• Using the HapMap genotype data and genome wide expression data, we assessed the distribution and functional implications of singleton SNPs in the human genome. (nature.com)
  • We further assessed whether singleton SNPs can be tagged using haplotypes of tagSNPs in the three genome wide chips, that is, GeneChip 500k of Affymetrix, HumanHap300 and HumanHap550 of Illumina, and discussed the general implications on genetic association studies. (nature.com)
  • It is now known that LD is not only present between SNPs in close physical proximity along the genome, but is also often present between widely spaced markers to form haplotype blocks. (nature.com)
  • In this study, we investigate the distribution and functional implications of singleton SNPs in the human genome using the phase II HapMap data. (nature.com)
  • Starting with the assumption that a single NGS read (or read pair) must come from one haplotype, we built a procedure for directly observing haplotypes at a local level by examining 2 or 3 adjacent single nucleotide polymorphisms (SNPs) which are close enough on the genome to be spanned by individual reads. (biomedcentral.com)
  • Thousands of loci were found in each genome where reads spanning 2 or 3 SNPs displayed more than two haplotypes, indicating that the locus is heterogeneous. (biomedcentral.com)
  • If individual reads span both SNPs, then these combinations are directly observable and it is possible to list haplotypes. (biomedcentral.com)
  • We have defined the complete gene, splice variant, and sequence variation contents of all three haplotypes, comprising over 259 annotated loci and over 20,000 single nucleotide polymorphisms (SNPs). (ox.ac.uk)
  • Our results show that present-day humans have two common FADS haplotypes-defined by 28 closely linked SNPs across 38.9 kb-that differ dramatically in their ability to generate LC-PUFAs. (ox.ac.uk)
  • In the present study, we used unphased genotype data for 12 common biallelic BRCA1 SNPs (located from exons 4 to 16) generated during sequence based clinical mutation testing to obtain BRCA1 SNP haplotypes for 5911 anonymised samples, by applying an expectation maximisation (EM) algorithm similar to those described elsewhere. (bmj.com)
  • 4- 8 An additional 17 samples were excluded from deletion testing because their haplotypes were defined by changes at two, non-adjacent haplotype defining SNPs, which could not be explained by a single deletion event. (bmj.com)
  • This pattern of SNPs on a block is a haplotype. (genome.gov)
  • Blocks may contain a large number of SNPs, but a few SNPs are enough to uniquely identify the haplotypes in a block. (genome.gov)
  • The HapMap is a map of these haplotype blocks and the specific SNPs that identify the haplotypes are called tag SNPs. (genome.gov)
  • Using just the tag SNPs, researchers are able to find chromosome regions that have different haplotype distributions in the two groups of people, those with a disease or response and those without. (genome.gov)
  • Several large-scale projects have combined the efforts of many institutions to identify and catalog all of the SNPs in the 3-billion-base pair human genome. (utah.edu)
  • SNPs occur throughout the human genome about one in every 300 nucleotide base pairs. (utah.edu)
  • This translates to about 10 million SNPs within the 3-billion-nucleotide human genome. (utah.edu)
  • dbSNP , a database of human SNPs, from the National Center for Biotechnology Information (NCBI). (utah.edu)
  • The human genome is estimated to contain one single nucleotide polymorphism (SNP) every 300 base pairs. (nature.com)
  • [8] A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation . (wikipedia.org)
  • Methods We fine-mapped the classical MHC (chr6: 29.6-33.1 Mb), imputing 216 human leukocyte antigen (HLA) alleles and 4 complement component 4 (C4) haplotypes in studies from the Psychiatric Genomics Consortium Major Depressive Disorder Working Group and the UK Biobank. (cardiff.ac.uk)
  • As human leukocyte antigen-DQ antigens present viral peptides to CD4 cells, we genotyped human leukocyte antigen -DQ alleles for 978 women enrolled in the cohort and performed cross-sectional and longitudinal analyses to identify associations of human leukocyte antigen -DQ with resistance/susceptibility to HIV-1. (edu.au)
  • The associations of these DQ alleles and haplotypes with resistance and susceptibility to HIV-1 were independent of the previously reported human leukocyte antigen-DRB*01, human leukocyte antigen A2/6802, and human leukocyte antigen-A*2301. (edu.au)
  • CONCLUSION: The associations of DQ alleles and haplotypes with resistance and susceptibility to HIV-1 emphasize the importance of human leukocyte antigen-DQ and CD4 in anti-HIV-1 immunity. (edu.au)
  • Other variables known to affect inhibitor risk including type of F8 mutation and human leucocyte antigen (HLA) were included in the. (lu.se)
