Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods
| Autor: | Wing Hung Wong, Narges Bani Asadi, Mark Gerstein, Xi Chen, Marghoob Mohiyuddin, John C. Mu, Hugo Y. K. Lam, Pegah Tootoonchi Afshar, Jian Li |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Population
Genomics Biology computer.software_genre Genome Article 03 medical and health sciences 0302 clinical medicine Humans education Illumina dye sequencing 030304 developmental biology 0303 health sciences education.field_of_study Multidisciplinary Genome Human Genetic Variation High-Throughput Nucleotide Sequencing Benchmarking Precision medicine Human genome Data mining computer 030217 neurology & neurosurgery |
| Zdroj: | Scientific Reports |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/srep14493 |
| Popis: | A high-confidence, comprehensive human variant set is critical in assessing accuracy of sequencing algorithms, which are crucial in precision medicine based on high-throughput sequencing. Although recent works have attempted to provide such a resource, they still do not encompass all major types of variants including structural variants (SVs). Thus, we leveraged the massive high-quality Sanger sequences from the HuRef genome to construct by far the most comprehensive gold set of a single individual, which was cross validated with deep Illumina sequencing, population datasets and well-established algorithms. It was a necessary effort to completely reanalyze the HuRef genome as its previously published variants were mostly reported five years ago, suffering from compatibility, organization and accuracy issues that prevent their direct use in benchmarking. Our extensive analysis and validation resulted in a gold set with high specificity and sensitivity. In contrast to the current gold sets of the NA12878 or HS1011 genomes, our gold set is the first that includes small variants, deletion SVs and insertion SVs up to a hundred thousand base-pairs. We demonstrate the utility of our HuRef gold set to benchmark several published SV detection tools. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|