger, Traci Pawlowski, Aswin Sekar, Gary Nunn, Matthew J. Huentelman, John V. Pearson, David Craig, Dietrich A. Stephan, Jason J. Corneveaux |
|---|---|
| Rok vydání: | 2008 |
| Předmět: |
0106 biological sciences
dbSNP Biology ENCODE Polymorphism Single Nucleotide 01 natural sciences Biochemistry Article DNA sequencing Deep sequencing 03 medical and health sciences Humans International HapMap Project Molecular Biology Genotyping Exome sequencing 030304 developmental biology Genetics Electronic Data Processing 0303 health sciences Genome Human Genetic Variation Cell Biology Human genome Sequence Alignment 010606 plant biology & botany Biotechnology |
| Zdroj: | Nature methods |
| ISSN: | 1548-7105 1548-7091 |
| DOI: | 10.1038/nmeth.1251 |
| Popis: | We developed a generalized framework for multiplexed resequencing of targeted regions of the human genome on the Illumina Genome Analyzer using degenerate indexed DNA sequence barcodes ligated to fragmented DNA prior to sequencing. Using this method, the DNA of multiple HapMap individuals was simultaneously sequenced at several ENCODE (ENCyclopedia of DNA Elements) regions. We then evaluated the use of Bayes factors for discovering and genotyping polymorphisms from aligned sequenced reads. If we required that predicted polymorphisms be either previously identified by dbSNP or be visually evident upon reinspection of archived ENCODE traces, we observed a false-positive rate of 11.3% using strict thresholds (Ks>1,000) for predicting variants and 69.6% for lax thresholds (Ks>10). Conversely, false-negative rates ranged from 10.8% to 90.8%, with those at stricter cut-offs occurring at lower coverage (< 10 aligned reads). These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|