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PubMed2006

High-resolution analysis of 9p loss in human cancer cells using single nucleotide polymorphism-based mapping arrays.

Single nucleotide polymorphism (SNP) mapping arrays were used to perform DNA copy number analysis of five human cancer cell lines (four malignant mesotheliomas; one non-small cell lung carcinoma) to identify and map the end-points of deletions of 9p. All five cell lines exhibited homozygous deletions encompassing the CDKN2A (alias INK4A/ARF) and CDKN2B loci. The DNA analysis profiles demarcated precisely two different, but overlapping, deletions in each mesothelioma cell line, but the lung cancer cells showed two copies of a single deletion. In the latter cell line, allele analysis revealed that virtually all SNPs for chromosome 9 were homozygous, suggestive of uniparental disomy. These findings demonstrate the utility of SNP-based mapping arrays for high-resolution analysis of genomic imbalances in cancer cells.

Cell Line, Tumor↗

PubMed2005

Different real time PCR approaches for the fine quantification of SNP's alleles in DNA pools: assays development, characterization and pre-validation.

Single nucleotide polymorphisms (SNPs) are becoming the most common type of markers used in genetic analysis. In the present report a SNP has been chosen to test the applicability of Real Time PCR to discriminate and quantify SNPs alleles on DNA pools. Amplification Refractory Mutation System (ARMS) and Mismatch Amplification Mutation Assay (MAMA) has been applied. Each assay has been pre-validated testing specificity and performances (linearity, PCR efficiency, interference limit, limit of detection, limit of quantification, precision and accuracy). Both the approaches achieve a precise and accurate estimation of the allele frequencies on pooled DNA samples in the range from 5 % to 95 % and don't require standard curves or calibrators. The lowest measurement that could be significantly distinguished from the background noise has been determined around the 1 % for both the approaches, allowing to extend the range of quantifications from 1 % to 99 %. Furthermore applicability of Real Time PCR assays for general diagnostic purposes is discussed.

Alleles↗

PubMed2026

Genome-wide cis-expression Quantitative Trait Loci (eQTL) and transcriptomic signals reveal distinct molecular regulation across correlated feed efficiency traits.

INTRODUCTION: Feed efficiency (FE) is a complex trait which determines livestock production profitability, yet the molecular mechanisms behind it remain unclear. This study investigated the blood transcriptomic profile of lambs, alongside genotype data with the aim to uncover the genetic basis of FE traits such as absolute dry matter intake (DMIabsolute), DMI adjusted for body size (DMIadjusted), average daily live weight gain (ADG), and residual feed intake (RFI). MATERIALS AND METHODS: Bulk RNA-Seq and genotype data were analysed using three complementary approaches: differential gene expression (DGE) analysis, weighted gene co-expression network analysis (WGCNA), and cis-expression Quantitative Trait Loci (cis-eQTL) mapping. These methods were used independently to identify genes and regulatory networks associated with FE traits and to investigate evidence supporting multi-trait candidate gene selection. RESULTS: DGE analysis revealed 2, 24, 85 and 4 differentially expressed genes for DMIabsolute, DMIadjusted, ADG, and RFI (Padjusted < 0.05), functionally enriched in sensory perception, ATP-dependent chromatin remodeling, Notch signaling and immune response pathways. 9 gene modules significantly associated with the FE traits (P ≤ 0.05) with correlations ranging from r = -0.56 to 0.49, were identified using WGCNA. Single nucleotide polymorphism (SNP)-level cis-eQTL analysis identified 93 eSNPs associated with 74 genes (false discovery rate (FDR) < 0.05), while permutation-derived gene level analysis identified 280 eGenes (FDR < 0.2, empirical P < 0.03). Across the three analyses, applying thresholds of DGE (Padjusted < 0.05), WGCNA (correlation, P ≤ 0.05), and cis-eQTL gene-level significance (empirical P < 0.05), multiple overlapping genes were identified including DNMT3A, KANSL1, NCOR1 for DMIadjusted, ACOX2, FANCF, CIMIP2B, LOC101115106, ARMH2, LOC132657496 for ADG, and LOC114114576 for RFI representing regulators of variations in FE. DISCUSSION: The integration of DGE, WGCNA, and cis-eQTL analyses identified key genes and regulatory mechanisms associated with variation in FE traits. These results highlight that integrated multi-trait candidate gene identification approaches can reveal key genes that lower feed intake while maintaining animal growth, supporting breeding strategies aimed at improving efficiency and long-term economic sustainability in sheep.

