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Journal articles on the topic 'Haplotypage'

Author: Grafiati

Published: 25 January 2025

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1

Kim, Ki-Bong. "Development of Haplotype Reconstruction System Using Public Resources." Journal of the Korea Academia-Industrial cooperation Society 11, no. 2 (February 28, 2010): 720–26. http://dx.doi.org/10.5762/kais.2010.11.2.720.

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2

Xu, Hanli, and Yongtao Guan. "Detecting Local Haplotype Sharing and Haplotype Association." Genetics 197, no. 3 (May 8, 2014): 823–38. http://dx.doi.org/10.1534/genetics.114.164814.

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3

Li, Ming, Roberto Romero, Wenjiang J. Fu, and Yuehua Cui. "Mapping Haplotype-haplotype Interactions with Adaptive LASSO." BMC Genetics 11, no. 1 (2010): 79. http://dx.doi.org/10.1186/1471-2156-11-79.

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4

Fellows, M. R., T. Hartman, D. Hermelin, G. M. Landau, F. Rosamond, and L. Rozenberg. "Haplotype Inference Constrained by Plausible Haplotype Data." IEEE/ACM Transactions on Computational Biology and Bioinformatics 8, no. 6 (November 2011): 1692–99. http://dx.doi.org/10.1109/tcbb.2010.72.

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5

Salem, M. M. I., G. Thompson, S. Chen, A. Beja-Pereira, and J. Carvalheira. "Linkage disequilibrium and haplotype block structure in Portuguese Holstein cattle." Czech Journal of Animal Science 63, No. 2 (January 19, 2018): 61–69. http://dx.doi.org/10.17221/56/2017-cjas.

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The objectives of this study were to estimate linkage disequilibrium (LD), describe and scan a haplotype block for the presence of genes that may affect milk production traits in Portuguese Holstein cattle. Totally 526 animals were genotyped using the Illumina BovineSNP50 BeadChip, which contained a total of 52 890 single nucleotide polymorphisms (SNPs). The final set of markers remaining after considering quality control standards consisted of 37 031 SNPs located on 29 autosomes. The LD parameters historical recombinations through allelic association (D') and squared correlation coefficient between locus alleles frequencies ( r<sup>2</sup>) were estimated and haplotype block analyses were performed using the Haploview software. The averages of D' and r<sup>2</sup> values were 0.628 and 0.122, respectively. The LD value decreased with increasing physical distance. The D' and r<sup>2</sup> values decreased respectively from 0.815 and 0.283 at the distance of 0–30 kb to 0.578 and 0.090 at the distance of 401–500 kb. The identified total number of blocks was 969 and consisted of 4259 SNPs that covered 159.06 Mb (6.24% of the total genome) on 29 autosomes. Several genes inside the haplotype blocks were detected; CSN1S2 gene in haplotype block 51 on BTA 6, IL6 and B4GALT1 genes in haplotype blocks 6 and 33 on BTA 8, IL1B and ID2 genes in haplotype blocks 19 and 29 on BTA 11, and DGAT1 gene in haplotype block 1 on BTA 14. The extension of LD using BovineSNP50 BeadChip did not exceed 500 kb and its parameters r<sup>2</sup> and D’ were less than 0.2 and 0.70, respectively, after 70–100 kb. Consequently, the 50K BeadChip would have a poor power in genome wide association studies at distances between adjacent markers lower than 70 kb.

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6

Kreisberg, Jason. "Haplotype roundup." Nature Biotechnology 30, no. 8 (August 2012): 768. http://dx.doi.org/10.1038/nbt.2337.

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7

Schwartz, Russell. "Haplotype Parsing." Applied Bioinformatics 3, no. 2 (2004): 181–91. http://dx.doi.org/10.2165/00822942-200403020-00012.

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8

Weitzman, Jonathan B. "Haplotype blocks." Genome Biology 3 (2002): spotlight—20020524–01. http://dx.doi.org/10.1186/gb-spotlight-20020524-01.

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9

Boleckova, J., F. Christensen O, P. Sørensen, and G. Sahana. "Strategies for haplotype-based association mapping in a complex pedigreed population." Czech Journal of Animal Science 57, No. 1 (January 27, 2012): 1–9. http://dx.doi.org/10.17221/5478-cjas.

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In association mapping, haplotype-based methods are generally regarded to provide higher power and increased precision than methods based on single markers. For haplotype-based association mapping most studies use a fixed haplotype effect in the model. However, an increase in haplotype length raises the number of parameters in the model, resulting in low accuracy of the estimates especially for the low-frequency haplotypes. Modeling of haplotype effects can be improved if they are assumed to be random effects, as only one parameter, i.e. haplotype variance, needs to be estimated compared to estimating the effects of all different haplotypes in a fixed haplotype model. Using simulated data, we investigated statistical models where haplotypes were fitted either as a fixed or random effect and we compared them for the power, precision, and type I error. We investigated five haplotype lengths of 2, 4, 6, 10 and 20. The simulated data resembled the Danish Holstein cattle pedigree representing a complex relationship structure and QTL effects of different sizes were simulated. We observed that the random haplotype models had high power and very low type I error rates (after the Bonferroni correction), while the fixed haplotype models had lower power and excessively high type I errors. Haplotype length of 4 to 6 gave the best results for random model in the present study. Though the present study was conducted on data structure more frequent in livestock, our findings on random vs. fixed haplotype effects in association mapping models are applicable to data from other species with a similar pedigree structure.  

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10

Rustgi, S., R. Bandopadhyay, H. S. Balyan, and P. K. Gupta. "EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure." Czech Journal of Genetics and Plant Breeding 45, No. 3 (October 6, 2009): 106–16. http://dx.doi.org/10.17221/16/2009-cjgpb.

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The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candidate EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1–18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.

