Linkage Disequilibrium and haplotype mapping : A number of packages provide haplotype estimation for unrelated individuals with ambiguous haplotypes (due to unknown linkage phase) and allow testing for associations between the estimated haplotypes and phenotypes (including co-variates) under a GLM framework. hapassoc performs likelihood inference of trait associations with haplotypes in GLMs. haplo.stats also contains tests for haplotype associations under a GLM framework, but also provides score tests of association as well as providing novel functionality for building haplotypes in a sequential manner, power and sample-size calculations and the preparation of data matrices for use in other methods. haplo.ccs utilises the haplotype estimation of haplo.stats and performs case-control association tests via weighted logistic regression. tdthap implements transmission/disequilibrium tests for extended marker haplotypes. LDheatmap creates a heat map plot of measures of pairwise LD ...
Linkage Disequilibrium and haplotype mapping : A number of packages provide haplotype estimation for unrelated individuals with ambiguous haplotypes (due to unknown linkage phase) and allow testing for associations between the estimated haplotypes and phenotypes (including co-variates) under a GLM framework. hapassoc performs likelihood inference of trait associations with haplotypes in GLMs. haplo.stats also contains tests for haplotype associations under a GLM framework, but also provides score tests of association as well as providing novel functionality for building haplotypes in a sequential manner, power and sample-size calculations and the preparation of data matrices for use in other methods. haplo.ccs utilises the haplotype estimation of haplo.stats and performs case-control association tests via weighted logistic regression. tdthap implements transmission/disequilibrium tests for extended marker haplotypes. LDheatmap creates a heat map plot of measures of pairwise LD ...
OBJECTIVES Associations of interleukin-10 (IL-10) promoter single nucleotide polymorphisms (SNPs) and their haplotypes with systemic lupus erythematosus (SLE) are unclear. We extended the analysis of established proximal IL-10 promoter haplotypes to a more distal SNP with functional capacity. METHODS Two hundred and ten German caucasian SLE patients fulfilling the ACR criteria and 160 ethnically, age and sex matched controls were genotyped for IL-10 -2849 G | A, -1082 A | G, -819 T | C and -592 C | A. Haplotypes were reconstructed via a mathematical model, then allele and haplotype distributions were compared between patients and controls and patients with different disease manifestations. RESULTS We detected at -2849, -1082, -819 and -592 the four predominant haplotypes GGCC (22% in patients vs. 29% in controls), AGCC (24% vs. 21%), GACC (30% vs. 25%) and GATA (24% vs. 24%). GGCC was underrepresented in SLE patients, suggesting a protective effect (odds ratio (OR) 0.67, 95% confidence interval (CI)
Haplotypes extracted from human DNA can be used for gene mapping and other analysis of genetic patterns within and across populations. A fundamental problem is, however, that current practical laboratory methods do not give haplotype information. Estimation of phased haplotypes of unrelated individuals given their unphased genotypes is known as the haplotype reconstruction or phasing problem. We define three novel statistical models and give an efficient algorithm for haplotype reconstruction, jointly called HaploRec. HaploRec is based on exploiting local regularities conserved in haplotypes: it reconstructs haplotypes so that they have maximal local coherence. This approach - not assuming statistical dependence for remotely located markers - has two useful properties: it is well-suited for sparse marker maps, such as those used in gene mapping, and it can actually take advantage of long maps. Our experimental results with simulated and real data show that HaploRec is a powerful method for the large
Tables 4 and 5 show the results of eight SNP haplotype analyses (rs941798, rs3787345, rs754118, rs2282147, rs718049, rs718050, rs3787348, and 1484insG) with Si (Table 4) and fasting glucose (Table 5), respectively. The SNPs were chosen to tag all common haplotypes (≥10% frequency) and ,85% of the variation in the LD block and, in addition, includes 1484insG. The Tables show the common (,1%) haplotypes, their frequency, P values for association under different models of inheritance, the mean trait values for the different haplotype combinations, and the effect of the specific haplotype on the trait. The haplotype ACTTCAG0 is significantly associated with lower Si (e.g., greater insulin resistance) and higher fasting glucose in the dominant model, and the haplotype GTCCTGT0 is significantly associated with higher Si (e.g., greater insulin sensitivity) and lower fasting glucose in the additive and recessive models. The remaining haplotype, ATCCTGG0, shows evidence of association with Si under the ...
