scholarly journals Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population

2012 ◽  
Vol 64 (1) ◽  
pp. 321-335 ◽  
Author(s):  
Elena Fabbri ◽  
R. Caniglia ◽  
Nadia Mucci ◽  
H.P. Thomsen ◽  
K. Krag ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Error Rates ◽  
Snp Genotyping ◽  
Genetic Monitoring ◽  
Taqman Probe ◽  
Degraded Dna ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Non Invasive ◽  
Probe Assay

Single nucleotide polymorphisms (SNPs) which represent the most widespread source of sequence variation in genomes, are becoming a routine application in several fields such as forensics, ecology and conservation genetics. Their use, requiring short amplifications, may allow a more efficient genotyping of degraded DNA. We provide the first application of SNP genotyping in an Italian non-invasive genetic monitoring project of the wolf. We compared three different techniques for genotyping SNPs: pyrosequencing, SNaPshot? and TaqMan? Probe Assay in Real-Time PCR. We successively genotyped nine SNPs using the TaqMan Probe Assay in 51 Italian wolves, 57 domestic dogs, 15 wolf x dog hybrids and 313 wolf scats collected in the northern Apennines. The obtained results were used to estimate genetic variability and PCR error rates in SNP genotyping protocols compared to standard microsatellite analysis. We evaluated the cost, laboratory effort and reliability of these different markers and discuss the possible future use of VeraCode, SNPlex and Fluidigm EP1 system in wild population monitoring.

A fully integrated SNP genotyping system for hereditary hearing-loss detection

Lab on a Chip ◽  
2022 ◽  
Author(s):  
Nan Li ◽  
Yuanyue Zhang ◽  
Minjie Shen ◽  
Youchun Xu
Keyword(s):  
Hearing Loss ◽  
Early Intervention ◽  
Single Nucleotide Polymorphisms ◽  
Snp Genotyping ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Fully Integrated ◽  
Hereditary Hearing Loss

Hereditary hearing loss is one of the most common human neurosensory disorder, and there is a great need for early intervention methods such as genetically screening newborns. Single nucleotide polymorphisms...

scholarly journals Correlation of TSHR and CTLA-4 Single Nucleotide Polymorphisms with Graves Disease

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Weihua Sun ◽  
Xiaomei Zhang ◽  
Jing Wu ◽  
Wendi Zhao ◽  
Shuangxia Zhao ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
T Lymphocyte ◽  
Cytotoxic T Lymphocyte ◽  
Thyroid Stimulating Hormone ◽  
Taqman Probe ◽  
Graves Disease ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Han Population ◽  
Positive Correlations

This study was designed to explore the association between Graves disease (GD) and thyroid-stimulating hormone receptor (TSHR) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) single nucleotide polymorphisms (SNPs). We studied a total of 1217 subjects from a Han population in northern Anhui province in China. Six SNPs within TSHR (rs179247, rs12101261, rs2284722, rs4903964, rs2300525, and rs17111394) and four SNPs within CTLA-4 (rs10197319, rs231726, rs231804, and rs1024161) were genotyped via a Taqman probe technique using a Fluidigm EP1 platform. The TSHR alleles rs179247-G, rs12101261-C, and rs4903964-G were negatively correlated with GD, whereas the rs2284722-A and rs17111394-C alleles were positively correlated with GD. Analyzing TSHR SNPs at rs179247, rs2284722, rs12101261, and rs4903964 yielded 8 different haplotypes. There were positive correlations between GD risk and the haplotypes AGTA and AATA (OR=1.27, 95%CI=1.07‐1.50, P=0.005; OR=1.45, 95%CI=1.21‐1.75, P<0.001, respectively). There were negative correlations between GD risk and the haplotype GGCG (OR=0.56, 95%CI=0.46‐0.67, P<0.001). With respect to haplotypes based on SNPs at the TSHR rs2300525 and rs17111394 loci, the CC haplotype was positively correlated with GD risk (OR=1.32, 95%CI=1.08‐1.60, P=0.006). Analyzing CTLA-4 SNPs at rs231804, rs1024161, and rs231726 yielded four haplotypes, of which AAA was positively correlated with GD risk (OR=1.21, 95%CI=1.02‐1.43, P=0.029). Polymorphisms at rs179247, rs12101261, rs2284722, rs4903964, and rs17111394 were associated with GD susceptibility. Haplotypes of both TSHR and CTLA-4 were additionally related to GD risk.

Chimerism Assay Using Single Nucleotide Polymorphisms Adjacent and in Linkage-Disequilibrium Enables Sensitive Disease Relapse Monitoring after Hematopoietic Stem-Cell Transplantation

2021 ◽  
Author(s):  
JinJu Kim ◽  
Woobin Yun ◽  
Yu Jin Park ◽  
Jieun Seo ◽  
Richard Dong Wook Lee ◽  
...  
Keyword(s):  
Stem Cell ◽  
Linkage Disequilibrium ◽  
Hematopoietic Stem Cell Transplantation ◽  
Single Nucleotide Polymorphisms ◽  
Stem Cell Transplantation ◽  
Error Rates ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Hematopoietic Stem ◽  
Baseline Error