  • Disease associated human leukocyte antigen (HLA) genes have been identified in humans where they are assumed to promote the susceptibility and/or progression of rheumatoid arthritis. (hu-berlin.de)
  • Narcolepsy is strongly associated with specific human leukocyte antigen (HLA) haplotypes, but the cause is not thought to be genetic. (msdmanuals.com)
  • The disease appears to be associated with the human leukocyte antigen B27 (HLA-B27) haplotype. (medscape.com)
  • and B14, DR1, DQw1 haplotypes could be involved with IgA-D susceptibility in RTIAG patients. (nih.gov)
  • The present study confirms some of the previous findings in other white populations and describes new possible alleles and haplotypes that could be implicated with IgA-D susceptibility and resistance. (nih.gov)
  • Taken together, our data provides evidence that carriage of the ATC/TTC haplotype in itself may increase the influx of neutrophils in inflammatory lesions and influence disease susceptibility. (nih.gov)
  • 4 had only the wild-type haplotype associated with CQ susceptibility (CVMNK). (cdc.gov)
  • Conclusions We found no evidence that an increased risk for depression was conferred by HLA alleles, which play a major role in the genetic susceptibility to autoimmune diseases, or C4 haplotypes, which are strongly associated with schizophrenia. (cardiff.ac.uk)
  • The finding of linkage together with significant transmission disequilibrium provides strong evidence for a susceptibility locus at 1q41 in human SLE. (elsevierpure.com)
  • SPSS 13.0 was used to determine associations of DQ alleles/haplotypes with HIV-1 resistance, susceptibility, and seroconversion rates. (edu.au)
  • A haplotype implicated in schizophrenia susceptibility is associated with reduced COMT expression in human brain. (snpedia.com)
  • and susceptibility to RAS, which segregates in families in association with HLA haplotypes. (medscape.com)
  • Haplotypes of IL-4 receptor and CD14 genetic polymorphisms are markers of susceptibility for diisocyanate asthma. (cdc.gov)
  • Although the functional significance of these findings is uncertain, these haplotypes could be susceptibility markers for DA and may be useful aids in the diagnosis of DA. (cdc.gov)
  • We discuss the advantages of determining genetic architecture in genetic isolates in order to begin to meet the grand challenge of human genetics. (nature.com)
  • In order to meet the grand challenge of human genetics, that is, to understand what causes disease and translate this knowledge to improve health outcomes, we need to know the number and population frequency of disease variants, the magnitude of their effects on phenotype and gene-gene and gene-environment interactions. (nature.com)
  • Current technologic advances in genetics, as demonstrated by Chahal et al, permit a fascinating insight into the causes of human diseases spanning probably over 57 generations. (medscape.com)
  • Data from the Hemophilia Inhibitor Genetics Study (HIGS) Combined Cohort were used to determine the association between F8 haplotype 3 (H3) vs. haplotypes 1 and 2 (H1 + H2) and inhibitor risk among individuals of genetically determined African descent. (lu.se)
  • American Journal of Human Genetics , 60, 103- 112. (bvsalud.org)
  • Two sgRNAs vectors targeting the IL-8 gene and the naked homologous repair DNA carrying different haplotypes were used to successfully generate HEK293T cells carrying the AT genotype at the first SNP - rs4073 (alias -251), TT genotype at the second SNP - rs2227307 (alias +396), TC or CC genotypes at the third SNP - rs2227306 (alias +781) at the IL-8 locus. (nih.gov)
  • Haplotype-specific expression of the N-terminal exons 2 and 3 at the human MAPT locus. (ox.ac.uk)
  • We have identified three polymorphic microsatellites (which we call TNFa, TNFb, and TNFc) within a 12-kilobase region of the human major histocompatibility complex (MHC) that includes the tumor necrosis factor (TNF) locus. (ox.ac.uk)
  • Most of the human SNP diversity at a given locus may be described as a set of "canonical" haplotypes, representing common haplotypes in a population. (bmj.com)
  • Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions. (lu.se)
  • For a given individual, there are nine possible configurations (haplotypes) at these two loci (shown in the Punnett square below). (wikipedia.org)
  • For individuals heterozygous at both loci, the gametic phase is ambiguous - in these cases, you do not know which haplotype you have, e.g. (wikipedia.org)
  • These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. (nygenome.org)
  • This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population. (nygenome.org)
  • These unusual haplotypes could represent hemizygous loci resulting from intragenic deletions. (bmj.com)
