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 Highlights from the 15th International Congress of Twin Studies/Twin Research: Differentiating MZ Co-twins Via SNPs; Mistaken Infant Twin-Singleton Hospital Registration; Narcolepsy With Cataplexy; Hearing Loss and Language Learning/Media Mentions: Broadway Musical Recalls Conjoined Hilton Twins; High Fashion Pair; Twins Turn 102; Insights From a Conjoined Twin Survivor

2015 ◽  
Vol 18 (1) ◽  
pp. 108-115
Author(s):  
Nancy L. Segal
Keyword(s):  
Hearing Loss ◽  
Single Nucleotide Polymorphisms ◽  
Language Learning ◽  
Twin Studies ◽  
Conjoined Twins ◽  
International Congress ◽  
Nucleotide Polymorphisms ◽  
Childhood Onset ◽  
Single Nucleotide ◽  
Broadway Musical

Highlights from the 15th International Congress of Twin Studies are presented. The congress was held November 16–19, 2014 in Budapest, Hungary. This report is followed by summaries of research addressing the differentiation of MZ co-twins by single nucleotide polymorphisms (SNPs), an unusual error in infant twin-singleton hospital registration, twins with childhood-onset narcolepsy with cataplexy, and the parenting effects of hearing loss in one co-twin. Media interest in twins covers a new Broadway musical based on the conjoined twins Violet and Daisy Hilton, male twins becoming famous in fashion, twins who turned 102 and unique insights from a conjoined twin survivor.

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 and automated microsystem for rapid pharmacogenetic typing of multiple warfarin-related single-nucleotide polymorphisms

Lab on a Chip ◽  
2016 ◽  
Vol 16 (1) ◽  
pp. 86-95 ◽  
Author(s):  
Bin Zhuang ◽  
Junping Han ◽  
Guangxin Xiang ◽  
Wupeng Gan ◽  
Shuaiqin Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dna Extraction ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pharmacogenetic Testing ◽  
Fully Integrated ◽  
Disposable Plastic

A fully integrated and automated microsystem consisting of disposable plastic chips for DNA extraction and PCR coupled with a reusable glass array-CE chip for rapid pharmacogenetic 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 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.

scholarly journals Single Nucleotide Polymorphisms of theGJB2andGJB6Genes Are Associated with Autosomal Recessive Nonsyndromic Hearing Loss

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Ana Paula Grillo ◽  
Flávia Marcorin de Oliveira ◽  
Gabriela Queila de Carvalho ◽  
Ruan Felipe Vieira Medrano ◽  
Sueli Matilde da Silva-Costa ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Single Nucleotide Polymorphisms ◽  
Autosomal Recessive ◽  
Nucleotide Polymorphisms ◽  
Nonsyndromic Hearing Loss ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Sequence Variations ◽  
Allele Specific ◽  
Allele Specific Pcr

Single nucleotide polymorphisms (SNPs) are important markers in many studies that link DNA sequence variations to phenotypic changes; such studies are expected to advance the understanding of human physiology and elucidate the molecular basis of diseases. TheDFNB1locus, which contains theGJB2andGJB6genes, plays a key role in nonsyndromic hearing loss. Previous studies have identified important mutations in this locus, but the contribution of SNPs in the genes has not yet been much investigated. The aim of this study was to investigate the association of nine polymorphisms located within theDFNB1locus with the occurrence of autosomal recessive nonsyndromic hearing loss (ARNSHL). The SNPs rs3751385 (C/T), rs7994748 (C/T), rs7329857 (C/T), rs7987302 (G/A), rs7322538 (G/A), rs9315400 (C/T), rs877098 (C/T), rs945369 (A/C), and rs7333214 (T/G) were genotyped in 122 deaf patients and 132 healthy controls using allele-specific PCR. There were statistically significant differences between patients and controls, in terms of allelic frequencies in the SNPs rs3751385, rs7994748, rs7329857, rs7987302, rs945369, and rs7333214 (P<0.05). No significant differences between the two groups were observed for rs7322538, rs9315400, and rs877098. Our results suggest that SNPs present in theGJB2andGJB6genes may have an influence on ARNSHL in humans.

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