Academic literature on the topic 'Alu polymorphism'
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Journal articles on the topic "Alu polymorphism"
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Al-Hamodi, Zaid, Riyadh Saif-Ali, Ikram S. Ismail, Khaled A. Ahmed, and Sekaran Muniandy. "Effect of Plasminogen Activator Inhibitor-1 and Tissue Plasminogen Activator Polymorphisms on Susceptibility to Type 2 Diabetes in Malaysian Subjects." Journal of Biomedicine and Biotechnology 2012 (2012): 1–6. http://dx.doi.org/10.1155/2012/234937.
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Elevated activity of plasminogen activator inhibitor-1 (PAI-1) and decreased tissue plasminogen activator (tPA) activity are considered to be important risk factors for type 2 diabetes mellitus (T2DM) and metabolic syndrome (MetS). The aim of this study was to investigate the association of the PAI-1 4G/5G and tPA Alu-repeat I/D polymorphisms with T2DM in Malaysian subjects. Serum insulin, coronary risk panel, plasma glucose, and PAI-1 4G/5G and tPA Alu-repeat I/D polymorphisms were studied in 303 T2DM subjects (227 with MetS and 76 without MetS) and 131 normal subjects without diabetes and MetS. Statistical analysis showed that the dominant and additive models of PAI-1 4G/5G polymorphism showed a weak association with T2DM without MetS (OR=2.35,P=0.045;OR=1.67,P=0.058). On the other hand, the recessive model of the tPA Alu-repeat I/D polymorphism showed an association with T2DM with MetS (OR=3.32,P=0.013) whereas the dominant and additive models of the tPA Alu-repeat I/D polymorphism were not associated with T2DM either with or without MetS.
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Ladenvall, Per, Ulrika Wall, Sverker Jern, and Christina Jern. "Identification of Eight Novel Single-Nucleotide Polymorphisms at Human Tissue-type Plasminogen Activator (t-PA) Locus: Association with Vascular t-PA Release In Vivo." Thrombosis and Haemostasis 84, no. 08 (2000): 150–55. http://dx.doi.org/10.1055/s-0037-1613990.
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SummaryRecently, we reported that an Alu insertion polymorphism of the tissue-type plasminogen activator (t-PA) gene is associated with vascular t-PA release rates in man. In the current study we searched the t-PA gene for putative functional genetic variants in linkage disequilibrium (LD) with this polymorphism. Healthy individuals with different Alu genotypes and contrasting t-PA release rates were studied. Regulatory and coding regions of the t-PA gene were sequenced. Eight singlenucleotide polymorphisms (SNPs) were identified. Three of these were in significant LD with the Alu polymorphism and consequently associated with t-PA release rates; one in the far upstream enhancer, one in exon 6, and one in intron 10. The enhancer SNP resides within a GC box. Electrophoretic mobility shift assay (EMSA) revealed a reduced binding affinity of Sp1 to the T allele, which is the allele associated with a low t-PA release rate. Variations in exon 6 and intron 10 were silent and without apparent effect on splicing, respectively.
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Zhou, Chen, Xiangman Zou, Xiaosha Wen, and Zifen Guo. "Association of the PROGINS PgR polymorphism with susceptibility to female reproductive cancer: A meta-analysis of 30 studies." PLOS ONE 17, no. 7 (2022): e0271265. http://dx.doi.org/10.1371/journal.pone.0271265.
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Aims The progesterone response of the nuclear progesterone receptor plays an important role in the female reproductive system. Changes in the function of the progesterone receptor gene may increase the risk of reproductive cancer. The present study performed a meta-analysis to examine whether the progesterone receptor gene PROGINS polymorphism was a susceptibility factor for female reproductive cancer. Materials and methods We searched the PubMed, Cochrane Library, Web of Science and EMBASE databases for literature on PROGINS polymorphisms and female reproductive cancer published before September 2020. We evaluated the risk using odds ratios [ORs] and 95% confidence intervals via fixed effects models and random-effects models, which were calculated for all five genetic models. We grouped the analyses by race, cancer, and HWE. Results Thirty studies comprised of 25405 controls and 19253 female reproductive cancer cases were included in this meta-analysis. We observed that the Alu insertion polymorphism and the V660L polymorphism were significantly associated with female reproductive cancer in the allele and dominant genetic models. The allele genetic model and (Alu-insertion polymorphism: OR = 1.22, 95% CI = 1.02–1.45; V660L polymorphism: OR = 1.02, 95% CI = 1.00–1.13) dominant genetic model (Alu-insertion polymorphism: OR = 1.27, 95% CI = 1.03–1.58; V660L polymorphism: OR = 1.10, 95% CI = 1.011.19) demonstrated a significantly increased risk of female reproductive cancer. A subgroup analysis according to ethnicity found that the Alu insertion was associated with female reproductive cancer incidence in white (Allele model: OR = 1.21, 95% CI = 1.00–1.45; Heterozygous model: OR = 3.44, 95% CI = 1.30–9.09) and Asian (Dominant model: OR = 3.12, 95% CI = 1.25–7.79) populations, but the association disappeared for African and mixed racial groups. However, the V660L polymorphism was significantly associated with female reproductive cancer in the African (Allele model: OR = 2.52, 95% CI = 1.14–5.56; Heterozygous model: OR = 2.83, 95% CI = 1.26–6.35) and mixed racial groups (Dominant model: OR = 1.28, 95% CI = 1.01–1.62). Subgroup analysis by cancer showed that the PROGINS polymorphism increased the risk of cancer in the allele model, dominant mode and heterozygous model, but the confidence interval for this result spanned 1 and was not statistically significant. This sensitivity was verified in studies with HWE greater than 0.5. Conclusion Our meta-analysis showed that the progesterone receptor gene Alu insertion and the V660L polymorphism contained in the PROGINS polymorphism were susceptibility factors for female reproductive cancer.
