ArticleBMC genomics2012
Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Development and validation of a multigene variant profiling assay to guide targeted and immuno therapy selection in solid tumors.PloS one · 2021Article
- Disjunction between canola distribution and the genetic structure of its recently described pest, the canola flower midge (Ecology and evolution · 2020Article
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- How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data.Genetics and molecular biology · 2018Article
- Identification and characterization of two functional variants in the human longevity gene FOXO3.Nature communications · 2017Article
- Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues.Scientific reports · 2017Article
- Mutated Ptpn11 alters leukemic stem cell frequency and reduces the sensitivity of acute myeloid leukemia cells to Mcl1 inhibition.Leukemia · 2015Article
- Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives.BioMed research international · 2015Review
- Mung bean nuclease treatment increases capture specificity of microdroplet-PCR based targeted DNA enrichment.PloS one · 2014Article
- Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics.Frontiers in oncology · 2014Review
- Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.BMC genomics · 2013Article
- A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.BMC bioinformatics · 2013Article
- Variant discovery in targeted resequencing using whole genome amplified DNA.BMC genomics · 2013Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany hypothesis-driven genetic studies require the ability to comprehensively and efficiently target specific regions of the genome to detect sequence variations. Often, sample availability is limited requiring the use of whole genome amplification (WGA). We evaluated a high-throughput microdroplet-based PCR approach in combination with next generation sequencing (NGS) to target 384 discrete exons from 373 genes involved in cancer. In our evaluation, we compared the performance of six non-amplified gDNA samples from two HapMap family trios. Three of these samples were also preamplified by WGA and evaluated. We tested sample pooling or multiplexing strategies at different stages of the tested targeted NGS (T-NGS) workflow.
resultsThe results demonstrated comparable sequence performance between non-amplified and preamplified samples and between different indexing strategies [sequence specificity of 66.0% ± 3.4%, uniformity (coverage at 0.2× of the mean) of 85.6% ± 0.6%]. The average genotype concordance maintained across all the samples was 99.5% ± 0.4%, regardless of sample type or pooling strategy. We did not detect any errors in the Mendelian patterns of inheritance of genotypes between the parents and offspring within each trio. We also demonstrated the ability to detect minor allele frequencies within the pooled samples that conform to predicted models.
conclusionOur described PCR-based sample multiplex approach and the ability to use WGA material for NGS may enable researchers to perform deep resequencing studies and explore variants at very low frequencies and cost.
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