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11

Li, Jun, Kui Zhang, and Nengjun Yi. "A Bayesian Hierarchical Model for Detecting Haplotype-Haplotype and Haplotype-Environment Interactions in Genetic Association Studies." Human Heredity 71, no. 3 (2011): 148–60. http://dx.doi.org/10.1159/000324841.

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12

Green, Jack, and Mamdouh Montasser. "HLA Haplotype Discordance." Biometrics 44, no. 4 (December 1988): 941. http://dx.doi.org/10.2307/2531725.

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13

Sebastiani, P., R. Lazarus, S. T. Weiss, L. M. Kunkel, I. S. Kohane, and M. F. Ramoni. "Minimal haplotype tagging." Proceedings of the National Academy of Sciences 100, no. 17 (August 4, 2003): 9900–9905. http://dx.doi.org/10.1073/pnas.1633613100.

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14

Forton, Julian, Dominic Kwiatkowski, Kirk Rockett, Gaia Luoni, Martin Kimber, and Jeremy Hull. "Accuracy of Haplotype Reconstruction from Haplotype-Tagging Single-Nucleotide Polymorphisms." American Journal of Human Genetics 76, no. 3 (March 2005): 438–48. http://dx.doi.org/10.1086/428439.

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15

Mueller, J. C., and C. Andreoli. "Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity." Bioinformatics 20, no. 5 (February 5, 2004): 786–87. http://dx.doi.org/10.1093/bioinformatics/btg481.

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16

Hardy, J., A. Pittman, A. Myers, K. Gwinn-Hardy, H. C. Fung, R. de Silva, M. Hutton, and J. Duckworth. "Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens." Biochemical Society Transactions 33, no. 4 (August 1, 2005): 582–85. http://dx.doi.org/10.1042/bst0330582.

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The tau (MAPT) locus exists as two distinct clades, H1 and H2. The H1 clade has a normal linkage disequilibrium structure and is the only haplotype found in all populations except those derived from Caucasians. The H2 haplotype is the minor haplotype in Caucasian populations and is not found in other populations. It shows no recombination over a region of 2 Mb with the more common H1 haplotype. The distribution of the haplotype and analysis of the slippage of dinucleotide repeat markers within the haplotype suggest that it entered Homo sapiens populations between approx. 10000 and 30000 years ago. However, sequence comparison of the H2 haplotype with the H1 haplotype and with the chimp sequence suggests that the common founder of the H1 and H2 haplotypes was far earlier than this. We suggest that the H2 haplotype is derived from Homo neanderthalensis and entered H. sapiens populations during the co-existence of these species in Europe from approx. 45000 to 18000 years ago and that the H2 haplotype has been under selection pressure since that time, possibly because of the role of this H1 haplotype in neurodegenerative disease.

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17

Makarasara, Wattanan, Natsuhiko Kumasaka, Anunchai Assawamakin, Atsushi Takahashi, Apichart Intarapanich, Chumpol Ngamphiw, Supasak Kulawonganunchai, et al. "pHCR: a Parallel Haplotype Configuration Reduction algorithm for haplotype interaction analysis." Journal of Human Genetics 54, no. 11 (November 2009): 634–41. http://dx.doi.org/10.1038/jhg.2009.85.

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18

Oliveira, Sofia A., William K. Scott, Fengyu Zhang, Jeffrey M. Stajich, Kenichiro Fujiwara, Michael Hauser, Burton L. Scott, Margaret A. Pericak-Vance, Jeffery M. Vance, and Eden R. Martin. "Linkage disequilibrium and haplotype tagging polymorphisms in the Tau H1 haplotype." Neurogenetics 5, no. 3 (June 8, 2004): 147–55. http://dx.doi.org/10.1007/s10048-004-0180-5.

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19

Bahlo, Melanie, Jim Stankovich, Terence P. Speed, Justin P. Rubio, Rachel K. Burfoot, and Simon J. Foote. "Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data." Human Genetics 119, no. 1-2 (December 14, 2005): 38–50. http://dx.doi.org/10.1007/s00439-005-0114-9.

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20

Sato, S., C. Ohnishi, Y. Uemoto, and E. Kobayashi. "Haplotype analysis within quantitative trait locus affecting intramuscular fat content on porcine chromosome." Czech Journal of Animal Science 56, No. 12 (December 22, 2011): 521–28. http://dx.doi.org/10.17221/4414-cjas.

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Previous results of fine mapping for quantitative trait loci affecting intramuscular fat content identified a 3.0-Mb chromosome interval on porcine chromosome 7, which contains at least 9 genes, based on the pig genome assembly. Therefore, we proposed these nine genes (LOC100154481, LOC100155711, LOC100155276, SPATA7, PTPN21, ZCH14, EML5, TTC8, and FOXN3) as positional candidate genes. The coding exons of the nine genes were characterized, and 45 polymorphisms were detected in F<sub>2</sub> Duroc × Meishan population. Within the nine genes, 10 non-synonymous substitutions and 1 insertion were genotyped among three European breeds (Landrace, Large White, and Duroc) and 1 Chinese breed (Meishan). Genotyping data was used to perform the haplotype analysis. Polymorphisms were found in all the studied genes, except ZCH14. We surveyed the frequency of 33 haplotypes that formed non-synonymous substitutions in four breeds. One of them was distributed widely in the Landrace, Large White, and Meishan breeds, but not in Duroc. Each breed had different major haplotypes.  

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21

Zhang, X., C. Ma, D. Yin, W. Zhu, C. Gao, J. Zhang, and T. Fu. "Characterization of S haplotype in a new self-compatible Brassica rapa cultivar Dahuangyoucai." Czech Journal of Genetics and Plant Breeding 49, No. 4 (November 26, 2013): 157–63. http://dx.doi.org/10.17221/159/2012-cjgpb.