In the original publications, the haplotypes identified as being of highest risk consisted of the combination of two SNPs together, rs1048661(G) and rs3825942(C), oriented with respect to the dbSNP entry. In the two populations studied combined (from Iceland and Sweden), the (G;C) haplotype has an odds ratio of 27.05, and the (T;C) haplotype has an OR of 8.90, relative to the (G;T) haplotype. The (T;T) haplotype is presumed to be at even lower risk than the (G;T) haplotype, but due at least in part to the high frequency of the rs1048661(G) allele, no individuals in this study carried it. In the populations studied, ~25% of all individuals in the population carry two copies of the (G;C), highest risk haplotype. If the risk of carrying two such haplotypes is multiplicative (which isnt known actually), the authors estimate that individuals carrying two copies of the (G;C) high risk haplotype would have 700 times the risk of developing this type of glaucoma compared to individuals carrying two ...
TY - JOUR. T1 - Complex SNP-based haplotypes in three human helicases. T2 - Implications for cancer association studies. AU - Trikka, Dimitra. AU - Fang, Zhe. AU - Renwick, Alex. AU - Jones, Sally H.. AU - Chakraborty, Ranajit. AU - Kimmel, Marek. AU - Nelson, David L.. PY - 2002/4/25. Y1 - 2002/4/25. N2 - We have initiated a candidate gene approach to study variation and predisposition to cancer in the four major ethnic groups that constitute the U.S. population (African Americans, Caucasians, Hispanics, and Asians). We resequenced portions of three helicase genes (BLM, WRN, and RECQL) identifying a total of 37 noncoding single nucleotide polymorphisms (SNPs). Haplotype inference predicted 50 haplotypes in BLM, 56 in WRN, and 47 in RECQL in a sample of 600 chromosomes. Approximately 10% of the predicted haplotypes were shared among all ethnic groups. Linkage disequilibrium and recombination effects showed that each locus has taken a diverse evolutionary path. Primate DNA analysis of the same ...
NK cells react to cells that lack self-MHC class I. Yet, since many NK cells cannot recognize self-MHC, mechanisms such as NK cell licensing protect against autoreactivity. To become licensed, i.e. functionally competent to be triggered through its activation receptors, an NK cell must engage host MHC class I via at least one of its MHC class I-specific inhibitory receptors, such as the Ly49 family of receptors in the mouse. However, the general determinants of this process remain largely unknown. Herein, we investigated the licensing impact of the b, d, f, k, q, r, and s H2 haplotypes on Ly49A+ NK cells in MHC-congenic mice. 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. Ly49A surface accessibility, a measure of cis binding with MHC class I, and Ly49A tetramer binding displayed a similar variability among the MHC haplotypes. Taken together, the ...
In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material; a substantial sample of individuals of the target species or other taxon is used; however, many current studies are based on single individuals. Haplotypes of individuals of closely related, yet different, taxa are also determined. Finally, haplotypes from a smaller number of individuals from a definitely different taxon are determined: these are referred to as an outgroup. The base sequences for the haplotypes are then compared. In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: this is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, for example, the insertion of a section of nucleic acid in one haplotype that is not present in another). The difference between organisms is usually re-expressed as a percentage divergence, by dividing the number ...
This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. ...
This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. ...
This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. ...
This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. ...
Background: In ecology and forensics, some population assignment techniques use molecular markers to assign individuals to known groups. However, assigning individuals to known populations can be difficult if the level of genetic differentiation among populations is small. Most assignment studies handle independent markers, often by pruning markers in Linkage Disequilibrium (LD), ignoring the information contained in the correlation among markers due to LD. 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. 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. Because complete exploration of all possible solutions for constructing haplotypes is computationally prohibitive, our approach uses a greedy algorithm ...
We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a ...
