• populations
  • Because haplotypes are highly likely to be preserved in populations, there are several algorithms for attempting to conduct pseudo-phasing on large number of unrelated people. (snpedia.com)
  • This can lead to over-estimation of the risk by including odds ratio of different SNP's along same haplotype, or flip-flop phenomenon where the effect of the SNP is opposite in different populations due to population-dependent variation in the haplotype. (snpedia.com)
  • Haplotype analyses revealed modest effects on susceptibility to prostate cancer across populations. (nih.gov)
  • Haplotype GGCC conferred increased risk in the African American and Nigerian populations. (nih.gov)
  • Haplotype convergence is the unrelated appearance of identical haplotypes in separate populations, through either convergent evolution or random chance. (wikipedia.org)
  • The members of this haplotype are found in high numbers in Anatolia and Armenia, with smaller numbers throughout Central Asia, the Middle East, the Balkans, the Caucus Mountains, and in Jewish populations. (wikipedia.org)
  • 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)
  • The submissions are then released to the public database, where the entries are retrievable by Search for haplotypes, populations, contributors or accession numbers. (wikipedia.org)
  • In the Dutch and German populations B-DR haplotypes have undergone more intense studies allowing the detection of haplotypes to very low frequencies (0.25% in the Dutch and 0.05% in the Germans) consequently the edge of B18-DR3 haplotype in Europe is evident. (wikipedia.org)
  • 2000
  • The MHC Haplotype Project was conducted between 2000 and 2006 at the Sanger Institute and offers a framework and resource for association studies of all MHC-linked-diseases. (ucl.ac.uk)
  • 2000) observed that the haplotype is of likely paleo North African origin, and later studies of North Africa support that finding. (wikipedia.org)
  • loci
  • These GRC haplotype contigs, called 'alternate loci', are constructed so that they begin with additional anchor sequence derived from the reference. (ucl.ac.uk)
  • 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 don't know which haplotype you have, e.g. (wikipedia.org)
  • gene
  • It provides the genomic sequences and gene annotation of 8 different HLA-homozygous typing haplotypes (listed below), their resulting variations (see Data below) and ancestral relationships. (ucl.ac.uk)
  • COX-2 gene promoter haplotypes and prostate cancer risk. (nih.gov)
  • β-globin gene cluster haplotypes in sickle cell patients from Panamá. (biomedsearch.com)
  • OBJECTIVE: To analyze the frequency of the haplotypes of β-globin gene cluster in randomly selected patients with sickle cell disease (SCD), attended in the Children's Hospital of Panama. (biomedsearch.com)
  • Fast forward into the future, and the gene pool will be dominated by the closely related haplotypes of the "adopters" and the haplotypes of the "non-adopters" will stand out in the total population as oddities. (blogspot.com)
  • We employed SNP, haplotype, and multiple-gene analysis to evaluate associations. (biomedsearch.com)
  • In some regions, due to low diversity in the Y-STR gene (often used to study surname origin), haplotype convergence may confuse analyses, concluding unrelated individuals to be very closely related. (wikipedia.org)
  • As an example of haplotype convergence due to convergent evolution in more distantly related groups, threespine stickleback in blackwater environments similar to that of the ancient bluefin killifish and black bream independently evolved the same haplotype in the SWS2 gene, which promotes better eyesight in those conditions. (wikipedia.org)
  • Preimplantation genetic haplotyping (PGH) is a clinical method of preimplantation genetic diagnosis (PGD) used to determine the presence of single gene disorders in offspring. (wikipedia.org)
  • allele
  • However, in the case of the Germans the Cw allele was not typed so it is undetermined whether the haplotype is of the 'Basque' variant or the ancestral 'Sardinian' type, In addition in Sardinia the A30 serotype has never been resolved by high resolution genetyping and therefore the A*3002 has not been confirmed. (wikipedia.org)
  • clade
  • To ensure that a group of Y-chromosomes are part of a clade, you must ensure that other Y-chromosomes have an even greater genetic distance than 3, so great indeed, that it is extremely unlikely that they are closely related to any Y-chromosomes in the haplotype cluster. (blogspot.com)
