Haplotype Block Analysis Research Articles

Novel and efficient tag SNPs selection algorithms

SNPs are the most abundant forms of genetic variations amongst species; the association studies between complex diseases and SNPs or haplotypes have received great attention. However, these studies are restricted by the cost of genotyping all SNPs; thus, it is necessary to find smaller subsets, or tag SNPs, representing the rest of the SNPs. In fact, the existing tag SNP selection algorithms are notoriously time-consuming. An efficient algorithm for tag SNP selection was presented, which was applied to analyze the HapMap YRI data. The experimental results show that the proposed algorithm can achieve better performance than the existing tag SNP selection algorithms; in most cases, this proposed algorithm is at least ten times faster than the existing methods. In many cases, when the redundant ratio of the block is high, the proposed algorithm can even be thousands times faster than the previously known methods. Tools and web services for haplotype block analysis integrated by hadoop MapReduce framework are also developed using the proposed algorithm as computation kernels.

Deletion Of Samsn1 Underlies Genetic Susceptibility To Monoclonal Gammopathy Of Undetermined Significance (MGUS) In Mice

KaLwRij/C57Bl (KaLwRij, “Kal-ridge”) is a spontaneous mutant mouse strain predisposed to monoclonal gammopathy of uncertain significance (MGUS) and parallels many features of human pathology including progression to multiple myeloma (MM). In African Americans, an increased prevalence of MM is due to an increased risk of MGUS development (rather than increased rate of progression from MGUS) and is likely therefore mediated by germline MGUS risk alleles. In both humans and mice, the genetic basis for MGUS/MM risk is unknown. We sought to identify the genetic basis for MGUS/MM risk in KaLwRij mice to shed light on genes or pathways that might mediate risk in humans. We employed a novel integrative computational analysis, combining KaLwRij/B6 modified haplotype block analysis and low-power human MM/control single nucleotide polymorphism (SNP) data. We used high-density SNP arrays to establish genetic distances of KaLwRij from 11 another diverse inbred strains and confirmed close homology to parent C57Bl/6. Haplotype block analysis identified genetic loci that diverged from C57Bl/6 and included over 500 genes. We filtered the haplotype list using previously published RNA expression data from the bone marrow of C57Bl/6 and KaLwRij mice, to identify 71 differentially expressed genes. As a final filter, we used SNP data from a genome wide association study (GWAS) of human Caucasian MM case and normal volunteer samples (∼300 each) to identify SNPs differentially represented in MM patients. Combining these sets yielded four (4) candidate genes. Our top candidate, Samsn1 (Hacs1), is a negative regulator of B-cell activation and interestingly, was first identified as a gene differentially expressed in MM. Strikingly, we found that KaLwRij mice had a complete germline deletion of the Samsn1 gene. Samsn1 is expressed within the hematopoetic compartment, including B-cells, macrophages, and osteoclasts (OC), key cell types that participate in MM pathology. Consistent with the reported inhibitory function of SAMSN1, KaLwRij had enhanced naïve B-cell response and constitutive Lyn phosphorylation. Further, we found that KaLwRij macrophages and OC also have constitutive Lyn activation consistent activation of cytokine signaling pathways in stromal cells. Absence of Samsn1 may lead to unregulated B-cell and macrophage/OC activation, priming both a pro-tumor bone microenvironment and B-cells for development of MGUS and predisposition to MM. Our approach focused on germline loci rather than malignant cell genetic alterations, advancing our understanding of host predisposition. Identification of the gene or genes predisposing patients to MGUS/MM will provide novel targets for identifying at-risk individuals and will potentially allow the develop of preventative therapeutics for MM. Disclosures:No relevant conflicts of interest to declare.

Exome Sequencing Of African American Siblings With Activated, B-Cell Like Diffuse Large B-Cell Lymphoma