The genetic diversity and phylogeny of western Palaearctic members of the Gerris lacustris group was investigated on the basis of 822 bp from the 3´end of the mitochondrial gene encoding COI obtained from 34 specimens of G. lacustris, 16 specimens of G. gibbifer, eight specimens of G. maculatus and seven specimens of G. brasili. Nine haplotypes represented G. lacustris, nine haplotypes represented G. gibbifer, six haplotypes represented G. maculatus, four haplotypes represented G. brasili, and a single haplotype was shared between G. gibbifer and G. brasili. Uncorrected p genetic distances within species averaged from 0.5% in G. gibbifer and G. brasili to 0.8 in G. lacustris and as much as 2.2 in G. maculatus. A phylogenetic analysis showed that G. gibbifer and G. brasili are not reciprocally monophyletic in their mtDNA probably due to relatively recent speciation and incomplete lineage sorting. G. maculatus was poorly supported as the sister taxon to G. gibbifer and G. brasili despite morphological
In 2009, Tregouet et al. identified the SLC22A3-LPAL2-LPA gene cluster as a risk cluster and haplotypes CTTG and CCTC formed by rs2048327, rs3127599, rs7767084 and rs10755578 as risk haplotypes for CAD in six White populations [1]. From then on, several GWHS have focused on this hot spot. In a study consisted of 3657 patients with MI and 1211 control individuals, Koch et al. observed significant association between haplotypes formed by the same four SNPs in the SLC22A3-LPAL2-LPA region and MI (P = 0.0005), and found 3 risk haplotypes (CTTG, CCTC, and TTTC) [10]. Later, Sawabe M etal analyzed rs2048327 (C/T) and rs10755578 (C/G) in 1,150 Japanese autopsy cases, and ascertained that haplotypes TC and TG worked as risk factors for both coronary sclerosis and CAD [12]. In addition, Shaw et al. found that genetic variants at the SLC22A3-LPAL2-LPA locus were associated with decreased early-outgrowth colony-forming units, thereby increased the risk of MI [13], which may support the findings in ...
Here you can Read online or download a free book: Algorithms for Haplotype Inference and Block Partitioning: Perfect Phylogeny Based Approaches for the Haplotype Inference Problem.pdf Language: English by Ravi Vijaya Satya (Author) A convenient format for reading on any device
The patterns of linkage disequilibrium (LD) between dense polymorphic markers are shaped by the ancestral population history. It is therefore possible to use multilocus predictors of LD to infer past population history and to infer sharing of identical alleles in quantitative trait locus (QTL) studies. We develop a multilocus predictor of LD for pairs of haplotypes, which we term haplotype homozygosity (HHn) : the probability that any two haplotypes share a given number of n adjacent identical markers or runs of homozygosity. Our method, based on simplified coalescence theory, accounts for recombination and mutation. We compare our HHn predictions, with HHn in simulated populations and with two published predictors of HHn. Our method performs consistently better across a range of population parameters, including populations with a severe bottleneck followed by expansion, compared to two published methods. We demonstrate that we can predict the pattern of HHn observed in dense single nucleotide ...
Khwaja, HA and Green, FR (2004) Analysis of the functional role of interleukin-6 promoter haplotype in a macrophage cell model In: 5th Annual Conference on Arteriosclerosis, Thrombosis, and Vascular Biology, 2004-05-06 - 2004-05-08, San Francisco, CA. Full text not available from this repository ...
The MDM2 protein is an ubiquitin ligase that plays a critical role in regulating the levels and activity of the p53 protein, which is a central tumor suppressor. A SNP in the human MDM2 gene (SNP309 T/G) occurs at frequencies dependent on demographic history and has been shown to have important differential effects on the activity of the MDM2 and p53 proteins and to associate with altered risk for the development of several cancers. In this report, the haplotype structure of the MDM2 gene is determined by using 14 different SNPs across the gene from three different population samples: Caucasians, African Americans, and the Ashkenazi Jewish ethnic group. The results presented in this report indicate that there is a substantially reduced variability of the deleterious SNP309 G allele haplotype in all three populations studied, whereas multiple common T allele haplotypes were found in all three populations. This observation, coupled with the relatively high frequency of the G allele haplotype in ...
Results In a Han population, the distribution of SNP3 (rs3890011) genotypes showed a significant difference between CAD and control subjects (p=0.030), the distribution of the recessive model of SNP3 (GG vs CC+GC) was significantly higher in CAD patients than control subjects (p=0.011), the significant difference was retained after adjustment for covariates (95%CI: 1.137-2.423, p=0.009). Three SNPs (SNP1, SNP3, SNP4) were located in one haplotype block, and the overall distribution of haplotypes constructed with these SNPs was significant (p=0.023). The G-G-T haplotype in CAD was significantly higher than that in control group (p=0.037). In a Uygur population, neither the distribution of genotypes and alleles for the 4 SNPs showed significant difference nor the distribution of haplotypes constructed with the same three SNPs between CAD and control subjects.. ...