  • Within the remaining samples, 42 contained rare haplotypes that appeared to arise from changes in one out of five SNP loci in exon 11, potentially indicative of a partial deletion of the exon. (bmj.com)
  • The functional biological mechanisms behind the genetic association have started to emerge with differences recently shown in haplotype splicing of the neuropathologically relevant exon 10. (ox.ac.uk)
  • Haplotyping is imperative for comprehensive analysis of genomes, imputation of genetic variants and interpretation of error-prone single-cell genomic data. (biorxiv.org)
  • Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. (ox.ac.uk)
  • The major histocompatibility complex (MHC) is recognised as one of the most important genetic regions in relation to common human disease. (ox.ac.uk)
  • Extensive genetic polymorphism in the human tumor necrosis factor region and relation to extended HLA haplotypes. (ox.ac.uk)
  • A saturated map of common genetic variants associated with human height. (umassmed.edu)
  • Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids. (ox.ac.uk)
  • A few days ago I pointed to a paper which suggests the possible utility of looking at selection on standing genetic variation on quantitative traits to get a sense of the role of adaptation in the human genome. (discovermagazine.com)
  • The haplotype map, or "HapMap," is a tool that allows researchers to find genes and genetic variations that affect health and disease. (genome.gov)
  • Scientists are identifying, cataloging, and studying small genetic variations among humans that will lead to more specialized and effective medical treatments. (utah.edu)
  • Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. (nordiag.com)
  • Functional analysis of genetic variation in catechol-O-methyltransferase (COMT): effects on mRNA, protein, and enzyme activity in postmortem human brain. (snpedia.com)
  • PMID 16786032 ] Impact of complex genetic variation in COMT on human brain function. (snpedia.com)
  • Genetic bases of human complement C7 deficiency. (lu.se)
  • Class I and II human leukocyte antigens were determined by a standard microlymphocytotoxity test in a group of 45 pediatric patients with selective immunoglobulin A deficiency (IgA-D), 33 of them with frequent respiratory tract infections, allergic diseases, or gastrointestinal disorders (RTIAG), and 12 with celiac disease (CD). (nih.gov)
  • Of the few unusual haplotypes not in the canonical set, some are found in a genotype context that is similar to a genotype expected from a combination of a pair of canonical haplotypes, except that one or several polymorphic positions appear, unexpectedly, homozygous. (bmj.com)
  • Here we present a novel sequencing-based approach for whole-genome SNP typing of single cells, and determine genome-wide haplotypes, the copy number of those haplotypes as well as the parental and segregational origin of chromosomal aberrations from sequencing- and array-based SNP landscapes of single cells. (biorxiv.org)
  • Genome-wide detection and characterization of positive selection in human populations. (genome.gov)
  • Two important objectives are pursued: (1) the generation of reliable frequency estimates for Y-STR haplotypes and Y-SNP haplotypes to be used in the quantitative assessment of matches in forensic and kinship cases and (2) the characterization of male lineages to draw conclusions about the origins and history of human populations. (wikipedia.org)
  • These results indicate that the differential disease associations of these two DR3 haplotypes are due to sequence variation outside this central 158-kb segment, and that shuffling of ancestral blocks via recombination is a potential mechanism whereby certain DR-DQ allelic combinations, which presumably have favoured immunological functions, can spread across haplotypes and populations. (ox.ac.uk)
  • We also analyzed available genomic data from human populations, archaic hominins, and more distant primates. (ox.ac.uk)
  • 10. Ancient European Haplotype Enrichment in Modern Eurasian Populations. (upenn.edu)
  • Among the CD-IgA-D group, the B14 allele and A1, B8, Cw7, DR3, DQw2 haplotype were found to confer a high risk of developing IgA-D. A possible protective role may be postulated for DR2 and DR4 in both types of IgA-D patients. (nih.gov)
  • Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele. (wikipedia.org)
  • We performed allele-specific gene expression analysis on a H1/H2 heterozygous human neuronal cell line model and 14 H1/H2 heterozygous human post-mortem brain tissues from two brain regions. (ox.ac.uk)
  • Major Histocompatibility Complex Class I Chain-Related A and B (MICA and MICB) Gene, Allele, and Haplotype Associations With Dengue Infections in Ethnic Thais. (umassmed.edu)
  • The Y Chromosome Haplotype Reference Database (YHRD) is an open-access, annotated collection of population samples typed for Y chromosomal sequence variants. (wikipedia.org)
