scholarly journals A Novel Test System for Genotyping rs43703016 Single-nucleotide Substitutions in the Bovine CSN3 Gene

2019 ◽  
pp. 1-5
Author(s):  
Svetlana Kovalchuk ◽  
Arina Tagmazyan ◽  
Eugene Klimov
Keyword(s):  
Nucleotide Substitution ◽  
Milk Proteins ◽  
Test System ◽  
Nucleotide Polymorphisms ◽  
Dna Testing ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Selection Of

Aims: Caseins are among the main milk proteins that determine many of its properties. Bovine kappa-casein (CSN3) is associated with the qualitative composition of milk, as well as with the quality of cheese obtained from this milk. The rs43703016 single-nucleotide substitution (g.88532332A>C; Asp148Ala) in exon 4 of the bovine CSN3 gene plays an important role in the production of quality hard cheeses. Various methods for the DNA testing of this substitution have been developed in the last three decades. Emergent DNA technologies provide an opportunity to modernize methods of genotyping single-nucleotide polymorphisms. Results: We have developed and verified a method to differentiate A/C alleles of the rs43703016 substitution in the bovine CSN3 gene by real-time PCR using allele-specific fluorescent probes. Conclusion: Our new method allows fast genotyping of animals, and may be used for selection of cows carrying the CC genotype, which determines good cheese-making properties of milk.

scholarly journals Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada

2009 ◽  
Vol 92 (7) ◽  
pp. 3431-3436 ◽  
Author(s):  
G.R. Wiggans ◽  
T.S. Sonstegard ◽  
P.M. VanRaden ◽  
L.K. Matukumalli ◽  
R.D. Schnabel ◽  
...  
Keyword(s):  
United States ◽  
Single Nucleotide Polymorphisms ◽  
Dairy Cattle ◽  
The United States ◽  
Nucleotide Polymorphisms ◽  
Genomic Evaluation ◽  
Single Nucleotide ◽  
Selection Of

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

Allele-specific long-range PCR/sequencing method for allelic assignment of multiple single nucleotide polymorphisms

2003 ◽  
Vol 55 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Michiyo Nagano ◽  
Takahiro Nakamura ◽  
Shogo Ozawa ◽  
Keiko Maekawa ◽  
Yoshiro Saito ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Long Range ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Sequencing Method ◽  
Allele Specific ◽  
Long Range Pcr

Genes Regulating Immune Response and Amelogenesis Interact in Increasing the Susceptibility to Molar-Incisor Hypomineralization

2018 ◽  
Vol 53 (2) ◽  
pp. 217-227 ◽  
Author(s):  
Diego Girotto Bussaneli ◽  
Manuel Restrepo ◽  
Camila Maria Bullio Fragelli ◽  
Lourdes Santos-Pinto ◽  
Fabiano Jeremias ◽  
...  
Keyword(s):  
Immune Response ◽  
Gene Interactions ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Nuclear Families ◽  
Molar Incisor Hypomineralization ◽  
Inflammatory Stimuli ◽  
Allele Specific ◽  
Family Based ◽  
And Function

Ameloblasts are sensitive cells whose metabolism and function may be affected by inflammatory stimuli. The aim of this study was to evaluate the possible association between polymorphisms in immune response-related genes and molar-incisor hypomineralization (MIH), and their interaction with polymorphisms in amelogenesis-related genes. DNA samples were obtained from 101 nuclear families that had at least 1 MIH-affected child. Eleven single-nucleotide polymorphisms (SNPs) were investigated in immune response genes using TaqMan® technology allele-specific probes. A transmission disequilibrium test was performed to verify overtransmission of alleles in all MIH families, as well as in families only with mild or severe MIH-affected children. Gene-gene interactions between the immune-related and amelogenesis-related polymorphisms were analyzed by determining whether alleles of those genes were transmitted from heterozygous parents more often in association than individually with MIH-affected children. In severe cases of MIH, significant results were observed for rs10733708 (TGFBR1, OR = 3.5, 95% CI = 1.1–10.6). Statistical evidence for gene-gene interactions between rs6654939 (AMELX) and the SNPs rs2070874 (IL4), rs2275913 (IL17A), rs1800872 (IL10), rs1800587 (IL1A), and rs3771300 (STAT1) was observed. The rs2070874 SNP (IL4) was also significantly overtransmitted from heterozygous parents with the rs7526319 (TUFT1) and the rs2355767 (BMP2) SNPs, suggesting a synergistic effect of the transmission of these alleles with susceptibility to MIH. This family-based study demonstrated an association between variation in TGFBR1 and MIH. Moreover, the polymorphisms in immune response and amelogenesis genes may have an additive effect on the risk of developing MIH.