average daily gain (ADG)↗

PubMed2006

Conserved extended haplotypes of the major histocompatibility complex: further characterization.

Since the complete sequencing of a human major histocompatibility complex (MHC) haplotype, interest in non-human leucocyte antigen (HLA) genes encoded in the MHC has been growing. Non-HLA genes, which outnumber the HLA genes, may contribute to or account for HLA and disease associations. Most information on non-HLA genes has been obtained in separate studies of individual loci. To comprehensively address polymorphisms of relevant non-HLA genes in 'conserved extended haplotypes' (CEH), we investigated 101 International Histocompatibility Workshop reference cell lines and nine additional anonymous samples representing all 37 unambiguously characterized CEHs at MICA, NFKBIL1, LTA, NCR3, AIF1, HSPA1A, HSPA1B, BF, NOTCH4 and a single nucleotide polymorphism (SNP) at HLA-DQA1 as well as MICA, NOTCH4, HSPA1B and all five tumour necrosis factor short tandem repeat (STR) polymorphisms. This work (1) provides an extensive catalogue of MHC polymorphisms in all CEHs, (2) unravels interrelationships between HLA and non-HLA haplotypical lineages, (3) resolves reported typing ambiguities and (4) describes haplospecific markers for a number of CEHs. Analysis also identified a DQA1 SNP and segments containing MHC class III polymorphisms that corresponded with class II (DRB3 and DRB4) lineages. These results portray the MHC where lineages containing non-HLA and HLA variants in linkage disequilibrium may operate in concert and can guide more thorough design and interpretation of HLA-disease relationships.

3' Untranslated Regions↗

PubMed2006

Genotyping of triallelic SNPs using TaqMan PCR.

Methods for analysis of single nucleotide polymorphisms (SNP) are well developed. However, most ready-made SNP genotyping kits (e.g., those that use TaqMan PCR) are based on the assumption that the SNP is biallelic. Thus, most kits are unsuitable for triallelic SNPs. We have experienced difficulty genotyping an SNP using TaqMan PCR. In the present study, we developed a method of genotyping a triallelic SNP (rs3091244: alleles C, A and T) using TaqMan PCR. We used 2 different genotyping kits: one for C/A allele genotyping, and one for C/T allele genotyping. The results of these 2 kits were combined to complete the genotyping. The subjects were 320 essentially healthy elderly Japanese. The frequencies of the C, A and T alleles were 0.78, 0.155 and 0.065, respectively. This double-tube method using TaqMan SNP Genotyping Assays was very accurate and convenient, and it should be useful for genotyping in case-control association studies or linkage studies.

Aged↗

PubMed2006

Evaluation of RGS4 as a candidate gene for schizophrenia.

Several studies have suggested that the regulator of G-protein signaling 4 (RGS4) may be a positional and functional candidate gene for schizophrenia. Three single nucleotide polymorphisms (SNP) located at the promoter region (SNP4 and SNP7) and the intron 1 (SNP18) of RGS4 have been verified in different ethnic groups. Positive results have been reported in these SNPs with different numbers of SNP combinatory haplotypes. In this study, these three SNP markers were genotyped in 218 schizophrenia pedigrees of Taiwan (864 individuals) for association analysis. Among these three SNPs, neither SNP4, SNP7, SNP18 has shown significant association with schizophrenia in single locus association analysis, nor any compositions of the three SNP haplotypes has shown significantly associations with the DSM-IV diagnosed schizophrenia. Our results fail to support the RGS4 as a candidate gene for schizophrenia when evaluated from these three SNP markers.

