• We investigated the association of single-nucleotide polymorphisms (SNPs) and haplotypes in EPHB4 with risk of ICH at clinical presentation in patients with BAVM. (kaiserpermanente.org)
  • METHODS AND RESULTS: Eight haplotype-tagging SNPs spanning approximately 29 kb were tested for association with ICH presentation in 146 white patients with BAVM (phase I: 56 ICH, 90 non-ICH) using allelic, haplotypic, and principal components analysis. (kaiserpermanente.org)
  • In principal components analysis, 2 components explained 91% of the variance and complemented haplotype results by implicating 4 SNPs at the 5′ end, including rs314308 and rs314313. (kaiserpermanente.org)
  • In spite of being exhaustively studied molecule, no attempt has been made till date to comprehensively and systematically analyze the SNPs of MBL2 gene. (springeropen.com)
  • The present study was carried out to identify and prioritize the SNPs of MBL2 gene for further genotyping and functional studies. (springeropen.com)
  • Out of total 661 SNPs, only 37 validated SNPs having minor allele frequency ≥0.10 were considered for the present study. (springeropen.com)
  • These 37 SNPs includes one in 3′ near gene, nine in 3′ UTR, one non-synonymous SNP (nsSNP), thirteen intronic SNPs and thirteen in 5′ near gene. (springeropen.com)
  • Out of these, 4 SNPs from 3′ UTR were found to play role in miRNA binding, 7 SNPs from 5′ near and intronic region were predicted to involve in transcription factor binding and expression of MBL2 gene. (springeropen.com)
  • Thus, findings of the present study indicated 12 SNPs of MBL2 gene to be functionally important. (springeropen.com)
  • 2007 ). SNPs of MBL2 gene cover both coding and non-coding regions. (springeropen.com)
  • Thirty SNPs of well-defined functional genes were investigated. (cancerindex.org)
  • Two SNPs in X-Ray Repair Cross Complementing 2 gene (XRCC2) rs2040639 and interferon gamma (IFNG) rs2069705 genes were found to be associated with ARSR. (cancerindex.org)
  • Dogs of various breeds, affected or unaffected with primary glaucoma, were genotyped for the Gly661Arg variant of ADAMTS10 , as well as 7 other nonsynonymous single nucleotide polymorphisms (SNPs) in other genes in the beagle POAG locus that segregate with disease. (arvojournals.org)
  • For the nonsynonymous SNPs other than the ADAMTS10 variant, control dogs were identified that were homozygous for the alternative alleles, ruling out those variants as causative. (arvojournals.org)
  • 1 Genotyping the eight nonsynonymous SNPs in 48 control beagles showed that the Gly661Arg variant of ADAMTS10 had the lowest minor allele frequency (MAF). (arvojournals.org)
  • The locations of the eight nonsynonymous SNPs that segregate with disease in the POAG beagle colony are indicated by arrows labeled according to the gene in which the SNPs are located. (arvojournals.org)
  • A functionally relevant SNP, as well as several SNPs either on the putatively selected core haplotypes or with significant iHS or XP-Rsb values, displayed allele frequencies strongly correlated with the absolute geographical latitude of the populations sampled. (biomedcentral.com)
  • Coupled with the extensive haplotype tagging SNP information being catalogued by the HapMap project ( 3 ), it now seems that that this density may be sufficient to permit indirect tests of association with the majority of all common SNPs ( 4 ), although this fundamental assumption has recently been questioned ( 5 ). (aacrjournals.org)
  • We used iterative association mapping to identify a susceptibility gene for age-related macular degeneration (AMD) on chromosome 10q26, which is one of the most consistently implicated linkage regions for this disorder. (nih.gov)
  • Classical recombinant studies located the D blood system on chicken chromosome 1, but the candidate gene was unknown. (bvsalud.org)
  • 1998 ). The MBL2 gene is composed of 7461 bases and lies between the regions 52765380 to 52772841 bp of chromosome no. 10 (NCBI reference sequence number NC_000010.11). (springeropen.com)
  • Clinical features associated with mutations in the chromosome 1 open-angle glaucoma gene (GLC1A). (jamanetwork.com)
  • In humans, MHC proteins are encoded by the Human Leukocyte Antigen (HLA), a group of more than 200 genes located closely together on the short arm of chromosome 6. (antibodies-online.com)
  • This gene encodes a member of the RecA/Rad51-related protein family that participates in homologous recombination to maintain chromosome stability and repair DNA damage. (cancerindex.org)