The systematic analysis of polymorphisms across large parts of the human genome has begun to provide the first information on haplotypes and the problem of linkage disequilibrium across large genomic regions. These data suggest that significant regions of the genome show highly conserved haplotypes, potentially enhancing the ability to detect disease associations.
This population-based cross-sectional study shows an association between a common genetic haplotype in IGF1 and absolute mammographic density in postmenopausal women after adjustment for age and BMI. Although not statistically significant, stratification by age and BMI revealed that the upper age tertiles and middle BMI tertile increased the mammographic density level. One haplotype in IGF2 was associated with the levels of both IGF1 and IGFBP3, while two haplotypes in the IGF2R gene were associated with the levels of IGF1. Within the IGFBP3 gene, two haplotypes were found associated with the IGFBP3 level indicating a regulation in cis.. The strength of our study is the large sample size and the fact that the samples were collected as part of a population-based screening project with high attendance rate[37]. Highly experienced personnel that were blinded to the characteristics of the women performed the reading and measurements of both the mammographic density and hormone levels. Also, we had ...
TY - JOUR. T1 - Four common HLA haplotypes and their association with diseases in the Japanese population. AU - Sasazuki, T.. AU - Kaneoka, H.. AU - Ohta, N.. AU - Hayase, R.. AU - Iwamoto, I.. PY - 1979/12/1. Y1 - 1979/12/1. UR - http://www.scopus.com/inward/record.url?scp=0018567739&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0018567739&partnerID=8YFLogxK. M3 - Article. C2 - 43610. AN - SCOPUS:0018567739. VL - 11. SP - 1871. EP - 1873. JO - Transplantation Proceedings. JF - Transplantation Proceedings. SN - 0041-1345. IS - 4. ER - ...
David R. Cox, of Perlegen Sciences in Santa Clara, California, and colleagues scanned 20 copies of chromosome 21 using high-density microarrays. In all, they found nearly 36,000 SNPs in the samples. Using the scan data, they identified groups of related SNPs, or haplotypes. Most of these structures turned up on all the chromosomes. Only eight percent of the haplotypes were specific to a particular ethnic group. It is remarkable that such a large fraction of globally diverse chromosomes are represented by such limited haplotype diversity, the researchers write in Science. Three common haplotypes accounted for 80 percent of the genetic diversity among the samples. This means that, for any region of the chromosome, the most common haplotype was found in 50 percent of individuals, the second most common in 25 percent of individuals, and the third most common in 12.5 percent of individuals. The discovery that chromosome 21 is less structurally diverse than expected is potentially good news. It may ...
In admixed populations originating from different base breeds, such as Nordic Red dairy cattle, haplotypes of chromosomal segments instead of single SNP are expected to improve prediction accuracy in genomic evaluations, because linkage disequilibrium with QTL is likely to be more consistent for haplotypes than for SNP. The suggested evaluation approach consists of (i) pre-selecting a limited number of chromosomal segments based on a genome-wide QTL-scan with BayesB, (ii) estimating relative variances of haplotype markers with BayesA, and (iii) obtaining solutions for haplotype effects from mixed model equations including pedigree-based animal effects. For three production traits (milk, protein, fat) and fertility, the highest validation test reliabilities R2 were 0.48, 0.41, 0.42 and 0.33, respectively. For milk, protein and fertility, we observed an improvement over G-BLUP of 3, 1 and 3 %-units, respectively, whereas for fat, a decline of 1 %-unit.. ...
The present invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase having a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e.g., oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the present invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases (Mb). Separation of the haplotypes of large genomic DNA fragments allows for linkage analysis of other HLA alleles
DESCRIPTION. Haploscope is a software package that facilitates flexible rendering of images to aid interpretation of model-based summaries of population haplotypes. Haploscope is designed to accept haplotype frequency input directly from output files of fastPHASE (Scheet & Stephens, 2006), though output from other cluster-based models for population haplotypes could be adapted for input to Haploscope.. ::DEVELOPER. paul scheet lab. :: SCREENSHOTS. N/A. :: REQUIREMENTS. ...