scholarly journals Selection of X-chromosome Inactivation Model

2017 ◽  
Vol 16 ◽  
pp. 117693511774727 ◽  
Author(s):  
Jian Wang ◽  
Rajesh Talluri ◽  
Sanjay Shete
Keyword(s):  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Association Test ◽  
Chromosome Inactivation ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Unified Approach ◽  
Cancer Genetic ◽  
Single Nucleotide ◽  
Selection Of

To address the complexity of the X-chromosome inactivation (XCI) process, we previously developed a unified approach for the association test for X-chromosomal single-nucleotide polymorphisms (SNPs) and the disease of interest, accounting for different biological possibilities of XCI: random, skewed, and escaping XCI. In the original study, we focused on the SNP-disease association test but did not provide knowledge regarding the underlying XCI models. One can use the highest likelihood ratio (LLR) to select XCI models (max-LLR approach). However, that approach does not formally compare the LLRs corresponding to different XCI models to assess whether the models are distinguishable. Therefore, we propose an LLR comparison procedure (comp-LLR approach), inspired by the Cox test, to formally compare the LLRs of different XCI models to select the most likely XCI model that describes the underlying XCI process. We conduct simulation studies to investigate the max-LLR and comp-LLR approaches. The simulation results show that compared with the max-LLR, the comp-LLR approach has higher probability of identifying the correct underlying XCI model for the scenarios when the underlying XCI process is random XCI, escaping XCI, or skewed XCI to the deleterious allele. We applied both approaches to a head and neck cancer genetic study to investigate the underlying XCI processes for the X-chromosomal genetic variants.

Whole Exome Sequencing in Patients With Ossification of the Spinal Ligaments

2021 ◽  
Author(s):  
Jiliang Zhai ◽  
Jiahao Li ◽  
Yu Zhao ◽  
Xing Wei
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Vital Role ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Whole Exome ◽  
Clinical Presentations ◽  
Spinal Ligaments ◽  
Neurological Pathology

Abstract Background The clinical presentations of ossification of spinal ligament (OSL) are majorly myelopathy and/or radiculopathy, with serious neurological pathology resulting in paralysis of extremities and disturbances of motility (motor function) lowering the quality of life. Currently, studies find that missense single nucleotide polymorphisms (SNPs) play a vital role in the susceptibility for complex diseases. Methods In the present study, we used whole exome sequencing (WES) method to explore variants in exomes and found out novel potential responsible genes for OSL. Genomic DNA was extracted from ligamentum flavum collected from 5 OSL patients and 5 control patients. Whole-exome sequencing was then performed, while variation forecasts and conservation examination were subsequently assessed. Results 8 common SNP variants were exhibited in all 5 subjects of OSL, presented in the genes of GRHL2, CUL3, WHAMM, IL17RD, POM121L12, SLC26A8 and PTPN23. After screened with numbers of samples and additional screenings with deleterious Polyphen2_HDIV_score, Polyphen2_HVAR_score and SIFT, 4 common SNP variants were displayed in 4 subjects of OSL, presented in the genes of KRT84, KIF1B, NRAP and CETN1. 7 common SNP variants were existed in 3 subjects of OSL, presented in the genes of CCT3, ANLN, ESRRB, SRBD1, ODF3L1, BRAT1 and RBP3. Conclusion We found out novel potential variants in several genes, especially WHAMM, KIF1B and ESRRB, which represented potentially pathogenic mutations in patients with OSL.

cDNA sequence of five mouse guanine deaminase (Gda) alleles and mapping to mouse chromosome 19

