Frequencies of haplotypes. Medical search. Frequent questions

Underlying this move was the HLA A1-B8-DR3-DQ2 haplotype, a haplotype that is in acute linkage disequilibrium in the European population. (wikipedia.org)
Two-point haplotype analysis between TNFB(B*01 allele) and HLA show that the allele is in linkage disequilibrium with HLA-A1, Cw7, B8, C4A(Null), DR3, DQ2.5. (wikipedia.org)
celaoforever/SHEsisPlus: a software package for analysis of genetic association, Hardy-weinberg equilibrium, linkage disequilibrium and haplotype construction at multiallelic polymorphism loci, compatible for both diploid and polyploid species. (github.com)
Linkage disequilibrium between markers was calculated and estimated haplotype frequencies were compared between groups. (lww.com)

Genotype frequencies of each SNP were compared according to the XFS phenotypes. (molvis.org)
There was no significant association between the genotype frequencies of the three SNPs and the XFS phenotypes. (molvis.org)
There was no significant difference in allele and genotype frequencies of +276G>T between type T2DM patients and controls. (who.int)

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)
We assert that the stability of whole genome adaptation is reflected in the frequencies of maintained diversity in these common variants (SNPs) for a population in its environment. (scirp.org)
As dynamic sites in the human genome, SNPs are often highly correlated into combinations referred to as haploblocks whose haplotypes are maintained throughout generations with fixed frequencies within a given population. (scirp.org)
Therefore, the dynamically independent statistical genomic units we use are SNP haplotypes together with alleles within SNP sites that are not in contiguous LD with any other SNPs. (scirp.org)
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)
ABSTRACT This study aimed to estimate the frequency of the SNPs (+45T>G and +276G>T) genotypes and investigate the association between the two SNPs and adiponectin concentration, metabolic parameters and risk of T2DM in the Bahraini population. (who.int)

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)

Stable Y-chromosomal polymorphism is difficult to reconcile with haplotype frequency variations without assuming frequency-dependent selection or specific interactions in the population dynamics of X- and Y-chromosomal genes, since otherwise the fittest haplotype would inevitably sweep to fixation. (oregonstate.edu)
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)
[8] A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation . (wikipedia.org)

This haplotype is 4.7 million nucleotides in length and the second longest haplotype identified within the human genome. (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)
These advances are adding value to short-read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. (lu.se)

This reflects that certain SNP allelic combinations never appear within the population, implying that only certain haplotypes are biologically viable and generationally maintained. (scirp.org)
These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (wikipedia.org)

The haplotype can be written in an extended form covering the major histocompatibility loci as follows: HLA A*01:01 : Cw*07:01 : B*08:01 However, there are many other gene-alleles within the haplotype. (wikipedia.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)
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)

We observed a considerable change in the frequencies of the rs145204276 allele and genotype among the IS patients and healthy control group. (hindawi.com)

No FCN2 promoter haplotypes were significantly distributed between mild and severe cases. (nih.gov)
The distributions of predicted haplotypes differed significantly between the two ethnicities where the Kyrgyz showed a higher genetic diversity. (aacrjournals.org)
The frequency of CD4+CD25+CD127- Tregs was significantly hig. (medworm.com)
In the haplotype analysis, the T-G-C haplotype composed of all three risk alleles was significantly overrepresented in XFS and conferred an 11.36 fold (95% CI=5.97-23.49) increased likelihood of XFS. (molvis.org)
The IC, QC and IQC haplotypes are significantly associated with the DA phenotype. (cdc.gov)
RAD50 687delT displayed significantly elevated frequency in the studied patients (8 out of 317, OR 4.3, 95% CI 1.5-12.5, P = 0.008), which indicates that it is a relatively common low-penetrance risk allele in this cohort. (lu.se)