Background and AimOne of the major challenges of using published genomic studies of diffuse large B-cell lymphoma (DLBCL) is that the majority of these data were generated from DLBCL patients of European American descent. Genes that were differentially mutated between activated B-cell-like (ABC) and germinal center B-cell-like (GCB) DLBCL in these populations may differ from the gene mutations associated with the increased frequency of ABC DLBCL in patients of African ancestry. We have shown that African-American (AA) DLBCL patients more commonly present with the ABC subtype (Flowers ASH 2012). Winship Cancer Institute provides the ideal patient population to investigate racial differences in lymphoma at the genome level. We have identified AA half-siblings who presented as new consults in the lymphoma clinic, both with ABC DLBCL. The female sibling had progressive disease after R-CHOP therapy, while the male sibling presented with de novo DLBCL. This observation of siblings of African descent with ABC DLBCL, one of whom had already demonstrated a poor clinical outcome with standard therapy, afforded the additional unique opportunity to examine differential prognosis among AA DLBCL patients using exome sequence. Materials and MethodsA tumor sample from a paraffin embedded tissue block was obtained at initial presentation from each sibling, with an additional fresh frozen lymph node obtained from the male subject. Peripheral blood samples were also obtained from each subject to assess DNA from the normal tissue. The NimbleGen SeqCap EZ v3 capture kit was used for whole exome library preparations according to established standard Illumina TruSeq protocols for FFPE samples. Exome sequencing data was generated using the 100x100 paired-end (PE) sequencing protocol for the Illumina HiSeq2000. The PE reads were mapped to Human Reference Genome NCBI36.1/hg19 using Burrow-Wheeler Aligner. VarScan 2 was used for detection of variants (germline and somatic), LOH, and copy number alterations (CNAs) using exome sequence data from the matched tumor and normal samples. Variants were further filtered according to sequencing- or alignment-related artifacts that include among other things, read position, strand bias, variant frequency, distance to 3′, homopolymer, and mapping quality, and visually confirmed by IGV. ResultsAmong the genes with variants identified, EP300, MTOR, MYOM2, and PIK3CD, all previously reported as associated with differentiating ABC from GCB DLBCL, were shown to have germline variants in common between the siblings. A single somatic variant in the EP300 gene was shown specific to the sister. In terms of novel genetic variants, post-filtering, we identified the following possibly damaging (non-benign) germline variants: 4 genes with variants in common between siblings, 5 genes with variants specific to the brother (common to FFPE and Fresh): 19 genes with variants specific to the sister. Novel somatic variants included the following: 1 gene variant specific to the brother (common to FFPE and Fresh), 8 genes with variants specific to the sister. The novel somatic variant specific to the brother also had a reported copy loss that was brother-specific. Exploration of publicly available expression data on ABC DLBCL patients with R-CHOP regimens showed significant associations with overall survival for the genes. We are further exploring haplotype block analysis to infer variant blocks shared by the half-siblings from the common parent to integrate with these results. ConclusionWe provide novel protein-altering variant results for AA half-siblings of differential prognosis that show to be promising novel markers for ABC DLBCL. The question of whether such markers are specific to AA remains yet to be investigated. Disclosures:No relevant conflicts of interest to declare.

Association mapping and haplotype analysis of a 3.1-Mb genomic region involved in Fusarium head blight resistance on wheat chromosome 3BS.

A previous study provided an in-depth understanding of molecular population genetics of European and Asian wheat gene pools using a sequenced 3.1-Mb contig (ctg954) on chromosome 3BS. This region is believed to carry the Fhb1 gene for response to Fusarium head blight. In this study, 266 wheat accessions were evaluated in three environments for Type II FHB response based on the single floret inoculation method. Hierarchical clustering (UPGMA) based on a Manhattan dissimilarity matrix divided the accessions into eight groups according to five FHB-related traits which have a high correlation between them; Group VIII comprised six accessions with FHB response levels similar to variety Sumai 3. Based on the compressed mixed linear model (MLM), association analysis between five FHB-related traits and 42 molecular markers along the 3.1-Mb region revealed 12 significant association signals at a threshold of P<0.05. The highest proportion of phenotypic variation (6.2%) in number of diseased spikelets (NDS) occurred at locus cfb6059, and the physical distance was about 2.9 Kb between umn10 and this marker. Haplotype block (HapB) analysis using a sliding window LD of 5 markers, detected six HapBs in the 3.1-Mb region at r2>0.1 and P<0.001 between random closely linked markers. F-tests among Haps with frequencies >0.05 within each HapB at r2>0.1 and P<0.001 showed significant differences between the Hap carried by FHB resistant resources, such as Sumai 3 and Wangshuibai, and susceptible genotypes in HapB3 and HapB6. These results suggest that Fhb1 is located within HapB6, with the possibility that another gene is located at or near HapB3. SSR markers and Haps detected in this study will be helpful in further understanding the genetic basis of FHB resistance, and provide useful information for marker-assisted selection of Fhb1 in wheat breeding.