mtDNA is usually treated as a non-recombining locus, and so it should evolve along a tree. A rooted global tree has therefore been produced for humans, based on parsimony analysis of the mtDNA genome (Torroni et al. 2000; van Oven and Kayser 2009). Groups and subgroups of this tree have been labelled as haplotypes, such as haplotype group M shown in the top figure, and sub-haplogroups, such as M4b, M49 and M61. These are (monophyletic) clades in the mtDNA tree that have been highlighted for convenience. Parsimony analysis has been used to reconstruct the ancestral sequences in the tree (Behar et al. 2012), and these ancestral sequences can be used to assign new sequences to their appropriate place in the rooted tree (Blanco et al. 2011 ...
mtDNA is usually treated as a non-recombining locus, and so it should evolve along a tree. A rooted global tree has therefore been produced for humans, based on parsimony analysis of the mtDNA genome (Torroni et al. 2000; van Oven and Kayser 2009). Groups and subgroups of this tree have been labelled as haplotypes, such as haplotype group M shown in the top figure, and sub-haplogroups, such as M4b, M49 and M61. These are (monophyletic) clades in the mtDNA tree that have been highlighted for convenience. Parsimony analysis has been used to reconstruct the ancestral sequences in the tree (Behar et al. 2012), and these ancestral sequences can be used to assign new sequences to their appropriate place in the rooted tree (Blanco et al. 2011 ...
A new type of insertion flanked by long stretches of TA repeats, hence named TAFTs for TA-flanked transposons, was discovered during the course of this investigation. TAFTs have the following properties. (i) They are flanked by TA microsatellites with as many as 50 copies of the TA repeat on either side of the insertion. (ii) The corresponding vacant site in haplotypes that lack TAFTs consists generally of a few (three or four) copies of the TA repeat, but there are exceptions. (iii) The elements identified so far possess imperfect TIRs of ≈40 bp and are relatively large (,2 kb). (iv) Related copies are found at other locations in the maize genome, where they are also flanked by TA repeats.. The TAFT1 element in CML258 and Coroico is 2.2-kb long and is flanked on either side by multiple copies of TA. The vacant site in the other haplotypes has three copies of the TA dinucleotide. TAFT1 is 85% identical to oligo-TA flanked sequences of similar length that occur in B73 locus 9009 (GenBank ...
The goal of this study was to determine whether variants associated with age at onset of CFRD affected the expression of SLC26A9. We discovered that the alleles of the CFRD-risk variants are coinherited as 2 common haplotypes, one that is associated with later onset of CFRD (LR), and another that is associated with earlier onset of CFRD (HR). A third less common haplotype similar to HR was also associated with earlier onset of diabetes, and it is possible that other, less common, haplotypes bearing the majority of the CFRD-risk variants also correlate with CFRD, but are not sufficiently frequent to allow detection of association in the 762 individuals studied here. There was no evidence that a coding or rare variant accounted for the CFRD association. Mapping of the major TSS indicated that the noncoding first exon of SLC26A9 was placed in the middle of the cluster of CFRD-risk variants in the 5′ region of SLC26A9. These results suggested that the HR and LR CFRD haplotypes affect ...
This study demonstrates that variation in the PPARα gene influences the onset and progression of type 2 diabetes, in concurrence with the recent observation that bezafibrate reduces the incidence and delays the onset of type 2 diabetes (11). Allele and haplotype frequencies were not different between healthy middle-aged U.K. men and the type 2 diabetes sample, but haplotype frequency was different between subjects with age at diagnosis ≤45 years and both those with later age at diagnosis and with healthy middle-aged U.K. men without overt type 2 diabetes, indicating that PPARα predisposes to early-onset type 2 diabetes. PPARα gene variants influenced age at diagnosis in combination and in haplotype analysis. Carriers of the intron 1 and 7 rare C-alleles had a dramatically younger age at diagnosis, an effect confirmed in haplotype analysis, in which haplotypes 6 and 8, comprising the intron 1 C- and intron 7 C-alleles with the L162 or V162 alleles, respectively, were associated with an age ...