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Bernard, Lynn E., and Stephen Wood. "Human chromosome 5 sequence primer amplifies Alu polymorphisms on chromosomes 2 and 17." Genome 36, no. 2 (1993): 302–9. http://dx.doi.org/10.1139/g93-042.
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Members of the Alu family of repetitive elements occur frequently in the human genome and are often polymorphic. Techniques involving Alu element mediated polymerase chain reactions (Alu PCR) allow the isolation of region-specific human DNA fragments from mixed DNA sources. Such fragments are a source of region-specific Alu elements useful for the detection of Alu-related polymorphisms. A clone from human chromosome 5, corresponding to locus D5F40S1, was isolated using Alu PCR differential hybridization. Alu elements within this clone were investigated for the presence of potentially polymorphic 3′ polyA tails. Primers were devised to amplify the 3′ polyA tail of an Alu element present within the clone. One primer, D5F40S1-T, was specific to the DNA flanking the 3′ end of the Alu element, and the other primer was homologous to sequences within the element. When these primers were used in PCR reactions, products from chromosomes 2 and 17 (loci D2F40S2 and D17F40S3) were amplified in addition to the expected product from chromosome 5. The most likely explanation for this nonspecific amplification is that the D5F40S1-T primer is located within a low-copy repetitive element that is 3′ of the Alu element. This phenomenon presents a potential problem for the identification of region-specific Alu polymorphisms.Key words: Alu polymorphism, human chromosome 5, polymerase chain reaction, D5F40S1, D2F40S2, D17F40S3.
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Zainab, A. Al-Mazaydeh, R. Yasin Salem, and H. Tahtamouni Lubna. "The implementation of Alu insertion polymorphism as a genetic marker for forensic investigation in a Jordanian population sample." African Journal of Biological Sciences 2, no. 3 (2020): 62–71. https://doi.org/10.33472/AFJBS.2.3.2020.62-71.
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Alu element is one of the most abundant short interspersed nuclear elements (SINE) in the human genome with great forensic potential. The current study focused on the analysis of the utility of Alu insertion polymorphism in forensic DNA typing in a Jordanian population sample (central Jordan). Alu insertions in seven different genetic loci were amplified using Polymerase Chain Reaction (PCR). The frequencies of the Alu insertions were 0.345 for <em>ACE</em>, 0.441 for <em>TPA25</em>, 0.291 for <em>PV92</em>, 0.845 for <em>APO</em>, 0.468 for <em>FXIIIB</em>, 0.727 for <em>HS</em>3.23 and 0.527 for <em>B65</em>. <em>APO</em> and <em>FXIIIB</em> Alu insertions were the most dominant alleles, while PV92 Alu insertion was the least frequent. Combined Power of Discrimination (P<sub>D</sub>) for those seven loci was 0.998285646, whereas the combined Power of Exclusion (P<sub>E</sub>) was 0.4987.Combining the seven Alu insertion/deletion data along with the Jordanian combined STR data should give an exceptional resolution power between Jordanian individuals.
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Arcot, S. S., A. W. Adamson, J. E. Lamerdin, et al. "Alu fossil relics--distribution and insertion polymorphism." Genome Research 6, no. 11 (1996): 1084–92. http://dx.doi.org/10.1101/gr.6.11.1084.
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Pidpala, O. V., and L. L. Lukash. "Distribution of the macaques genus-specific Alu repeat AluMacYa3 in the MGMT gene orthologs of old world monkeys." Faktori eksperimental'noi evolucii organizmiv 32 (September 1, 2023): 148–54. http://dx.doi.org/10.7124/feeo.v32.1552.
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Aim. To follow the distribution and evolution of the macaques genus-specific Alu repeat AluMacYa3 in Cercopithecidae MGMT gene orthologs. Methods. The homology between nucleotide sequences has been determined by the BLAST 2.6.1 program. The results of the search and identification of MGE have been obtained by the CENSOR program. Results. It has been shown on the example of Cercopithecidae MGMT gene orthologs that the genus-specific Alu repeat AluMacYa3 is present not only in the intron sequences of macaques, but also in other representatives of the Old World monkeys and in its evolutionary history not a deletion degradation of nucleotide sequences, as it is in the case of species-specific Alu repeats, but a single nucleotide polymorphism is dominated. Conclusions. Thus, the macaque genus-specific Alu repeat AluMacYa3 has been identified in different representatives of the Old World monkeys and its evolutionary history combines nucleotide polymorphism and deletion degradation of nucleotide sequences.
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Tyuryupov, M. S., K. S. Shulenin, T. S. Svyoklina, et al. "Genetic predictors of survival and development of MACE in the acute COVID-19 in patients with high cardiovascular risk." Therapist’s Bulletin 63, no. 2 (2024): 9–18. http://dx.doi.org/10.31550/2712-8601-vt-2024-2-2.