A common TPH2 haplotype regulates the neural processing of a cognitive control demand

The monoamine neurotransmitter, serotonin, critically regulates the function of the cerebral cortex and is involved in psychiatric disorders. Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the synthesis of serotonin with the neuron-specific TPH2 isoform present exclusively in the brain and encoded by the TPH2 gene on chromosome 12q21. The haplotype structure of TPH2 was defined for 16 single-nucleotide polymorphisms (SNPs) in a healthy subject population and a haplotype block analysis confirmed the presence of a six SNP haplotype in a yin configuration that has previously been associated with risk for suicidality, depression, and anxiety disorders. Functional magnetic resonance imaging (fMRI) was used to assess the influence of TPH2 variation on brain function related to cognitive control using the Multi-Source Interference Task (MSIT). The MSIT-related blood oxygen level-dependent (BOLD) response was increased with increasing copies of the TPH2 yin haplotype for the dorsal anterior cingulate cortex (dACC), right inferior frontal cortex (IFC), and anterior striatum. A functional connectivity analysis further revealed that increasing numbers of the TPH2 yin haplotype was associated with diminished functional coupling between the dACC and the right IFC, precentral gyrus, parietal cortex and dlPFC. A moderation analysis indicated that the relationship between neural processing networks and cognitive control was significantly modulated by allelic variation for the TPH2 yin haplotype. These findings suggest that the association of risk for psychiatric disorders with a common TPH2 yin haplotype is related to the inefficient functional engagement of cortical areas involved in cognitive control and alterations in the mode of functional connectivity of dACC pathways.

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r(2) ≥ 0.3) in both traditional and village chickens at pairwise marker distances of ~10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling ~75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.

A multicenter study confirms CD226gene association with systemic sclerosis-related pulmonary fibrosis

IntroductionCD226 genetic variants have been associated with a number of autoimmune diseases and recently with systemic sclerosis (SSc). The aim of this study was to test the influence of CD226 loci in SSc susceptibility, clinical phenotypes and autoantibody status in a large multicenter European population.MethodsA total of seven European populations of Caucasian ancestry were included, comprising 2,131 patients with SSc and 3,966 healthy controls. Three CD226 single nucleotide polymorphisms (SNPs), rs763361, rs3479968 and rs727088, were genotyped using Taqman 5'allelic discrimination assays.ResultsPooled analyses showed no evidence of association of the three SNPs, neither with the global disease nor with the analyzed subphenotypes. However, haplotype block analysis revealed a significant association for the TCG haplotype (SNP order: rs763361, rs34794968, rs727088) with lung fibrosis positive patients (PBonf = 3.18E-02 OR 1.27 (1.05 to 1.54)).ConclusionOur data suggest that the tested genetic variants do not individually influence SSc susceptibility but a CD226 three-variant haplotype is related with genetic predisposition to SSc-related pulmonary fibrosis.

Genetic variants of 11 telomere-pathway gene loci and the risk of incident type 2 diabetes mellitus: The Women's Genome Health Study

ObjectiveLeukocyte telomere length shortening has recently been associated with type 2 diabetes mellitus (T2D). Whether this observation was modulated by genetic variation within the telomere-pathway genes remains elusive. To date, no prospective epidemiological data on the relationship of telomere-pathway gene variation with T2D are available. MethodsThe association between 150 tagging-SNPs (tSNPs) of 11 telomere-pathway genes (TERC, UCP1, TERT, POT1, TNKS, TERF1, TNKS2, TEP1, ACD, TERF2 and TERF2IP) and incident T2D was investigated in 22,715 Caucasian female participants of the prospective Women's Genome Health Study. All were free of known cardiovascular disease, cancer and diabetes at baseline. During a 13-year follow-up period, 1445 participants developed an incident T2D. Multivariable Cox regression analysis was performed to investigate the relationship between genotypes and T2D risk assuming an additive genetic model. Haplotype block analysis was also performed. ResultsA total of eleven tSNPs within TERF1, TNKS, TEP1, ACD, and TERF2 were associated with T2D risk (all p-uncorrected <0.050). Further investigation using the haplotype-block analysis again revealed an association of several prespecified haplotypes of TERF1, and TEP1 with T2D risk (all p-uncorrected <0.040). ConclusionIf corroborated in other prospective studies, the present findings suggest that genetic variation within the telomere-pathway gene loci examined may be useful predictor for T2D risk assessment.

