Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.
Authors
Kenny, Elaine MCormican, Paul
Gilks, William P
Gates, Amy S
O'Dushlaine, Colm T
Pinto, Carlos
Corvin, Aiden P
Gill, Michael
Morris, Derek W
Affiliation
Trinity Genome Sequencing Laboratory, Neuropsychiatric Genetics Research Group, Department of Psychiatry, Institute of Molecular Medicine, Trinity College Dublin, Ireland. elaine.kenny@tcd.ieIssue Date
2011-02MeSH
DNAExons
High-Throughput Nucleotide Sequencing
Polymorphism, Single Nucleotide
RNA, Complementary
Metadata
Show full item recordCitation
Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection. 2011, 18 (1):31-8 DNA Res.Journal
DNA research : an international journal for rapid publication of reports on genes and genomesDOI
10.1093/dnares/dsq029PubMed ID
21163834Abstract
Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an advanced method that combines DNA samples using indexes or barcodes prior to target enrichment to facilitate this type of experiment. Sequencing libraries for multiple individual DNA samples, each incorporating a unique 6-bp index, are combined in equal quantities, enriched using a single in-solution target enrichment assay and sequenced in a single reaction. Sequence reads are parsed based on the index, allowing sequence analysis of individual samples. We show that the use of indexed samples does not impact on the efficiency of the enrichment reaction. For three- and nine-indexed HapMap DNA samples, the method was found to be highly accurate for SNP identification. Even with sequence coverage as low as 8x, 99% of sequence SNP calls were concordant with known genotypes. Within a single experiment, this method can sequence the exonic regions of hundreds of genes in tens of samples for sequence and structural variation using as little as 1 μg of input DNA per sample.Item Type
ArticleLanguage
enISSN
1756-1663ae974a485f413a2113503eed53cd6c53
10.1093/dnares/dsq029
Scopus Count
Collections
Related articles
- Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.
- Authors: Kiialainen A, Karlberg O, Ahlford A, Sigurdsson S, Lindblad-Toh K, Syvänen AC
- Issue date: 2011 Feb 9
- Mitigating the effects of reference sequence bias in single-multiplex massively parallel sequencing of the mitochondrial DNA control region.
- Authors: Huszar TI, Wetton JH, Jobling MA
- Issue date: 2019 May
- A novel three-round multiplex PCR for SNP genotyping with next generation sequencing.
- Authors: Chen K, Zhou YX, Li K, Qi LX, Zhang QF, Wang MC, Xiao JH
- Issue date: 2016 Jun
- Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences.
- Authors: Peng Z, Fan W, Wang L, Paudel D, Leventini D, Tillman BL, Wang J
- Issue date: 2017 Oct
- Target capture enrichment of nuclear SNP markers for massively parallel sequencing of degraded and mixed samples.
- Authors: Bose N, Carlberg K, Sensabaugh G, Erlich H, Calloway C
- Issue date: 2018 May