  • But, any test that would identify these haplotypes as descendants of the "founder" node, despite 4 generations of mutations, would also erroneously identify all the smallcase nodes, also at most 4 generations away from the "founder" as members of the clade. (blogspot.com)
  • A haplotype cluster centered on a presumed founder who lived g generations ago will invariably include a set of Y chromosomes that do not form a clade. (blogspot.com)
  • Whereas a clade includes all the descendants of a single founder, a haplotype cluster will invariably include many men who are g generations away from the founder, whether they are his descendants or not. (blogspot.com)
  • 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)
  • Clade here refers to a set of haplotypes sharing a common ancestor. (wikipedia.org)
  • markers
  • Results: To improve the accuracy of population assignment, we present an algorithm, implemented in the HaploPOP software, that combines markers into haplotypes, without requiring independence. (diva-portal.org)
  • The algorithm is based on the Gain of Informativeness for Assignment that provides a measure to decide if a pair of markers should be combined into haplotypes, or not, in order to improve assignment. (diva-portal.org)
  • The use of the microsatellite markers D6S260, D6S89 and D6S274 provided evidence that the expanded SCA1 repeats segregated with three distinct haplotypes in the six families. (springer.com)
  • Erroneously determining two individuals do be identical due to haplotype convergence becomes much less likely when more genetic markers are tested, since that would require a larger amount of extremely rare coincidences. (wikipedia.org)
  • This examination of generational variation then allows for a haplotype of genetic markers statistically associated with the target disease to be identified, rather than searching merely for a mutation. (wikipedia.org)
  • This locus in part of the HLA A1-B8-DR3-DQ2 haplotype (markers are A1, CW7, B8, BfS, C4AQ0, C4B1, DR3, DQ2) therefore one study concluded that C4AQ0 could explain the increased infectivity to HIV. (wikipedia.org)
  • haplogroups
  • Similarly, a study of New World mitochondrial DNA haplogroups observed that similarities in haplotypes between Native Americans and Asians were a result of the hypervariability of the HVSI region in mitochondrial DNA, rather than common ancestry. (wikipedia.org)
  • Chromosomal
  • Because strong correlations between geographic areas and Y chromosomal variants exist, the YHRD population database was structured to display the geographic, linguistic and phylogenetic relationship of searched haplotype profiles. (wikipedia.org)
  • phenotype
  • Ex vivo PK136 (anti-NK1.1) stimulation assays indicated that licensing may not be a binary phenomenon as some Ly49A-MHC class I haplotype combinations produced an intermediate licensing phenotype. (jimmunol.org)
  • However, some of this reaction can be attributed to the linkage of the HLA A1-B8-DR3-DQ2 haplotype to the IgA-less phenotype. (wikipedia.org)
  • generations
  • While a UEP at the founder defines a watershed moment, separating the founder's descendants (who possess the UEP derived state) from his other relatives (who do not), Y-STRs do not define such a moment: node "m", a cousin of the founder, will possess a haplotype that is 4-generations removed from the "founder", just as node "Q" who is a great great grandson. (blogspot.com)
  • probability
  • However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals. (wikipedia.org)
  • Substitution bias further increases the likelihood of haplotype convergence, as this increases the probability of mutations occurring at the same site. (wikipedia.org)
  • sequence
  • For single nucleotide polymorphisms 'variation' consists of two letters, firstly, the base in the reference sequence, and secondly, the base in the other haplotype. (ucl.ac.uk)
  • Here, we used DNA sequences from the SRK and SCR genes of the wild Brassica species Brassica cretica , together with publicly available sequence data from other Brassicaceae species, to investigate the evolutionary relationships among S haplotypes in the Brassicaceae family. (genetics.org)
  • Haplotype convergence is rare, due to the sheer odds involved of two unrelated individuals independently evolving the exact same genetic sequence in the site of interest. (wikipedia.org)
  • genes
  • A haplotype map is thus created, not only exhibiting genes the offspring will contain, but also the parental origin of the genes. (wikipedia.org)