Quantitative lymphatic vessel trait analysis suggests Vcam1 as candidate modifier gene of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic debilitating disease resulting from a complex interaction of multiple genetic factors with the environment. To identify modifier genes of IBD, we used an F2 intercross of IBD-resistant C57BL/6J-Il10(-/-) mice and IBD-susceptible C3H/HeJBir-Il10(-/-) (C3Bir-Il10(-/-)) mice. We found a prominent involvement of lymphatic vessels in IBD and applied a scoring system to quantify lymphatic vascular changes. Quantitative trait locus (QTL) analyses revealed a large-effect QTL on chromosome 3, mapping to an interval of 43.6 Mbp. This candidate interval was narrowed by fine mapping to 22 Mbp, and candidate genes were analyzed by a systems genetics approach that included quantitative gene expression profiling, search for functional polymorphisms, and haplotype block analysis. We identified vascular adhesion molecule 1 (Vcam1) as a candidate modifier gene in the interleukin 10-deficient mouse model of IBD. Importantly, VCAM1 protein levels were increased in susceptible C3H/HeJ mice, compared with C57BL/6J mice; systemic blockade of VCAM1 in C3Bir-Il10(-/-) mice reduced their inflammatory lymphatic vessel changes. These results indicate that genetically determined expression differences of VCAM1 are associated with susceptibility to colon inflammation, which is accompanied by extensive lymphatic vessel changes. VCAM1 is, therefore, a promising therapeutic target for IBD.

Practical Applications of the Bioinformatics Toolbox for Narrowing Quantitative Trait Loci

Dissecting the genes involved in complex traits can be confounded by multiple factors, including extensive epistatic interactions among genes, the involvement of epigenetic regulators, and the variable expressivity of traits. Although quantitative trait locus (QTL) analysis has been a powerful tool for localizing the chromosomal regions underlying complex traits, systematically identifying the causal genes remains challenging. Here, through its application to plasma levels of high-density lipoprotein cholesterol (HDL) in mice, we demonstrate a strategy for narrowing QTL that utilizes comparative genomics and bioinformatics techniques. We show how QTL detected in multiple crosses are subjected to both combined cross analysis and haplotype block analysis; how QTL from one species are mapped to the concordant regions in another species; and how genomewide scans associating haplotype groups with their phenotypes can be used to prioritize the narrowed regions. Then we illustrate how these individual methods for narrowing QTL can be systematically integrated for mouse chromosomes 12 and 15, resulting in a significantly reduced number of candidate genes, often from hundreds to <10. Finally, we give an example of how additional bioinformatics resources can be combined with experiments to determine the most likely quantitative trait genes.

BDNF variability in opioid addicts and response to methadone treatment: preliminary findings

Brain-derived neurotrophic factor (BDNF) signaling pathways have been shown to be essential for opioid-induced plasticity. We conducted an exploratory study to evaluate BDNF variability in opioid addict responders and nonresponders to methadone maintenance treatment (MMT). We analyzed 21 single nucleotide polymorphisms (SNPs) across the BDNF genomic region. Responders and nonresponders were classified by means of illicit opioid consumption detected in random urinalysis. Patients were assessed by a structured interview (Psychiatric Research Interview for Substance and Mental Disorders (PRISM)-DSM-IV) and personality was evaluated by the Cloninger's Temperament and Character Inventory. No clinical, environmental and treatment characteristics were different between the groups, except for the Cooperativeness dimension (P < 0.001). Haplotype block analysis showed a low-frequency (2.7%) haplotype (13 SNPs) in block 1, which was more frequent in the nonresponder group than in the responder group (4/42 vs. 1/135; P(corrected) = 0.023). Fine mapping in block 1 allows us to identify a haplotype subset formed by only six SNPs (rs7127507, rs1967554, rs11030118, rs988748, rs2030324 and rs11030119) associated with differential response to MMT (global P sim = 0.011). Carriers of the CCGCCG haplotype had an increased risk of poorer response, even after adjusting for Cooperativeness score (OR = 20.25 95% CI 1.46-280.50, P = 0.025). These preliminary results might suggest the involvement of BDNF as a factor to be taken into account in the response to MMT independently of personality traits, environmental cues, methadone dosage and psychiatric comorbidity.