Differential cultural adaption by populations from the North Lebanese Mountains are clearly aligned with the L1b haplotype STR haplogroup clusters, indicating pre-existing and persistent cultural barriers marked by the transmission of L1b lineages. (nature.com)
Our findings highlight the value of uniparental haplogroups and STR haplotype data for elucidating biosocial events among these populations. (nature.com)
This paper mathematically models environmentally induced adaptive forces that quantify changes in the distribution of SNP frequencies between populations. (scirp.org)
The importance of low frequency and rare variation in complex disease genetics is difficult to estimate in patient populations. (frontiersin.org)
Frequency differences of common haplotypes from widely dispersed populations of L. Iineolaris indicate the possibility of some geographically based population structure for this species. (usda.gov)
In addition, databases that aggregate allele frequencies, such as gnomAD are also biased toward European populations and contain very little information from individuals of African or other ancestries. (cdc.gov)
The lack of diverse ethnic representation in these data has created a gap in knowledge about the alleles present in non-White populations and their relative frequencies. (cdc.gov)

Our results highlight the need for new methods to analyze genomic variation because existing ones do not systematically consider local haplotypes. (biomedcentral.com)

Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio. (oregonstate.edu)
RESULTS: Here we show temporal correlations between Y-chromosomal haplotype frequencies and foetal sex ratios in the KNP buffalo population, suggesting SR genes. (oregonstate.edu)
In some cases, the increased risk is related to a group of specific variants in several genes, a combination known as a C3 glomerulopathy at-risk haplotype. (medlineplus.gov)

In this approach, unphased SNP genotypes are compared to pairs of canonical haplotypes to identify potentially hemizygous regions. (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)
Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing techniques. (wikipedia.org)
Genotypes and allele frequencies were compared between groups using χ 2 contingency analysis. (lww.com)

The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. (ox.ac.uk)
To determine whether genetic variations of IGF modify pancreatic cancer risk, we compared the frequency of six single nucleotide polymorphisms of IGF1 and IGF2 in a large-scale case control study. (aacrjournals.org)
C1 identification during diagnosis suggests the need to increase the frequency of medical examination compared to other genetic variants. (conicet.gov.ar)
Haplotypes of IL-4 receptor and CD14 genetic polymorphisms are markers of susceptibility for diisocyanate asthma. (cdc.gov)

Morphometrics and haplotype analyses were used to investigate the frequency of African markers in honey bees from Sonora (SON), the north and south of Baja California (BCN and BCS). (apidologie.org)
2) Radar observations indicated that most of the moths' migration took place at a height of 600 m, often in a dense layer which formed at heights of 350-800 m. (3) Analyses of adult ovarian development and larval haplotypes showed third-generation larvae were progeny of both locally produced progeny and immigrant moths. (bioone.org)
4) Based on our back-tracking and haplotype analyses, immigration led to an outbreak originated in the same source area to the southwest. (bioone.org)
Phylogenetic analyses of 62 multi-species Lygus haplotype sequences representing North America and Europe show that L. Iineolaris, L. hesperus, L. rugulipennis, L. plagiatus, L. elisus, and L. vanduzeei are clustered by species, with a few exceptions. (usda.gov)

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)
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 gene-alleles are markers for a haplotype, a stretch of chromosome 6 that contains many gene alleles. (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)
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)

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)

However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals. (wikipedia.org)
These algorithms estimate population haplotype frequencies from pooled SNP data and can make use of a list of the haplotypes that are known to exist in the population. (helsinki.fi)
The SSS measure is a likelihood estimate based on the frequency of identical and closely related (>99%) haplotypes. (africanancestry.com)

Among the 58 samples, 29 haplotypes belonging to 18 different haplogroups were analyzed. (blogspot.com)
Extensive Eastern Eurasian lineages exist in the Daheyan population in which Northern-prevalent haplogroups present higher frequencies. (blogspot.com)

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)

There were no significant differences between groups on the allele, genotype or haplotype level for any of the tested single nucleotide polymorphisms. (lww.com)

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. (ox.ac.uk)
Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. (ox.ac.uk)
We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. (ox.ac.uk)
For dense genotyping arrays, imputation is able to predict nearly all missing common variation with high accuracy, but as the variant minor allele frequency (MAF) decreases, so does the accuracy of imputation, depending mainly on the size of the reference panel and the ancestry of the imputed samples, with the best efficiencies in European cohorts, mainly due to the sufficiently large size of the European reference panels ( 7 - 13 ). (frontiersin.org)