Alleles↗

PubMed1996

Neuronal apoptosis by glial NO: involvement of inhibition of glyceraldehyde-3-phosphate dehydrogenase.

In primary cocultures of neurons and glial cells prepared from the neonatal rat brain, lipopolysaccharide (LPS) reduced the numbers of neuronal cells but the effects were markedly inhibited by NG-monomethyl-L-arginine, indicating the involvement of NO and LPS-induced NO synthase in neuronal death. LPS stimulated the expression of inducible NOS (iNOS) in preparations of primary cultured microglias/astrocytes, but not in primary cultured neurons. In addition, LPS caused DNA fragmentation only in NG108-15 cells but not in primary cultured astrocytes as well as astrocytes in cocultures of the two cell types, suggesting that NOS induces the apoptosis of neurons but not glial cells. We then examined the NO-induced neuronal death in NG108-15 cells using NO donors. SNP, and NO donor, caused NO-2 accumulation in the reaction medium and lactate dehydrogenase (LDH) leakage from NG108-15 cells. Although SNP stimulated guanylyl cyclase and accumulated cGMP, cGMP analogs did not affect LDH leakage. In addition, SNP induced chromosomal condensation and fragmentation of nuclei in NG108-15 cells. Gel electrophoretic analysis of cellular DNA extracted from SNP-treated cells, confirmed the internucleosomal DNA fragmentation typical of apoptosis in this culture. SNP increased the amount of radioisotopic labeled glyceraldehyde-3 phosphate dehydrogenase (GAPDH) in the presence of [32P]NAD and inhibited the enzyme activity. The results suggested that SNP-induced cell death is partly due to the NO-induced inhibition of GAPDH, perhaps by stimulating the binding of NAD to GAPDH.

Animals↗

PubMed2006

LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters.

UNLABELLED: We present a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates population genetic parameters from genetic data. LAMARC can co-estimate subpopulation Theta = 4N(e)mu, immigration rates, subpopulation exponential growth rates and overall recombination rate, or a user-specified subset of these parameters. It can perform either maximum-likelihood or Bayesian analysis, and accomodates nucleotide sequence, SNP, microsatellite or elecrophoretic data, with resolved or unresolved haplotypes. It is available as portable source code and executables for all three major platforms. AVAILABILITY: LAMARC 2.0 is freely available at http://evolution.gs.washington.edu/lamarc

Bayes Theorem↗

PubMed2002

Human non-synonymous SNPs: server and survey.

Human single nucleotide polymorphisms (SNPs) represent the most frequent type of human population DNA variation. One of the main goals of SNP research is to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases. Non-synonymous coding SNPs (nsSNPs) comprise a group of SNPs that, together with SNPs in regulatory regions, are believed to have the highest impact on phenotype. Here we present a World Wide Web server to predict the effect of an nsSNP on protein structure and function. The prediction method enabled analysis of the publicly available SNP database HGVbase, which gave rise to a dataset of nsSNPs with predicted functionality. The dataset was further used to compare the effect of various structural and functional characteristics of amino acid substitutions responsible for phenotypic display of nsSNPs. We also studied the dependence of selective pressure on the structural and functional properties of proteins. We found that in our dataset the selection pressure against deleterious SNPs depends on the molecular function of the protein, although it is insensitive to several other protein features considered. The strongest selective pressure was detected for proteins involved in transcription regulation.

Databases, Genetic↗

PubMed2026

Development of Genome-Derived InDel Markers and Genetic Diversity Analysis of Caragana acanthophylla in Xinjiang, China.