  • It is thought that identifying these statistical associations and a few alleles of a specific haplotype sequence can facilitate identifying all other such polymorphic sites that are nearby on the chromosome. (wikipedia.org)
  • To address this issue, we are employing a bacterial artificial chromosome (BAC) cloning strategy to sequence entire MHC haplotypes from consanguineous cell lines as part of the MHC Haplotype Project. (ox.ac.uk)
  • Analysis of the two DR3 haplotypes allowed delineation of the shared sequence between two HLA class II-related haplotypes differing in disease associations and the identification of at least one of the sites that mediated the original recombination event. (ox.ac.uk)
  • We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. (nordiag.com)
  • The promoters of the disease associated HLA-DR4 to the neutral DR7 and DR9 haplotypes were analyzed for sequence polymorphisms resulting in functional differences. (hu-berlin.de)
  • Members of the apolipoprotein gene cluster (APOA1/C3/A4/A5) on human chromosome 11q23 play an important role in lipid metabolism. (doe.gov)
  • Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. (nygenome.org)
  • We present 64 assembled haplotypes from 32 diverse human genomes. (nygenome.org)
  • Primate epigenetic evolution: An analysis of CpG island evolution in the human, chimpanzee, gibbon, and rhesus monkey genomes. (upenn.edu)
  • The close genomic locations of these two genes as well as their functional similarity have hindered efforts to define whether each gene independently influences human triglyceride concentrations. (doe.gov)
  • These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (wikipedia.org)
  • Our results highlight the need for new methods to analyze genomic variation because existing ones do not systematically consider local haplotypes. (biomedcentral.com)
  • 3 Interestingly, two BRCA1 haplotypes account for the bulk of the genotypes, the consensus at 59% frequency, and the most common non-consensus haplotype at 21% (fig 1). (bmj.com)
  • The frequency of the IC haplotype (shared between I75V and C159T) was 0.44 in DA + workers vs. 023 among DA- subjects (p=0.04). (cdc.gov)
  • The QC haplotype frequency (Q576R, C159T) of 0.667 in the DA + group was more frequent (0.425) than in the DA- groups (p=0.03). (cdc.gov)
  • Furthermore, the frequency of IQC haplotype (l75V, Q576R, C159T) was 0.44 in DA + workers vs. 0.217 in the DA - group (p=0.04). (cdc.gov)
  • In this paper we present observations in human whole genome data, human whole exome data and in mouse whole genome data to challenge this assumption. (biomedcentral.com)
  • Highly duplicated and polymorphic regions of the human genome such as the MHC are, however, somewhat refractory to some whole-genome analysis methods. (ox.ac.uk)
  • Two- and three-marker haplotypes from the 1q41 region similarly showed strong transmission distortion in the collection of 332 SLE families. (elsevierpure.com)
  • Complement C7 deficiency: seven further molecular defects and their associated marker haplotypes. (lu.se)
  • We have now established a new data pre-processing procedure to eliminate artifacts caused by a 5'-RACE library generation process, reanalyzed a previously studied data set defining human immunoglobulin heavy chain genes, and identified novel upstream regions, as well as previously identified upstream regions that may have been identified in error. (lu.se)
  • Structure of the human C7 gene and comparison with the C6, C8A, C8B, and C9 genes. (lu.se)
  • Among subjects of all racial ancestries enrolled in HIGS who reported early use of recombinant products (N = 223), mismatch in endogenous haplotype and the FVIII proteins constituting the products used did not confer greater risk for inhibitor development. (lu.se)
  • However, the functional roles of IL-8 gene haplotypes have not been investigated. (nih.gov)
  • To test whether ATC/TTC haplotype is functional, we used a trans-well assay to measure the transmigration of primary neutrophils incubated with supernatants from the Poly I:C stimulation experiment. (nih.gov)
  • ATC/TTC haplotype cells significantly increased transmigration of neutrophils confirming the functional role for this IL-8 haplotype. (nih.gov)
  • Certain coding sequences vary significantly between different haplotypes, making them candidates for functional and disease-association studies. (ox.ac.uk)
  • All three haplotypes carry as a second functional DRB gene the DRB4 gene, which is regulated by the DRB4A or -B promoter. (hu-berlin.de)
  • We introduce the technique of Local Haplotyping Analysis (LHA) which shows that evidence for heterogeneity is strong and directly observable in Next Generation Sequencing (NGS) data. (biomedcentral.com)
