Genetic screening and testing by induced heteroduplex formation

Wood, Natalie J.; Bidwell, J. L.

doi:10.1002/elps.1150170143

Cited by 31 publications

(32 citation statements)

References 24 publications

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“…UHGs are DNA molecules designed to increase the electrophoretic separation of sequence variants with which they form DNA heteroduplexes (7,12,60,63,79,80,82,83). The protease UHG probe used here (pro1) was based on the HIV-1 subtype B protease gene consensus sequence and was constructed using a series of 18 overlapping oligomers (see Materials and Methods).…”

Section: Resultsmentioning

confidence: 99%

Sequencing-Based Detection of Low-Frequency Human Immunodeficiency Virus Type 1 Drug-Resistant Mutants by an RNA/DNA Heteroduplex Generator-Tracking Assay

Kapoor

Jones

Shafer

et al. 2004

J Virol

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Drug-resistant viruses may be present as minority variants during early treatment failures or following discontinuation of failed antiretroviral regimens. A limitation of the traditional direct PCR population sequencing method is its inability to detect human immunodeficiency virus type 1 (HIV-1) variants present at frequencies lower than 20%. A drug resistance genotyping assay based on the isolation and DNA sequencing of minority HIV protease variants is presented here. A multiple-codon-specific heteroduplex generator probe was constructed to improve the separation of HIV protease genes varying in sequence at 12 codons associated with resistance to protease inhibitors. Using an RNA molecule as probe allowed the simple sequencing of protease variants isolated as RNA/DNA heteroduplexes with different electrophoretic mobilities. The protease gene RNA heteroduplex generator-tracking assay (RNA-HTA) was tested on plasma quasispecies from 21 HIV-1-infected persons in whom one or more protease resistance mutations emerged during therapy or following initiation of salvage regimens. In 11 of 21 cases, RNA-HTA testing of virus from the first episode of virologic failure identified protease resistance mutations not seen by population-based PCR sequencing. In 8 of these 11 cases, all of the low-frequency drug resistance mutations detected exclusively by RNA-HTA during the first episode became detectable by population-based PCR sequencing at the later time point. Distinct sets of protease mutations could be linked on different genomes in patients with high-frequency protease gene lineages. The enhanced detection of minority drug resistance variants using a sequencing-based assay may improve the efficacy of genotype-assisted salvage therapies.

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Section: Resultsmentioning

confidence: 99%

Sequencing-Based Detection of Low-Frequency Human Immunodeficiency Virus Type 1 Drug-Resistant Mutants by an RNA/DNA Heteroduplex Generator-Tracking Assay

Kapoor

Jones

Shafer

et al. 2004

J Virol

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“…Population location, morphotypes, and numbers of samples (N) used for a phylogeographic analysis of the Piriqueta caroliniana complex in North America and the Bahamas. Hybrid zone populations are described in Martin and Cruzan (1999;N ϭ 8-20 (Wood and Bidwell 1996;Delwart et al 1997).…”

Section: Methodsmentioning

confidence: 99%

Patterns of Intraspecific Diversification in the Piriqueta Caroliniana Complex in Southeastern North America and the Bahamas

Maskas

Cruzan

2000

Evolution

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Abstract. We use chloroplast DNA (cpDNA) variation and nested clade phylogeographic analyses to infer the historical processes that have contributed to the high level of morphological and ecological diversification present in a group of herbaceous perennials (the Piriqueta caroliniana complex) in North America and the Bahamas. The presence of morphologically distinct and intercompatible varieties (morphotypes) that can be distinguished based on suites of taxonomic characters (e.g., leaf shape, pubescence type, stature) and contrasting habitat affinities (from marshes to dry pinelands and sand scrub) makes this group particularly appropriate for studies of intraspecific diversification. To examine the distribution of haplotypes among populations, we sampled 467 individuals from 55 locations in Florida, Georgia, and the northern Bahamas (Grand Bahama and Abaco) and screened each individual for cpDNA variation using restriction fragment length polymorphism (RFLP) and heteroduplex analyses. We develop a one-step haplotype phylogeny for this group and use the geographic distributions of haplotypes and clades to test specific phylogeographic hypotheses using the methods developed by Templeton and his colleagues (Templeton 1998). In general, the distribution of haplotypes was strongly influenced by limited dispersal distances, with the more recently derived haplotypes having much lower levels of dispersion and lower frequencies in populations than the ancestral haplotypes. The patterns of clade and haplotype dispersion and displacement and the distribution of morphotypes imply at least three cases of long-distance dispersal and one case of historical fragmentation. The historical patterns inferred for populations of Piriqueta are consistent with known biogeographical events, historical vegetation change, and the concordant patterns of multiple Pleistocene refugia that have been observed for a number of other taxa in southeastern North America.

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“…For the IL1R1 -227 A4G SNP, induced heteroduplex generator (IHG) analysis was used, incorporating an [AAAA] insertion adjacent to the polymorphic site. 34 The same method was used to identify the polymorphisms IL1A -889 C4T, IL1B Exon 5 þ 14 C4T, IL1B -31 C4T, IL1B -511 G4A, IL1RN IVS3 þ 59 T4C and IL1RN Exon 4 þ 72 T4C (Table 1).…”

Section: Snp and Vntr Genotypingmentioning

confidence: 99%

Extended haplotypes and linkage disequilibrium in the IL1R1–IL1A–IL1B–IL1RN gene cluster: association with knee osteoarthritis

et al. 2004

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The interleukin-1 gene cluster is a key regulator in a number of chronic disease processes. We explored the linkage between nine polymorphic loci in the IL1R1 promoter, eight in the IL1A-IL1B-IL1RN gene complex, and their association with osteoarthritis (OA), a common complex disease associated with low-level inflammation. Using 195 healthy controls, we identified eight novel polymorphisms in the IL1R1 exon 1A region. We found limited LD between IL1R1 and the IL1A-IL1B-IL1RN cluster, although LD within these two individual groups was high. To test association with knee OA, we genotyped 141 patients from Bristol (UK) at the 17 loci. IL1R1 promoter haplotypes showed no association with disease. However, within the IL1A-IL1B-IL1RN complex, we identified a common haplotype conferring a four-fold risk of OA (P ¼ 0.00043; P c ¼ 0.0043) and one IL1B-IL1RN haplotype conferring a four-fold reduced risk (P ¼ 0.0036; P c ¼ 0.029). To replicate these associations, we subsequently examined 163 knee OA patients from London. Here, the effects of the haplotypes were confirmed: the risk IL1A-IL1B-IL1RN haplotype conferred a two-fold risk of OA (P ¼ 0.02), and the protective IL1B-IL1RN haplotype conferred a fivefold reduced risk of OA (P ¼ 0.0000008). These results may help to explain the genome-wide scan linkage data and functional observations concerning association between IL-1 and OA.

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Genetic screening and testing by induced heteroduplex formation

Cited by 31 publications

References 24 publications

Sequencing-Based Detection of Low-Frequency Human Immunodeficiency Virus Type 1 Drug-Resistant Mutants by an RNA/DNA Heteroduplex Generator-Tracking Assay

Sequencing-Based Detection of Low-Frequency Human Immunodeficiency Virus Type 1 Drug-Resistant Mutants by an RNA/DNA Heteroduplex Generator-Tracking Assay

Patterns of Intraspecific Diversification in the Piriqueta Caroliniana Complex in Southeastern North America and the Bahamas

Extended haplotypes and linkage disequilibrium in the IL1R1–IL1A–IL1B–IL1RN gene cluster: association with knee osteoarthritis

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