Caragana acanthophylla Kom. is an ecologically important drought-tolerant shrub in Xinjiang, China, but species-specific molecular markers for germplasm characterization remain limited. We sampled 93 individuals from 11 localities representing the currently known distribution of C. acanthophylla in Xinjiang. Three individuals per locality (33 in total) were whole-genome resequenced, yielding 2,873,410 high-quality SNPs and 5,679,915 InDels. Genome-wide SNP-based PCA and genetic relationship analysis provided an independent high-resolution assessment of the 33 resequenced individuals. From 34 candidate primer pairs, eight polymorphic InDel markers with stable amplification and clear genotyping profiles were retained and applied to all 93 individuals. The SNP dataset revealed clear regional differentiation and finer locality-associated relationships. Analysis of the same 33 individuals with the eight InDel loci recovered part of this broad pattern, particularly the differentiation of the western YL materials, but showed lower fine-scale resolution. Across all 93 individuals, the InDel panel revealed moderate to low marker-level genetic diversity and detectable regional differentiation. AMOVA attributed 67.00% of the variation to differences among the 11 original sampling localities, while the five exploratory analytical groups showed a similar among-group component (68.37%). The Mantel correlation detected across all 93 individuals (r = 0.801, p < 0.001) disappeared after YL was excluded (r = -0.032, p = 0.724), indicating that the overall spatial signal was largely driven by the geographic separation of YL. These results support the eight-marker panel as a practical, low-cost tool for preliminary germplasm characterization and broader sample screening, while genome-wide SNP data provide substantially greater resolution for population-level inference.

Caragana acanthophylla↗

PubMed2003

Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map.

An international effort is underway to generate a comprehensive haplotype map (HapMap) of the human genome represented by an estimated 300,000 to 1 million 'tag' single nucleotide polymorphisms (SNPs). Our analysis indicates that the current human SNP map is not sufficiently dense to support the HapMap project. For example, 24.6% of the genome currently lacks SNPs at the minimal density and spacing that would be required to construct even a conservative tag SNP map containing 300,000 SNPs. In an effort to improve the human SNP map, we identified 140,696 additional SNP candidates using a new bioinformatics pipeline. Over 51,000 of these SNPs mapped to the largest gaps in the human SNP map, leading to significant improvements in these regions. Our SNPs will be immediately useful for the HapMap project, and will allow for the inclusion of many additional genomic intervals in the final HapMap. Nevertheless, our results also indicate that additional SNP discovery projects will be required both to define the haplotype architecture of the human genome and to construct comprehensive tag SNP maps that will be useful for genetic linkage studies in humans.

Base Sequence↗

PubMed2004

Characterization of a new SNP c767A/T (Arg222Trp) in the candidate TSG FUS2 on human chromosome 3p21.3: prevalence in Asian populations and analysis of association with nasopharyngeal cancer.

The FUS2 gene, encoding a novel cytoplasmic acetyltransferase, resides in the tumor suppressor gene region on human chromosome 3p21.3 and is considered a promising candidate tumor suppressor gene. We have identified a new single nucleotide polymorphism (SNP), c767A/T, in the coding region of the gene. The polymorphism leads to a non-conservative amino acid change (R222W) located between the acetyltransferase (GNAT) and the proline-rich domains of the protein. We have analyzed 254 subjects included in 14 sub-populations. The occurrence of the SNP varies with the ethnicity of the population, suggesting that this SNP could be a valuable biomarker for population genetics. It is most prevalent in various Asian populations (T allele frequency>0.54), followed by the Canadian polar Inuit (T allele frequency=0.3), African American (T allele frequency=0.17), and Caucasian population (T allele frequency=0.1). Since nasopharyngeal carcinoma (NPC) is frequent in Southern China, Taiwan, Borneo and polar Canada, we further tested for the possible association of the FUS2 SNP with this form of endemic cancer. Our analysis, albeit limited, suggests no likely association between NPC and the FUS2 gene polymorphism. Further large-scale case-control studies are necessary and warranted to prove the strength of this contention.

Acetyltransferases↗

PubMed2006

[SNP polymorphism of LGALS3BP gene in patients with benign and malignant thyroid tumours].

