Whole human exome capture for high-throughput sequencing

Kim, Dae-Won KimD.; Nam, Sang Ki; Kim, Ryong Nam KimR.N.; Choi, Sang-Haeng; Park, Hong-Seog ParkH.

doi:10.1139/g10-025

Cited by 14 publications

(10 citation statements)

References 15 publications

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“…A large-scale DNA fragment collection of specific genomic regions was previously established based on the sequence capture method [39], which employs the hybridization of oligonucleotides that are complementary to known genomic DNA sequences containing the target DNA fragments. Commercially available sequence capture tools allow for the collection of large genomic regions or exon regions of multiple genes in a high-throughput manner [40], and a reference genome sequence is required for this method. Briggs et al [21] employed PEC to recover and reconstruct the mitochondrial genome from ancient DNA.…”

Section: Discussionmentioning

confidence: 99%

Mapping of the Gynoecy in Bitter Gourd (Momordica charantia) Using RAD-Seq Analysis

et al. 2014

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Momordica charantia is a monoecious plant of the Cucurbitaceae family that has both male and female unisexual flowers. Its unique gynoecious line, OHB61-5, is essential as a maternal parent in the production of F1 cultivars. To identify the DNA markers for this gynoecy, a RAD-seq (restriction-associated DNA tag sequencing) analysis was employed to reveal genome-wide DNA polymorphisms and to genotype the F2 progeny from a cross between OHB61-5 and a monoecious line. Based on a RAD-seq analysis of F2 individuals, a linkage map was constructed using 552 co-dominant markers. In addition, after analyzing the pooled genomic DNA from monoecious or gynoecious F2 plants, several SNP loci that are genetically linked to gynoecy were identified. GTFL-1, the closest SNP locus to the putative gynoecious locus, was converted to a conventional DNA marker using invader assay technology, which is applicable to the marker-assisted selection of gynoecy in M. charantia breeding.

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Section: Discussionmentioning

confidence: 99%

Mapping of the Gynoecy in Bitter Gourd (Momordica charantia) Using RAD-Seq Analysis

et al. 2014

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“…2010). Arrays can be scaled to population studies by barcoding individual samples uniquely and then pooling multiple samples prior to targeted capture and sequencing (Kim et al. 2010).…”

Section: Discussionmentioning

confidence: 99%

Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens

Rowe

Singhal

MacManes

et al. 2011

Molecular Ecology Resources

129

128

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Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.

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“…User feedback indicates that the CCDS data set is a valued definition of high confidence coding exons and it is used in large-scale epigenomic studies, production of exon arrays (40), the design of exome capture kits (41) and the design of an in silico set of oligonucleotides (the Human OligoExome) (42). The CCDS data set is also integrated into the GENCODE (http://www.gencodegenes.org) (4) gene annotation project (one of the projects of the ENCODE consortium, http://www.genome.gov/10005107) (43, 44).…”

Section: Discussionmentioning

confidence: 99%

Tracking and coordinating an international curation effort for the CCDS Project

et al. 2012

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The Consensus Coding Sequence (CCDS) collaboration involves curators at multiple centers with a goal of producing a conservative set of high quality, protein-coding region annotations for the human and mouse reference genome assemblies. The CCDS data set reflects a ‘gold standard’ definition of best supported protein annotations, and corresponding genes, which pass a standard series of quality assurance checks and are supported by manual curation. This data set supports use of genome annotation information by human and mouse researchers for effective experimental design, analysis and interpretation. The CCDS project consists of analysis of automated whole-genome annotation builds to identify identical CDS annotations, quality assurance testing and manual curation support. Identical CDS annotations are tracked with a CCDS identifier (ID) and any future change to the annotated CDS structure must be agreed upon by the collaborating members. CCDS curation guidelines were developed to address some aspects of curation in order to improve initial annotation consistency and to reduce time spent in discussing proposed annotation updates. Here, we present the current status of the CCDS database and details on our procedures to track and coordinate our efforts. We also present the relevant background and reasoning behind the curation standards that we have developed for CCDS database treatment of transcripts that are nonsense-mediated decay (NMD) candidates, for transcripts containing upstream open reading frames, for identifying the most likely translation start codons and for the annotation of readthrough transcripts. Examples are provided to illustrate the application of these guidelines. Database URL : http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi

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Whole human exome capture for high-throughput sequencing

Cited by 14 publications

References 15 publications

Mapping of the Gynoecy in Bitter Gourd (Momordica charantia) Using RAD-Seq Analysis

Mapping of the Gynoecy in Bitter Gourd (Momordica charantia) Using RAD-Seq Analysis

Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens

Tracking and coordinating an international curation effort for the CCDS Project

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