scholarly journals High-Quality and -Quantity DNA Extraction from Frozen Archival Blood Clots for Genotyping of Single-Nucleotide Polymorphisms

2013 ◽  
Vol 17 (6) ◽  
pp. 501-503 ◽  
Author(s):  
Steffen Bank ◽  
Bjørn Andersen Nexø ◽  
Vibeke Andersen ◽  
Ulla Vogel ◽  
Paal Skytt Andersen
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dna Extraction ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Blood Clots

scholarly journals Whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the Black Bengal goat

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 318
Author(s):  
Md. Bazlur Rahman Mollah ◽  
Md. Shamsul Alam Bhuiyan ◽  
M.A.M. Yahia Khandoker ◽  
Md. Abdul Jalil ◽  
Gautam Kumar Deb ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Genome Wide ◽  
High Quality Snps ◽  
Black Goat ◽  
Black Bengal Goat

The Black Bengal goat (BBG) is a dwarf sized heritage goat (Capra hircus) breed from Bangladesh, and is well known for its high fertility, excellent meat and skin quality. Here we present the first whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the BBG. A total of 833,469,900 raw reads consisting of 125,020,485,000 bases were obtained by sequencing one male BBG sample. The reads were aligned to the San Clemente and the Yunnan black goat genome which resulted in 98.65% (properly paired, 94.81%) and 98.50% (properly paired, 97.10%) of the reads aligning, respectively. Notably, the estimated sequencing coverages were 48.22X and 44.28X compared to published San Clemente and the Yunnan black goat genomes respectively. On the other hand, a total of 9,497,875 high quality SNPs (Q ≥ 20) along with 1,023,359 indels, and 8,746,849 high quality SNPs along with 842,706 indels were identified in BBG against the San Clemente and Yunnan black goat genomes respectively. The dataset is publicly available from NCBI BioSample (SAMN10391846), Sequence Read Archive (SRR8182317, SRR8549413 and SRR8549904), with BioProject ID PRJNA504436. These data might be useful genomic resources in conducting genome wide association studies, identification of quantitative trait loci (QTLs) and functional genomic analysis of the Black Bengal goat.

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 Next generation sequencing of African and Indicine cattle to identify single nucleotide polymorphisms

2012 ◽  
Vol 52 (3) ◽  
pp. 133 ◽  
Author(s):  
W. Barris ◽  
B. E. Harrison ◽  
S. McWilliam ◽  
R. J. Bunch ◽  
M. E. Goddard ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Sequence ◽  
Genetic Selection ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Dna Variation ◽  
High Quality Sequence ◽  
Large Stretch ◽  
Generation Sequencing

We sequenced the genomes of a Brahman, an Africander and a Tuli bull because tropically adapted breeds of cattle have so far not been well characterised at the level of DNA variation. In excess of 16 Gb of Illumina GA-II sequence was obtained for each animal in the form of 75-bp paired-end reads, generating more than 6× coverage of each genome, and between 86.7 and 88.8% of the bases of each genome sequence was covered by one or more sequence reads. A total of 6.35 million single nucleotide polymorphisms (SNP) were discovered in the three animals, adding 3.56 million new SNP to dbSNP. The Brahman animal had nearly twice as many SNP as either the Tuli or the Africander. Comparing genome sequence to genotypic array data, genotype accuracy from sequencing was more than 98% for homozygotes that had at least six high quality sequence reads and for heterozygotes that had at least two high quality reads containing the alternative allele. Intergenic and intronic SNP were found at higher densities closer to coding sequences, and there was a reduction in numbers of SNP within 5 bp of a splice site, features consistent with genetic selection. On average, slightly more SNP per Mb, and slightly higher average reads per SNP per Mb, were found towards the ends of chromosomes, especially towards the telomeric end of the chromosome. At least one autosome in each animal showed a large stretch of homozygosity, the largest was 58 Mb long in the Tuli, although the animals are not known to have recent inbreeding.

scholarly journals Analysis of MC1R, MITF, TYR, TYRP1, and MLPH Genes Polymorphism in Four Rabbit Breeds with Different Coat Colors

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 81
Author(s):  
Xianbo Jia ◽  
Peng Ding ◽  
Shiyi Chen ◽  
Shaokang Zhao ◽  
Jie Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dna Sequencing ◽  
Genetic Resources ◽  
Genetic Background ◽  
Coat Color ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Genotypic Profile

Pigmentation genes such as MC1R, MITF, TYR, TYRP1, and MLPH play a major role in rabbit coat color. To understand the genotypic profile underlying coat color in indigenous Chinese rabbit breeds, portions of the above-mentioned genes were amplified and variations in them were analyzed by DNA sequencing. Based on the analysis of 24 Tianfu black rabbits, 24 Sichuan white rabbits, 24 Sichuan gray rabbits, and 24 Fujian yellow rabbits, two indels in MC1R, three SNPs in MITF, five SNPs (single nucleotide polymorphisms) in TYR, one SNP in TYRP1, and three SNPs in MLPH were discovered. These variations have low-to-moderate polymorphism, and there are significant differences in their distribution among the different breeds (p < 0.05). These results provide more information regarding the genetic background of these native rabbit breeds and reveal their high-quality genetic resources.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide
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