INTRODUCTION: The aim of the study was estimation of occurrence of SNP (single nucleotide polymorphism) sites in LGALS3BP gene in patients with benign and malignant thyroid tumors and analysis of correlation between their frequency and the histological type of thyroid lesions. MATERIAL AND METHODS: The studied group consisted of 58 patients, 24 with papillary thyroid carcinomas, 19 with nodular goiters and 15 with follicular adenomas. Control group included 180 healthy volunteers. Four different SNP polymorphisms were analysed in PCR products using the SNaPshot test, on genetic analyser ABI Prism 310; these can be found in NCBI database under rs numbers: 1803938 (a/g), 11024 (g/c), 1801463 (a/c) and 1131516 (c/t). RESULTS: In all patients analysis of SNP sites revealed: lack of polymorphism in a/g rs 18039380; polymorphism identical to database in g/c rs 11024 and polymorphism different from database in a/g rs 1801463 and c/g rs 131516. There were no significant differences between patients with thyroid lesions and group of healthy controls. CONCLUSION: Single nucleotide polymorphism (SNP) of LGALS3BP gene (found in NCBI) database are not characteristic for papillary thyroid cancer, follicular adenomas and nodular goiter.

Adenoma↗

PubMed2006

Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene.

BACKGROUND: Cholesterol 7-alpha-hydroxylase (CYP7A1) is the rate limiting enzyme for converting cholesterol into bile acids. Genetic variations in the CYP7A1 gene have been associated with metabolic disorders of cholesterol and bile acids, including hypercholesterolemia, hypertriglyceridemia, arteriosclerosis, and gallstone disease. Current genetic studies are focused mainly on analysis of a single nucleotide polymorphism (SNP) at A-278C in the promoter region of the CYP7A1 gene. Here we report a genetic approach for an extensive analysis on linkage disequilibrium (LD) blocks and haplotype structures of the entire CYP7A1 gene and its surrounding sequences in Africans, Caucasians, Asians, Mexican-Americans, and African-Americans. RESULT: The LD patterns and haplotype blocks of CYP7A1 gene were defined in Africans, Caucasians, and Asians using genotyping data downloaded from the HapMap database to select a set of haplotype-tagging SNPs (htSNP). A low cost, microarray-based platform on thin-film biosensor chips was then developed for high-throughput genotyping to study transferability of the HapMap htSNPs to Mexican-American and African-American populations. Comparative LD patterns and haplotype block structure was defined across all test populations. CONCLUSION: A constant genetic structure in CYP7A1 gene and its surrounding sequences was found that may lead to a better design for association studies of genetic variations in CYP7A1 gene with cholesterol and bile acid metabolism.

Black or African American↗

PubMed2005

QTLs influencing panicle size detected in two reciprocal introgressive line (IL) populations in rice (Oryza sativa L.).

Two sets of reciprocal introgression line (IL) populations, i.e., ILs with Lemont as recurrent parent (IL_LT) and ILs with Teqing as recurrent parent (IL_TQ), were developed and evaluated for traits representing panicle size, including primary branch number (PBN), secondary branch number (SBN), and spikelet number per panicle (SNP). Together with the regression to recurrent parent by advanced backcross, transgressive segregations were observed for all traits. Correlation and regression analysis showed that SBN had much higher contribution to SNP than PBN. It was confirmed by the QTL analysis that many common loci were detected between SBN and SNP, in comparison with single common locus between PBN and SNP. One and three main effect QTLs (M-QTLs) were detected for PBN in IL_LT and IL_TQ, respectively. Six M-QTLs per trait per populations were associated with SBN and SNP. Less number and lower contribution of epistasis were detected in IL populations in comparison with mapping result from F2 or RI population. There were only four QTLs in fourteen loci (near 30%) commonly detected in both reciprocal IL populations implying the large impact of genetic background on QTLs expression.

Chromosome Mapping↗

PubMed2004

Nitric oxide-induced apoptosis is mediated by Bax/Bcl-2 gene expression, transition of cytochrome c, and activation of caspase-3 in rat vascular smooth muscle cells.