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Twenty four CML-patients, 22 (91.7%) with chronic phase and 2 (8.3%) under blast crisis, were studied. Thirteen (54.2%) were males, and 11 (45.8%) were females. The Sokal risk was low in 7 (29.2%), intermediate in 7 (29.2%), high in 6 (25%), and not evaluated in 4 (16.6%). Age, gender, phase of disease, TKI treatment and doses, molecular responses (at 6, 12, and 18 months) and haplotypes are listed in Table 1.. A total of seventeen different haplotypes were identified in CML-patients and controls. The frequency distribution indicates that 6 were only detected in CML-patients, 7 only in controls, and 4 in both groups. Heterozygous T-variant genotypes were observed in all 25 controls (100%), and in 18 CML-patients (75%). In this last group, 9 different T-variant haplotypes were identified as follows: full mutated-homozygote (TT-TT-TT) in 3 (12.5%), full mutated-heterozygous (CT-GT/A-CT) in 6 (25%), and other combinations of T-variants in 9 cases (37.5%). The remaining 6 (25%) CML-patients were ...
Recent advances in RNA sequencing technology can generate deep coverage data containing millions of reads. RNA-Seq data are used to identify genetic variants and alternatively spliced isoforms, a common mechanism for diversity in a gene, that may play a role in heritable traits and diseases. Using this type of data, connections can be drawn between genetic expression and one of the two parental haplotypes identified in a diploid organisms transcript. In other words, we can potentially identify the parent from which an individual inherited a group of genes.. These multi-kilobase reads are longer than most transcripts and enable sequencing of complete haplotype isoforms. New computational methods are required for efficient analysis of this highly complex data. In a recent paper, we present HapIso (Haplotype-specific Isoform Reconstruction), a comprehensive method that can accurately reconstruct the haplotype-specific isoforms of a diploid cell. Our software package is the first method capable of ...
AIM: To examine the association between the four haplotypes of IL-7Rα gene and a cohort of HIV infected patients who have commenced HAART with varying CD4+ T lymphocyte responses.. METHODS: IL-7Rα gene SNPs and haplotypes will be measured by constructing DNA pools, and PCR amplification and DNA sequencing. IL-7Rα expression will be examined using constitutive expression of IL-7Rα, IL-7Rα gene expression, and inducible expression of IL7Rα. ...
Imaging genetic studies of large control cohorts such as UK Biobank enable to assess the range of normal variations in brain structures. Previous studies by our group have shown that the width of several cortical sulci is associated with a variant in the upstream region of KCNK2 gene even if this effect is corrected with age. Here we propose to analyze in a multivariate setup the associations between sets of genetic variants and multiple sulci widths. The genetic variants we consider are sets of SNPs of known phase called haplotypes, taken from the upstream region of KCNK2 gene. To the best of our knowledge, multivariate analysis in imaging genetics has never been used in haplotype studies. Our method was able to recover the expected association signal and uncover new associations between imaging data and genetic variants.
Disclaimer: Like the OP, I know very little about genetics and I suppose other people in the site can give better answers than me. Anyway, since the question has been unanswered for months Im posting my answer. Hopefully someone will improve it.. Just beware that "possible" in this context doesnt mean all haplotypes that we can imagine. As the paper says, "$\mathcal{H}_G$ denote the set of all possible diplotypes that are consistent with the genotype data $G$" and that is an additional restriction that allows just some diplotypes - the seven ones listed, not the 32 we can imagine.. Furthermore, please notice that sum of frequencies in the table equals 1, therefore there can be no more haplotypes in the set.. However, it would help if you linked the source where you got those data and quotes.. ...
Three MDM2 promoters have been identified and numerous genetic polymorphisms in these promoter regions have been reported in the HapMap and dbSNPs databases. Therefore, besides the reported functional SNP309 in the MDM2 promoter (13), we thought that the other genetic variants of the MDM2 gene may also be important and that their roles in human cancer susceptibility should be evaluated. In the present study, we used a haplotype-based approach to identify tagSNPs and evaluated their associations with risk of bladder cancer. Although we did not observe an association between any of the haplotypes and risk of bladder cancer, we observed a statistically significant association between the C1797G polymorphism in the MDM2 promoter and risk of bladder cancer and showed that the C to G substitution of this polymorphism significantly enhanced the binding affinity of the transcriptional activator C/EBPα and increased the transcription activity of the MDM2 gene in vitro. Furthermore, we found that of the ...