  • cluster
  • Suppose you identify a cluster of haplotypes, and every pair of them has a genetic distance of at most 3. (blogspot.com)
  • First, it must be shown that the genetic distance between any haplotype in the cluster and any other haplotype (not in the cluster), must be greater than 3. (blogspot.com)
  • Suppose you have identified a cluster of haplotypes {a, b, c} and dist( a , b )=3. (blogspot.com)
  • Needless to say, none of the folks who propose various "clades" on the basis of Y-STR haplotypes have bothered to prove that their haplotype clusters share a common ancestor that is more recent than that between cluster members and non-cluster members. (blogspot.com)
  • Second , suppose that you have identified a very distinctive haplotype cluster that addresses the first concern. (blogspot.com)
  • Suppose that every pair of haplotypes within this cluster is within a short genetic distance (e.g., 3) and very far from any other haplotype (e.g., more than 15). (blogspot.com)
  • The AMH 1.15 set of haplotypes is also referred to as the Atlantic modal cluster or AMC. (wikipedia.org)
  • thus
  • Next Gen Sequencing can thus provide not only perfectly phased genome, but also a haplotype map which can be used to impute untested SNP's from nearby known ones. (snpedia.com)
  • Haplotypes are important for example because many of the SNP's found by genome-wide association studies aren't the true cause but simply occur on same haplotype and are thus inherited together. (snpedia.com)
  • human
  • 31,500 sequenced whole genomes, aggregated over 20 studies of predominantly European ancestry, to create a very large reference panel of human haplotypes where ~50M genetic variants are observed 5 or more times. (ashg.org)
  • The AMH is the most frequently occurring haplotype amongst human males in Atlantic Europe. (wikipedia.org)
  • detect
  • For any collection of haplotypes, the first step should be to calculate the distribution of pairwise distances to detect outliers. (blogspot.com)
  • It is perhaps possible to devise a test that would be able to detect all these haplotypes as related. (blogspot.com)
  • estimates
  • Estimates within J1 [6.5kybp(4K-12K)] and J2 [13kybp(7K-27K)] were substantially deeper than previous figures obtained from a heavily weighted Jewish sampling, indicating a likely origin of the compound haplotype prior to the establishment of the Hebrew population. (blogspot.com)
  • This method used a Gibbs sampling approach in which each individuals haplotypes were updated conditional upon the current estimates of haplotypes from all other samples. (wikipedia.org)
  • These methods iteratively update the haplotype estimates of each sample conditional upon a subset of K haplotype estimates of other samples. (wikipedia.org)
  • variants
  • Our full resource is available to the community through imputation servers that enable scientists to impute missing variants in any study and respect the privacy of subjects contributing to the studies that constitute the Haplotype Reference Consortium. (ashg.org)
  • Haplotype information contributes to the understanding of the potential functional effects of variants in cis or in trans. (wikipedia.org)
  • among
  • Ly49A surface accessibility, a measure of cis binding with MHC class I, and Ly49A tetramer binding displayed a similar variability among the MHC haplotypes. (jimmunol.org)
  • By October 2017 more than 197,000 9-locus haplotypes, among them 145,816 17-locus haplotypes, 39,414 23-locus haplotypes, 22,832 27-locus haplotypes and 20,495 Y SNP profiles sampled at 1128 locations in 133 countries have been directly submitted by more than 300 institutes and laboratories. (wikipedia.org)
  • mainly
  • A large number of S haplotypes have been identified, mainly in cultivated species of the Brassica and Raphanus genera, but recently also in wild Arabidopsis species. (genetics.org)
  • independently
  • The first proposes that after the Arabidopsis/Brassica split, diversification of S haplotypes took place independently in the two descendant lineages. (genetics.org)
  • distinct
  • Once the chromosomes have been isolated and amplified any molecular haplotyping can be applied as long as the chromosomes remain distinct. (wikipedia.org)
  • species
  • This is a simplistic description of the general mechanism of SI, which is more complicated, and in some species the S-haplotype contains more than two protein coding regions. (wikipedia.org)