A Novel Single Nucleotide Polymorphism in Exon 4 of Insulin-Like Growth Factor-1 Associated with Production Traits in Bali Cattle

Insulin-like growth factor-1 (IGF-1) is one of the gene candidates that can be used in selection strategy by using DNA markers (marker assisted selection). Gene candidate strategy is a molecular biology techniques to identify quantitative trait loci directly, with the assumption that genetic variation associated to quantitative trait variation. This study was designed to identify any new mutations in exon 4 that can cause the IGF-1 gene polymorphism and then affect the production traits on Bali cattle. Single nucleotide polymorphism (SNP) discovery was conducted by using the direct sequencing technique. Genetic variation of the genes candidate was identified by using PCR-RFLP technique. The results of this study indicate the presence of a new SNP in exon 4 of IGF-1 gene caused by the T/C transition, which can be identified using Rsa1 restriction enzyme. Genotypic polymorphism of IGF-1/Rsa1 has a significant influence on birth weight, weaning weight and average daily gain of Bali cattle. CC genotype had a birth weight rate, weaning weight and average daily gain of: 15.64±1.83; 83.15±9.00, and 0.439±0.07 respectively, higher than the TT and CT genotype. IGF-1/Rsa1 can be used as a genetic marker for selection of birth weight, weaning weight, and daily body weight gain

Single Nucleotide Polymorphism Promoter -765g/C Gen Cox-2 sebagai Faktor Risiko Terjadinya Karsinoma Kolorektal

Karsinoma kolorektal (KKR) merupakan keganasan yang berasal dari transformasi neoplastik sel-sel epitel kolon dan rektum, menempati urutan ketiga terbanyak dari seluruh kanker di seluruh dunia.Berbagai Perubahan DNA dapat terjadi akibat paparan dengan lingkungan dan karsinogen. DNA yang gagal berpasangan menimbulkan instabilitas genetik, mutagenesis, dan kematian sel, disebut sebagai single nucleotide polymorphisms (SNPs). Polimorfisme adalah Perubahan atau mutasi pada gen yang tidak menimbulkan Perubahan struktur protein hanya mengakibatkan variasi fungsi protein, tidak bermanifestasi klinis, hanya bisa menentukan kerentanan terhadap penyakit. Jenis penelitian ini adalah deskriptif observasional pada gen COX-2 dengan metode PCRRFLP. Desain penelitian yang digunakan pada penelitian ini adalah case series, dilakukan di Laboratorium Klinik RSUP dr. Mohammad Hoesin Palembang selama 4 bulan, dari bulan Mei sampai dengan November 2012. Terdapat empat puluh (40) orang subjek penelitian yang merupakan penderita KKR, semuanya berasal dari seluruh etnis yang berdomisili di Sumatera Selatan dan bersedia ikut serta dalam penelitian. Penderita karsinoma kolorektal yang berjenis kelamin laki-laki (52,5%) lebih banyak daripada wanita (47,5%), lokasi karsinoma pada daerah kolon (25%) lebih banyak daripada daerah rektum (75%), dan penderita dengan adenokarsinoma (77,5%) merupakan jenis terbanyak diikuti musinus adenokarsinoma (17.5%) dan adenoskuamous karsinoma (5%). Distribusi genotip CC (mutan) sebanyak 10%, genotip GC (heterozygot) sebanyak 10%, dan, genotif GG (normal) sebanyak 80%. Sedangkan Distribusi alel C (mutan) sebanyak 16% dan alel G (normal) sebanyak 84%. Penelitian ini terbatas pada identifikasi polimorfisme gen COX2 pada kasus KKR, tidak melihat hubungan atau pengaruh polimorfisme gen COX-2 terhadap kejadian KKR. Perlu dilakukan wawancara lebih lanjut terhadap pasien mengenai suku, etnis, riwayat keluarga. Perlu dilakukan penelitian lebih lanjut untuk mengetahui hubungan polimorfisme promoter -765G/C Gen COX-2 dengan kejadian karsinoma kolorektal

Identifikasi Single Nucleotide Polymorphism (SNP) Gen Pvmdr1 Pada Penderita Malaria Vivaks Di Minahasa Tenggara (Sulawesi Utara)