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The GATK Pipeline is an implementation of GATK Haplotype Variant Caller from the Broad Institute on the DRAGEN Platform. The GATK Pipeline is accelerated by using the APIs of the DRAGEN Bio-IT Processor. The result is a haplotype variant calling pipeline that is able to analyze a 30x coverage whole human genome in 18 minutes. Customers with a valid GATK license from the Broad Institute are able to run GATK on the DRAGEN Platform.. ...
The GATK Pipeline is an implementation of GATK Haplotype Variant Caller from the Broad Institute on the DRAGEN Platform. The GATK Pipeline is accelerated by using the APIs of the DRAGEN Bio-IT Processor. The result is a haplotype variant calling pipeline that is able to analyze a 30x coverage whole human genome in 18 minutes. Customers with a valid GATK license from the Broad Institute are able to run GATK on the DRAGEN Platform.. ...
Haplotype: A specific combination of SNPs all occuring together on the same chromosome (i.e. all occuring on the chromosome inherited from Dad, or, inherited from Mom). Common DNA microarrays such as 23andMe, FTDNA and AncestryDNAs will at most identify the number of different alleles at each SNP location - 0, 1 or 2 - but cant identify which sides of the pair of chromosomes they came from. If matching SNPs are available for both parents, its possible to determine which side they came from with high precision based on Mendelian inheritance, called phasing. 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. Sequencing, on the other hand, directly reads the sequence of nucleotides on a single strand of DNA, therefore preserving phasing. Next Gen Sequencing can thus provide not only perfectly phased genome, but also a haplotype map which can be used to impute untested ...
This book constitutes the post-proceedings of the DIMACS/RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotype Inference held in Piscataway, NJ, USA, in November 2002. The book presents ten revised full papers as well as abstracts of the remaining workshop papers. All
The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.. ...
In addition, an independent laboratory verified the sequence based on amplification from a third sample tooth from the same individual, both by direct sequencing and cloning (in two overlapping fragments: 16 055-16 218 and 16 209-16 356). For the first cloned fragment, all 3 clones showed the T→A transversion at 16 189. For the second fragment, all 5 clones for the Romani sequence were consistent for variable sites 16 271 and 16 278, and 4 clones for site 16 223. Clones also showed other unique, non-reproducible variable sites, as was expected due to random lesions in the aDNA. If consistent variable sites were the result of non-random lesions, this should be evident by cloning amplicons from different individuals. However, none of the four variable sites observed in the Romani haplotype were found in any of the 21 clones from a second cloned Norwich sample. Thus, we rule out the possibility that any of the variable sites, including the specific T→A transversion, are due to amplification ...
Today, I obtained genotype data comprising MCM6 SNPs from HapMap for 2436 individuals from 26 HapMap populations (ESN, GWD, LWK, MSL, YRI, ACB, ASW, CLM, MXL, PEL, PUR, CDX, CHB, CHS, FIN, GBR, IBS, TSI, CEU, BEB, ITU, JPT, KHV, PJL, STU, GIH). Haplotype annotation of each individual can be downloaded here. I focused on all the SNPs that show more variation (more than 1% of the alternative base). I excluded all SNPs that have varying numbers of bases (insertion/deletion), and I excluded rs4988274 and rs55809728 because they did not show a clear pattern (hypervariability?). I excluded all haplotypes that were only present in 2 or less individuals. Using the remaining 203 SNPs I was able to identify 76 haplogroups. Please note that there are many more haplotypes (especially in Africa); I just focused on most common ones as stated above. Please also note that I changed the nomenclature at this stage because the following three reasons ...
Today, I obtained genotype data comprising MCM6 SNPs from HapMap for 2436 individuals from 26 HapMap populations (ESN, GWD, LWK, MSL, YRI, ACB, ASW, CLM, MXL, PEL, PUR, CDX, CHB, CHS, FIN, GBR, IBS, TSI, CEU, BEB, ITU, JPT, KHV, PJL, STU, GIH). Haplotype annotation of each individual can be downloaded here. I focused on all the SNPs that show more variation (more than 1% of the alternative base). I excluded all SNPs that have varying numbers of bases (insertion/deletion), and I excluded rs4988274 and rs55809728 because they did not show a clear pattern (hypervariability?). I excluded all haplotypes that were only present in 2 or less individuals. Using the remaining 203 SNPs I was able to identify 76 haplogroups. Please note that there are many more haplotypes (especially in Africa); I just focused on most common ones as stated above. Please also note that I changed the nomenclature at this stage because the following three reasons ...