ArticleGenome research2009
Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 51 citations in OpenAlex.
- Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis.Pathology oncology research : POR · 2017Review
- Targeted Capture of Complete Coding Regions across Divergent Species.Genome biology and evolution · 2017Article
- Microbial Ecology: Where are we now?Postdoc journal : a journal of postdoctoral research and postdoctoral affairs · 2016Article
- Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.BMC genomics · 2012Article
- Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities.Hearing research · 2012Review
- Potential value of nutrigenomics in Crohn's disease.Nature reviews. Gastroenterology & hepatology · 2012Review
- Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation.Genetics in medicine : official journal of the American College of Medical Genetics · 2011Article
- Next-generation sequencing for cancer diagnostics: a practical perspective.The Clinical biochemist. Reviews · 2011Article
- Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing.BMC genomics · 2011Article
- The impact of next-generation sequencing on genomics.Journal of genetics and genomics = Yi chuan xue bao · 2011Review
- Article
- Targeted resequencing of candidate genes using selector probes.Nucleic acids research · 2011Article
- Exome sequencing: the sweet spot before whole genomes.Human molecular genetics · 2010Review
- Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.Genome research · 2010Article
- Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development.BMC bioinformatics · 2010Article
- Next generation sequencing for clinical diagnostics-principles and application to targeted resequencing for hypertrophic cardiomyopathy: a paper from the 2009 William Beaumont Hospital Symposium on Molecular Pathology.The Journal of molecular diagnostics : JMD · 2010Review
- Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.Nucleic acids research · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The lack of efficient high-throughput methods for enrichment of specific sequences from genomic DNA represents a key bottleneck in exploiting the enormous potential of next-generation sequencers. Such methods would allow for a systematic and targeted analysis of relevant genomic regions. Recent studies reported sequence enrichment using a hybridization step to specific DNA capture probes as a possible solution to the problem. However, so far no method has provided sufficient depths of coverage for reliable base calling over the entire target regions. We report a strategy to multiply the enrichment performance and consequently improve depth and breadth of coverage for desired target sequences by applying two iterative cycles of hybridization with microfluidic Geniom biochips. Using this strategy, we enriched and then sequenced the cancer-related genes BRCA1 and TP53 and a set of 1000 individual dbSNP regions of 500 bp using Illumina technology. We achieved overall enrichment factors of up to 1062-fold and average coverage depths of 470-fold. Combined with high coverage uniformity, this resulted in nearly complete consensus coverages with >86% of target region covered at 20-fold or higher. Analysis of SNP calling accuracies after enrichment revealed excellent concordance, with the reference sequence closely mirroring the previously reported performance of Illumina sequencing conducted without sequence enrichment.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.