High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification

Faruqi, A. Fawad; Hosono, Seiyu; Driscoll, Mark D.; Dean, Frank B.; Alsmadi, Osama; Bandaru, Rajanikanta; Kumar, Gaurav; Grimwade, Brian G.; Zong, Qiuling; Sun, Zhenyu; Du, Yunpeng; Kingsmore, Stephen F.; Knott, Tim; Lasken, Roger S.

doi:10.1186/1471-2164-2-4

Cited by 115 publications

(64 citation statements)

References 24 publications

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“…Samples of both amplified and unamplified genomic DNA from 24 individuals were genotyped by using RFLP for a SNP located on chromosome 13q32 (10). In all 24 cases the amplified DNA gave the correct genotype (Table 2).…”

Section: Resultsmentioning

confidence: 99%

“…In all 24 cases the amplified DNA gave the correct genotype (Table 2). A 10,000-fold amplified MDA product was also tested at another 10 loci by using a high-throughput, ligation-based SNP assay (Table 3) (10). Results were indistinguishable from unamplified genomic DNA genotyped by the same method (Table 2).…”

Section: Resultsmentioning

confidence: 99%

“…Assays were carried out by using Coriell Human Variation Panel samples (nos. 12, 70, 75, and 86) as described (10). The 24 RFLP genotypes of Table 1 were obtained from MDA carried out with genomic DNA from Coriell Human Variation Panel sample catalog 73-96.…”

Section: Amplification Of Human Genomic Dna By Primer Extension Preammentioning

confidence: 99%

“…TaqI enzyme digested the 1822 (C) allele into two fragments (250 bp and 100 bp) whereas the 1822 (T) allele was undigested. The genotypes obtained were compared with the known sequences of SNP1822 determined for these Coriell DNA samples by DNA sequencing (10).…”

Section: Amplification Of Human Genomic Dna By Primer Extension Preammentioning

confidence: 99%

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Comprehensive human genome amplification using multiple displacement amplification

Dean¹,

Hosono²,

Fang³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotideprimed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multiple displacement amplification (MDA), which provides a highly uniform representation across the genome. Amplification bias among eight chromosomal loci was less than 3-fold in contrast to 4 -6 orders of magnitude for PCR-based WGA methods. Average product length was >10 kb. MDA is an isothermal, strand-displacing amplification yielding about 20 -30 g product from as few as 1-10 copies of human genomic DNA. Amplification can be carried out directly from biological samples including crude whole blood and tissue culture cells. MDA-amplified human DNA is useful for several common methods of genetic analysis, including genotyping of single nucleotide polymorphisms, chromosome painting, Southern blotting and restriction fragment length polymorphism analysis, subcloning, and DNA sequencing. MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.F or genomic studies, the quality and quantity of DNA samples is critical. High-throughput genetic analysis requires large amounts of template for testing, yet typically the yield of DNA from individual patient samples is limited. Forensic and paleoarcheology work also can be severely limited by DNA sample size. An important goal is to supply a sufficient amount of genomic sequence for a variety of procedures as well as longterm storage for future work and archiving of patient samples. Methods include the time-consuming process of creating of Epstein-Barr virus-transformed cell lines and whole genome amplification (WGA) by random or degenerate oligonucleotideprimed PCR (DOP-PCR) (1-3). However, PCR-based WGA methods may generate nonspecific amplification artifacts (2), give incomplete coverage of loci (4), and generate DNA less than 1 kb long (1-3) that cannot be used in many applications.Recently, a rolling circle amplification (5) method was developed for amplifying large circular DNA templates such as plasmid and bacteriophage DNA (6). Using 29 DNA polymerase and random exonuclease-resistant primers, DNA was amplified in a 30°C reaction not requiring thermal cycling. This is made possible in part by the great processivity of 29 DNA polymerase, which synthesizes DNA strands 70 kb in length (7). Here we extend the use of exonuclease-resistant primers and 29 DNA polymerase to WGA. The amplification is surprisingly uniform across the genomic target, with the relative representation of different loci differing by less than 3-fold. In contrast, PCR-based WGA methods exhibited strong amplification bias ranging fr...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Amplification Of Human Genomic Dna By Primer Extension Preammentioning

confidence: 99%

Section: Amplification Of Human Genomic Dna By Primer Extension Preammentioning

confidence: 99%

See 2 more Smart Citations

Comprehensive human genome amplification using multiple displacement amplification

Dean¹,

Hosono²,

Fang³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

1,309

1,198

View full text Add to dashboard Cite

show abstract

“…On the other hand, the 3' region is in an association dissociation equilibrium with the target be cause of a calculated dissociation temperature that is 10 8C lower than the reaction temperature of 60 8C. [50] Accordingly the specificity of the ligation reaction is enhanced owing to the favorable hybridization of the perfectly matched OCP. After ligation, linear isothermal RCA can be used to determine whether the probe was circularized or not.…”

Section: Genotyping Through the 5'-3'-exonuclease Activity Of Dna Polmentioning

confidence: 99%