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Introduction. Despite the fact that the SARS-CoV-2 virus is highly contagious, the clinical manifestations of the disease caused by it can have significant differences: from a low-symptom course to extremely severe forms with the development of a fatal outcome. It is obvious that the observed polymorphism of the development of infection caused by SARS-CoV-2 is due, among other things, to genetic factors. These include single-nucleotide polymorphisms of genes involved in the stages of the pathogenesis of infection: from the penetration of the virus into target cells, the expression of its RNA to the response of the host organism. The study of genetic predictors that cause changes in susceptibility to the SARS-CoV-2 virus and differences in the severity of infection will help to better understand the pathogenesis of this disease and give an idea of promising areas of therapy and prevention. Aim. To study the relationship of genetic biomarkers with the severity of infection caused by SARS-CoV-2, cardiovascular complications and the risk of death in the early period of the disease. Design. A single-center retrospective study. Materials and methods. The study included 164 patients (90 men, 74 women) with infection caused by SARS-CoV-2. All patients were classified as high and very high cardiovascular risk. Concomitant somatic pathology: arterial hypertension in 164 (100%), coronary heart disease in 80 (48.9%), alimentary obesity in 100 (61%), prediabetes in 52 (31.74%), chronic kidney disease in 34 (20.7%) patients. At the first stage of the study, the relationship of genetic biomarkers with the severity of the disease was evaluated, at the second — with cardiovascular complications, and at the third — with the onset of death. Results. In the group of patients with severe disease, variant DD of ACE Alu I/D gene polymorphism, rs4646994 (p = 0.004), variant GG of IL-10 polymorphism 1082 G/A, rs1800896 (p = 0.043), allele *11 HLA-DRB1 (p = 0.015) were significantly more common. The genetic predictors of the development of cardiovascular complications were the genotype DD of the ACE gene (rs4646994) (p = 0.038), the allele *3 HLA-DRB1 (p = 0.041), the allele *13 HLA-DRB1 (p = 0.047) was less common. When searching for a correlation between the selected genetic biomarkers and mortality, only a negative contribution of the ACE Alu I/D polymorphism variant DD, rs4646994 (p = 0.015) was revealed. The survival analysis showed that in the DD variant of the ACE Alu polymorphism I/D, rs4646994, the median survival rate is lower than in the II variant (13 (9–15) days and 21 (12–n/o) days, respectively (p = 0.03)), and lower than in the ID (31 variant (14–n/ o) day (p < 0.0001)). The survival rate of patients with the heterozygous variant of the polymorphism MTRR –66 A/G, rs1801394 was 11.5 (9–16) days, with variant AA — 7 (3–n/o), and with variant GG — 6 (4–14), p = 0.013. With the *16 HLA DRB1 allele, survival was only 5.5 (2–n/o) days versus 22 (17–n/o) days in patients without it, p = 0.04. Conclusion. Predictors of an increased risk of severe infection caused by SARS-CoV-2 include the DD variant of the ACE Alu I/D gene polymorphism, rs4646994, the GG variant of the IL-10 1082 G/A gene polymorphism, rs1800896 and the *11 HLA-DRB1 allele. The negative effect of the DD variant of the polymorphism of the ACE Alu I/D gene, rs4646994, the *3 HLA-DRB1 allele and the protective effect of the *13 HLA-DRB1 allele have been proven in relation to the overall risk of major cardiovascular complications. The carriage of the *16 HLA-DRB1 allele and the DD variant of the ACE Alu I/D gene polymorphism, rs4646994, correlate with an increased risk of early hospital mortality in patients. At the same time, the heterozygous variant of the MTRR –66 A/G polymorphism, rs1801394, is a protective biomarker and is associated with better survival. Key words: COVID-19, SARS-CoV-2 virus, mortality, cardiovascular complications, cardiovascular risk, genetic biomarkers
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Sekridova, A. V., A. M. Varizhuk, O. N. Tatarinova, et al. "Conformational polymorphysm of G-rich fragments of DNA ALU-repeats. I. Potential noncanonical structures." Biomeditsinskaya Khimiya 62, no. 5 (2016): 535–43. http://dx.doi.org/10.18097/pbmc20166205535.
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In this paper, we report results of systematic studies of conformational polymorphism of G-rich DNA fragments from Alu repeats. Alu retrotransposones are primate-specific short interspersed elements. Using the Alu sequence from the prooncogen bcl2 intron and the consensus AluSx sequence as representative examples, we determined characteristic Alu sites that are capable of adopting G-quadruplex (GQ) conformations (i.e., potential quadruplex sites – PQSAlu), and demonstrated by bioinformatics methods that those sites are Alu-specific in the human genome. Genomic frequencies of PQSAlu were assessed (~1/10000 b.p.). The sites were found to be characteristic of young (active) Alu families (Alu-Y). A recombinant DNA sequence bearing the Alu element from the human bcl2 gene (304 b.p.) and its PQS-mutant (Alu-PQS) were constructed. The formation of noncanonical structures in Alubcl2 dsDNA and the absence of such structures in the case of Alu-PQS were shown using DMS-footprinting and AFM microscopy. Expression vectors bearing wild-type and mutant Alu insertions in the promoter regions were obtained, and the effects of these insertions on the expression of the reporter gene in НЕК293 and HeLa cell lines were compared. Our findings on the spatial organization of Alu repeats may provide insight into the mechanisms of genomic rearrangements which underlie many oncological and neurodegenerative diseases.
