The HbS gene had a limited number of origins during history, and these can be defined by the haplotype (a set of DNA polymorphisms inherited together) of the associated β-globin gene. Five major haplotypes have been identified, and associated with different ethnic groups. These are the Arab Indian haplotype, the Benin haplotype, the Cameroonian haplotype, the Central African Republic (CAR) or Bantu haplotype, and the Senegal haplotype. The polymorphisms defining these haplotypes are associated with fetal hemoglobin, the major modifier of sickle cell disease phenotype and severity. The Arab Indian haplotype, in particular, is associated with unusually high HbF levels (20%), and a significantly less severe clinical presentation. We found a novel (C>T) SNP -68 bp 5' to HBD in this region, expressed in patients with the Arab Indian haplotype, but not sickle cell disease patients expressing other β-globin cluster haplotypes. There is evidence that this -68 (C>T) polymorphism may play a functional role in the hemoglobin expression of these patients, and its effect on globin levels and disease severity is the long-term interest of this study. A previous reporter assay in K562 cells determined that the -68 SNP was associated with decreased δ-globin gene expression. This study aims to clone the HBD region of a patient positive for this SNP into a lentiviral firefly luciferase reporter vector, for use in more physiologically accurate CD34+ erythropoietic progenitor cells. If the mutations in these β-globin gene haplotypes, such as the HBD mutation described in this study, are responsible for the protective effects seen in patients, perhaps some of these genetic locations can serve as targets for therapeutics in sickle cell disease or other blood disorders.

Hierarchical sampling from populations, incipient and recognized varieties within Phacelia dubia and P. maculata has revealed high levels of intraspecific polymorphism in chloroplast DNA. Much of the variation is partitioned between populations as evidenced by population-specific variants at fixation in all three populations of P. dubia var. interior and in both populations of P. maculata. Nine of 16 populations were polymorphic for cpDNA haplotypes. A total of 16 haplotypes was found in a sample of 106 individuals; the most common occurred in eight of the 16 populations and in 31 per cent of the individuals in the entire sample. A phylogenetic analysis revealed four basic plastome types. The two major groups of plastomes were separated by four independent base-pair mutations which suggests an ancient split in the evolution of plastid genomes. Representatives from each major plastome division were found in each of five populations spanning two allopatric varieties of P. dubia. The geographical distribution of haplotypes and lack of evidence for recent admixture argue against migration as a source of the polymorphism. It is more likely that the current taxonomic varieties are descendants of a polymorphic common ancestor.

High-throughput DNA sequencing technologies are currently revolutionizing the fields of biology and medicine by elucidating the structure and function of the components of life. Modern DNA sequencing machines typically produce relatively short reads of DNA which are then assembled by software in an attempt to produce a representation of the entire genome. Due to the complex structure of all but the smallest genomes, especially the abundant presence of exact or almost exact repeats, all genome assemblers introduce errors into the final sequence and output a relatively large set of contigs instead of full-length chromosomes (a contig is a DNA sequence built from the overlaps between many reads). These problems are dramatically worse when homologous copies of the same chromosome differ substantially. Currently such genomes are usually avoided as assembly targets and, when they are not avoided, they generally produce assemblies of relatively low quality. An improved algorithm for the assembly of such data would dramatically improve our understanding of the genetics of a large class of organisms. We present a unique algorithm for the assembly of diploid genomes which have a high degree of variation between homologous chromosomes. The approach uses coverage, graph patterns and machine-learning classification to identify haplotype-specific sequences in the input reads. It then uses these haplotype-specific markers to guide an improved assembly. We validate the approach with a large experiment that isolates and elucidates the effect of single nucleotide polymorphisms (SNPs) on genome assembly more clearly than any previous study. The experiment conclusively demonstrates that the Bioluminescence heterozygous genome assembler produces dramatically longer contigs with fewer haplotype-switch errors than competing algorithms under conditions of high heterozygosity.

No description available.

No description available.

No description available.

The positional Burrows-Wheeler transform (PBWT) is a foundational data structure for representing haplotype matches of biobank scale. Once the PBWT panel of a set of haplotypes are constructed, efficient algorithms are available for “All vs. All” positional substring matching, finding exact matches of substrings in pre-aligned strings, for haplotypes within the panel, and “One vs. All” positional substring match query for an out-of-panel haplotype against all haplotypes in the panel. While the original PBWT was designed from linear reference genomes, GBWT was proposed to extend PBWT to genome graphs that allow large insertions and deletions. However, there are no GBWT algorithms for haplotype matching. In this work, we develop the efficient algorithms for “All vs. All” and “One vs. All” haplotype set-maximal and long matching algorithms for GBWT. For a GBWT containing a panel of paths P, we show algorithms similar to the matching algorithms of PBWT. Our algorithms achieves theoretically optimal time complexity to output all “All vs. All” matches in time linear to the size of the input panel (O(∑|Pi| + |out put|)), and quasilinear time to the length of the query path for “One vs. All” path match queries (O(|Q| log σ + |out put| log σ ), where σ is the maximum out- degree in the GBWT and out put is the set of discovered path matches). Under the constant σ assumption made by gPBWT and GBWT, these algorithms are in fact linear. Our algorithms open the possibilities for applications of efficient positional substring matching in pangenome references such as identical-by-descent (IBD) segment identification and genotype imputation.