In this study, we determined the phased haplotypes of 291 patients using family members and segregation analysis. (unige.ch)

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)

Chromosomal recombination fragments multigene haplotypes as the distance to that ancestor increases in number of generations. (wikipedia.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)

and B14, DR1, DQw1 haplotypes could be involved with IgA-D susceptibility in RTIAG patients. (nih.gov)
and susceptibility to RAS, which segregates in families in association with HLA haplotypes. (medscape.com)

The haplotype without mutations was more common in Kyrgyz (40.1% in Kyrgyz, 29.3% in Romanians). (aacrjournals.org)

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)
The sum of ranks of the haplotypes carried by patients was used as a surrogate predictor of a successful unrelated donor search. (unige.ch)
This could cause health inequities because the results of PGx tests that were designed based on allele frequencies of Europeans are being applied to patients of other ethnicities, causing physicians to prescribe drugs and doses that are ineffective or may cause adverse reactions in non-White patients. (cdc.gov)
Nous avons génotypé les deux polymorphismes mononucléotidiques du gène ADIPOQ chez 140 patients atteints de DNID sans lien de parenté et 66 témoins non diabétiques en recourant à l'analyse du polymorphisme de longueur des fragments de restriction par réaction en chaîne de polymérase. (who.int)
SSCP Frequency Weekly Samples 12 patients /year Prices 482 EUR/patient, 180 EUR/carrier Comment Patient samples are only accepted for analysis after Comment prior consultation and submission of clinical and Comment laboratory data. (lu.se)

High-resolution HLA phased haplotype frequencies to predict the success of unrelated donor searches and clinical outcome following hematopoietic stem cell transplantation. (unige.ch)
Some studies have proposed that further matching at the haplotype level could be beneficial for clinical outcome. (unige.ch)
This study provides useful data for the optimization of unrelated bone marrow donor searches, but does not confirm previous reports that matching at the haplotype level has a clinical impact following HSCT. (unige.ch)
Reactivation of the disease was defined both by clinical symptoms appearance and/or direct larvae detection from 30 days after treatment.The analysis of the 41 stool samples described ten cox1.404 haplotypes organized in two clusters (C1 and C2). (conicet.gov.ar)
HP24 and HP93 were the most frequent haplotypes in our patient?s population, distributed in American and Asian continents and cluster founders in median-joining network analysis (C1 and C2, respectively).Clinical presentation (intestinal, severe, cutaneous, and asymptomatic), immunological status and eosinophil count were not associated with specific haplotypes or clusters. (conicet.gov.ar)
Haplotype/cluster determination could assist in the management of strongyloidiasis clinical evolution. (conicet.gov.ar)
Cruz Garcia Rodriguez Address Unidad de Inmunologia, Hospital La Paz, Paseo de Address la Castellana 261, 28046 Madrid, Spain Telephone +34-91-7277095 Fax +34-91-7277095 Email [email protected] Method SSCP, Direct sequencing Frequency Whenever required Samples 2 samples per year Prices 300 EUR/patient 112/carrier Comment Patient samples are only accepted for analysis after Comment prior consultation and submission of clinical and Comment laboratory data. (lu.se)

The putative impact of haplotypes was then analyzed in a cohort of 211 recipients transplanted with 10/10 matched unrelated donors. (unige.ch)

A logistic regression analysis showed a highly significant effect of the haplotypes in the outcome of a search, but we did not find any significant effect on overall survival, graft versus host disease or relapse/progression following HSCT. (unige.ch)
In contrast, the frequency of the allele related to rs55829688 was not statistically correlated with IS in all analysis. (hindawi.com)
This group was selected for molecular analysis because of its abundance, representing 18% of the unusual haplotypes. (bmj.com)
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)
Haplotype analysis and the screening of altogether 512 additional breast cancer cases from Sweden, Norway and Iceland suggest that RAD50 687delT is a Finnish founder mutation, not present in the other Nordic cohorts. (lu.se)