  • Y chromosome markers can complement the use of autosomal markers, for example when a forensic scientist is confronted with a DNA mixture or needs to amplify male specific markers in paternity cases where the father is not available. (uclan.ac.uk)
  • The Cohanim Modal Haplotype (CMH) is the Y-chromosome (paternal) profile most frequently found in men with an oral tradition of Cohen ancestry. (familytreedna.com)
  • It is a Y-chromosome DNA STR (Short Tandem Repeat) haplotype. (familytreedna.com)
  • Dr. Scheet's lab has helped pioneer methods to more accurately distinguish these alterations using information on the order of inherited alleles on a chromosome, i.e. the haplotypes. (mdanderson.org)
  • The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians. (blogspot.com)
  • The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent,' Looks to me more like between West Asia (minus Arabia) and western part of South_Central Asia (minus India). (blogspot.com)
  • The parental haplotypes causing for this mutation are also found in Americas and East Asians. (blogspot.com)
  • When you sequence, phasing refers to the process of identifying those unique variants on each DNA sequencing read and then separating (phasing) those reads into their respective parental haplotypes. (seqanswers.com)
  • Additional strategies can be implemented to help improve phasing such as using sequence data from parents to bin long reads into their respective parental haplotypes during the assembly process, known as trio-binning, and/or by including long-range chromosomal contact information from Hi-C sequencing," Korlach stated. (seqanswers.com)
  • homologous regions between genomes are compressed into a single representative of all alleles present in the pangenome. (biorxiv.org)
  • 2006 ). Mice have two homologous genes of MBL i.e. (springeropen.com)
  • This gene is involved in the repair of DNA double-strand breaks by homologous recombination and it functionally complements Chinese hamster irs1, a repair-deficient mutant that exhibits hypersensitivity to a number of different DNA-damaging agents. (cancerindex.org)
  • Meanwhile, Paraphase is a tool capable of phasing haplotypes from highly homologous, medically significant genes, such as SMN1/SMN2 , within targeted sequencing HiFi datasets 3 . (seqanswers.com)
  • Low circulating levels of MBL have been associated with common genetic variants in the MBL2 gene, which is the only functional human gene for MBL. (biomedcentral.com)
  • We investigated a panel of 34 known high/moderate-risk cancer genes, including 16 related to breast or ovarian cancer (BC/OC) genes, and 63 candidate genes to BC/OC in 192 clinically suspicious of hereditary breast/ovarian cancer (HBOC) Spanish families without pathogenic variants in BRCA1 or BRCA2 (BRCA1/2). (cancerindex.org)
  • Each set of this DNA we inherit will contain a unique collection of variants, which is often referred to as a haplotype. (seqanswers.com)
  • The reason that this process is so important is that accurate phasing allows researchers to connect one or more genetic variants on the same parental allele, or gene copy. (seqanswers.com)
  • For example, if you discovered two variants at different locations within a gene that had the potential to disrupt the expression of that gene, it would be important to know if those variants resided on the same copy (one bad and one good copy) or both copies (two bad copies of the gene). (seqanswers.com)
  • After the appropriate sequencing reads are generated, the next steps are to assemble the reads, detect the variants, and phase the haplotypes. (seqanswers.com)
  • Age-related macular weakening (AMD) has a solid anatomical element with a main locus at 1q31, such as complement aspect L (CFH) gene. (4egi-1inhibitor.com)
  • The intention of these types of studies was to assess the share of newly defined CFHR1 alleles on the association of the 1q31 locus with AMD. (4egi-1inhibitor.com)
  • An allele is a genetic variant at a specific point, locus , in our genetic code. (familytreedna.com)
  • The high-temperature requirement factor A1 (HTRA1) gene located at 10q26 locus has been associated with age-related macular degenerative (AMD), with the significantly related polymorphism being (rs11200638, −625G/A), however, above association is not consistent. (biomedcentral.com)
  • Nature Genetics) of the first new susceptibility genes for 17 years defined a pivotal moment in Alzheimer's genetics research. (cardiff.ac.uk)
