Akhiyan Hadi Susanto, Widodo, Mohammad Saifur Rohman, Didik Huswo Utomo and Mifetika Lukitasari
Singlenucleotidepolymorphisms (SNPs) are estimated to occur in 1 of every 1,000 nucleotides in the human genome [ 1 , 2 ]. Depending on where a SNP occurs, it might have various consequences at the phenotypic level. SNPs that alter the function or structure of the encoded proteins are a necessary and sufficient cause of most of the known recessively or dominantly inherited monogenic disorders. These SNPs are found in the coding regions of genes and are routinely analyzed for medical purposes [ 3 ]. SNPs in the promoter region of genes affect the
Matej Horvat, Uros Potocnik, Katja Repnik, Rajko Kavalar, Vesna Zadnik, Stojan Potrc and Borut Stabuc
practice. 16 , 17
Singlenucleotidepolymorphisms (SNPs) are molecular factors that might be useful as prognostic markers in CRC. Preliminary genome wide association (GWA) study in non-caucasian population has indicated a role of SNPs in resectable CRC. 18 We hypothesized that SNPs participating in genetic risk for CRC and metastasis might prove as a prognostic factor in resectable CRC. In our study, we have selected SNPs with higher frequency in patients with either local lymph node involvement or systemic dissemination in genes participating in CRC carcinogenesis
P Noveski, S Trivodalieva, G Efremov and D Plaseska-Karanfilska
Y Chromosome Single Nucleotide Polymorphisms Typing by SNaPshot MINISEQUENCING
Analysis of Y chromosome haplogroups, defined by single nucleotide polymorphisms (SNPs), is now a standard approach for study of the origin of human populations and measurement of the variability among them. It is also a new forensic tool, because it may allow determination of the origin of any male sample of interest. We have used a strategy for rapid, simple and inexpensive Y chromosome SNP typing of 343 male DNA samples, of which 211 were Macedonians, 111 Albanians and 21 Roma, Serbs or Turks. Using multiplex polymerase chain reaction (mPCR) and a SNaPshot multiplex kit for single nucleotide extension reaction, 28 markers were grouped into five multiplexes. Twenty different Y haplogroups were found in these samples. The most common Y haplogroups in Macedonians were I2a-P37b (27.5%), E1b1b1a-M78 (15.6%), R1a1-SRY1532 (14.2%) and R1b1-P25 (11.4%). In the Albanians E1b1b1a-M78 accounted for 28.8%, R1b1-P25 for 18.0%, J2b2-M241 for 13.5% and R1a1-SRY1532 for 12.6%. We conclude that five haplogroups (E1b1b1a-M78, I2a-P37b, J2b2-M241, R1a1-SRY1532 and R1b1-P25) comprised 72.6% of the Y chromosomes, this being characteristic of the typical European Y chromosome gene pool.
D.P. Berry, N. McHugh, E. Wall, K. McDermott and A.C. O’Brien
be robust, technically accurate, inexpensive, and require minimal effort by producers and breeders. Moreover, the tools should ideally be such as not to stifle collaboration in (genomic) data exchange.
The exploitation of genomic technologies in animal production systems is intensifying, primarily in response to improved accuracy of prediction of true genetic merit when the genotype of an animal is incorporated into genetic evaluations ( Hayes et al ., 2009 ; Spelman et al ., 2013 ). The cost of the commonly termed singlenucleotidepolymorphism (SNP) chips
Jaromír Kadlec, Božena Hosnedlová, Václav Řehout, Jindřich Čítek, Libor Večerek and Lenka Hanusová
Amills M, Jiménez N, Villalba D, Tor M, Molina E, Cubiló D, Marcos C, Francesch A, Sanchez A, Estany J (2003): Identification of three singlenucleotidepolymorphisms in the Chicken - Insulin-Like Growth Factor 1 and 2 genes and their associations with growth and feeding traits. Poultry Sci 82: 1485-1493.