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)

While type 1 diabetes shows an extended association on the HLA A1-B8-DR3-DQ2 haplotype, the association appears not to extend beyond the HLA-B locus. (wikipedia.org)
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)

Creation of the comprehensive PGx data set proposed in this project will, for the first time, help to establish the allele frequencies in 150 pharmacogenes across ethnicities in the US population. (cdc.gov)

Natural selection quickly increases in frequency any alleles which confer protection against the exogenous stress. (discovermagazine.com)

common multigene haplotypes are generally the result of identity by descent from a common ancestor (share a recent common ancestor for that segment of the chromosome). (wikipedia.org)
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)
Clade here refers to a set of haplotypes sharing a common ancestor. (wikipedia.org)

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)
We identified 78 (1.3%) samples with non-canonical haplotypes, which in 62 cases were paired with a canonical haplotype. (bmj.com)
Several other samples were identified with haplotypes that may have been the result of intragenic deletions. (bmj.com)
SLC40A1 Q248H allele frequencies and associated SLC40A1 haplotypes in three West African population samples. (unl.pt)
http://www.ncbi.nlm.nih.gov/pubmed/?term=SLC40A1+Q248H+allele+frequencies+and+associated+SLC40A1+haplotypes+in+three+West+African+population+samples. (unl.pt)
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)

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)

Database comparisons of the NAT2 minor allele frequencies support that Romanians belong to Caucasians and Kyrgyz are in between Caucasians and East Asians. (aacrjournals.org)

HLA A*01:01-C*07:01-B*08:01) is a multigene haplotype that covers the MHC Class I region of the human major histocompatibility complex on chromosome 6. (wikipedia.org)
The disease appears to be associated with the human leukocyte antigen B27 (HLA-B27) haplotype. (medscape.com)

Estimating population haplotype frequencies from pooled SNP data using incomplete prior information. (helsinki.fi)

BACKGROUND: The Y-chromosomal diversity in the African buffalo (Syncerus caffer) population of Kruger National Park (KNP) is characterized by rainfall-driven haplotype frequency shifts between year cohorts. (oregonstate.edu)

Of amino acids are underlined) haplotype emerged in 2010 these SP-based interventions, IPTi with SP is safe and effec- that was closely related to pre-existing double-mutant SGEA tive ( 2 ), IPT in children receiving SP and amodiaquine has haplotypes, suggesting local origination in Malawi. (cdc.gov)
The increase in frequency of the mutant gene though is balanced by the fact that mutant homozygotes have decreased fitness. (discovermagazine.com)

In at least 2 diseases, the risk of autoimmune disease extends beyond the class II region of the haplotype. (wikipedia.org)

Nevertheless, presence of C1 haplotypes during diagnosis increased the risk of reactivation with an OR of 7.51 (CI 95% 1.38-44.29, p=0.026). (conicet.gov.ar)
If the NRTI abacavir (ABC) is considered as part of treatment, HLA-B*5701 must be obtained and ABC only prescribed if the patient is negative for this haplotype, as persons who are positive are at risk for a potentially serious hypersensitivity reaction to the drug. (medscape.com)

The del -T haplotype was substantially more prevalent in the IS cases compared to the control individuals. (hindawi.com)
Cases and controls were frequency matched by age (±5 years), race, and sex. (aacrjournals.org)

Both wet and dry periods were associated with a specific haplotype indicating a SR distorter and SR suppressor, respectively. (oregonstate.edu)

In Europe A1-B8 is found, generally as part of the HLA A1-B8-DR3-DQ2 haplotype. (wikipedia.org)

The high frequency of SSS and low frequency of consanguineous marriages in this study may reflect a high rate of heterozygous carriers. (who.int)
12: Gustafsson P, Jestin P, Gunnarsson U, Lindforss U. Higher frequency of anastomotic leakage with stapled compared to hand-sewn ileocolic anastomosis in a large population-based study. (cancercentrum.se)

Anatomy2

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