Ce travail concerne des hémopathies myéloïdes malignes appelés Néoplasmes Myéloprolifératifs (NMP) qui incluent les Polyglobulies de Vaquez (PV), les Thrombocythémies Essentielles (TE) et les Myélofibroses Primaires (MFP). Ces maladies résultent de la transformation d’une cellule souche hématopoïétique (CSH) avec hyperprolifération mais sans blocage de différentiation. Leur défaut moléculaire le plus fréquent est la mutation JAK2V617F résultant dans l’activation de la signalisation des récepteurs aux cytokines utilisant JAK2. Au cours de ce travail, nous avons développé un modèle murin « Knock-In » (KI) constitutif et conditionnel pour la mutation JAK2V617F. Ces animaux développent une maladie mimant la PV humaine évoluant vers la MF secondaire. Ces animaux présentent augmentation en fonction de l’âge du nombre de cellules immatures (phénotypes Lin-, LSK et SLAM: LSK/CD48-/CD150+). Dans un système compétitifs in vivo nous montrons que les cellules KI ont un avantage prolifératif dés le stade CSH et qu'un faible nombre de CSH peuvent déclencher la maladie. Ces résultats suggèrent que la mutation JAK2V617F seule est suffisante pour (1) le phénotype et (2) l'émergence de ces maladies. Nous avons aussi testé l'effet de l'interféron-a (IFNa) sur le développement des NMP en utilisant ces souris JAK2V617F KI. Nous montrons que l'IFNa traite le phénotype de la maladie en bloquant la propagation des cellules KI dés le stade immature avec éradication des cellules souches néoplasiques, entraînant comme chez certains patients PV une rémission hématologique et aussi moléculaire. Enfin, en combinant l’analyse quantitative de l’haplotype 46/1 et de la mutation JAK2V617F sur les cellules sanguines nous développons une nouvelle méthode prédictive de la fréquence des clones hétérozygotes et homozygotes JAK2V617F chez les patients PV. Cette étude suggère que l'IFNa cible préférentiellement le clone homozygote JAK2V617F et que sa réponse est fonction de l’intensité de la signalisation JAK2. / This work concerns malignant myeloid hemopathies called classical BCR-ABL-negative Myeloproliferative Neoplasms (MPN) and include Polycythemia Vera (PV), Essential Thrombocythemia (ET) and Primary Myelofibrosis (PMF). They result from the transformation of a multipotent hematopoietic stem cell (HSC) with hyperproliferation but no blockade of differentiation. The most common molecular defect is the acquired point mutation JAK2V617F resulting into the activation of the cytokine receptor/JAK2 pathway. We have developed a mouse constitutive and a conditional JAK2V617F knock-in (KI) mouse models. These animals developed a disease mimicking human PV evolving into secondary MF. They also displayed an age dependent increase in the total numbers of early hematopoietic cells (phenotype LK, LSK and SLAM: LSK/CD48-/CD150+). Using In vivo competitive repopulation assays we demonstrated that cells from KI origin outcompeted their WT counterparts and that a low number of JAK2V617F KI SLAM cells propagates the disease. These results show that the sole JAK2V617F mutation, without any additional mutations, is sufficient for disease phenotype and emergence. Using this KI mouse model, we tested the effect of interferon-a (IFNa) treatment on MPN development. We found that IFNa treats the disease phenotype by blocking the propagation of early JAK2V617F cells and eradicates disease-initiating cells, showing that IFNα could cure the disease in mice, as shown in some PV patients. Finally, we developed a new method combining the measurement of 46/1 SNPs and JAK2V617F allele burdens in blood predicting the frequency of normal, heterozygous and homozygous JAK2V617F clones in PV patients. This study suggested that IFNa preferentially targets the homozygous JAK2V617F clone in PV patients suggesting a link between the levels of JAK2 signaling and the success of the IFNa response.

BACKGROUND:General, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency - residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) - were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.RESULTS:For the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value<0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value<0.001) including, 9nucleotide binding / ion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.CONCLUSIONS:The general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.

Genotype microarrays assay hundreds of thousands of genetic variants on an individual's genome. The availability of this high throughput genotyping capability has transformed the field of genetics over the past decade by enabling thousands of individuals to be rapidly assayed. This has lead to the discovery of hundreds of genetic variants that are associated with disease and other phenotypes in genome wide association studies (GWAS). These data have also brought with them a number of new statistical and computational challenges. This thesis deals with two primary analysis problems involving microarray data; genotype calling and haplotype inference. Genotype calling involves converting the noisy bivariate fluorescent signals generated by microarray data into genotype values for each genetic variant and individual. Poor quality genotype calling can lead to false positives and loss of power in GWAS so this is an important task. We introduce a new genotype calling method that is highly accurate and has the novel capability of fusing microarray data with next-generation sequencing data for greater accuracy and fewer missing values. Our new method compares favourably to other available genotype calling software. Haplotype inference (or phasing) involves deconvolving these genotypes into the two inherited parental chromosomes for an individual. The development of phasing methods has been a fertile field for statistical genetics research for well over ten years. Depending on the demography of a cohort, different phasing methods may be more appropriate than others. We review the popular offerings and introduce a new approach to try and unify two distinct problems; the phasing of extended pedigrees and the phasing of unrelated individuals. We conduct an extensive comparison of phasing methods on real and simulated data. Finally we demonstrate some preliminary results on extending methodology to sample sizes in the tens of thousands.