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The most important Brassica species, B. rapa, is naturally self-incompatible. Self-compatible mutants would be useful for dissecting the molecular mechanism of self-incompatibility (SI), a process that promotes outcrossing by recognizing and refusing self-pollens. The S haplotype in a new self-compatible B. rapa cultivar, Dahuangyoucai, was characterized for the first time in this study. Sequence analysis of the S-locus genes, SLG (S-locus glycoprotein), SRK (S-locus receptor kinase) and SCR (S-locus cysteine-rich protein) revealed that Dahuangyoucai contained S haplotype highly similar to S-f2, a non-functional class I S haplotype identified in another self-compatible B. rapa cultivar, Yellow Sarson. Mutations of MLPK (M-locus protein kinase) and non-transcription of the male determinant, SCR, were observed in this cultivar, which is similar to the situation reported in Yellow Sarson. With respect to the female determinant, SRK, no transcript was detected in Yellow Sarson but two fragments were detected in Dahuangyoucai. One fragment was highly similar to SRK-f2, but the other fragment was different from the signal factors previously identified in the SI reaction. The results suggest that Dahuangyoucai and Yellow Sarson have the same origin and a similar mechanism of self-compatibility, but diverge after mutations in SRK, SCR and MLPK. Further studying the self-compatibility of Dahuangyoucai might identify novel factors involved in the SI signalling cascade and provide new insights into the mechanisms of SI in Brassicaceae.

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22

Anantaphruti, Malinee, Urusa Thaenkham, Teera Kusolsuk, Wanna Maipanich, Surapol Saguankiat, Somjit Pubampen, and Orawan Phuphisut. "Genetic Variation and Population Genetics ofTaenia saginatain North and Northeast Thailand in relation toTaenia asiatica." Journal of Parasitology Research 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/310605.

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Taenia saginatais the most common humanTaeniain Thailand. Bycox1sequences, 73 isolates from four localities in north and northeast were differentiated into 14 haplotypes, 11 variation sites and haplotype diversity of 0.683. Among 14 haplotypes, haplotype A was the major (52.1%), followed by haplotype B (21.9%). Clustering diagram of Thai and GenBank sequences indicated mixed phylogeny among localities. By MJ analysis, haplotype clustering relationships showed paired-stars-like network, having two main cores surrounded by minor haplotypes. Tajima’sDvalues were significantly negative inT. saginataworld population, suggesting population expansion. Significant Fu’sFsvalues in Thai, as well as world population, also indicate that population is expanding and may be hitchhiking as part of selective sweep. Haplotype B and its dispersion were only found in populations from Thailand. Haplotype B may evolve and ultimately become an ancestor of future populations in Thailand. Haplotype A seems to be dispersion haplotype, not just in Thailand, but worldwide. High geneticT. saginataintraspecies divergence was found, in contrast to its sister species,T. asiatica; among 30 samples from seven countries, its haplotype diversity was 0.067, while only 2 haplotypes were revealed. This extremely low intraspecific variation suggests thatT. asiaticacould be an endangered species.

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23

Armstrong, M. A., G. V. McDonnell, C. A. Graham, C. W. Kirk, A. G. Droogan, and S. A. Hawkins. "Relationship between tumour necrosis factor-alpha (TNFα) production and a specific multiple sclerosis (MS) associated TNF gene haplotype." Multiple Sclerosis Journal 5, no. 3 (June 1999): 165–70. http://dx.doi.org/10.1177/135245859900500305.

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Objective: To determine if monocyte TNFa production from patients homozygous for a specific MS associated TNF gene haplotype is different from that produced in patients either heterozygous for, or without this haplotype. Background: The balance between pro- and anti-inflammatory cytokines is important in the clinical outcome of inflammatory reactions. Levels of TNFa, a pro-inflammatory cytokine, is raised in MS as well as being found in acute and chronic MS lesions. A previous population based study in Northern Ireland with polymorphisms spanning the TNF gene region identified a conserved MS associated haplotype in relation to three markers (130: 118: 127 TNF d: a: b) for which 19 MS patients were homozygous. Methods: Venous blood collected in EDTA to give a concentration of 1073 M was drawn from 16 patients with the conserved MS associated haplotype, 19 patients heterozygous for the haplotype and 17 patients without the haplotype. Mononuclear cells were separated and cultured by standard techniques and levels of TNFa and of TNF binding proteins I and II were determined by commercial enzyme-linked immunosorbent assays. Results: There were no significant differences in TNFa production in the 3 h (P=0.28) or 24 h cultures (P=0.18) or following stimulation with interferon-g (P=0.17) between the group positive for the conserved haplotype and the group negative for this haplotype. There was also no significant difference when compared to the heterozygote group. No association was found between the MS associated haplotype and levels of either TNF binding protein. A greater proportion of patients with the conserved haplotype had a benign clinical course (P=0.06). Conclusion: We conclude that whilst a trend exists, we have found no significant association between peripheral TNFa production and a specific MS associated TNF haplotype in this population. Paradoxically this haplotype may also predict a more favourable clinical course.

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24

White, Perrin C., and Liliya Slutsker. "Haplotype analysis of CYP11B2." Endocrine Research 21, no. 1-2 (January 1995): 437–42. http://dx.doi.org/10.3109/07435809509030459.

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25

MORTON, NEWTON E., S. PATRICIA SIMPSON, RUTH LEW, and SHIRLEY YEE. "Estimation of haplotype frequencies." Tissue Antigens 22, no. 4 (December 11, 2008): 257–62. http://dx.doi.org/10.1111/j.1399-0039.1983.tb01201.x.

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26

Flintoft, Louisa. "Haplotype maps go global." Nature Reviews Genetics 7, no. 12 (December 2006): 906. http://dx.doi.org/10.1038/nrg2014.

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27

Weerasekara, Vajira Samanthi. "Genome-wide haplotype analysis." Sri Lanka Journal of Bio-Medical Informatics 3, no. 1 (January 8, 2013): 20. http://dx.doi.org/10.4038/sljbmi.v3i1.2564.

