Rapid single nucleotide polymorphism based method for hematopoietic chimerism analysis and monitoring using high-speed droplet-allele-specific PCR and allele-specific quantitative PCR.

Rapid single nucleotide polymorphism based method for hematopoietic chimerism analysis and monitoring using high-speed droplet-allele-specific PCR and allele-specific quantitative PCR.

Clin Chim Acta. 2015 Mar 19;

Authors: Taira C, Matsuda K, Yamaguchi A, Uehara M, Sugano M, Okumura N, Honda T

Abstract
BACKGROUND: Chimerism analysis is important for evaluation of engraftment and predicting relapse following hematopoietic stem cell transplantation (HSCT). We developed a chimerism analysis for single nucleotide polymorphisms (SNPs), including rapid screening of the discriminable donor/recipient alleles using droplet allele-specific PCR (droplet-AS-PCR) pre-HSCT and quantitation of recipient DNA using AS-quantitative PCR (AS-qPCR) following HSCT.
METHODS: SNP genotyping of 20 donor/recipient pairs via droplet-AS-PCR and the evaluation of the informativity of 5 SNP markers for chimerism analysis were performed. Samples from six follow-up patients were analyzed to assess the chimerism via AS-qPCR. These results were compared with that determined by short tandem repeat PCR (STR-PCR).
RESULTS: Droplet-AS-PCR could determine genotypes within 8 min. The total informativity using all 5 loci was 95% (19/20). AS-qPCR provided the percentage of recipient DNA in all 6 follow-up patients without influence of the stutter peak or the amplification efficacy, which affected the STR-PCR results.
CONCLUSION: The droplet-AS-PCR had an advantage over STR-PCR in terms of rapidity and simplicity for screening before HSCT. Furthermore, AS-qPCR had better accuracy than STR-PCR for quantification of recipient DNA following HSCT. The present chimerism assay compensates for the disadvantages of STR-PCR and is readily performable in clinical laboratories.

PMID: 25797898 [PubMed - as supplied by publisher]

A case study on strains of Buša cattle structured into a metapopulation to show the potential for use of single-nucleotide polymorphism genotyping in the management of small, cross-border populations of livestock breeds and varieties.

A case study on strains of Buša cattle structured into a metapopulation to show the potential for use of single-nucleotide polymorphism genotyping in the management of small, cross-border populations of livestock breeds and varieties.

Front Genet. 2015;6:73

Authors: Broxham ET, Kugler W, Medugorac I

PMID: 25798144 [PubMed]

SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing.

SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing.

Appl Plant Sci. 2015 Mar;3(3)

Authors: Logan-Young CJ, Yu JZ, Verma SK, Percy RG, Pepper AE

Abstract
PREMISE OF THE STUDY: Single-nucleotide polymorphism (SNP) marker discovery in plants with complex allotetraploid genomes is often confounded by the presence of homeologous loci (along with paralogous and orthologous loci). Here we present a strategy to filter for SNPs representing orthologous loci.
METHODS AND RESULTS: Using Illumina next-generation sequencing, 54 million reads were collected from restriction enzyme-digested DNA libraries of a diversity of Gossypium taxa. Loci with one to three SNPs were discovered using the Stacks software package, yielding 25,529 new cotton SNP combinations, including those that are polymorphic at both interspecific and intraspecific levels. Frequencies of predicted dual-homozygous (aa/bb) marker polymorphisms ranged from 6.7-11.6% of total shared fragments in intraspecific comparisons and from 15.0-16.4% in interspecific comparisons.
CONCLUSIONS: This resource provides dual-homozygous (aa/bb) marker polymorphisms. Both in silico and experimental validation efforts demonstrated that these markers are enriched for single orthologous loci that are homozygous for alternative alleles.

PMID: 25798340 [PubMed]

Role of Interferon Gamma and Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand Receptor 1 Single Nucleotide Polymorphism in Natural Clearance and Treatment Response of HCV Infection.

Role of Interferon Gamma and Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand Receptor 1 Single Nucleotide Polymorphism in Natural Clearance and Treatment Response of HCV Infection.

Viral Immunol. 2015 Mar 23;

Authors: Azam S, Manzoor S, Imran M, Ashraf J, Ashraf S, Resham S, Ghani E

Abstract
Hepatitis C virus (HCV) pathogenesis and treatment outcomes are multifactorial phenomena involving both viral and host factors. This study was designed to determine the role of tumor necrosis factor-related apoptosis-inducing ligand receptor 1(TRAIL-R1) and interferon gamma (IFN-γ) genetic mutations in susceptibility and response to interferon-based therapy of hepatitis C virus (HCV) infection. The detection of TRAIL-R1 rs4242392 and IFN-γ rs2069707 single nucleotide polymorphisms was completed in 118 chronic HCV patients and 96 healthy controls by allele-specific polymerase chain reaction and restriction fragment length polymorphisms polymerase chain reaction. Patients were further categorized into sustained virological responder (SVR) and nonresponder (NR) groups on the basis of their response to interferon-based therapy for HCV infection. Real-time PCR was used for HCV quantification. HCV genotyping was performed by Ohno's method. The results demonstrated that the distribution of the TRAIL-R1 rs4242392TT genotype was significantly higher in the SVR group (78%) compared to the NR group (36%). It showed that chronic HCV patients possessing the TRAIL-R1 rs4242392TT genotype are better responders to interferon-based therapy (p<0.05). The prevalence of the TRAIL-R1 rs4242392TT genotype in healthy controls and chronic HCV patients was 56% and 65% respectively. It indicated that there is the TRAIL-R1 rs4242392 genetic variation plays no role in the spontaneous clearance of HCV infection (p>0.05). The distribution of IFN-γ rs2069707 was the opposite to TRAIL-R1 rs4242392 prevalence, that is, there was high distribution of the IFN-γ rs2069707GG genotype in patients and healthy controls (p<0.05), while the prevalence of IFN-γ rs2069707GG in SVR and NR groups was comparable (p>0.05). In conclusion, genetic variation of TRAIL-R1 rs4242392 is linked with response to interferon-based therapy for HCV infection, and genetic variation IFN-γ rs2069707 is associated with natural clearance of HCV infection.

PMID: 25798684 [PubMed - as supplied by publisher]

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