Parasite resistance to antimalarial drugs is an obstacle to malaria elimination. In Plasmodium vivax, up to now, a marker to distinguish between resistant and susceptible is no available yet. Identify Single Nucleotide Polymorphisms (SNP) in P. vivax for multidrug resistance (pvmdr1)is potential approach due to pvmdr1 gene is orthologous to the pfmdr1 of P.falciparum, have been related to multidrug resistance. The purpose of this study was to identify SNPs/mutations on pvmdr1 gene of malaria vivax patients who came to the Primary Healthe Centers, Touluaan and Tombatu Minahasa Tenggara (North Sulawesi).Blood samples and slide of blood smears were collected from patients who infected with P.vivax or mixed infection of P.vivax and P.falciparum. After the species were cross checked by certified microscopist then confirmed by PCR, SNP identification were performed by sequencing technique. Only 83 of 99 recruited subjects were included inclution criteria. Sequensing result showed that 59 of 83 subjects were analysed to identify the SNP. We found 5 nonsynonymous SNPs, namely at the point G698S, M908L, Y976F, L1076F, and K1261E

Identification of Single Nucleotide Polymorphisms on Cattle Breeds in Indonesia Using Bovine 50k

Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmenta-tion, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia

Detection of Single Nucleotide Polymorphism Rs2013162 of IRF6 Gene in Patient with Cleft Lip and Palate

Background: Cleft lip and palate are congenital disorders which induce affected individuals medically, socially and psychologically. The objective of this study was to investigate the association of Single Nucleotide Polymorphism(SNP); rs2013162 of IRF6 Gene in Patient with Cleft Lip and Palate. Materials and Methods: Fifty patients with non-syndromic CL/P were included in present study alongwith fifty individuals with no psychiatric history as controls. In all of the these individuals, search for Single nucleotide polymorphism was carried out by designing sequence specific primers. The sequence was amplified by using Real time PCR and products were investigated by visualizing high resolution melting curve upon HRM-PCR. Results: The logistic regression and Hardy-Weinberg equilibrium were applied to investigate the association of IRF6 SNP rs2013162 with disease. Results revealed no association of this polymorphism with non-syndromic CL/P. Conclusion: We found no association of IRF6 SNP rs2013162 in patients with non-syndromic CL/P. Further study is required with larger sample size to validate the findings of the present study in Pakistani population and along with this SNP other polymorphisms of the same gene should be analyzed to find out the association with the non-syndromic CL/P

Single nucleotide polymorphisms in the bovine leptin gene and their association with carcass and efficiency traits, and endocrine profiles, in female Angus cows

One hundred and fifty female Angus cattle were genotyped for the bovine leptin gene SNPs UASMS1, UASMS2, E2FB and E2JW. Net Feed Intake (NFI) Estimated Breeding Values (EBVs) and E2JW SNP data was also acquired from 169 Angus cattle that originated from Trangie Research Station, NSW, and were selected for a divergence in feed efficiency. The E2JW SNP was associated with NFI, NFI EBV and P8 fatness. The UASMS1 and UASMS2 SNPs were associated with circulating leptin concentrations. These particular associations have not been reported previously but similar associations have reported in North American studies. The inconsistent associations suggest that these SNPs are not good candidates for marker-assisted selection for NFI. Also, the investigation of associations with endocrine profiles that reflect body composition such as leptin, requires genotyping of a larger number of Australian cattle than was possible in this experiment

Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm

The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies

MMP-2 geno-phenotype is prognostic for colorectal cancer survival, whereas MMP-9 is not.

The prognostic significance of single-nucleotide polymorphisms (SNPs) and tumour protein levels of MMP-2 and MMP-9 was evaluated in 215 colorectal cancer patients. Single-nucleotide polymorphism MMP-2(-1306T) and high MMP-2 levels were significantly associated with worse survival. Extreme tumour MMP-9 levels were associated with poor prognosis but SNP MMP-9(-1562C>T) was not. Tumour MMP levels were not determined by their SNP genotypes

Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm

The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies