• We previously identified a ~1.5 Mb locus on canine chromosome 27 associated with CAD in German shepherd dogs (GSDs). (biomedcentral.com)
  • Linkage studies have identified several quantitative trait loci (QTLs) for RD. The QTL on chromosome 6p21.3 has been independently replicated by several groups and spans a 16.4-Mb (13.8 cM) interval from D6S109 to D6S291. (nih.gov)
  • In addition, we identify common X-chromosome loci at IGSF1 (rs762080, P =9.4 × 10 −13 ) and FAAH2 (rs5914101, P =4.9 × 10 −10 ). (nature.com)
  • On the whole, a susceptibility locus for disc herniation and autosomal recessive spastic paraplegia was found on chromosome 6q23.3-q24.1. (bmj.com)
  • The structure of female (mtDNA) and male (Y-chromosome haplotypes) lineages in the Yakut population was examined. (blogspot.com)
  • The search led to a haplotype falling in a chromosome 4 locus that's undergone balancing selection early in the human lineage. (genomeweb.com)
  • After accounting for known malaria risky loci and other potential confounders such as parasite diversity, they narrowed in on a suspicious new chromosome 4 site falling between the FREM3 gene and the GYPE, GYPB, and GYPA genes, which code for glycophorin proteins expressed in the red blood cell membrane. (genomeweb.com)
  • 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)
  • For example, consider a diploid organism and two bi-allelic loci (such as SNPs ) on the same chromosome. (wikipedia.org)
  • A genome-wide linkage search in family F1 identified a 6.5 Mb locus for this disorder on chromosome 16q23.2-24.1. (molvis.org)
  • The higher risk of SLE in women and men with Klinefelter syndrome may be associated with enhanced expression of toll-like receptor 7 (TLR7), a key pathogenic factor in SLE that is encoded on an X chromosome locus. (medscape.com)
  • 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)
  • Sixteen single-nucleotide polymorphisms (SNPs) were genotyped at and around the G72/G30 locus, which covered a 157-kb region encompassing the entire complementary DNA sequences of G72 and G30. (nih.gov)
  • Although statistically significant association was not detected for individual SNPs in the NIMH data set, the same haplotype was consistently overtransmitted in both series. (nih.gov)
  • There are two main ways that the term "haplotype block" is defined: one based on whether a given genomic sequence displays higher linkage disequilibrium than a predetermined threshold, and one based on whether the sequence consists of a minimum number of single nucleotide polymorphisms (SNPs) that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of unique haplotypes). (wikipedia.org)
  • proposed the following definition of the term: "Suppose we have a number of haplotypes consisting of a set of consecutive SNPs. (wikipedia.org)
  • The objectives of this study are to evaluate the association of the genotype and haplotype distributions of three single-nucleotide polymorphisms (SNPs) (G-217A, A-6G, and M235T) in the AGT gene with hypertension. (tmu.edu.tw)
  • Three SNPs from each QTL region were used for haplotype association analysis. (usda.gov)
  • We performed transmission/disequilibrium testing (TDT) and haplotype analysis, since a linkage-disequilibrium block was present at this gene locus. (nih.gov)
  • According to the haplotype-block model, such blocks should show high levels of linkage disequilibrium and be separated from one another by numerous recombination events. (wikipedia.org)
  • These loci, corresponding to seven genomic regions based on linkage disequilibrium decay distance, explained 9.3 to 26.0% of the total phenotypic variation. (unboundmedicine.com)
  • This was confirmed when linkage analysis showed that family F2 also mapped to the 16q locus. (molvis.org)
  • We applied a strategy to identify predisposition loci for breast cancer by using mathematical models to identify early somatic genetic deletions in tumor tissues followed by targeted linkage analysis. (lu.se)
  • The results were further evaluated by simulation to assess the probability of obtaining significant evidence in favor of linkage by chance as well as to take into account the possible influence of the BRCA2 locus, located at a recombination fraction of 0.25 from the new locus. (lu.se)
  • Haplotype analysis, linkage disequilibrium, and homozygosity mapping indicated that HLA-DQ/DR is the major IGAD1 locus, and suggest the autoimmune pathogenesis of IgAD/CVID. (lu.se)
  • No single causative variant alone, but rather multiple variants combined in a risk haplotype likely contribute to an altered expression of the PKP2 gene, and possibly nearby genes, in immune and epithelial cells, and predispose GSDs to CAD. (biomedcentral.com)
  • Marker associations were detected in five of the ten genes, results that were corroborated by our haplotype TDT analysis. (nih.gov)
  • After the exclusion of type II collagen and vitamin D receptor genes and the recessive loci for HSPs, a genome wide search was performed with about 500 fluorescent markers. (bmj.com)
  • We investigated the patterns of genetic differentiation in two mitochondrial DNA genes (cyt- b and ND2) and eight microsatellite loci among and within colonies of A. fuciphagus from across recently established man-made colonies in Thailand. (bioone.org)
  • NEW YORK (GenomeWeb) - The severity of malaria infections caused by Plasmodium falciparum in African children appears to be partly influenced by a locus falling near genes coding for glycophorin proteins involved in red blood cell invasion. (genomeweb.com)
  • This new resistance locus is particularly interesting because it lies so close to genes that are gatekeepers for the malaria parasite's invasion machinery," co-corresponding author Dominic Kwiatkowski, with the Wellcome Trust Sanger Institute and the Wellcome Trust Centre for Human Genetics, said in a statement. (genomeweb.com)
  • By scouring other regions in the genome that have reportedly undergone balancing selection events, meanwhile, the researchers identified half a dozen other variants with less pronounced ties to malaria that fell near genes belonging to ancient balanced polymorphism haplotypes. (genomeweb.com)
  • A genome-wide study in a northern European population replicated the association of SLE with susceptibility genes related to B-cell receptor pathway signaling, as well as confirmed the association of SLE with genes at the interferon regulatory factor 5 (IRF5)-TNPO3 locus. (medscape.com)
  • These results highlight the necessity of a thorough analysis of all reported variants of a candidate gene in the elucidation of genetic susceptibility to a complex disease like hypertension, even when the variants are in the same haplotype block. (tmu.edu.tw)
  • Haplotype variants of QTL QYr.sicau-2BS showed subspecies-specific inheritance of the stripe rust resistance locus. (unboundmedicine.com)
  • In one of the Nature articles-"A global reference for human genetic variation"-the 1000 Genomes Project identified "over 88 million variants (84.7 million single nucleotide polymorphisms, 3.6 million short insertions/deletions, and 60,000 structural variants), all phased onto high-quality haplotypes. (genengnews.com)
  • We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. (genengnews.com)
  • This study also uncovered appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. (genengnews.com)
  • A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31. (karmastudy.org)
  • From a genetic point of view, little information has so far been available on possible susceptibility loci. (bmj.com)
  • The single nucleotide polymorphism microarray analysis excluded a shared founder haplotype between the families and refined the locus to 3.1 Mb. (molvis.org)
  • Dutch myotonic dystrophy type 2 patients and a North-African DM2 family carry the common European founder haplotype. (cdc.gov)
  • Two alleles were found at this locus, D17Tu5 a and D17Tu5 b , defined by Taq I restriction fragment length polymorphism. (psu.edu)
  • Overall estimates of interpopulation variance in microsatellite alleles ( F ST = 0.011 ) and mtDNA haplotypes ( Φ ST = 0.126 ) were low and not significantly different from zero. (usgs.gov)
  • A haplotype ( haploid genotype ) is a group of alleles in an organism that are inherited together from a single parent. (wikipedia.org)
  • To obtain a more complete picture of the PGx alleles present in a diverse US population, approximately 5,000 DNA samples from the population-based NHANES will be tested to determine the PGx allele frequencies of 970 unique haplotypes in 150 pharmacogenes. (cdc.gov)
  • To determine mtDNA haplotypes, sequencing of hypervariable segment I and typing of haplotype-specific point substitutions in the other parts of the mtDNA molecule were performed. (blogspot.com)
  • Chromosomes of haplogroup N3 displayed the presence of 19 microsatellite haplotypes, the most frequent of which encompassed 54% chromosomes of this haplogroup. (blogspot.com)
  • The microsatellite haplotypes within HG were constructed using 7 STR loci. (blogspot.com)
  • Based on analysis of microsatellite haplotypes within main Y- chromosomal haplogroups, molecular diversity within monophyletic lineages were calculated and phylogenetic trees for most common haplogroups were reconstructed. (blogspot.com)
  • B. burgdorferi is transmitted to humans disequilibrium among genetic loci can result from several during the blood meal of an infected Ixodes tick, predomi- evolutionary and ecologic forces in addition to small popu- nantly Ixodes scapularis in North America ( 2 ). (cdc.gov)
  • One hundred and six genomic loci for this highly heritable trait have been mapped by genome-wide association studies (GWAS), implicating many previously unsuspected mechanisms 1 . (nature.com)
  • We used eight microsatellite DNA loci and mitochondrial DNA control-region sequence data to assess population structure of Northern Goshawks breeding in Utah. (usgs.gov)
  • genotypes from these divergent haplotypes can be used in pea resistance breeding to avoid genetic homogeneity and genetic vulnerability. (nature.com)
  • In the former scenario, reproductive isolation may be unlikely to evolve because the chance that loci under divergent selection will be linked to a trait that causes reproductive isolation is slim, and a genome-wide correlated response to divergent selection is lacking 16 , 17 . (biorxiv.org)
  • 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)
  • We analysed the association of these factors with Hb F levels in 112 SS patients living in France who are homozygous for the three common African β-globin haplotypes (Benin, Bantu or Central African Republic and Senegal). (johnshopkins.edu)
  • On the basis of likelihood ratio test, only the set of haplotypes that constituted the A-6G and the M235T polymorphisms was associated with hypertension (χ 2 = 20.91, P = 0.0008), which was mainly due to the increased frequency of the recombinant haplotypes (-6A ≡ 235M and -6G ≡ 235T), and a pathophysiological role in the predisposition to hypertension was hence indicated. (tmu.edu.tw)
  • So far, 16 loci have been identified, both on autosomal and X chromosomes. (bmj.com)
  • The total part of the lineages of western Eurasian origin ("Caucasoid") was about 6% (4 haplotypes, haplogroups H, J, and U). Most of Y chromosomes in the Yakut population (87%) belonged to haplogroup N3 (HG16), delineated by the T-C substitution at the Tat locus. (blogspot.com)
  • Five quantitative trait loci (QTLs) on chromosomes 1A, 2B, 7B, and 7D overlapped or were in close proximity to previously reported QTLs based on the consensus and physical maps using the reference sequence of bread wheat (IWGSC RefSeq v1.0). (unboundmedicine.com)
  • The haploid genotype (haplotype) is a genotype that considers the singular chromosomes rather than the pairs of chromosomes. (wikipedia.org)
  • 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)
  • This group was selected for molecular analysis because of its abundance, representing 18% of the unusual haplotypes. (bmj.com)
  • Analysis of the decay of haplotype sharing gave a location estimate that included G72/G30 in its 95% confidence interval. (nih.gov)
  • Marker-trait associations were assessed by using QTDT (a general test of association for quantitative traits) and the family-based association test (FBAT), and haplotype analysis was performed by using FBAT and the GeneHunter Transmission/Disequilibrium Test TDT. (nih.gov)
  • Epub 2011 Aug 17) and in the targeted analysis of JAK2 risk locus. (mskcc.org)
  • Locus refinement was undertaken with single nucleotide polymorphism (SNP) microarray analysis. (molvis.org)
  • Haplotype analysis of the myotonic dystrophy type 1 (DM1) locus in the Korean population. (cdc.gov)
  • Genetic analyses included a genome-wide association study (GWAS), haplotype assessment, and a risk profile analysis using cumulative genetic risk scores. (lu.se)
  • To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). (mdpi.com)
  • Therefore, we investigated the 17 Yfiler Y-STRs in 1,730-1,764 DNA-confirmed father-son pairs per locus and found 84 sequence-confirmed mutations among the 29,792 meiotic transfers covered. (springer.com)
  • Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. (lu.se)
  • These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (wikipedia.org)
  • Thus, at least three QTL (quantitative trait loci) for BCWD resistance were validated in the 2015TLUM generation. (usda.gov)
  • Three haplotypes, Omy3TGG, Omy8GCG and Omy25CGG, were found to be associated with BCWD resistance in the 2015TLUM generation. (usda.gov)
  • Retrospective analyses were then performed to evaluate the accuracy of MAS for BCWD resistance using these three favorable haplotypes. (usda.gov)
  • The phenotypic datasets were used for 55K single-nucleotide polymorphism (SNP) array-based genome-wide association studies to identify effective resistance loci. (unboundmedicine.com)
  • Resistant loci among Chinese endemic wheat germplasms could be introduced into common wheat cultivars, and the high-confidence SNP markers will aid in marker-assisted selection in breeding for stripe rust disease resistance. (unboundmedicine.com)
  • The locus proved to be polymorphic among inbred strains and wild mice. (psu.edu)
  • DNA samples of the affected members of our cohort of USH families were tested using an USH genotyping array, and/or genotyped with polymorphic markers specific for the USH3A locus. (molvis.org)
  • In genetics, a haplotype block is a region of an organism's genome in which there is little evidence of a history of genetic recombination, and which contain only a small number of distinct haplotypes. (wikipedia.org)
  • By testing of recombinant inbred strains and partial t haplotypes, the D17Tu5 locus could be mapped to a position between the D17Leh66E and D17Rp17 loci within the t complex. (psu.edu)
  • Sex-determining regions (SDRs) or mating-type (MT) loci in two sequenced volvocine algal species, Chlamydomonas reinhardtii and Volvox carteri, exhibit major differences in size, structure, gene content, and gametolog differentiation. (wustl.edu)
  • These data begin to polarize important changes that occurred in volvocine MT loci, and highlight the potential for discontinuous and dynamic evolution in SDRs. (wustl.edu)
  • Three such regions are the major histocompatibility complex (MHC), sex-determining regions (SDRs) and the plant self-incompatibility locus (S-locus). (lu.se)
  • Despite these findings, SP remains a explored emerging lineages of dhps mutant haplotypes in Malawi,theDemocraticRepublicoftheCongo,andTanza- major tool for malaria control when administered as a partner niabyusinganalysesofgeneticmicrosatellitesflankingthe drug with artemisinins and as intermittent preventive therapy dhps locus. (cdc.gov)
  • Haplotypes within haplogroups were analyzed with seven microsatellite loci. (blogspot.com)
  • 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)
  • We, therefore, targeted this research to find the pathogen-resistant pea lines and further decipher the diversity at er locus among resistant pea lines. (nature.com)
  • The level of genetic diversity for microsatellite loci was high, but FST values were not significant. (bioone.org)
  • This discovery increased the likelihood that the unusual haplotype in this sample, and perhaps others in this group, were the result of intragenic deletions, and not just recombination. (bmj.com)
  • Additional genotyping and association analyses in GSDs combined with control dogs from five breeds with low-risk for CAD revealed the top SNP 27:19,086,778 ( p = 1.4 × 10 −7 ) and a rare ~48 kb risk haplotype overlapping the PKP2 gene and shared only with other high-risk CAD breeds. (biomedcentral.com)
  • Analyses of haplotype relationships did not show genetic structure across the sampled distribution. (bioone.org)
  • Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. (lu.se)
  • 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)
  • 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)
  • We reveal that repeated ecological and morphological diversification along a common environmental axis is associated with both genome-wide allele frequency shifts and a specific, larger effect, locus, associated with the gene edar . (biorxiv.org)
  • Genome-wide association studies have identified more than 100 genetic loci for SLE susceptibility across populations, with most of the genetic risk shared across borders and ethnicities. (medscape.com)
  • In addition, we nominate an unconfirmed and potentially population-specific genome-wide significant association in the PLPP4 locus (rs12771445). (lu.se)
  • Molecular studies revealed that the Erysiphe resistant ( er1 ) gene was present in 40 lines out of selected 50 pea lines and the mutational character was conferred up to 36 genotypes with 11 haplotype groups. (nature.com)
  • These resistant lines have er ( Erysiphe resistant) locus having MLO gene (responsible for resistant mechanism in pea) which was detected using various molecular approaches. (nature.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)