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28

Bahcall, Orli. "Single-haplotype genome assembly." Nature Genetics 46, no. 12 (November 24, 2014): 1257. http://dx.doi.org/10.1038/ng.3157.

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29

Zhang, K., and L. Jin. "HaploBlockFinder: haplotype block analyses." Bioinformatics 19, no. 10 (July 1, 2003): 1300–1301. http://dx.doi.org/10.1093/bioinformatics/btg142.

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30

Arnold, Paula Y., Sheila Shurtleff, and Victoria Turner. "4-OR Haplotype loss." Human Immunology 72 (October 2011): S2. http://dx.doi.org/10.1016/j.humimm.2011.07.009.

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31

Wigger, Leonore, Julia E. Vogt, and Volker Roth. "Malaria haplotype frequency estimation." Statistics in Medicine 32, no. 21 (April 23, 2013): 3737–51. http://dx.doi.org/10.1002/sim.5792.

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32

Terwilliger, Joseph D., and Jurg Ott. "A Haplotype-Based Haplotype Relative Risk’ Approach to Detecting Allelic Associations." Human Heredity 42, no. 6 (1992): 337–46. http://dx.doi.org/10.1159/000154096.

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33

Jin, Lina, Wensheng Zhu, and Jianhua Guo. "Genome-wide association studies using haplotype clustering with a new haplotype similarity." Genetic Epidemiology 34, no. 6 (August 17, 2010): 633–41. http://dx.doi.org/10.1002/gepi.20521.

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34

Mendoza, Yamandú, Estela Gramajo, Ciro Invernizzi, and Ivanna H. Tomasco. "Mitochondrial haplotype analyses of the mite Varroa destructor (Acari: Varroidae) collected from honeybees Apis mellifera (Hymenoptera, Apidae) in Uruguay." Systematic and Applied Acarology 25, no. 8 (September 1, 2020): 1526–29. http://dx.doi.org/10.11158/saa.25.8.14.

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The ectoparasite Varroa destructor is currently the main health problem faced by honeybees Apis mellifera in the world. It has been identified that two haplotypes were able of infecting and reproducing in this species: the “Korean haplotype” (K) and the “Japanese haplotype” (J). Both haplotypes differ in their virulence, being the K haplotype more harmful than the J. V. destructor was detected for the first time in Uruguay in 1978, but its effect on honeybees is very different depending on the region of the country. Although the K haplotype predominates in South America, the presence of J haplotype in Uruguay is possible, and may be the cause of different virulence of the mites. The aims of this study were to identify the haplotype of V. destructor existing throughout Uruguay and, at the same time, to present a new strategy of RFLP which that presents an internal positive control of digestion. Despite the differences in the effect of V. destructor on honeybees in different areas of the country, all the colonies evaluated presented the K haplotype. The presence in the past of haplotype J cannot be ruled out, and could be assessed with independent nuclear markers.

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35

Haapalainen, Minna, Satu Latvala, Annika Wickström, Jinhui Wang, Minna Pirhonen, and Anne I. Nissinen. "A novel haplotype of ‘Candidatus Liberibacter solanacearum’ found in Apiaceae and Polygonaceae family plants." European Journal of Plant Pathology 156, no. 2 (November 28, 2019): 413–23. http://dx.doi.org/10.1007/s10658-019-01890-0.

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AbstractA previously unknown haplotype of the plant pathogen ‘Candidatus Liberibacter solanacearum’ (Lso) was found in cultivated carrots and parsnips in eastern Finland. That same haplotype was found in western Finland, over 300 km away, in the family Polygonaceae, the species Fallopia convolvulus (wild buckwheat) and Persicaria lapathifolia (pale persicaria) growing as weeds within carrot and parsnip fields. The infected plants, both apiaceous and polygonaceous, showed symptoms of foliar discolouration. This is the first report of Lso bacteria in plants of the family Polygonaceae. The finding that the polygonaceous plants infected with a previously unknown haplotype of Lso were growing among the apiaceous plants infected with Lso haplotype C suggests that these two haplotypes might be transmitted by different vectors. Phylogenetic analyses showed that the new haplotype, called haplotype H, is distinct from the previously characterized haplotypes and appears to have diverged early from their common ancestor. Multi-locus sequence analysis revealed four different sequence types (strains) within the haplotype H. These findings suggest that the haplotype H is likely to be endemic in northern Europe and that the genetic diversity within the Lso species is higher than previously assumed.

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36

Thompson, Sarah M., Chris P. Johnson, Ashley Y. Lu, Rebekah A. Frampton, Kerry L. Sullivan, Mark W. E. J. Fiers, Ross N. Crowhurst, et al. "Genomes of ‘Candidatus Liberibacter solanacearum’ Haplotype A from New Zealand and the United States Suggest Significant Genome Plasticity in the Species." Phytopathology® 105, no. 7 (July 2015): 863–71. http://dx.doi.org/10.1094/phyto-12-14-0363-fi.

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‘Candidatus Liberibacter solanacearum’ contains two solanaceous crop-infecting haplotypes, A and B. Two haplotype A draft genomes were assembled and compared with ZC1 (haplotype B), revealing inversion and relocation genomic rearrangements, numerous single-nucleotide polymorphisms, and differences in phage-related regions. Differences in prophage location and sequence were seen both within and between haplotype comparisons. OrthoMCL and BLAST analyses identified 46 putative coding sequences present in haplotype A that were not present in haplotype B. Thirty-eight of these loci were not found in sequences from other Liberibacter spp. Quantitative polymerase chain reaction (qPCR) assays designed to amplify sequences from 15 of these loci were screened against a panel of ‘Ca. L. solanacearum’-positive samples to investigate genetic diversity. Seven of the assays demonstrated within-haplotype diversity; five failed to amplify loci in at least one haplotype A sample while three assays produced amplicons from some haplotype B samples. Eight of the loci assays showed consistent A–B differentiation. Differences in genome arrangements, prophage, and qPCR results suggesting locus diversity within the haplotypes provide more evidence for genetic complexity in this emerging bacterial species.

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37

Dahan, Jennifer, Erik J. Wenninger, Brandon D. Thompson, Sahar Eid, Nora Olsen, and Alexander V. Karasev. "Prevalence of ‘CandidatusLiberibacter solanacearum’ Haplotypes in Potato Tubers and Psyllid Vectors in Idaho From 2012 to 2018." Plant Disease 103, no. 10 (October 2019): 2587–91. http://dx.doi.org/10.1094/pdis-11-18-2113-re.

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‘Candidatus Liberibacter solanacearum’ (Lso) is an uncultured, phloem-associated bacterium causing a severe tuber disease in potato called zebra chip (ZC). Seven haplotypes of Lso have been described in different hosts, with haplotypes A and B found associated with infections in potato and tomato. In the field, Lso is transmitted by the potato psyllid (Bactericera cockerelli), and between 2011 and 2015, a significant change in Lso haplotype prevalence was previously reported in Idaho: from exclusively A haplotype found in tested psyllids in 2012 to mainly B haplotype found in collected psyllids in 2015. However, prevalence of Lso haplotypes in Idaho was not analyzed in potato tubers exhibiting symptoms of ZC. To fill in this knowledge gap, prevalence of Lso haplotypes was investigated in potato tubers harvested in southern Idaho between 2012 and 2018, and it was found to change from exclusively A haplotype in the 2012 season to an almost equal A and B haplotype distribution during the 2016 season. During the same period, haplotype distribution of Lso in psyllid vectors collected using yellow sticky traps also changed, but in psyllids, the shift from A haplotype of Lso to B haplotype was complete, with no A haplotype detected in 2016 to 2018. The changes in the haplotype prevalence of the Lso circulating in potato fields in southern Idaho may be, among other factors, responsible for a decrease in the ZC incidence in Idaho potato fields between an outbreak of the disease in 2012 and a very low level of ZC afterward.

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38

Nadeau, J. H., D. Varnum, and D. Burkart. "Genetic evidence for two t complex tail interaction (tct) loci in t haplotypes." Genetics 122, no. 4 (August 1, 1989): 895–903. http://dx.doi.org/10.1093/genetics/122.4.895.

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Abstract The t complex on chromosome 17 of the house mouse is an exceptional model for studying the genetic control of transmission ratio, gametogenesis, and embryogenesis. Partial haplotypes derived through rare recombination between a t haplotype and its wild-type homolog have been essential in the genetic analysis of these various properties of the t complex. A new partial t haplotype, which was derived from the complete tw71 haplotype and which is called tw71Jr1, was shown to have unexpected effects on tail length and unique recombination breakpoints. This haplotype, either when homozygous or when heterozygous with the progenitor tw71 haplotype, produced short-tailed rather than normal-tailed mice on certain genetic backgrounds. Genetic analysis of this exceptional haplotype showed that the recombination breakpoints were different from those leading to any other partial t haplotype. Based on this haplotype, a model is proposed that accounts for genetic interactions between the brachyury locus (T), the t complex tail interaction (tct) locus, and their wild-type homolog(s) that determine tail length. An important part of this model is the hypothesis that the tct locus, which enhances the tail-shortening effect of T mutations, is in fact at least two, genetically separable genes with different genetic activities. Genetic analysis of parental and recombinant haplotypes also suggests that intrachromosomal recombination involving an inverted duplicated segment can account for the variable orientation of loci within an inverted duplication on wild-type homologs of the t haplotype.

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TAN, QIHUA, LENE CHRISTIANSEN, KAARE CHRISTENSEN, LISE BATHUM, SHUXIA LI, JING HUA ZHAO, and TORBEN A. KRUSE. "Haplotype association analysis of human disease traits using genotype data of unrelated individuals." Genetical Research 86, no. 3 (November 25, 2005): 223–31. http://dx.doi.org/10.1017/s0016672305007792.

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Haplotype inference has become an important part of human genetic data analysis due to its functional and statistical advantages over the single-locus approach in linkage disequilibrium mapping. Different statistical methods have been proposed for detecting haplotype – disease associations using unphased multi-locus genotype data, ranging from the early approach by the simple gene-counting method to the recent work using the generalized linear model. However, these methods are either confined to case – control design or unable to yield unbiased point and interval estimates of haplotype effects. Based on the popular logistic regression model, we present a new approach for haplotype association analysis of human disease traits. Using haplotype-based parameterization, our model infers the effects of specific haplotypes (point estimation) and constructs confidence interval for the risks of haplotypes (interval estimation). Based on the estimated parameters, the model calculates haplotype frequency conditional on the trait value for both discrete and continuous traits. Moreover, our model provides an overall significance level for the association between the disease trait and a group or all of the haplotypes. Featured by the direct maximization in haplotype estimation, our method also facilitates a computer simulation approach for correcting the significance level of individual haplotype to adjust for multiple testing. We show, by applying the model to an empirical data set, that our method based on the well-known logistic regression model is a useful tool for haplotype association analysis of human disease traits.

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Adabale, Abosede, Samira Batista Lobo Makanjuola, Akinsegun Akinbami, Adedoyin Dosunmu, Alani Akanmu, Farideh A. Javid, and Louis C. Ajonuma. "Frequency of beta S globin gene haplotypes among sickle cell patients in Nigeria." Journal of International Medical Research 49, no. 6 (June 2021): 030006052110199. http://dx.doi.org/10.1177/03000605211019918.

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Objective To determine the frequency of beta s globin gene haplotypes in Nigerian patients with sickle cell disease (SCD) and to measure their correlation with clinical and haematological characteristics. Methods This study enrolled patients with SCD and collected their peripheral blood for restriction fragment length polymorphism analysis in order to identify five polymorphic sites in the β-globin gene cluster. Results A total of 245 homozygous SCD patients (490 alleles) were included in the study. Among the analysed alleles, 426 (86.9%) had the Benin (BEN) haplotype; 19 (3.9%) had the Senegal (SEN) haplotype; 31 (6.3%) had the Cameroon haplotype; five (1.0%) had the Bantu/Central African Republic haplotype; and nine 9 (1.8%) had atypical haplotypes. No significant association was observed between the haplotypes and haematological events, although patients with the BEN/SEN haplotype showed improved red blood cell counts, haemoglobin levels and red blood cell width index. No significant association was observed between the haplotypes and the three clinical manifestations, although patients with the BEN/SEN haplotype showed a four-fold lower frequency of painful episodes. Conclusion These findings suggest that the SEN haplotype combined with the BEN haplotype might contribute toward a better haematological profile and milder clinical severity in SCD.

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SAZONOVA, NADEZHDA, and E. JAMES HARNER. "HAPLOTYPE INFERENCE AND BLOCK PARTITIONING IN MIXED POPULATION SAMPLES." Journal of Bioinformatics and Computational Biology 06, no. 06 (December 2008): 1177–92. http://dx.doi.org/10.1142/s0219720008003898.

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Multi-population haplotype inference and block partitioning is a difficult task when dealing with mixed genotype samples. A number of studies have shown that the haplotype block structures, as well as the collections of common haplotypes and their frequencies, vary significantly among world populations. These differences are more extreme when the geographical locations for the populations are more distant. Some of the previous studies performed haplotype inference in multi-population samples with known population assignment. Others developed algorithms for clustering of the mixed haplotype or genotype samples with different block structures or genetic marker profiles. We present a new algorithm that performs haplotype inference and block partitioning in a mixed sample of genotypes from two populations when the population assignments are not known. Given a mixed genotype sample, the proposed algorithm (HAPLOCLUST) extracts two clusters of genotypes with different block structures in addition to performing haplotype inference on each of these clusters. When tested on a set of unrelated individuals, our algorithm provides correct assignments comparable to those of two state-of-the-art algorithms for population stratification. The contribution of HAPLOCLUST consists of performing haplotype/block-based population stratification and simultaneously finding the haplotype resolution and block partitioning for the extracted clusters.

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Chen, Wen-Pei, Che-Lun Hung, and Yaw-Ling Lin. "Efficient Haplotype Block Partitioning and Tag SNP Selection Algorithms under Various Constraints." BioMed Research International 2013 (2013): 1–13. http://dx.doi.org/10.1155/2013/984014.

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Patterns of linkage disequilibrium plays a central role in genome-wide association studies aimed at identifying genetic variation responsible for common human diseases. These patterns in human chromosomes show a block-like structure, and regions of high linkage disequilibrium are called haplotype blocks. A small subset of SNPs, called tag SNPs, is sufficient to capture the haplotype patterns in each haplotype block. Previously developed algorithms completely partition a haplotype sample into blocks while attempting to minimize the number of tag SNPs. However, when resource limitations prevent genotyping all the tag SNPs, it is desirable to restrict their number. We propose two dynamic programming algorithms, incorporating many diversity evaluation functions, for haplotype block partitioning using a limited number of tag SNPs. We use the proposed algorithms to partition the chromosome 21 haplotype data. When the sample is fully partitioned into blocks by our algorithms, the 2,266 blocks and 3,260 tag SNPs are fewer than those identified by previous studies. We also demonstrate that our algorithms find the optimal solution by exploiting the nonmonotonic property of a common haplotype-evaluation function.

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Bossone, Anna, Donatella Coalizzo, Giovanna D’Andrea, Vincenzo Brancaccio, Antonio Ciampa, Elvira Grandone, Giovanni Di Minno, and Maurizio Margaglione. "FV HR2 Haplotype as Additional Inherited Risk Factor for Deep Vein Thrombosis in Individuals with a High-Risk Profile." Thrombosis and Haemostasis 87, no. 01 (2002): 32–36. http://dx.doi.org/10.1055/s-0037-1612939.

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SummaryA number of strongly linked polymorphisms within the Factor V gene (FV HR2 haplotype) has been identified as a cause of resistance to activated protein C, and has suggested a modest risk factor for vein thrombosis. We investigated the frequency of the HR2 haplotype in 433 consecutive patients with confirmed deep vein thrombosis and 326 controls. The HR2 haplotype was more frequent in patients (15.2%) than in controls (10.1%). The risk of thrombosis among carriers of this haplotype was significantly increased (odds ratio: 1.6 [95% CI: 1.0-2.5]). The estimated risk associated with the HR2 haplotype was 1.8 (95% CI: 1.1-2.9) in subjects with (n = 255), and 1.4 (95% CI: 0.8-2.4) in those without (n = 178) acquired risk factors for vein thrombosis. After adjustment for sex, FV Leiden and FII A20210 mutations, the estimated risk of vein thrombosis among carriers of the HR2 haplotype was 1.8 (95% CI: 1.1-2.8). Present data indicate that the HR2 haplotype is independently associated with vein thrombosis among individuals with a highrisk profile.

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Gummere, Gregory R., Paulette J. McCormick, and Dorothea Bennett. "THE INFLUENCE OF GENETIC BACKGROUND AND THE HOMOLOGOUS CHROMOSOME 17 ON t-HAPLOTYPE TRANSMISSION RATIO DISTORTION IN MICE." Genetics 114, no. 1 (September 1, 1986): 235–45. http://dx.doi.org/10.1093/genetics/114.1.235.

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ABSTRACT Transmission ratio distortion is a characteristic of complete t-haplotypes, such that heterozygous males preferentially transmit the t-haplotype bearing chromosome 17 to the majority of their progeny. At least two genes contained within the t-haplotype have been identified as being required for such high transmission ratios. In this study we examine the effects of the genetic background and the chromosome homologous to the t-haplotype on transmission ratio distortion. We use two different congenic lines: (1) BTBRTF/Nev.Ttf/t12, in which the t12 haplotype has a transmission ratio of 52%, and (2) C3H/DiSn.Ttf/t12, in which the t12 haplotype has a transmission ratio of 99%. By intercrossing these two strains to produce reciprocal F1 and F2 generations, we have isolated the effects of the homologous chromosome 17 from the effects of the genetic background. We demonstrate that both the homologous chromosome and the genetic background have profound effects on t-haplotype transmission ratio distortion. Furthermore, it is evident that the t-haplotype transmission ratio behaves as a quantitative character rather than an intrinsic property of t-haplotypes.

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Flores Carrasco, Sergio, Mariela Olguín-Barraza, and Angel Roco-Videla. "Population analysis of the CLOCK rs3749474T-rs4864548A haplotype and its relationship with obesity." Medwave 23, no. 09 (October 3, 2023): e2735-e2735. http://dx.doi.org/10.5867/medwave.2023.09.2735.

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It has been suggested that the rs3749474T/rs4864548A haplotype of the CLOCK gene increases the risk of obesity, but the population variability of these alleles and the haplotype is unknown. This research aims to determine the linkage between the rs3749474T and rs4864548A alleles from the database of 1000Genomes to confirm the existence of the TA haplotype polymorphisms of these alleles and their frequency in five macro populations. Linkage disequilibrium and haplotype frequencies for 2504 individuals from 26 populations were analyzed using the r statistic and Fisher's exact test. There is a high frequency of the TA haplotype in Latin America (44.8%), a high linkage disequilibrium (r2= 0.92) worldwide between these alleles, a high differentiation between macro populations, and a high homogeneity. The evidence warrants further studies on the association between this haplotype and the risk of obesity and overweight in Latin American populations.

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Wang, Jiayi. "Research Status of Haplotype Assembly Technology." International Journal of Computer Science and Information Technology 2, no. 1 (March 25, 2024): 466–75. http://dx.doi.org/10.62051/ijcsit.v2n1.49.

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Haplotype, also called haploid genotype, refers to the combination of a series of variant loci located on the same chromosome. Most of the current assembly algorithms ignore the heterozygous SNP variant sites on the chromosome and assemble a pseudohaplotype sequence. Due to the importance of haplotypes for the treatment of diseases, the mining of pathogenic genes and other medical organisms, haplotype analysis methods have become particularly important. At present, the indirect haplotype inference technology mainly includes two types: the alignment-based haplotyping algorithm and the assembly-based haplotyping method. This paper briefly summarizes the current typical haplotype indirect regression technology, and also looks forward to the future of haplotype typing technology.

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Oner, C., AJ Dimovski, C. Altay, A. Gurgey, YC Gu, TH Huisman, and KD Lanclos. "Sequence variations in the 5' hypersensitive site-2 of the locus control region of beta S chromosomes are associated with different levels of fetal globin in hemoglobin S homozygotes." Blood 79, no. 3 (February 1, 1992): 813–19. http://dx.doi.org/10.1182/blood.v79.3.813.813.

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Abstract We have compared the sequence of the 5′ hypersensitive site-2 (5′-HS-2) of the locus control region (LCR) from a sickle cell anemia (SS) patient homozygous for haplotype 19 and with low levels of fetal hemoglobin (HbF), with the same sequence from an SS patient homozygous for haplotype 3 and with high levels of HbF. Several nucleotide variations were present in the 5′HS-2 of the haplotype 19 individual. One is the A----G at position -10905 that creates an Sp1 binding site GCCCC (A----G)CCCC. A second is the T----G at position -10924 in a sequence that binds both erythroid and ubiquitous factors and exhibits high homology to the long terminal repeat of the Moloney leukemia viruses and Friend murine leukemia virus. Other differences were in the two AT-rich stretches of DNA, and an A----T substitution at position - 10390. Dot-blot analyses of amplified DNA from several SS patients showed that these variations are specific for beta S chromosomes with haplotype 19. We also examined the 5′HS-2 sequence from an SS patient who is homozygous for haplotype 19, but has abnormally high levels of HbF (greater than 20%). We observed a cross-over that has placed sequences similar to the 5′HS-2 of haplotype 3 in juxtaposition to the 5′ flanking regions of haplotype 19. Thus, a beta S chromosome with haplotype 19 but having a 5′HS-2 (LCR) characteristic for haplotype 3 is associated with high gamma-chain expression. We postulate that factors produced under conditions of hematopoietic stress, together with genetic determinants on the haplotype 3-like LCR sequences, allow for high level expression of gamma-globin genes.

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Oner, C., AJ Dimovski, C. Altay, A. Gurgey, YC Gu, TH Huisman, and KD Lanclos. "Sequence variations in the 5' hypersensitive site-2 of the locus control region of beta S chromosomes are associated with different levels of fetal globin in hemoglobin S homozygotes." Blood 79, no. 3 (February 1, 1992): 813–19. http://dx.doi.org/10.1182/blood.v79.3.813.bloodjournal793813.

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We have compared the sequence of the 5′ hypersensitive site-2 (5′-HS-2) of the locus control region (LCR) from a sickle cell anemia (SS) patient homozygous for haplotype 19 and with low levels of fetal hemoglobin (HbF), with the same sequence from an SS patient homozygous for haplotype 3 and with high levels of HbF. Several nucleotide variations were present in the 5′HS-2 of the haplotype 19 individual. One is the A----G at position -10905 that creates an Sp1 binding site GCCCC (A----G)CCCC. A second is the T----G at position -10924 in a sequence that binds both erythroid and ubiquitous factors and exhibits high homology to the long terminal repeat of the Moloney leukemia viruses and Friend murine leukemia virus. Other differences were in the two AT-rich stretches of DNA, and an A----T substitution at position - 10390. Dot-blot analyses of amplified DNA from several SS patients showed that these variations are specific for beta S chromosomes with haplotype 19. We also examined the 5′HS-2 sequence from an SS patient who is homozygous for haplotype 19, but has abnormally high levels of HbF (greater than 20%). We observed a cross-over that has placed sequences similar to the 5′HS-2 of haplotype 3 in juxtaposition to the 5′ flanking regions of haplotype 19. Thus, a beta S chromosome with haplotype 19 but having a 5′HS-2 (LCR) characteristic for haplotype 3 is associated with high gamma-chain expression. We postulate that factors produced under conditions of hematopoietic stress, together with genetic determinants on the haplotype 3-like LCR sequences, allow for high level expression of gamma-globin genes.

