Ultraspecific probes for high throughput HLA typing

Chen, Feng; Putonti, Catherine; Zhang, Meizhuo; Eggers, R.F.; Mitra, Rahul; Hogan, Mike; Jayaraman, Krishna; Fofanov, Yuriy

doi:10.1186/1471-2164-10-85

Cited by 10 publications

(6 citation statements)

References 25 publications

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“…The logical extension of the SSOP approach is microarray analysis, which should enable high throughput parallel genotyping of multiple alleles and loci. However, the extreme polymorphism of the HLA led to considerable difficulties with establishing universally applicable microarrays and research is still ongoing (Zhang et al 2005;Lee et al 2008;Feng et al 2009). A technique that may be useful for typing known variation as well as for de novo mutation detection is PCR-RFLP, where variation in MHC amplicons is detected by restriction enzyme digestion.…”

Section: Genotyping Methods Based On Interrogation Of Known Variationmentioning

confidence: 99%

Methods for MHC genotyping in non‐model vertebrates

Babik

2010

Molecular Ecology Resources

131

192

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Genes of the major histocompatibility complex (MHC) are considered a paradigm of adaptive evolution at the molecular level and as such are frequently investigated by evolutionary biologists and ecologists. Accurate genotyping is essential for understanding of the role that MHC variation plays in natural populations, but may be extremely challenging. Here, I discuss the DNA-based methods currently used for genotyping MHC in non-model vertebrates, as well as techniques likely to find widespread use in the future. I also highlight the aspects of MHC structure that are relevant for genotyping, and detail the challenges posed by the complex genomic organization and high sequence variation of MHC loci. Special emphasis is placed on designing appropriate PCR primers, accounting for artefacts and the problem of genotyping alleles from multiple, co-amplifying loci, a strategy which is frequently necessary due to the structure of the MHC. The suitability of typing techniques is compared in various research situations, strategies for efficient genotyping are discussed and areas of likely progress in future are identified. This review addresses the well established typing methods such as the Single Strand Conformation Polymorphism (SSCP), Denaturing Gradient Gel Electrophoresis (DGGE), Reference Strand Conformational Analysis (RSCA) and cloning of PCR products. In addition, it includes the intriguing possibility of direct amplicon sequencing followed by the computational inference of alleles and also next generation sequencing (NGS) technologies; the latter technique may, in the future, find widespread use in typing complex multilocus MHC systems.

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Section: Genotyping Methods Based On Interrogation Of Known Variationmentioning

confidence: 99%

Methods for MHC genotyping in non‐model vertebrates

Babik

2010

Molecular Ecology Resources

131

192

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“…The binding between the probe and amplicon is highly specifi c with single-nucleotide discrimination [ 36 ]. The number of probes required per array is optimized for the highest resolution, and the cis-trans linkage of SNPs in a heterozygous sample is ensured [ 37 ]. Another feature of the unique "ribbonlike" structure of the probe-amplicon structure is single-nucleotide discrimination with room temperature hybridization.…”

Section: Microarraysmentioning

confidence: 99%

Molecular Typing of Blood Cell Antigens

Bugert¹

2015

Methods in Molecular Biology

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“…, 2001). The number of probes required per array is optimized for the highest resolution, and the cis–trans linkage of SNPs in a heterozygous sample is ensured (Feng et al. , 2009).…”

Section: Microarraysmentioning

confidence: 99%

“…The binding between the probe and amplicon is highly specific with single-nucleotide discrimination at room-temperature hybridization (Lemeshko et al, 2001). The number of probes required per array is optimized for the highest resolution, and the cistrans linkage of SNPs in a heterozygous sample is ensured (Feng et al, 2009). Room-temperature hybridization is possible, so there is no requirement for complex washing ⁄ hybridization machinery; this is because of the novel 'ribbon-like' structure and because probes described in the arrays here are sufficiently short.…”

Section: Microarraysmentioning

confidence: 99%

Human leucocyte antigen typing: techniques and technology, a critical appraisal

Dunn¹

2011

Int J Immunogenetics

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Methods for the identification of Human Leukocyte Antigens (HLA) have changed significantly since this group of polymorphic proteins were first characterized by serological reagents in the 1960s and 1970s. The invention and development of the Polymerase Chain Reaction (PCR) has been key in the progress of methods for HLA genotyping. As the complexity of HLA polymorphism has unravelled so it has exposed the weaknesses in techniques such as PCR - Restriction Fragment Length Polymorphism (RFLP) and Reference Strand Mediated Conformation Analysis (RSCA), which are no longer in use today. Methods which have been considered routine laboratory tools in recent years, such as Sequence-Specific Primer - PCR and Sequencing Based Typing (SBT) are now also threatened with extinction, not only because of the depth of HLA variation but also because of the rapid development of Next Generation Sequencing and technologies which will follow this. This review describes the merits and disadvantages of current technologies available to HLA Typing laboratories, future trends and the problems posed by new alleles.

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Ultraspecific probes for high throughput HLA typing

Cited by 10 publications

References 25 publications

Methods for MHC genotyping in non‐model vertebrates

Methods for MHC genotyping in non‐model vertebrates

Molecular Typing of Blood Cell Antigens

Human leucocyte antigen typing: techniques and technology, a critical appraisal

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