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 276-281
Author(s):  
Raymond D Giese ◽  
Floyd F Snyder
Keyword(s):  
Mouse Chromosome ◽  
Nucleotide Polymorphisms ◽  
Mus Spretus ◽  
Chromosome 19 ◽  
Single Nucleotide ◽  
Guanine Deaminase ◽  
Key Words Mouse ◽  
Allele Specific ◽  
Guanine Base ◽  
Codon Change

Guanine deaminase catalyses the conversion of guanine to xanthine and ammonia, thereby irreversibly removing the guanine base from the pool of guanine-containing metabolites. We have identified five alleles at the mouse guanine deaminase locus by cDNA sequencing. These alleles were defined by single-nucleotide polymorphisms at a total of 19 positions. For each allele the representative strains are as follows: Gdaa, C57BL/6J and DBA/2J; Gdab, A/J; Gdac, MOLF/Ei; Gdad, CAST/Ei; and Gdae, SPRET-1. The only codon change resulting in an amino acid substitution was found at nucleotide 523, where GAT was replaced by AAT in Mus spretus resulting in the deduced substitution of Asp-174 by Asn. The single-nucleotide difference between the a and b alleles was also typed by allele-specific oligonucleotide amplification for 17 common strains of Mus musculus susbp. musculus. By typing the A×B and B×A recombinant inbred (RI) strain sets, Gda was mapped to mouse chromosome 19, a region syntenic with human chromosome 9q11–q22.Key Words: mouse guanine deaminase, alleles, mapping.

scholarly journals Genome-Wide Association Study of Body Weight Traits in Chinese Fine-Wool Sheep

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 170 ◽  
Author(s):  
Zengkui Lu ◽  
Yaojing Yue ◽  
Chao Yuan ◽  
Jianbin Liu ◽  
Zhiqiang Chen ◽  
...  
Keyword(s):  
Body Weight ◽  
Muscle Development ◽  
Genome Wide Association Study ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Economic Trait ◽  
Significance Levels ◽  
Genomic Regions ◽  
Selection Of

Body weight is an important economic trait for sheep and it is vital for their successful production and breeding. Therefore, identifying the genomic regions and biological pathways that contribute to understanding variability in body weight traits is significant for selection purposes. In this study, the genome-wide associations of birth, weaning, yearling, and adult weights of 460 fine-wool sheep were determined using resequencing technology. The results showed that 113 single nucleotide polymorphisms (SNPs) reached the genome-wide significance levels for the four body weight traits and 30 genes were annotated effectively, including AADACL3, VGF, NPC1, and SERPINA12. The genes annotated by these SNPs significantly enriched 78 gene ontology terms and 25 signaling pathways, and were found to mainly participate in skeletal muscle development and lipid metabolism. These genes can be used as candidate genes for body weight in sheep, and provide useful information for the production and genomic selection of Chinese fine-wool sheep.

Fabrication and Application of Single Nucleotide Polymorphisms Library on Magnetic Nanoparticles Using Adaptor PCR

2008 ◽  
Vol 8 (1) ◽  
pp. 405-409 ◽  
Author(s):  
Hongna Liu ◽  
Song Li ◽  
Meiju Ji ◽  
Libo Nie ◽  
Jianrong Chen ◽  
...  
Keyword(s):  
Magnetic Nanoparticles ◽  
Single Nucleotide Polymorphisms ◽  
Reliable Method ◽  
Nucleotide Polymorphisms ◽  
Probe Signal ◽  
Single Nucleotide ◽  
Novel Approach ◽  
Mismatch Probe ◽  
Allele Specific ◽  
Agt Gene

We have developed a novel approach to fabricate single nucleotide polymorphisms (SNPs) library on magnetic nanoparticles (MNPs) based on adaptor PCR. Each SNP locus in the library was interrogated by hybridization with a pair of allele specific dual-color fluorescence (Cy3, Cy5) probes to determine SNP. Two SNPs loci (M235T and A-6G) associated with essential hypertension in the angiotensinogen (AGT) gene were detected by this method and their fluorescent signals were quantified. The fluorescent ratios (match probe: mismatch probe signal) of homozygous genotypes were over 3.0, whereas heterozygous genotypes had ratios near to 1.0. Without any complex multiplex PCR procedure, it is a simple, efficient and reliable method for the multiplex SNPs detection using limited amount of DNA samples from individuals.

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