  • Standard linkage analysis has the potential to localize major susceptibility genes to within a few million base pairs using as few as 300 microsatellite markers for a genome-wide scan. (aacrjournals.org)
  • Alternate allele frequencies were calculated with 95% confidence intervals and comparisons made to expected allele frequency relative to disease prevalence or between cases and controls. (arvojournals.org)
  • Mannose binding lectin gene 2 ( MBL2 ) polymorphisms are reported to be associated with various diseases. (springeropen.com)
  • Regulatory polymorphisms in cis-acting elements result in the unequal expression of alleles. (springer.com)
  • Alex Hastie, Ph.D., Vice President of Clinical and Scientific Affairs at Bionano, added that in addition to assessing pathogenicity, "Accurate phasing can enable complex haplotype reconstruction, allowing researchers to discriminate different structures in the most variable and functionally interesting regions of the genome (e.g. (seqanswers.com)
  • This model approximated important features of the established "coalescent" model but allowed for computationally efficient inference of important features, such as haplotypes and missing genotypes from panels of reference data. (mdanderson.org)
  • To incorporate the two most important known AMD risk factors--smoking and the Y402H variant of the complement factor H gene (CFH)--we used logistic regression modeling to test for gene-gene and gene-environment interactions in the case-control data set and used the ordered-subset analysis to account for genetic linkage heterogeneity in the family-based data set. (nih.gov)
  • Non-secretion of mutant proteins of the glaucoma gene myocilin in cultured trabecular meshwork cells and in aqueous humor. (jamanetwork.com)
  • Taking the 12.4ky estimate and multiplying by two (for the slower autosomal mutation rate) yields an estimate of 25ky, so it seems that this allele did not accompany the earliest modern human colonists of West Eurasia but emerged in some region and spread from there. (blogspot.com)
  • To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. (blogspot.com)
  • Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. (blogspot.com)
  • The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. (blogspot.com)
  • But than we still don't know when exactly this mutation took place it could very well be that the West Eurasian admixture Amerindians got stems from a time when West Eurasian still hadn't developed this light skin allele. (blogspot.com)
  • A third cluster of HLAs (class III HLAs), situated between class I and class II HLAs, encodes components of the complement system and is not involved in the adaptive immune response. (antibodies-online.com)
  • Additionally, we explored for signals of natural selection within humans by sequencing the gene in 20 Europeans, 20 East Asians and 20 Yorubas and by analysing SNP variation in a 2 Mb region centered on FOXI1 in 39 worldwide human populations from the HGDP-CEPH diversity panel. (biomedcentral.com)
  • Resulting gene expression data were analyzed combining traditional statistics with machine learning to obtain signature gene lists for functional analysis. (bvsalud.org)
  • MBL1 and MBL2 , but in human the first of them is pseudogene leaving one functional gene MBL2 (Guo et al. (springeropen.com)
  • We used an integrative approach to comprehensively assess the interactions between 1.6 million data points, encompassing a range of environmental exposures, health, and gene expression levels, coupled with whole-genome genetic variation. (nature.com)
  • Normal gene expression variation is thought to play a central role in inter-individual variation and susceptibility to disease. (springer.com)
  • We are also investigating the variation in lipoprotein-associated genes in families with various dyslipidaemias. (otago.ac.nz)
  • Here, we present the Optimized Dynamic Genome/Graph Implementation (ODGI) toolkit, a pangenome graph interrogation and transformation system specifically implemented to handle the data scales encountered when working with pangenomes built from hundreds of haplotype-resolved genomes. (biorxiv.org)
  • He leads or co-leads projects to discover risk alleles for pancreatic cancer and study the evolution to metastasis from primary lung cancer. (mdanderson.org)
  • The maternal HLA-E*01:06 allele was significantly associated with a higher fraction of anti-HLA I immunization (20.0% vs. 4.8%, p = 0.048). (frontiersin.org)
  • Antibody response is a complex genetic trait and characterizing differences in gene expression could facilitate better understanding of physiological changes due to selection and antigen exposure. (bvsalud.org)