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Al-Mamoori, Ali Shakir Obeed, and Mona N. Al-Terehi. "The Efficiency of the Alu Insertion Sequence in Discrimination Among some Individuals." JOURNAL OF UNIVERSITY OF BABYLON for Pure and Applied Sciences 32, no. 2 (2024): 62–79. http://dx.doi.org/10.29196/jubpas.v32i2.5267.
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Background: The Alu element is a widely distributed short interspersed nuclear element (SINE) in the human genome and has important applications in forensic science. The current study focused on assessing the effectiveness of Alu insertion polymorphism in forensic DNA profiling to identifying samples of some individuals living in the Babylon Governorate. Materials and methods: DNA was extracted From frozen blood samples (60) individuals were collected from Babylon - Al-Hilla Governorate from 8/8/2022 until 8/9/2022. Results: purified then a PCR technique Alu insertions were A(2q21.1)(111-115bp) 0.75, Alu deletion (0.25), B(8q23.1) (0.375) (0.625) C(13q34) (0.5)(0.5), D(15q23) (0.775) (0.225), E(16q23.3) (0.692) (0.308) and F(19q13.12)(0.616)(0.384) respectively.The alleles with Alu insertions at (2q21.1) were the most prevalent, whereas the Alu insertions at (8q23.1) were the least common. The similarity coefficient among individuals varied from 0.4 to 1, based on the proportion of genetic relatedness between them. Conclusions: Alu elements have efficacy in families’ discrimination it can be used more than one site, set of Alu insertion sequences should be used to accurate results.
Dissertations / Theses on the topic "Alu polymorphism"
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Sekeryapan, Ceran. "An Extended Study On The Alu Insertion Polymorphisms In Anatolian Human Population." Master's thesis, METU, 2005. http://etd.lib.metu.edu.tr/upload/12606573/index.pdf.
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In the present study, for estimating the Central Asia contribution to the Anatolia, nine Alu insertion polymorphisms (ACE, PV92, FXIIIB, APO, A25, B65, TPA25, D1, HS4.32 ) in 100 individuals from Anatolia were examined. Alu insertion frequency for these loci were calculated as 0,410<br>0,220<br>0,579<br>0,963<br>0,067<br>0,667<br>0,390<br>0,427<br>and 0,637 respectively and they were found to be in Hardy-Weinberg equilibrium (p<<br>0,05). Observed insertion frequencies of each loci were compared with those of the previous observations (Dinç<br>, 2003<br>Comas et al., 2004) and it was found that the present study results were not different than those obtained by Comas et al. (2004). Thus, these two data were pooled (N = 143) and used to examine genetic relationships between populations from Eurasia and Africa.
Pairwise Fst statistics indicated that there is higher genetic similarity between Anatolia and all of the Balkans and some of the Caucasian populations. Neighbor Joining (NJ) tree based on Reynold&rsquo<br>s genetic distances and Principal Component Analysis (PCA) both grouped the Anatolian populations with Balkans and some of the Caucasian populations and show clear differentiation of Asian populations from the Anatolian population.
The relative genetic contribution of Central Asian genes to the current Anatolian gene pool was quantified using Admix analysis, considering for comparison populations of Balkans (Greek, Romania, Albania and Hungarian) and Central Asia (Uighur, Uzbeks, Tajicks, Kazaks, Kyrgyzes, Dungans). Estimates suggest roughly 28 % contribution from Asia to Anatolia in concordance with the previous estimation (Benedetto et al., 2001).
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Dinc, Havva. "Alu Insertion Polymorphisms In Anatolian Turks." Master's thesis, METU, 2003. http://etd.lib.metu.edu.tr/upload/1169929/index.pdf.
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In the present study<br>ten autosomal human-specific Alu insertion polymorphisms<br>ACE, APO, A25, B65, D1, FXIIIB, HS4.32, HS4.69, PV92 and TPA25 were analyzed in approximately 100 unrelated individuals from Anatolia. Alu insertion polymorphisms offer several advantages over other nuclear DNA polymorphisms for human evolution studies.
The frequencies of the ten biallelic Alu insertions in Anatolians were calculated and all systems were found to be in Hardy-Weinberg equilibrium (p><br>0.05).
By combining the results of this study with results of previous studies done on worldwide populations, the genetic distance (Nei&rsquo<br>s DA) between each pair of populations was calculated and neighbor joining trees were constructed. In general, geographically closer populations were found to be also genetically similar. Principal component analysis (PCA) was performed and Anatolia was found to be in the European cluster. As a result of PCA<br>it was concluded that FXIIIB, PV92 and ACE were the variables contributing the most to the explanation of the variation between the populations. Additionally<br>canonical variates analysis (CVA) concluded that the most discriminative markers for the groups of populations were PV92, D1, ACE and HS4.32.
Pair-wise Fst values were also calculated between Anatolians and some of the populations for which the data was available. It was concluded that, Anatolians have non-significant pair-wise Fst values with Swiss and French Acadian populations.