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Michaelis, Sebastian, Markus Mezger, Martin Bornhauser, Rudolf Trenschel, Gernot Stuhler, Matthias Stelljes, Lutz P. Mueller, et al. "KIR Haplotype B Donors but Not KIR-Ligand Mismatch Result in a Reduced Risk of Relapse After Haploidentical Hematopoietic Stem Cell Transplantation Using Reduced Intensity Conditioning and a CD3/CD19 Depleted Graft." Blood 120, no. 21 (November 16, 2012): 3101. http://dx.doi.org/10.1182/blood.v120.21.3101.3101.

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Abstract Abstract 3101 Natural killer (NK) cell alloreactivity, after allogeneic hematopoietic cell transplantation (HCT) is influenced by the interaction of killer-cell immunoglobulin-like receptors (KIRs) on donor NK cells and human leukocyte antigen (HLA) class I ligands on recipient cells. Recently, a positive influence of KIR haplotype B versus haplotype A donors on the outcome of HLA-matched allogeneic HCT was demonstrated (Cooley et al., Blood 2010). Previously, Ruggeri et al. (Science 2002) reported the positive influence of KIR-ligand mismatch (MM) on outcome of haploidentical HCT (HHCT). Here we investigated the influence of the donor KIR haplotype and KIR-ligand MM on relapse of 57 patients with hematologic malignancies receiving HHCT after reduced intensity conditioning and graft CD3/CD19 depletion. 36 patients with AML, eight with ALL, four with multiple myeloma, four with NHL and one with MCL, CML, CMML, MDS, CLL, respectively (median age 45 years, range 19–61 years) were evaluated. Patients were “high risk” because of relapse (n=8), prior HCT (n=23), refractory disease (n=20) or cytogenetic risk (n=6). At HHCT, 29 patients were in complete remission (CR) and 28 in partial remission (PR). 15 KIR genes were determined by real-time PCR as described (Vilches et al., Tissue Antigens 2007, Alves et al., Tissue Antigens 2009), and donors were assigned the A/A or B/x haplotype. Patients and donors were HLA-typed by high-resolution molecular methods. Of the 57 donors, 17 had KIR haplotype A (29.8%) and 40 KIR haplotype B (70.2%). A KIR-ligand MM was found in 34 of 57 patients (59.6%). Cumulative incidence adjusted for competing risk showed no difference between KIR haplotype A or B patients regarding non-relapse mortality (NRM) (Gray's test: p=0.200), but a significantly reduced incidence of relapse for patients with a haplotype B donor (p=0.001). In particular, patients in PR benefited more from a haplotype B graft (p=0.008) than patients in CR (p=0.297). This resulted in a trend in the Kaplan-Meier estimated event free (EFS) at 3 years of 26.8 % for KIR haplotype B and 11.7 % for KIR haplotype A (HR=1.33 [CI=0.66–2.70], log rank test: p=0.422). In detail, all patients in PR died within 1.2 years when haplotype A donor cells were transplanted whereas 25% of haplotype B recipients were still alive after 3 years (HR=1.27 [CI=0.49–3.30], p=0.631). In comparison, 16.6% of haplotype A and 28.1% of haplotype B recipients in CR survived for more than 3 years (HR=1.46 [CI=0.54–3.94], p=0681). Surprisingly, KIR-ligand MM cumulative incidence curves were not statistically different for relapse (p=0680) or NRM (p=0.579). In addition, KIR-ligand MM resulted in a trend for decreased EFS rate for MM patients (17.6%) in contrast to matched patients (33.7%; HR=1.47 [CI=0.89–2.75], p=0.230). These effects were even more pronounced when analyzing the patient cohort with AML. Of the 36 donors, 10 showed KIR haplotype A (27.8%), 26 KIR haplotype B (72.2%) and KIR-ligand MM was present in 25 patients (69.4%). EFS at 3 years was prolonged for KIR haplotype B graft recipients (EFS: HR=2.29 [CI=0.88–5.96], p=0.087). In addition, cumulative incidence adjusted for competing risk analysis revealed a reduced incidence of relapse for patients with a haplotype B donor (all AML patients: p=0.079, AML in PR: p=0.049), but not for NRM (all AML patients: p=0.806, AML in PR: p=0.674). Again, KIR-ligand MM cumulative incidence curves were not significantly different for both relapse (p=0.126) and NRM (p=0.535). In line, KIR-ligand MM led to decreased EFS rate for MM patients (16.0%) in contrast to matched patients (53.0%; HR=2.27 [CI=1.08–5.06], p=0.045). Taken together, in the setting of RIC and CD3/CD19 depleted HHCT we could not confirm the positive data with KIR-ligand MM but observed a significant lower risk of relapse with a KIR haplotype B donor. We therefore conclude from our results that a donor KIR B haplotype should be favored as donor for HHCT using RIC and CD3/CD19 depletion in patients with hematological malignancies, particularly if no complete remission has been achieved prior to HHCT. Disclosures: Off Label Use: off lable use of drugs for conditioning.

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Turner, Daniel J., Chris Tyler-Smith, and Matthew E. Hurles. "Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotyping." Nucleic Acids Research 36, no. 13 (June 18, 2008): e82-e82. http://dx.doi.org/10.1093/nar/gkn373.

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