Abstract Background Short tandem repeat (STR)-based chimerism analysis has been widely used for chimerism monitoring after hematopoietic stem-cell transplantation (HSCT), but technical artifacts can be problematic. We designed a chimerism assay using single nucleotide polymorphisms (SNPs) adjacent and in linkage-disequilibrium (CASAL), which doubly checked for SNP pairs, and thus could reduce background errors and increase analytical sensitivity. Methods CASAL targeted 84 SNP pairs within 10 bp distance and in perfect linkage-disequilibrium. Using undiluted and serially diluted samples, baseline error rates, and linearity was calculated. Clinical performance of CASAL was evaluated in comparison with a conventional STR assay, using 191 posttransplant samples from 42 patients with HSCT. Results CASAL had ∼10 times lower baseline error rates compared to that of ordinary next-generation sequencing. Limit of detection and quantification of CASAL were estimated to be 0.09 and 0.39%, respectively, with a linear range of 0.1–100%. CASAL correlated well with STR assay (r2 = 0.99) and the higher sensitivity enabled detection of low-level recipient chimerism and earlier prediction of relapse. Conclusions CASAL is a simple, analytically sensitive and accurate assay that can be used in clinical samples after HSCT with a higher performance compared to that of traditional assays. It should also be useful in other forensic and archeological testing.

scholarly journals An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms

2007 ◽  
Vol 2007 ◽  
pp. 1-7 ◽  
Author(s):  
B. Jayashree ◽  
Manindra S. Hanspal ◽  
Rajgopal Srinivasan ◽  
R. Vigneshwaran ◽  
Rajeev K. Varshney ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Sequence Data ◽  
Snp Genotyping ◽  
Model Organisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Web Interfaces

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.

scholarly journals More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing

2019 ◽  
Author(s):  
Charlotte E. Eriksson ◽  
Joel Ruprecht ◽  
Taal Levi
Keyword(s):  
Amplicon Sequencing ◽  
Error Rates ◽  
Snp Genotyping ◽  
Individual Identification ◽  
Degraded Dna ◽  
Nucleotide Polymorphisms ◽  
Success Rates ◽  
Noninvasive Methods ◽  
Promising Alternative ◽  
Management Actions

AbstractNon-invasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates, and high error rates. The information lost when genotyping success is low may lead to decreased precision in animal population densities which could misguide conservation and management actions. Single nucleotide polymorphisms (SNPs) provide a promising alternative to traditionally used microsatellites as SNPs allow amplification of shorter DNA fragments, are less prone to genotyping errors, and produce results that are easily shared among laboratories. Here, we outline a detailed protocol for cost-effective and accurate noninvasive SNP genotyping using highly multiplexed amplicon sequencing optimized for degraded DNA. We validated this method for individual identification by genotyping 216 scats, 18 hairs and 15 tissues from coyotes (Canis latrans). Our genotyping success rate for scat samples was 93%, and 100% for hair and tissue, representing a substantial increase compared to previous microsatellite-based studies at a cost of under $5 per PCR replicate (excluding labor). The accuracy of the genotypes was further corroborated in that genotypes from scats matching known, GPS-collared coyotes were always located within the territory of the known individual. We also show that different levels of multiplexing produced similar results, but that PCR product cleanup strategies can have substantial effects on genotyping success. By making noninvasive genotyping more affordable, accurate, and efficient, this research may allow for a substantial increase in the use of noninvasive methods to monitor and conserve free-ranging wildlife populations.

Reverse line probe assay for cheap detection of Single Nucleotide Polymorphisms in Mycobacterium tuberculosis

Tuberculosis ◽  
2018 ◽  
Vol 110 ◽  
pp. 52-55 ◽  
Author(s):  
Memona Yasmin ◽  
Guislaine Refregier ◽  
Rubina Tabassum Siddiqui ◽  
Rizwan Iqbal ◽  
Shahid Ahmad Abbasi ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Line Probe Assay ◽  
Single Nucleotide ◽  
Probe Assay

scholarly journals Genotyping of Single Nucleotide Polymorphisms Using Allele-Specific qPCR Producing Amplicons of Small Sizes Directly from Crude Serum Isolated from Capillary Blood by a Hand-Powered Paper Centrifuge

Diagnostics ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 9 ◽  
Author(s):  
Gustavo Barra ◽  
Ticiane Santa Rita ◽  
Daniella Jardim ◽  
Pedro Mesquita ◽  
Camila Nobre ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Base Pair ◽  
Genomic Dna ◽  
Room Temperature ◽  
Capillary Blood ◽  
Snp Genotyping ◽  
Nucleotide Polymorphisms ◽  
Base Pairs ◽  
Single Nucleotide ◽  
Allele Specific

The cell-free genomic DNA (gDNA) concentration in serum ranges from 1500 to 7500 copies/mL within 2 h after phlebotomy (6–24 times the concentration observed in plasma). Here, we aimed to evaluate the gDNA size distribution in serum with time after coagulation and to test if crude serum can be directly used as a source of gDNA for qPCR. Next, we investigated if single nucleotide polymorphisms (SNPs) could be genotyped directly from the crude serum isolated from capillary blood using a hand-powered paper centrifuge. All tested PCR targets (65, 100, 202 and 688 base pairs) could be successfully amplified from DNA extracted from serum, irrespective of their amplicon size. The observed qPCR quantitation cycles suggested that the genomic DNA yield increased in serum with incubation at room temperature. Additionally, only 65 and 101 base pair qPCR targets could be amplified from crude serum soon after the coagulation. Incubation for 4 days at room temperature was necessary for the amplification of PCR targets of 202 base pairs. The 688 base pair qPCR target could not be amplified from serum directly. Lastly, serum was successfully separated from capillary blood using the proposed paper centrifuge and the genotypes were assigned by testing the crude serum using allele-specific qPCR, producing small amplicon sizes in complete agreement with the genotypes assigned by testing the DNA extracted from whole blood. The serum can be used directly as the template in qPCR for SNP genotyping, especially if small amplicon sizes are applied. This shortcut in the SNP genotyping process could further molecular point-of-care diagnostics due to elimination of the DNA extraction step.

Sign in / Sign up

Export Citation Format

Share Document