Lastly, heterozygosity vs. distance from centroid graph was constructed and it was found that Anatolians and India-Hindu had exactly the expected heterozygosity value predicted by the model of Harpending and Ward (1982).
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Varzari, Alexander. "Population History of the Dniester-Carpathians: evidence from Alu insertion and Y-chromosome polymorphisms." Diss., [S.l.] : [s.n.], 2006. http://edoc.ub.uni-muenchen.de/archive/00005868.
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au, ddunn@cbbc murdoch edu, and David Suliman Dunn. "Studies on polymorphic alu insertions and genomic diversity within the major histocompatibility complex." Murdoch University, 2005. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20061121.94752.
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After the initiation of the human genome sequencing project and the introduction of the field of bioinformatics, interest in human genetic diversity studies has been increased. Sequence diversity has helped define differences between genes and genomic regions that were previously unknown or difficult to determine. In this thesis I have undertaken to study sequence diversity in the human genome in three areas; 1) investigated diversity in the MHC as represented by the MICA alleles with respect to the known HLA alleles, 2) investigated the structure and diversity in the intergenic region from an MHC related (paralogous) genomic region and related the structural and diversity findings to the knowledge available on the MHC and the wider genome, and 3) described the identification of three and characterization of five new MHC class I polymorphic markers (Alu) and their polymorphic characteristics in worldwide populations and their associations with skin cancer.
1. Phylogenetic analysis of MICA alpha-domain (extracellular) sequences demonstrated relationships with HLA-B cross-reactive serogroups. The HLA-B and MICA loci are in linkage disequilibrium. The data indicated that MICA and HLA-B have evolved in concert from their common ancestors and that the transmembrane polymorphisms have arisen independently and more recently.
2. Sequence analysis of the CD1 genomic region confirmed the presence of five CD1 genes and revealed that there are four unrelated intergenic regions (IGRs). The IGRs are composed mostly of retroelements including five full-length L1 PA sequences and various pseudogenes. Genomic and phylogenetic analyses support the view that the human CD1 gene copies were duplicated prior to the evolution of primates and the bulk of the HLA class I genes found in humans.
3. Five polymorphic Alu insertions (POALINs) were identified (two from previous studies) and located within the 1.8 megabase of the MHC class I genomic region. All five POALINs are polymorphic, and are positively associated with the HLA-A and HLA-B alleles. The AluyHJ insertion was found most frequently associated with HLA-A1 or A24, AluyHG with HLA-A2, AluyHF with HLA-A2, A-10 or -A26 and AluyTF showed a marginal association with HLA-A29. The AluyMICB insertion was strongly associated with HLA-B17 (HLA-B57, HLA-B58) and HLA-B13. The presence of three Alu insertions (AluyHJ, AluyHG and AluyHF) was found in only one HLA class I haplotype (HLA-A1, -B57, -Cw6) in the 10th IHW cell lines. A novel positive association between the presence of AluyMICB and the MICAdel/MICBnull/HLA-B48 haplotype was determined. The AluyMICB insertion was also associated with at least three different MICB alleles (*0102, *0107N and *0105) and three different HLA-B alleles (B13, B48 and B57). Based on the analysis of associations between different polymorphic markers within the beta block, the MICB*0102 allele was inferred to be the ancestral form of the MICB*0105 and MICB*0107N alleles. The AluyMICB polymorphism can be used to further investigate haplotype relationship and consequently their lineage origins. Some of the MHC POALINs are haplospecific and associate strongly with certain groups of HLA class I alleles and MHC ancestral haplotypes. The AluyTF frequency was significantly associated with skin cancer (p<0.005).
MICA gene diversity is derived from two different evolving paths, therefore one or the other alone cannot reliably mark an ancestral haplotype. The CD1 duplicons originated well before the HLA class I duplicons. The MHC POALINs provide new lineage and linkage markers for the fine mapping study of different haplotypes and variations in linkage groups across 1.8 Mb of the MHC class I region. The POALINs may also prove useful in investigating the origins and history of human populations and in determining the role of human genetic diversity in disease risk.
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Dunn, David Suliman. "Studies on polymorphic alu insertions and genomic diversity within the major histocompatibility complex." Thesis, Dunn, David Suliman (2005) Studies on polymorphic alu insertions and genomic diversity within the major histocompatibility complex. PhD thesis, Murdoch University, 2005. https://researchrepository.murdoch.edu.au/id/eprint/28/.
Full textAbstract:
After the initiation of the human genome sequencing project and the introduction of the field of 'bioinformatics', interest in human genetic diversity studies has been increased. Sequence diversity has helped define differences between genes and genomic regions that were previously unknown or difficult to determine. In this thesis I have undertaken to study sequence diversity in the human genome in three areas; 1) investigated diversity in the MHC as represented by the MICA alleles with respect to the known HLA alleles, 2) investigated the structure and diversity in the intergenic region from an MHC related (paralogous) genomic region and related the structural and diversity findings to the knowledge available on the MHC and the wider genome, and 3) described the identification of three and characterization of five new MHC class I polymorphic markers (Alu) and their polymorphic characteristics in worldwide populations and their associations with skin cancer.