  • In addition to verifying this association in another 14,000 African individuals, the team estimated that individuals with a protective version of the haplotype are roughly 33 percent less likely to suffer from severe malaria than their counterparts without it. (genomeweb.com)
  • The protective, derived version of the allele at this locus was more common in East Africa, the study's authors noted, and showed the most pronounced ties to malaria in the Kenyan population. (genomeweb.com)
  • Medians from Bayesian estimation of locus-specific mutation rates ranged from 0.0003 for DYS448 to 0.0074 for DYS458, with a median rate across all 17 Y-STRs of 0.0025. (springer.com)
  • [8] A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation . (wikipedia.org)
  • Five factors have been hypothesized to influence the 20-fold variation in fetal haemoglobin (Hb F) levels in sickle cell anaemia (SS): age sex, α-globin gene number, β-globin haplotype, and the X-linked F-cell production locus (FCP) that regulates the production of Hb F containing erythrocytes (F cells). (johnshopkins.edu)
  • We found that: (1) FCP accounts for about 40% of the overall variation in Hb F levels, (2) when the FCP influence is removed, β-globin haplotype is associated with 14% of the remaining Hb F variation, and (3) the other factors have little influence. (johnshopkins.edu)
  • We now need to drill down at this locus to characterize these complex patterns of genetic variation more precisely and to understand the molecular mechanisms by which they act," Kwiatkowski added. (genomeweb.com)
  • Goshawks had moderate levels of genetic variation at microsatellite loci (observed heterozygosity = 50%), similar to levels found in other medium-sized, highly mobile birds. (usgs.gov)
  • In this approach, unphased SNP genotypes are compared to pairs of canonical haplotypes to identify potentially hemizygous regions. (bmj.com)
  • Genetic Variability and Structure of SNP Haplotypes in the DMPK Gene in Yakuts and Other Ethnic Groups of Northern Eurasia in Relation to Myotonic Dystrophy]. (cdc.gov)
  • At least two P. falciparum proteins bind host blood cells via interactions with the glycophorin proteins Glycophorin A and Glycophorin B, the team noted, consistent with a potential role for the glycophorin locus in helping to dodge severe malaria infection. (genomeweb.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)
  • 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)
  • In functional assays, the promoter activities of the haplotypes -217A ≡ -6A and -217G ≡ -6G were significantly higher than the most common haplotype -217G ≡ -6A. (tmu.edu.tw)
  • Clade here refers to a set of haplotypes sharing a common ancestor. (wikipedia.org)
  • Lyme disease, caused by the bacterium Borrelia burg- Genetic loci are found in perfect or near-perfect association dorferi , is the most common vector-borne disease in the in B. burgdorferi in the Northeast ( 9-12 ). (cdc.gov)
  • Here, we determined the sequences of the minus and plus MT haplotypes of the isogamous 16-celled volvocine alga, Gonium pectorale, which is more closely related to the multicellular V. carteri than to C. reinhardtii. (wustl.edu)
  • The B gene expressed at each locus in each line had unique DNA sequences from the B gene expressed in other lines. (usda.gov)
  • The results warrant studies of this putative breast cancer predisposition locus in other populations. (lu.se)
  • Understanding the origin of these differences requires investigation of MT loci from related species. (wustl.edu)
  • 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 accuracies of MAS using these two haplotypes together were consistently around 0.5, which was equal or greater than the accuracy of the conventional family-based selection in the same generation. (usda.gov)
  • All complete t haplotypes tested carry the D17Tu5 a allele and all tested wild mice of the species M. musculus, with the exception of those bearing t haplotypes, carry the D17Tu5 b allele. (psu.edu)
  • These gene loci are deleted in mice having the a (e.g. (bdbiosciences.com)
  • However, some evidence suggests that different algorithms for identifying haplotype blocks give very different results when used on the same data, though another study suggests that their results are generally consistent. (wikipedia.org)
  • The National Institutes of Health funded the HapMap project to catalog haplotype blocks throughout the human genome. (wikipedia.org)