  • Human mobility patterns in Falbygden were studied by applying strontium isotope analysis combined with archaeological and bioarchaeological data, including mtDNA and sex assessment on a large dataset encompassing 141 individuals from 21 megalithic graves. (springer.com)
  • This group was selected for molecular analysis because of its abundance, representing 18% of the unusual haplotypes. (bmj.com)
  • Linkage disequilibrium maps: 'blocks' without haplotyping and application to disease mapping. (soton.ac.uk)
  • Because strong correlations exist between geographic areas and Y chromosomal variants, the YHRD population database was structured to display the geographic, linguistic and phylogenetic relationship of searched haplotype profiles. (wikipedia.org)
  • Ancestral background, specifically African descent, confers higher risk for development of inhibitory antibodies to factor VIII (FVIII) in haemophilia A. It has been suggested that differences in the distribution of FVIII gene (F8) haplotypes, and mismatch between endogenous F8 haplotypes and those comprising products used for treatment could contribute to risk. (lu.se)
  • The protein kinase complement of the human genome. (nordiag.com)
  • In both cell culture and post-mortem brain tissue, we show that the protective MAPT H2 haplotype significantly expresses two-fold more 2N (exons 2+3+) MAPT transcripts than the disease-associated H1 haplotype. (ox.ac.uk)
  • Omega-3 and omega-6 long-chain polyunsaturated fatty acids (LC-PUFAs) are essential for the development and function of the human brain. (ox.ac.uk)
  • This human-specific haplotype increases the efficiency of synthesizing essential long-chain fatty acids from precursors and thereby might have provided an advantage in environments with limited access to dietary LC-PUFAs. (ox.ac.uk)
  • The detailed balance of demographic, stochastic and selective parameters in shaping human evolution in a general and regionally specific sense are still to be worked out. (discovermagazine.com)
  • They found that specific MLH1 haplotypes were associated with the presence and family history of the disease in both CD and UC. (bmj.com)
  • Cell-type specific and multiscale dynamics of human focal seizures in limbic structures. (medscape.com)
  • In this approach, unphased SNP genotypes are compared to pairs of canonical haplotypes to identify potentially hemizygous regions. (bmj.com)
  • Among these samples, 14 were identified with rare haplotypes created by a change at the SNP in exon 16 (fig 1), suggestive of a possible deletion of this exon. (bmj.com)
  • The more efficient, evolutionarily derived haplotype appeared after the lineage split leading to modern humans and Neanderthals and shows evidence of positive selection. (ox.ac.uk)
  • The term ' haplogroup ' refers to the SNP/ unique-event polymorphism (UEP) mutations that represent the clade to which a collection of particular human haplotypes belong. (wikipedia.org)
  • Haplotype 3 was associated with higher inhibitor risk among those genetically identified (N = 49) as of African ancestry, but the association did not remain significant after adjustment for F8 mutation type and the HLA variables. (lu.se)
  • However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals. (wikipedia.org)
  • Clade here refers to a set of haplotypes sharing a common ancestor. (wikipedia.org)
  • This patient shared common haplotypes with the recent families studied. (medscape.com)
  • However, these could also be bona fide haplotypes that are too rare to be represented in the canonical set, resulting from recombinations between common haplotypes, or single base changes. (bmj.com)
  • In humans, aneuploidy would be any number of chromosomes other than the usual 46. (genome.gov)
  • An expectation maximisation based prediction algorithm was created to identify unusual haplotypes in patient samples that may be caused by small intragenic deletions. (bmj.com)
  • These results indicate that CQ-resistant haplotype P. falciparum malaria parasites are present in Haiti. (cdc.gov)
  • Here we present 4.25 Mb of the human haplotype QBL (HLA-A26-B18-Cw5-DR3-DQ2) and compare it with the MHC reference haplotype and with a second haplotype, COX (HLA-A1-B8-Cw7-DR3-DQ2), that shares the same HLA-DRB1, -DQA1, and -DQB1 alleles. (ox.ac.uk)
  • Granted, we can start with the assumption that on the order of 50,000 years before the present there was a rapid demographic expansion of anatomically modern humans out of the continent of Africa. (discovermagazine.com)
  • The microtubule-associated protein tau (MAPT) H1 haplotype shows a strong association to the sporadic neurodegenerative diseases, progressive supranuclear palsy and corticobasal degeneration. (ox.ac.uk)
  • The submissions are then registered to the public database, where the entries are retrievable by Search for haplotypes, contributors or accession numbers. (wikipedia.org)