1. Phylogenetic analysis of MICA alpha-domain (extracellular) sequences demonstrated relationships with HLA-B cross-reactive serogroups. The HLA-B and MICA loci are in linkage disequilibrium. The data indicated that MICA and HLA-B have evolved in concert from their common ancestors and that the transmembrane polymorphisms have arisen independently and more recently.
2. Sequence analysis of the CD1 genomic region confirmed the presence of five CD1 genes and revealed that there are four unrelated intergenic regions (IGRs). The IGRs are composed mostly of retroelements including five full-length L1 PA sequences and various pseudogenes. Genomic and phylogenetic analyses support the view that the human CD1 gene copies were duplicated prior to the evolution of primates and the bulk of the HLA class I genes found in humans.
3. Five polymorphic Alu insertions (POALINs) were identified (two from previous studies) and located within the 1.8 megabase of the MHC class I genomic region. All five POALINs are polymorphic, and are positively associated with the HLA-A and HLA-B alleles. The AluyHJ insertion was found most frequently associated with HLA-A1 or A24, AluyHG with HLA-A2, AluyHF with HLA-A2, A-10 or -A26 and AluyTF showed a marginal association with HLA-A29. The AluyMICB insertion was strongly associated with HLA-B17 (HLA-B57, HLA-B58) and HLA-B13. The presence of three Alu insertions (AluyHJ, AluyHG and AluyHF) was found in only one HLA class I haplotype (HLA-A1, -B57, -Cw6) in the 10th IHW cell lines. A novel positive association between the presence of AluyMICB and the 'MICAdel/MICBnull/HLA-B48' haplotype was determined. The AluyMICB insertion was also associated with at least three different MICB alleles (*0102, *0107N and *0105) and three different HLA-B alleles (B13, B48 and B57). Based on the analysis of associations between different polymorphic markers within the beta block, the MICB*0102 allele was inferred to be the ancestral form of the MICB*0105 and MICB*0107N alleles. The AluyMICB polymorphism can be used to further investigate haplotype relationship and consequently their lineage origins. Some of the MHC POALINs are haplospecific and associate strongly with certain groups of HLA class I alleles and MHC ancestral haplotypes. The AluyTF frequency was significantly associated with skin cancer (p<0.005).
MICA gene diversity is derived from two different evolving paths, therefore one or the other alone cannot reliably mark an ancestral haplotype. The CD1 duplicons originated well before the HLA class I duplicons. The MHC POALINs provide new lineage and linkage markers for the fine mapping study of different haplotypes and variations in linkage groups across 1.8 Mb of the MHC class I region. The POALINs may also prove useful in investigating the origins and history of human populations and in determining the role of human genetic diversity in disease risk.
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Dunn, David Suliman. "Studies on polymorphic alu insertions and genomic diversity within the major histocompatibility complex." Dunn, David Suliman (2005) Studies on polymorphic alu insertions and genomic diversity within the major histocompatibility complex. PhD thesis, Murdoch University, 2005. http://researchrepository.murdoch.edu.au/28/.
Full textAbstract:
After the initiation of the human genome sequencing project and the introduction of the field of 'bioinformatics', interest in human genetic diversity studies has been increased. Sequence diversity has helped define differences between genes and genomic regions that were previously unknown or difficult to determine. In this thesis I have undertaken to study sequence diversity in the human genome in three areas; 1) investigated diversity in the MHC as represented by the MICA alleles with respect to the known HLA alleles, 2) investigated the structure and diversity in the intergenic region from an MHC related (paralogous) genomic region and related the structural and diversity findings to the knowledge available on the MHC and the wider genome, and 3) described the identification of three and characterization of five new MHC class I polymorphic markers (Alu) and their polymorphic characteristics in worldwide populations and their associations with skin cancer.
1. Phylogenetic analysis of MICA alpha-domain (extracellular) sequences demonstrated relationships with HLA-B cross-reactive serogroups. The HLA-B and MICA loci are in linkage disequilibrium. The data indicated that MICA and HLA-B have evolved in concert from their common ancestors and that the transmembrane polymorphisms have arisen independently and more recently.
2. Sequence analysis of the CD1 genomic region confirmed the presence of five CD1 genes and revealed that there are four unrelated intergenic regions (IGRs). The IGRs are composed mostly of retroelements including five full-length L1 PA sequences and various pseudogenes. Genomic and phylogenetic analyses support the view that the human CD1 gene copies were duplicated prior to the evolution of primates and the bulk of the HLA class I genes found in humans.
3. Five polymorphic Alu insertions (POALINs) were identified (two from previous studies) and located within the 1.8 megabase of the MHC class I genomic region. All five POALINs are polymorphic, and are positively associated with the HLA-A and HLA-B alleles. The AluyHJ insertion was found most frequently associated with HLA-A1 or A24, AluyHG with HLA-A2, AluyHF with HLA-A2, A-10 or -A26 and AluyTF showed a marginal association with HLA-A29. The AluyMICB insertion was strongly associated with HLA-B17 (HLA-B57, HLA-B58) and HLA-B13. The presence of three Alu insertions (AluyHJ, AluyHG and AluyHF) was found in only one HLA class I haplotype (HLA-A1, -B57, -Cw6) in the 10th IHW cell lines. A novel positive association between the presence of AluyMICB and the 'MICAdel/MICBnull/HLA-B48' haplotype was determined. The AluyMICB insertion was also associated with at least three different MICB alleles (*0102, *0107N and *0105) and three different HLA-B alleles (B13, B48 and B57). Based on the analysis of associations between different polymorphic markers within the beta block, the MICB*0102 allele was inferred to be the ancestral form of the MICB*0105 and MICB*0107N alleles. The AluyMICB polymorphism can be used to further investigate haplotype relationship and consequently their lineage origins. Some of the MHC POALINs are haplospecific and associate strongly with certain groups of HLA class I alleles and MHC ancestral haplotypes. The AluyTF frequency was significantly associated with skin cancer (p<0.005).
