Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.
Cohort Studies* ; Polymorphism, Single Nucleotide

D2GSNP is a web-based server for the selection of single nucleotide polymorph isms (SNPs) within genes related to human diseases. The D2GSNP is based on a relational database created by downloading and parsing OMIM, GAD, and dbSNP, and merging it with positional information of UCSC Golden Path. Totally our server provides 5,142 and 1,932 non-redundant disease genes from OMIM and GAD, respectively. With the D2GSNP web interface, users can select SNPs within genes responding to certain diseases and get their flanking sequences for further genotyping experiments such as association studies.
Databases, Genetic ; Humans* ; Polymorphism, Single Nucleotide*

Humans ; Occupational Health ; Polymorphism, Single Nucleotide

Single nucleotide polymorphisms (SNPs) have been very widely used in the study of diseases and characters since the completion of the Human Genome Project. SNPs are mostly used as mere genetic markers in studying complex disease. Geneticists began to focus on the direct relationship between SNPs and complex diseases after the "Encyclopedia Of DNA Elements Project". SNPs can pay a regulative role alone, while the collected SNPs in genome can significantly affect the biological characters and disease development.
DNA ; Disease ; genetics ; Humans ; Polymorphism, Single Nucleotide

Humans ; Polymorphism, Single Nucleotide ; Rhinitis, Allergic ; genetics

Background: Extrahepatic biliary atresia (EHBA) causes a rare obstructive cholestasis in infants. Kasai portoenterostomy if done before the third month of life may relieve obstruction. Genetic predisposition has been implicated in EHBA etiopathogenesis with rs17095355 polymorphism having the strongest association. We determined the association between rs17095355 and EHBA susceptibility of Filipino children, and described the outcome in each genotype among timely operated patients. Methods: Thirty-four histologically diagnosed EHBA patients and thirty-three age- and sex-matched controls were recruited. Genomic DNA was extracted from peripheral blood and subjected to PCR and direct sequencing. Success of surgery among patients operated before 90 days of life was assessed by jaundice clearance six months post-surgery and native liver survival two and five years post-surgery. Results: There was no significant difference among individuals carrying T and C alleles in developing EHBA (OR:1.36; 95%CI:0.65–2.86). Jaundice persisted post-operatively in 75%, 33% and 27% of Kasai-operated homozygous T (T/T), homozygous C (C/C) and heterozygous (C/T) patients, respectively. Fifty percent of Kasai-operated C/C and C/T patients retained their native liver whereas all Kasai-operated T/T patients required liver transplantation two years post-surgery. Conclusion There is insufficient evidence to associate rs17095355 in EHBA development among Filipinos. Further investigation is warranted to elucidate genetic mechanisms in EHBA etiopathogenesis.
Biliary Atresia ; Polymorphism, Single Nucleotide ; Portoenterostomy, Hepatic

Background. Low levels of high-density lipoprotein cholesterol (HDL-c) is a well-recognized risk factor in the development of cardiovascular diseases. Associated gene variants for low HDL-c have already been demonstrated in various populations. Such associations have yet to be established among Filipinos who reportedly have a much higher prevalence of low HDL-c levels compared to other races.

Objective. To determine the association of selected genetic variants and clinical factors with low HDL-c phenotype in Filipinos.

Methods. An age- and sex-matched case-control study was conducted among adult Filipino participants with serum HDL-c concentration less than 35 mg/dL (n=61) and those with HDL-c levels of more than 40 mg/dL (n=116). Genotyping was done using DNA obtained from blood samples. Candidate variants were correlated with the low HDL-c phenotype using chi-squared test and conditional logistic regression analysis.

Results. Twelve single nucleotide polymorphisms (SNPs) were associated with low HDL-c phenotype among Filipinos with univariate regression analysis. The variant rs1260326 of glucokinase regulator (GCKR) (CT genotype: adjusted OR=5.17; p-value=0.007; TT genotype: adjusted OR=6.28; p-value=0.027) remained associated with low HDL-c phenotype, together with hypertension and elevated body mass index, after multiple regression analysis.

Conclusion. The variant rs1260326 near GCKR is associated with low HDL-c phenotype among Filipinos. Its role in the expression of low HDL-c phenotype should be further investigated prior to the development of possible clinical applications.

Single-nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variation. These variable sites are present at high density in the genome, making them powerful tool for the diagnosis of genetic and genetic-related diseases, population genetics research and drug development. They are also found widespread application to the forensic medicine. This report mainly describe the SNPs characteristics and its potential applications to the forensic medicine including the possibility, the problems and high-throughput automation detection methods.
Forensic Medicine ; Humans ; Polymorphism, Single Nucleotide

With the development of far advanced techniques in biomedical areas, individual identification using genetic polymorphism has become powerful tool in forensics. Nowadays, use of several commercial kits and automatic fluorescence dye using system have been regarded as the standard method. Short Tandem Repeat(STR) locus, whose polymorphism could be classified as length polymorphism, is usually the target for test. As time goes on, more and more have been revealed about genetic polymorphism, and new type of polymorphisms, so called Single Nucleotide Polymorphism(SNP), has come to the concerns of forensic scientists. Forensic scientists hope that SNPs would give some clues even when conventional STR loci are restricted in practical cases. Degraded sample in which we cannot get appropriate results is one of the cases. Forensic scientists also want to get some phenotype related information. SNP is hoped to solve this problems. As the mechanism for polymorphism is different from that of STR though, special consideration must be given if we want to use SNP routinely in forensic field. We review the brief history of individual identification, the background of introduction of SNP in forensics and the special points that must be discussed before the routine introduction in the field with some important characteristics of SNP.
Fluorescence ; Forensic Sciences ; Phenotype ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide

OBJECTIVETo investigate the sequence polymorphism of mtDNA HV1,HV2 overlapping fragments and coding region encompassing position 8430-8673 in Hebei Han population.

METHODSPolymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) combined with sequencing method was used to detect the haplotype distribution of mtDNA in 100 Hebei Han individuals.

RESULTSNinety-one haplotypes were noted in 100 unrelated individuals. The gene diversity is 0.9985 and the random match probability is 0.0115. Compared with the Anderson sequence, 65 sites of different nucleotide sequences were noted, of which 44 sites were previously registered in MITOMAP, 12 sites were not registered and the gene mutations were different from MITOMAP at 9 positions.

CONCLUSIONThe obtained data suggest that these loci are valuable genetic markers for personal identification and thus could be used as basic data for the forensic application of mtDNA in Hebei province.