Beccavin C, Chevalier B, Cogburn LA, Simon J, Duclos MJ (2001): Insulin-like growth factors and body growth in chickens divergently selected for high or low growth rate. J Endocrinol 168: 297
Vivi Yuskianti, Fa Xin Huang, Bian Xiang Zhang and Susumu Shiraishi
A chere , V., P. F aivre R ampant , L. E. P aques and D. P rat (2004): Chloroplast and mitochondrial molecular tests identify European x Japanese larch hybrids. Theoretical Applied Genetics 108 : 1643–1649.
A itken , N., S. S mith , C. S chwarz and P. A. M orins (2004): Singlenucleotidepolymorphism (SNP) discovery in mammals: a targeted-gene approach. Molecular Ecology 13 : 1423–1431.
B atley , J., R. M ogg , D. E dwards , H. O’S ullivan and K. J. E dwards (2003): A high-throughput SNuPE assay for genotyping SNPs in the
J Krsteski, S Jurgec, M Pakiž, I But and U Potočnik
(rs11575934) and IL23R (rs7517847) SingleNucleotidePolymorphisms
The rs2070874 ( IL4) and rs1801275 ( IL4R) SNPs were selected according to their known functional role in IL expression. Singlenucleotidepolymorphisms rs11575934 ( IL12RBI) , rs6887695 ( IL12B) , rs20541 ( IL13) and rs7517847 ( IL23R) were previously reported to be associated with other ULM-related immune-mediated diseases, such as inflammatory bowel disease [ 22 ], glioblastoma [ 23 ], cervical adenocarcinoma and an increased risk of tuberculosis [ 24 ].
Genotyping of IL4 (rs2070874
pedigrees is that they neither exist nor are accurate for many of the livestock breeds, which negates or seriously hampers any effort to assess genetic diversity.
With the availability of molecular markers such as microsatellites, and more recently singlenucleotidepolymorphisms (SNP) and whole genome sequence data, it is possible to analyze diversity on a genomic level. The dense marker genotypes negate the necessity to have historical records, and thus, all problems associated with pedigrees. It allows a more precise assessment of relatedness accounting for Mendelian
Ramin Saravani, Elahe Esmaeilzaei, Nafiseh Noorzehi and Hamid Reza Galavi
SingleNucleotidePolymorphism in its Receptor MTNR1B Gene with Breast Cancer. Middle East J Cancer. 2015;6(1):11-20.
23. Li C, Shi Y, You L, Wang L, Chen Z-J. Association of rs10830963 and rs10830962 SNPs in the melatonin receptor (MTNR1B) gene among Han Chinese women with polycystic ovary syndrome. Mol Hum Reprod. 2011;17(3):193-8. DOI: 10.1093/molehr/gaq087
24. Xia Q, Chen Z-X, Wang Y-C, Ma Y-S, Zhang F, Che W, et al. Association between the melatonin receptor 1B gene polymorphism on the risk of type 2 diabetes, impaired glucose
Li-jun Peng, Jin-sheng Guo, Zhe Zhang, Li-li Liu, Yi-rong Cao, Hong Shi, Jian Wang, Scott L. Friedman, John J. Sninsky and Ji-yao Wang
risk of liver fibrosis in Caucasians with chronic hepatitis C infection. J Hepatol 2009;51:750-757.
19 Beutler B. Inferences, questions and possibilities in Toll-like receptor signalling. Nature 2004;430:257-263.
20 Seki E, De Minicis S, Osterreicher CH, Kluwe J, Osawa Y, Brenner DA, et al. TLR4 enhances TGF-beta signaling and hepatic fibrosis. Nat Med 2007;13:1324-1332.
21 Guo J, Loke J, Zheng F, Hong F, Yea S, Fukata M, et al. Functional linkage of cirrhosis-predictive singlenucleotidepolymorphisms of Toll