MICA gene diversity is derived from two different evolving paths, therefore one or the other alone cannot reliably mark an ancestral haplotype. The CD1 duplicons originated well before the HLA class I duplicons. The MHC POALINs provide new lineage and linkage markers for the fine mapping study of different haplotypes and variations in linkage groups across 1.8 Mb of the MHC class I region. The POALINs may also prove useful in investigating the origins and history of human populations and in determining the role of human genetic diversity in disease risk.
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Bettin, Bettina [Verfasser]. "MDR1-Polymorphismen als Suszeptibilitätsfaktor für das Harnblasenkarzinom / Bettina Bettin." Berlin : Medizinische Fakultät Charité - Universitätsmedizin Berlin, 2009. http://d-nb.info/1023464918/34.
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Pitt, Alison Patricia. "Comparison of Middle Eastern Bedouin genotypes with previously studies populations using polymorphic Alu insertions." University of Western Australia. Centre for Forensic Science, 2009. http://theses.library.uwa.edu.au/adt-WU2009.0119.
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[Truncated abstract] Polymorphic Alu insertions (POALINs) are known to contribute to the variation and genetic diversity of the human genome. In this report specific POALINs of the Major Histocompatibility Complex (MHC) were studied. Previous population studies on the MHC POALINs have focused on individuals of African, European and Asian descent. In this study, we expand the research by studying a new and previously uncharacterised population, focusing on the Bedouin from the Middle East. Specifically we report on the individual insertion frequencies of four POALINs within the MHC class I region of this population. POALINs are members of a young Alu subfamily that have only recently been inserted into the human genome. POALINs are either present or absent at particular sites. Individuals that share the inserted (or deleted) polymorphism inherited the insertion (or deletion) from a common ancestor, making Alu alleles identical by decent. In population genetics a comparison of the resulting products from each population can then be done by comparing the lengths of the PCR products in a series of unrelated individuals and may also detect polymorphisms with regard to the presence or absence of the Alu repeats. As a direct result of their abundance and sequence identity, they promote genetic recombination events that are responsible for large-scale deletions, duplication and translocations. The deletions occur mostly in the A-T rich regions and have found to be unlikely to have been created independently of the insertions of the Alu elements (Callinan et al, 2005) The easy genotyping of the POALINs has proven to be very valuable as lineage markers for the study of human population genetics, pedigree and forensics as well as genomic diversity and evolution. POALINs have been used in a range of applications, primarily focusing on anthropological analysis of human populations. As a result of its ease of use and its utility as a marker in human evolutions studies, combining the POALINs along with other markers used in forensics could lead to improved identity testing in forensic science. More specifically, in combination with more traditional markers, race specific genotypes and haplotypes could be used for profiling crime scene samples. ... This is supported by previously reported molecular data using various types of genetic markers. In a study using six separate Alu genes, Antunez-de-Mayolo et al were able to generate a phylogenetic tree, in which the biogeographical groups followed a pattern. The biogeographical groups started with African populations that were found to relate closely to the hypothetical ancestral African population. The African populations were then followed in order by Southwest Asian populations, European populations which include Middle Eastern groups (Antunez-de-Mayolo et al, 2002). This study shows the similarities and differences between the frequencies of the Middle Eastern Bedouin and the rest of the compared populations. Though no clear results were determined, the information from the POALINs along with information provided from other genetic markers can lead to further research on the Bedouin population and the improvement of the forensic population database in order to accurately test individual ethnic background of samples to be analysed.
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Tanrikut, Cihan. "Dna Repair Genes, Xrcc3 And Rad51, Polymorphisms And Risk Of Childhood Acute Lymphoblastic Leukemia." Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12612836/index.pdf.
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In this study, the role of two DNA repair genes, X-ray repair cross complementing group 3 (XRCC3) Thr241Met and Rad51 G135C polymorphisms were investigated in the risk of development of childhood ALL in Turkish population among 193 healthy controls and 184 ALL patients, by using PCR-RFLP technique. For XRCC3 Thr241Met polymorphism, the frequencies of both heterozygous and homozygous mutant genotypes were found to be higher in the controls compared to ALL patients (OR: 0.59, p = 0.02<br>OR: 0.48, p = 0.02, respectively). In addition, either heterozygous (Thr/Met) or homozygous mutant (Met/Met) genotypes were significantly more common in the controls than the ALL patients (OR: 0.55, p =0.005). In case of Rad51 G135C polymorphism, no significant associations have been found with the risk of childhood ALL. Combination of XRCC3 heterozygote and Rad51 heterozygote genotypes increased the protective effect for risk of childhood ALL. (OR=0.35<br>p =0.02). Combination of homozygote mutant genotype of XRCC3 with homozygote wild type genotype of Rad51 gave a highly statistically proved protective effect for the development of disease (OR= 0.36<br>p= 0.004). To our knowledge, this is the first study showing the protective role of XRCC3 Thr241Met polymorphism either alone or in combination with Rad51 G135C variant on the risk of development of childhood ALL.