  • and gene expression of HASI vs. HASN further suggests this basal ATP production is sufficient for robust antibody responses. (bvsalud.org)
  • Conversely, LASI vs. LASN jejunal gene expression implies a physiological need for increased ATP production with only minimal correlating antibody production. (bvsalud.org)
  • Maternal blood serum was screened for HLA class I and II antibodies, identification of Donor Specific Antibody (DSA), activation of complement measured by C1q and IgG4 concentrations. (frontiersin.org)
  • The Gly661Arg variant of ADAMTS10 was the only variant with minor allele frequency consistent with the prevalence of primary glaucoma in the general beagle population. (arvojournals.org)
  • Time will tell whether these early reports represent true positives, but the simultaneous publication in Science of two confirmatory studies ( 11, 12 ) for the Complement Factor H association with age-related macular degeneration along with the GWA scan has sparked great enthusiasm, and several reports have seemed subsequently confirming the association. (aacrjournals.org)
  • The Gly661Arg variant of ADAMTS10 was identified as the likely cause of POAG in the beagle colony because it was the only rare nonsynonymous variant that caused a highly nonconservative amino acid substitution in a highly conserved region of a gene. (arvojournals.org)
  • 2.0001) and show the unusual genotype-phenotype connection between the CFHR1 alleles and various diseases which could have crucial ramifications with regard to comprehending the pathophysiology regarding AMD. (4egi-1inhibitor.com)
  • However, it has increasingly been recognized that linkage analysis may not be powerful enough to detect genes involved in "complex diseases" like cancer, which are caused by multiple genes and multiple environmental factors, interacting in complicated ways. (aacrjournals.org)
  • A recent study shows that individuals with the allele HLA-B*46:01 have the fewest predicted binding peptides for SARS-CoV-2, suggesting they may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS. (antibodies-online.com)
  • Individuals carrying A-allele or AA genotype may have an increased risk to be AMD disease. (biomedcentral.com)
  • Our meta-analysis demonstrated that HTRA1 rs11200638 polymorphism may be related to the AMD development, especially about individuals carrying A-allele or AA genotype, who may be as identified targets to detect and intervene in advance. (biomedcentral.com)
  • We compared the distribution of allelic ratios of gene expression in fresh blood (B cells and total mononuclear cells), transformed lymphoblasts, and breast tissue from unmatched healthy individuals. (springer.com)
  • It binds to carbohydrates on the surface of mannose-rich pathogens and mediates clearing by phagocytosis or complement activation (Nepomuceno et al. (springeropen.com)
  • MBL directly mediates opsonophagocytosis and acvation of the C-type lectin complement pathway by binding microbial mannose and N-acetylglucosamine surface residues. (biomedcentral.com)
  • AD and Parkinson's disease, ALS, schizophrenia) and complex statistical analyses (e.g. gene-wide/burden, pathway analyses). (cardiff.ac.uk)
  • What is striking about her group's findings is that the genes identified show patterns of relationship, which implicate novel disease mechanisms, including immunity, endocytosis, lipid transport and ubiquination. (cardiff.ac.uk)
  • Multiple resources were utilized to identify the chicken D system candidate gene, including genome sequence information from both research and elite egg production lines for which D system alloantigen alleles were reported, and DNA from both pedigree and non-pedigree samples with known D alleles. (bvsalud.org)
  • The ancestral state of an allele is the assumed initial condition (value) of the allele and is often represented by the sequence reference. (familytreedna.com)
  • Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
  • The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. (blogspot.com)
  • However, the Long Range Haplotype (LRH) test, as well as the iHS and XP-Rsb statistics revealed significantly extended tracks of homozygosity around FOXI1 in Africa, suggesting a recent episode of positive selection acting on this gene. (biomedcentral.com)
  • We present evidence for recent positive selection in the FOXI1 gene region in Africa. (biomedcentral.com)
  • A study was done on the olfactory receptor gene clusters where they questioned if there was an association between normal rearrangement of 8p and the repeated inverted sequences. (wikipedia.org)