BACKGROUND: In contrast to the anti-apoptotic action of nitric oxide (NO) on endothelial cells, NO exerts a pro-apoptotic effect on vascular smooth muscle cells (VSMCs). This study was designed to elucidate the mechanism underlying NO-induced apoptosis in rat VSMCs. METHODS AND RESULTS: (1) Using the terminal deoxynucleotidyl transferase-mediated digoxigenin-11-dUTP nick end labeling (TUNEL) assay and fluorescence activated cell sorter (FACS) analyses, apoptosis of rat VSMCs were confirmed after exposure to sodium nitroprusside (SNP) (0.5 to 4 mmol/l), an exogenous NO donor. The effects of SNP were blocked by hemoglobin. (2) A universal caspase inhibitor, z-VAD-fmk, dose-dependently inhibited NO-induced apoptosis. VSMCs degraded Ac-DEVD-pNA rather than Ac-WHED-pNA after exposure to SNP, which suggested that the activation of caspase 3 rather than caspase 1 was involved in the process. Immunoblot analysis confirmed the activation of caspase-3. (3) Exposure to SNP induced the release of cytochrome c from the mitochondria to the cytosol, which was detected by immunoblot analysis of mitochondrial and cytosol fractions. (4) SNP exposure increased the ratio of Bax/Bcl-2 protein expression twofold by immunoblot analysis. CONCLUSIONS: The mechanism of NO-induced apoptosis in rat VSMCs involves an increase in the ratio of Bax/Bcl-2 gene expression, which leads to the release of cytochrome c from the mitochondria to the cytosol, finally activating caspase-3 and resultant apoptosis.

Animals↗

PubMed2001

The single-nucleotide polymorphism lottery: how useful are a few common SNPs in identifying disease-associated alleles?

It has been proposed that using association analysis of single nucleotide polymorphism (SNP) markers in candidate genes may be more successful in identifying disease susceptibility genes for complex diseases. Finding all the SNPs within a candidate gene and genotyping a large case-control cohort is a resource-intensive process. As linkage disequilibrium extends across small regions of the genome, the expectation is that a few common anonymous SNPs will be sufficient to detect functional disease-associated alleles. The aim of this investigation was to compare the ability of a number of family- and population-based association methods to identify known susceptibility loci using the Genetic Analysis Workshop 12 simulated data set. As expected, case-control methods were more likely to detect association with individual SNPs but family-based haplotyping methods appeared better able to localize the position of functional polymorphism.

Adult↗

PubMed2004

Linkage and association analysis at the serotonin transporter (SLC6A4) locus in a rigid-compulsive subset of autism.

Autism is a complex genetic neurodevelopmental disorder in which affected individuals display deficits in language, social relationships, and patterns of compulsive and stereotyped behaviors and rigidity. Linkage analysis in our dataset of 57 New England and 80 AGRE multiplex autism families reveals a multipoint heterogeneity LOD (HLOD) score of 2.74 at D17S1871 in 17q11.2. Analysis of phenotypic subsets shows an increased HLOD of 3.62 in families with compulsive behaviors and rigidity. The serotonin transporter locus (SLC6A4) maps nearby and is considered a functional candidate gene in autism and obsessive-compulsive disorder. We genotyped an insertion/deletion polymorphism in the promoter (5-HTTLPR), and seven single nucleotide polymorphisms (SNPs) across the 38-kb transcriptional unit. Transmission disequilibrium (TD) analysis reveals nominal association at a SNP in intron 5 (P = 0.02) as well as 5-HTTLPR (P = 0.01), corresponding to over-transmission of the short allele. TD analysis in the rigid-compulsive subset shows no evidence for association. Intermarker linkage disequilibrium was determined. All SNPs define a single haplotype block, while 5-HTTLPR lies 5' to this block. Three SNPs are sufficient to detect all common alleles (> or =5%) in this > 26-kb block. Analysis of haplotypes for these markers demonstrates no evidence for association to autism. These data indicate that a common allele within the coding region of SLC6A4 is not responsible for the observed linkage. However, the presence of heterogeneous disease variants within the block or the existence of a common disease-associated allele either upstream or downstream of this block is possible. In fact, such variants may well account for linkage to 17q11.2 in our families.

Autistic Disorder↗