Single Nucleotide Polymorphisms

Kwok, Pui‐Yan

doi:10.1385/1592593275

Cited by 83 publications

(90 citation statements)

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“…A length-modified SBE protocol from Applied Biosystems (AB, Foster City, CA, USA) was used for genotyping SNPs. Exonuclease I and shrimp alkaline phosphatase (SAP) enzymes were used to clean the amplification products, and SBE was performed using the SNaPshot Kit made by AB (Foster City, CA, USA), 65,66 which attaches a fluorescently labeled ddNTP to the extension primer. An additional SAP clean-up was performed to modify unincorporated ddNTPs using SAP.…”

Section: Methodsmentioning

confidence: 99%

Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance

et al. 2005

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Hepatitis C virus (HCV) is an infectious blood-borne pathogen that usually persists as a chronic infection. However, approximately 15% of the time, patients can clear the virus, indicating that host differences could be critical in determining the course of HCV infection. The inflammatory response is crucial to resolving or failing to resolve an acute HCV infection. Some previous reports have implicated interleukin 10 (IL10) polymorphisms with successful anti-HCV therapy and natural viral clearance. We tested 54 single nucleotide polymorphisms (SNPs) in the IL10 region (7300 kb and 24 within the IL10 gene itself), which contains 13 genes including the IL10 immunomodulatory paralogs IL19, IL20, and IL24, for association with HCV clearance vs persistence. SNPs from two haplotype block regions, one at IL10 and the other from IL19/IL20, were associated with HCV clearance in African Americans (91 clearance cases and 183 chronically infected matched controls; P ¼ 0.05-0.002) while with expectation-maximization algorithm-reconstructed haplotypes, these associations remained (P ¼ 0.05-0.002). However, no significant associations were detected in European Americans (108 clearance and 245 chronic). Our results indicate that variants of the immunomodulatory IL10 and IL19/IL20 genes may be involved in natural clearance of HCV in the African-American population.

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Section: Methodsmentioning

confidence: 99%

Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance

et al. 2005

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“…There are currently several SNP genotyping methods available (Kwok 2001). The recently developed DHPLC technique has a reported sensitivity and specificity of consistently greater than 96%, surpassing other mutation detection methods such as single-strand conformation analysis and denaturing gradient gel electrophoresis (Spiegelman et al 2000).…”

Section: Prospects For Snp Discovery and Est Mappingmentioning

confidence: 99%

Identification and mapping of SNPs from ESTs in sunflower

et al. 2005

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More than 67,000 expressed sequence tags (ESTs) have recently been generated for sunflower (Helianthus), including 44,000 from cultivated confectionery (RHA280) and oilseed (RHA801) lines of Helianthus annuus and 23,000 from droughtand salt-tolerant wild sunflowers, H. argophyllus and H. paradoxus, respectively. To create a transcript map for sunflower, we identified 605 ESTs that displayed small insertion-deletion polymorphism (SNP) variation in silico, had apparent tissuespecific expression patterns, and/or were ESTs with candidate functions in traits such as development, cell transport, metabolism, plant defense, and tolerance to abiotic stress. Primer pairs for 535 of the loci were designed from the ESTs and screened for polymorphism in recombinant inbred lines derived from a cross between the same cultivars (RHA280 × RHA801) employed for sequencing. In total, 273 of the loci amplified polymorphic products, of which 243 mapped to the 17 linkage groups previously identified for sunflower. Comparisons with previously mapped QTL revealed some cases where ESTs with putatively related functions mapped near QTLs identified in other crosses for salt tolerance and for domestication traits such as stem diameter, shattering, flowering time, and achene size.

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“…Numerous assays for SNP genotyping have been described (1). The methods differ in their molecular mechanisms, which can be one of following types: allele-specific hybridization, primer extension, oligonucleotide ligation, invasive cleavage discrimination, and allele-specific digestion.…”

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confidence: 99%

“…Despite the large quantity of available assays, there is no single method that lives up to all the norms of what could be called a "gold standard" in SNP genotyping. The major requirements for the ideal genotyping method are easy setup, low cost, robustness, simplicity, and flexibility (1). Moreover, the assay should be easily automated and scalable, thus allowing a few hundred to a million assays per day with a minimized cost per call.…”

mentioning

confidence: 99%

SNP genotyping using microsphere‐linked PNA and flow cytometric detection

Rockenbauer

Petersen²,

Vogel

et al. 2005

Cytometry Pt A

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Background: Single nucleotide polymorphisms (SNPs) represent the most frequent form of genetic variations. Some of the most sensitive methods for SNP genotyping employ synthetic oligonucleotides, such as the peptide nucleic acid (PNA). We introduce a new method combining allele-specific hybridization, PNA technology, and flow cytometric detection. We tested the design by genotyping a Danish basal cell carcinoma cohort of 80 individuals for an A/C SNP in exon 6 of the XPD gene. Methods: Genomic DNA was amplified by a two-step polymerase chain reaction (PCR) in the presence of fluorescein-dyed primers and fluorescein-12-dUTP. The allelespecific PNA molecules were covalently coupled to carboxylated microspheres with and without rhodamine. Allele-specific hybridization between PCR products and

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Single Nucleotide Polymorphisms

Cited by 83 publications

References 0 publications

Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance

Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance

Identification and mapping of SNPs from ESTs in sunflower

SNP genotyping using microsphere‐linked PNA and flow cytometric detection

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