Single nucleotide polymorphism

Single nucleotide polymorphism analysis of the endopolygalacturonase gene in peach and its potential use in crossbreeding programs

Y. Jiao, Ma, R., and Yu, M., “Single nucleotide polymorphism analysis of the endopolygalacturonase gene in peach and its potential use in crossbreeding programs”, vol. 14, pp. 4090-4101, 2015.

Single nucleotide polymorphisms (SNPs) are the most abundant sequence variations found in plant genomes and are widely used as molecular genetic markers in genetic diversity studies and crossbreeding programs. In this study, we examined 113 DNA sequences of the endopolygalacturonase (endo-PG) gene from 67 peach accessions and found a total of 56 SNPs and 6 insertion/deletions (indels), with a frequency of 3, 1, and 3% for the transitions, transversions, and indels, respectively.

A single nucleotide polymorphism in the promoter region of let-7 family is associated with lung cancer risk in Chinese

L. Q. Shen, Xie, Y. Z., Qian, X. F., Zhuang, Z. X., Jiao, Y., and Qi, X. F., “A single nucleotide polymorphism in the promoter region of let-7 family is associated with lung cancer risk in Chinese”, vol. 14, pp. 4505-4512, 2015.

Lung cancer is a complex polygenic disease and many genetic factors are involved in the development of the disease. As one of the most important and widely studied families of microRNA, let-7 appears to play an important role in initiation and progression of lung cancer. Any small changes in miRNA level or its target point can cause significant changes in gene function. In this study, we examined whether a single-nucleotide polymorphism in the promoter region of the let-7 family (rs10877887) is associated with the susceptibility to and prognosis of lung adenocarcinoma cancer.

Characterization and phylogenetic analysis of the swine leukocyte antigen 3 gene from Korean native pigs

H. Y. Chung, Choi, Y. C., and Park, H. N., “Characterization and phylogenetic analysis of the swine leukocyte antigen 3 gene from Korean native pigs”, vol. 14, pp. 5270-5279, 2015.

We investigated the phylogenetic relationships between pig breeds, compared the genetic similarity between humans and pigs, and provided basic genetic information on Korean native pigs (KNPs), using genetic variants of the swine leukocyte antigen 3 (SLA-3) gene. Primers were based on sequences from GenBank (accession Nos. AF464010 and AF464009). Polymerase chain reaction analysis amplified approximately 1727 bp of segments, which contained 1086 bp of coding regions and 641 bp of the 3'- and 5'-untranslated regions.

Genome-wide association with residual body weight gain in Bos indicus cattle

M. H. A. Santana, Gomes, R. C., Utsunomiya, Y. T., Neves, H. H. R., Novais, F. J., Bonin, M. N., Fukumasu, H., Garcia, J. F., Alexandre, P. A., Junior, G. A. Oliveira, Coutinho, L. L., and Ferraz, J. B. S., “Genome-wide association with residual body weight gain in Bos indicus cattle”, vol. 14. pp. 5229-5233, 2015.

Weight gain is a key performance trait for beef cattle; however, attention should be given to the production costs for better profitability. Therefore, a feed efficiency trait based on performance can be an interesting approach to improve performance without increasing food costs. To identify candidate genes and genomic regions associated with residual body weight gain (RWG), we conducted a genome-wide association study (GWAS) with 720 Nellore cattle using the GRAMMAR-Gamma association test.

Clinical significance of SHMT1 rs1979277 polymorphism in Asian solid tumors: evidence from a meta-analysis

T. T. Zhao, Shen, L. L., Zhang, X. L., Gu, D. Y., Zhang, Q., Huo, X. Y., Tang, C. J., and Chen, J. F., “Clinical significance of SHMT1 rs1979277 polymorphism in Asian solid tumors: evidence from a meta-analysis”, vol. 14, pp. 5602-5614, 2015.

Published data regarding the association between the cytosolic serine hydroxymethyltransferase (SHMT1) C1420T (Leu474Phe) polymorphism and solid tumor risk have shown inconclusive results. To derive a more precise estimation of the relationship, we performed a meta-analysis of 23 published studies that included 14,409 cancer cases and 16,996 controls. A comprehensive search was conducted to identify all eligible studies of the SHMT1 rs1979277 polymorphism and solid tumor risk.

