ArticleGenome research2009
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations.
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 39 papers.
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Who cites it
39 citing papers in PubMed.
- An optimized ligation-mediated PCR method for chromosome walking and fusion gene chromosomal breakpoints identification.Biology methods & protocols · 2024Article
- NGS allele counts versus called genotypes for testing genetic association.Computational and structural biotechnology journal · 2022Article
- Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.Nucleic acids research · 2021Article
- Ultrasensitive detection of circulating tumour DNA via deep methylation sequencing aided by machine learning.Nature biomedical engineering · 2021Article
- Evaluation of molecular inversion probe versus TruSeq® custom methods for targeted next-generation sequencing.PloS one · 2020Article
- Efficient in situ barcode sequencing using padlock probe-based BaristaSeq.Nucleic acids research · 2018Article
- A generic, cost-effective, and scalable cell lineage analysis platform.Genome research · 2016Article
- Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries.Nature communications · 2015Article
- RNA-binding proteins in neurodegeneration: Seq and you shall receive.Trends in neurosciences · 2015Review
- microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes.Nucleic acids research · 2015Article
- MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing.Bioinformatics (Oxford, England) · 2014Article
- Large-scale de novo DNA synthesis: technologies and applications.Nature methods · 2014Review
- Molecular inversion probe: a new tool for highly specific detection of plant pathogens.PloS one · 2014Article
- Single-cell sequencing-based technologies will revolutionize whole-organism science.Nature reviews. Genetics · 2013Review
- DNA methylation analysis in human cancer.Methods in molecular biology (Clifton, N.J.) · 2013Article
- A public resource facilitating clinical use of genomes.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation.BMC microbiology · 2012Article
- Review of massively parallel DNA sequencing technologies.The HUGO journal · 2011Article
- Review
- Landscape of next-generation sequencing technologies.Analytical chemistry · 2011Review
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable CpG regions across human chromosome 21. From approximately 3 million reads derived from a single Illumina Genome Analyzer lane, approximately 94% (approximately 50,500) target sites can be observed with at least one read. The uniformity of coverage was also greatly improved; up to 93% and 57% of all targets fell within a 100- and 10-fold coverage range, respectively. Alleles at >400,000 target base positions were determined across six subjects and examined for single nucleotide polymorphisms (SNPs), and the concordance with independently obtained genotypes was 98.4%-100%. We detected >500 SNPs not currently in dbSNP, 362 of which were in targeted CpG locations. Transitions in CpG sites were at least 13.7 times more abundant than non-CpG transitions. Fractions of polymorphic CpG sites are lower in CpG-rich regions and show higher correlation with human-chimpanzee divergence within CpG versus non-CpG sites. This is consistent with the hypothesis that methylation rate heterogeneity along chromosomes contributes to mutation rate variation in humans. Our success suggests that targeted CpG resequencing is an efficient way to identify common and rare genetic variations. In addition, the significantly improved padlock capture technology can be readily applied to other projects that require multiplex sample preparation.
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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.