Hepcidin, transferrin (exon 7), and hemochromatosis genotyping suggests that haplotype block analysis is the best strategy for predicting iron deficiency phenotype in women

Strategies to draw associations between disease, genes and nutrients include the investigation of mutations and/or haplotypes. We studied the relationship between certain mutations in hepcidin (HAMP, exon 1, 2 and 3), transferrin (Tf, exon 7), and hemochromatosis (HFE, H63D and C282Y) genes,aswellastheirassociationsinhaplotypes,andirondeficiency,withorwithoutanemia,inyoung women. One hundred and sixty-two young, menstruating women were recruited. Hemoglobin (Hb [g/ dL]), ferritin (Ft [μg/L]), total iron binding capacity, Tf saturation, hematocrit, and mean corpuscular volume were determined, and subjects were divided in 3 iron status groups: sufficient (Hb ≥12, Ft ≥20; n = 63), deficient (Hb ≥12, Ft b20 or Hb b12, Ft ≥20; n = 77), and deficient-anemic (Hb b12, Ft b20; n = 22). Mutations in the HAMP gene were detected by means of single strand conformational polymorphism analysis, in exon 7 of the Tf gene using DNA sequencing, whereas C282Yand H63D mutations in theHFEgene were detected using restriction enzymes. Among the iron-deficient women, 8 were G277S/L247L-heterozygous (except 1 L247L homozygote), and 1 was I7V-heterozygous for the mutation in the HAMP gene. Three iron-deficient, anemic women were G277S/L247L/H63Dheterozygous (except 1 H63D homozygote), and1 was I7V-heterozygous. Two iron-sufficientfemales were G277S/L247L/H63D-heterozygous, 1 was G277S/L247L/H268H-heterozygous, and 2 were G277S/L247L-heterozygous. In conclusion, (1) the iron-deficient anemic group presented the highest proportion of subjects carrying mutations; (2) there are 3 possible haplotypes: G277S /L247L, G277S/ L247L/H63D, and G277S/L247L/H268H, nonrestricted to any iron status; and (3) analysis of haplotype blocks is the best strategy to associate genes and iron deficiency. © 2007 Elsevier Inc. All rights reserved.

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HtSNPer1.0: software for haplotype block partition and htSNPs selection

BackgroundThere is recently great interest in haplotype block structure and haplotype tagging SNPs (htSNPs) in the human genome for its implication on htSNPs-based association mapping strategy for complex disease. Different definitions have been used to characterize the haplotype block structure in the human genome, and several different performance criteria and algorithms have been suggested on htSNPs selection.ResultsA heuristic algorithm, generalized branch-and-bound algorithm, is applied to the searching of minimal set of haplotype tagging SNPs (htSNPs) according to different htSNPs performance criteria. We develop a software htSNPer1.0 to implement the algorithm, and integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning. It is a software with powerful Graphical User Interface (GUI), which can be used to characterize the haplotype block structure and select htSNPs in the candidate gene or interested genomic regions. It can find the global optimization with only a fraction of the computing time consumed by exhaustive searching algorithm.ConclusionhtSNPer1.0 allows molecular geneticists to perform haplotype block analysis and htSNPs selection using different definitions and performance criteria. The software is a powerful tool for those focusing on association mapping based on strategy of haplotype block and htSNPs.

A Haplotype Block Model for Fine Mapping of Quantitative Trait Loci Regulating HIV-1 Pathogenesis

The dynamic change of human immunodeficiency virus type-1 (HIV-1) particles that cause AIDS displays considerable variation from patients to patients. It is likely that such variation in HIV-1 pathogenesis is correlated with the genetic architecture of hosts. Traditional genetic analysis of HIV-1 infection is based on various biochemical approaches, but it has been little successful because HIV-1 dynamics, as a complex trait, is under polygenic control and sensitive to environmental changes. Here, we present a novel model for integrating mathematical functions for HIV-1 dynamics that have been well constructed into a multivariate mixture model for genetic mapping. This integrative mapping model on the foundation of linkage disequilibrium (LD)-based haplotype block analysis provides unique power to precisely detect human quantitative trait loci (QTL) determining HIV-1 dynamics and facilitates positional cloning of target QTL. The model allows for a number of hypothesis tests for the effects of the dynamic QTL on the virion clearance rate, the infected cell life-span and the average viral generation timein vivo, all of which provide theoretical principles to guide the development of efficient gene therapy strategies.