  • Association of various HLA haplotypes with SARS-CoV-2 infection and the course of COVID-19 could improve assessment of viral severity in the population. (antibodies-online.com)
  • The results support an association of certain HLA class Ib alleles with allo-immunization during pregnancy. (frontiersin.org)
  • Thus, molecular epidemiologists are turning to candidate-gene association studies or studies of entire candidate pathways, driven by specific biological hypotheses, as an alternative approach. (aacrjournals.org)
  • Our results strongly implicate a coding change (Ala69Ser) in the LOC387715 gene as the second major identified AMD-susceptibility allele, confirming earlier suggestions. (nih.gov)
  • Further, in order to capture gene-by-environment interactions through eQTL analyses, we combine whole-transcriptome RNA-Sequencing profiles with whole-genome genotyping and extensive fine-scale environmental exposure data. (nature.com)
  • Further studies using Larger sample size studies, including information about gene-environment interactions will be necessary to carry out. (biomedcentral.com)
  • Identification of a gene that causes primary open angle glaucoma. (jamanetwork.com)
  • A different allele, HLA-B*15:03, showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting it could enable cross-protective T-cell based immunity. (antibodies-online.com)
  • We show that differential allelic expression is common among these 12 candidate genes and is comparable between breast and blood (fresh and transformed lymphoblasts) in a significant proportion of them. (springer.com)
  • What's more, it shows that CFHR1*A is strong linkage disequilibrium with all the CFH 402His allele, which gives additional candidate versions inside the key chance haplotype with 1q31, promoting it's connection to AMD. (4egi-1inhibitor.com)
  • In genetic genealogy, this most often refers to the part of the mitochondrial genome that contains genes. (familytreedna.com)
  • In addition, an excess of oxidative free radicals also increases the expression of proinflammatory genes and activates the inflammation process [ 18 , 19 ]. (hindawi.com)
  • Air pollution impacts gene expression and pathways affecting cardio-metabolic and respiratory traits, when controlling for genetic ancestry. (nature.com)
  • After attributing a regional and/or continental ancestry to each individual using genome-wide polymorphism data, we are able to capture the effect of different environmental exposures on gene expression and health-related traits, while simultaneously controlling for genetic relatedness and migration. (nature.com)
  • 2 These observations point towards a potential influence of different HLA composition - the haplotype - in the present SARS-CoV-2 pandemic. (antibodies-online.com)
  • The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. (blogspot.com)
  • The human FOXI1 gene codes for a transcription factor involved in the physiology of the inner ear, testis, and kidney. (biomedcentral.com)
  • Using three interspecies comparisons, it has been suggested that this may be a gene under human-specific selection. (biomedcentral.com)
  • Overall, these findings have led to the hypothesis that mutations in the human FOXI1 gene might cause sensorineural deafness with distal renal tubular acidosis and male infertility [ 4 ]. (biomedcentral.com)
  • A study found that forty percent of haemophilia A patients had a factor 8 gene inversion of a certain region that was four hundred kb in size. (wikipedia.org)
  • Upon exposure to ROS, Keap1 undergoes a conformational change that allows Nrf2 to translocate to the nucleus, bind to the ARE region, and initiate transcription of target genes [ 24 ]. (hindawi.com)
  • Oxidized Keap1 dissociates from Nrf2, allowing Nrf2 to translocate to the nucleus, bind to the ARE region, and initiate transcription of target genes. (hindawi.com)
  • A coding region is DNA that contains genes. (familytreedna.com)
  • To identify statistically the most likely AMD-susceptibility allele, we used the Genotype-IBD Sharing Test (GIST) and conditional haplotype analysis. (nih.gov)
  • This gene-environment interaction is supported by statistically independent family-based and case-control analysis methods. (nih.gov)
  • To complement interests in large-scale genetic data and population genetics, he pursued studies in Statistics, with a master's (Iowa, 2000) and Ph.D. (Washington, 2006), followed by a postdoctoral fellowship at Univ. (mdanderson.org)