Cyclin D1 G870A polymorphism is associated with an increased risk of multiple myeloma

S. Wang, Huang, Y., Su, R., Fang, Z., and Han, M., “Cyclin D1 G870A polymorphism is associated with an increased risk of multiple myeloma”, vol. 14, pp. 5856-5861, 2015.

Cyclin D1 is an important cell cycle regulator implicated in the pathogenesis of many cancer types. In particular, translocation and overexpression of cyclin D1 are common events in multiple myeloma (MM), suggesting that it may drive the initiation and progression of this malignancy. However, the association between genetic polymorphisms of cyclin D1 and the risk for developing MM remains poorly characterized. We performed a case-control study with 67 patients with MM and 66 healthy controls in a Chinese population.

Genomic cloning, expression, and single nucleotide polymorphism association analysis of the insulin-like androgenic gland hormone gene in the oriental river prawn (Macrobrachium nipponense)

F. J. Li, Jiang, F. W., Bai, H. K., Fu, H. T., Jin, S. B., Sun, S. M., Qiao, H., and Zhang, W. Y., “Genomic cloning, expression, and single nucleotide polymorphism association analysis of the insulin-like androgenic gland hormone gene in the oriental river prawn (Macrobrachium nipponense)”, vol. 14, pp. 5910-5921, 2015.

Increasing evidence suggests that the insulin-like androgenic gland hormone (IAG) gene plays an important role in male sexual differentiation, metabolism, and growth in crustaceans. In the present study, we isolated the full-length genome sequence of IAG by genome walking based on the cDNA sequence in Macrobrachium nipponense. Four novel single nucleotide polymorphisms (SNPs) were studied, including 509G>T, 529G>T, 590A>T in intron 1, and 2226A>G in intron 2.

Association between XRCC1 Arg280His polymorphism and risk of hepatocellular carcinoma: a systematic review and meta-analysis

W. Xu, Liu, S., Li, L., Shen, Z. Y., and Wu, Y. L., “Association between XRCC1 Arg280His polymorphism and risk of hepatocellular carcinoma: a systematic review and meta-analysis”, vol. 14, pp. 7122-7129, 2015.

Hepatocellular carcinoma (HCC) is one of the most life-threatening malignancies worldwide. Defects in DNA repair genes may increase the risk of HCC. X-ray cross-complementing group 1 gene (XRCC1) is a major DNA repair gene involved in base excision repair. Recently, several studies have indicated that an association exists between XRCC1 polymorphism and HCC, particularly the Arg280His polymorphism. However, the data is inconsistent and incomplete.

Association between a single nucleotide polymorphism of the XRCC1 gene and hepatocellular carcinoma susceptibility in the Chinese Han population

X. F. Li, Chen, Y. X., Ye, W. W., Tao, X. F., Zhu, J. H., Wu, S., and Lou, L. Q., “Association between a single nucleotide polymorphism of the XRCC1 gene and hepatocellular carcinoma susceptibility in the Chinese Han population”, vol. 13, pp. 160-166, 2014.

The human X-ray repair cross-complementing protein 1 (XRCC1) gene is a potentially gene determining hepatocellular carcinoma (HCC) susceptibility. The purpose of this study was to evaluate the association between XRCC1 and susceptibility to HCC. The association of XRCC1 polymorphisms with HCC susceptibility was investigated in 460 HCC patients and 463 controls using the created restriction site-polymerase chain reaction method.

Toll-like receptor 3 polymorphism is not associated with neovascular age-related macular degeneration and polypoidal choroidal vasculopathy in the Chinese

Y. Cheng, Li, M. W., Li, H. P., Zeng, W. T., Zhou, P., Huang, L. Z., Li, X. X., and Sun, Y. Y., “Toll-like receptor 3 polymorphism is not associated with neovascular age-related macular degeneration and polypoidal choroidal vasculopathy in the Chinese”, vol. 13, pp. 302-309, 2014.

Toll-like receptor 3 (TLR3) variants in mainland northern Chinese patients with polypoidal choroidal vasculopathy (PCV) and neovascular age-related macular degeneration (nAMD) were investigated. The complete genes of TLR3, including all exons and the promoter region, were assessed using direct sequencing technology of 284 unrelated mainland northern Chinese individuals: 96 nAMD patients, 92 PCV patients, and 96 controls. Six single nucleotide polymorphisms were identified: rs5743303, rs5743305, rs5743312, rs3775291, rs3775290, and rs6830345.

Single nucleotide polymorphism