Assessment of Whole Genome Amplification for Sequence Capture and Massively Parallel Sequencing
| Autor: | Cedric Orear, Max Käller, Joakim Lundeberg, Mikael Huss, Pierre Validire, Henrik Gréen, Johanna Hasmats |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Cancer genome sequencing
Male Medicin och hälsovetenskap Lung Neoplasms lcsh:Medicine Genomics Bioengineering Biology Medical and Health Sciences Lung and Intrathoracic Tumors Engineering Diagnostic Medicine Carcinoma Non-Small-Cell Lung Genetics Cancer Genetics Humans Genome Sequencing lcsh:Science Exome Exome sequencing Whole Genome Amplification Multidisciplinary Massive parallel sequencing Genome Human Sequence Analysis RNA lcsh:R Multiple displacement amplification Computational Biology Cancers and Neoplasms Genetic Variation High-Throughput Nucleotide Sequencing Reproducibility of Results Sequence Analysis DNA Non-Small Cell Lung Cancer Oncology Mutation Medicine Human genome lcsh:Q Female Sequence Analysis Population Genetics Research Article Test Evaluation |
| Zdroj: | PLoS ONE PLoS ONE, Vol 9, Iss 1, p e84785 (2014) |
| ISSN: | 1932-6203 |
| Popis: | Exome sequence capture and massively parallel sequencing can be combined to achieve inexpensive and rapid global analyses of the functional sections of the genome. The difficulties of working with relatively small quantities of genetic material, as may be necessary when sharing tumor biopsies between collaborators for instance, can be overcome using whole genome amplification. However, the potential drawbacks of using a whole genome amplification technology based on random primers in combination with sequence capture followed by massively parallel sequencing have not yet been examined in detail, especially in the context of mutation discovery in tumor material. In this work, we compare mutations detected in sequence data for unamplified DNA, whole genome amplified DNA, and RNA originating from the same tumor tissue samples from 16 patients diagnosed with non-small cell lung cancer. The results obtained provide a comprehensive overview of the merits of these techniques for mutation analysis. We evaluated the identified genetic variants, and found that most (74%) of them were observed in both the amplified and the unamplified sequence data. Eighty-nine percent of the variations found by WGA were shared with unamplified DNA. We demonstrate a strategy for avoiding allelic bias by including RNA-sequencing information. |
| Databáze: | OpenAIRE |
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