In addition, interactions of these polymorphisms with non-genetic risk factors were investigated. Only in terms of paternal exposure, the heterozygote (Thr/Met) genotype for XRCC3 gene in children whose father exposed to cigarette smoke demonstrated a significant risk of 3.0 fold (p=0.05). Moreover, the frequency of Rad51 135C allele was determined for the first time in Turkish population. The frequency of the mutant allele was found to be very similar to that observed in other Caucasian populations.
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Wolf, Reinhard. "Arylamin-N-Acetyltransferase 2 - genetische Polymorphismen als Suszeptibilitätsfaktoren für das Mammakarzinom?" Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2004. http://dx.doi.org/10.18452/15052.
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Gegenstand der Untersuchung: Vorliegende Arbeit stellt eine molekularbiologische Studie dar, die der Frage nachging, ob der Genotyp für die NAT2 eine Rolle bei der Pathogenese des Mammakarzinoms spielt. Das Mammakarzinom hat eine erbliche Komponente. Neben hoch-penetranten genetischen Mutationen des BRCA1- und BRCA2-Gens stehen polymorphe Enzyme des Fremdstoffwechsels im Verdacht, Präkanzerogene zu aktivieren und somit das Karzinomrisiko zu erhöhen. Die NAT2 detoxifiziert aromatische Amine, wie sie z. B. im Zigarettenrauch enthalten sind und weist eine ausgesprochene bimodale Aktivitätsverteilung auf. Nach systematischer Aufklärung des genetischen Polymorphismus der NAT2 ist eine Vorhersage des Phänotyps mit hoher Sicherheit möglich. Design: Es wurde eine prospektive Fall-Kontroll-Studie an 248 Patientinnen mit Mammakarzinom und 248 Kontrollen (Patientinnen mit anderen, nicht malignen Erkrankungen und Gesunde) durchgeführt. Zusätzlich wurde eine Blutprobe entnommen, aus der DNA isoliert wurde. Damit wurden folgende Mutationen des NAT2-Gens bestimmt: G191A, C282T, T341C, C481T, G590A, A803G, G857A. Anhand dieser Mutationen erfolgte die Zuordnung zu Haplotypen. Da bekannt ist, welche mittlere Aktivität der NAT2 bei den einzelnen Genotypen zu erwarten ist, konnte mit dieser Information eine Vorhersage der Aktivität als "schnelle" und "langsame" Acetylierer vorgenommen werden. Methode: Die Genotypisierung erfolgte durch Amplifikation des NAT2 -Gens mit verschiedenen Primern in der PCR, anschließendem Verdau mit Restriktionsenzymen und Charakterisierung der Fragmente mittels Gelelektrophorese. Statistik: Mit der Berechnung von "Odds ratios" und multivariaten logistischen Regressionsanalysen zur Berücksichtigung möglicher Einflussfaktoren wurde der Zusammenhang zwischen NAT2-Genotyp bzw. daraus vorhergesagtem Phänotyp und Mammakarzinom überprüft. Ergebnisse: Es wurden acht verschiedene NAT2-Haplotypen nachgewiesen. 2 Haplotypen (*4 und *12A) kodieren für einen schnellen Acetylierer-Typ, 6 Haplotypen (5A, 5B, 5C, 6A, 7B und 14*B) für den langsamen Acetylierer-Typ. 55,6% der MC-Patientinnen und 58% der Kontrollpersonen Genotypen wiesen den langsamen Acetyliererstatus auf. Dies entspricht in etwa der von anderen Untersuchern beschriebenen Häufigkeit bei Kaukasiern. Es fand sich keine Überrepräsentierung bestimmter Genotypen oder Haplotypen in der Gesamtgruppe der Patientinnen mit Mammakarzinom im Vergleich zur Kontrollgruppe. Die Odds ratio betrug 1,12 (CI: 0,03 - 1,60). In einer Subgruppenanalyse fanden sich keine signifikante Unterschiede in bezug auf das mittlere Alter, das Ausmaß des Zigarettenkonsums und auch von Blutgruppenmerkmalen. Innerhalb des Patientenkollektivs wurde die Verteilung von schnellen und langsamen Acetylierern stratifiziert nach Menopausenstatus, Menstruationsdauer, TNM-Klassifikation und Grading. Bei den Patientinnen mit invasiv-lobulärer Tumorhistologie waren die schnellen Acetylierer in der Auswertung signifikant häufiger als bei invasiv-duktalem Mammakarzinom. Ein weiterer signifikanter Unterschied wird bezüglich des Hormonrezeptorstatus berichtet: Schnelle Acetylierer waren bei Patientinnen mit positivem Hormonrezeptorstatus deutlich häufiger als bei solchen mit negativem Rezeptorstatus. Bezüglich der Tumorhistologie fiel auf, dass die 33 Patientinnen mit einem invasiv-lobulären Mammakarzinom signifikant häufiger schnelle Acetylierer waren. Langsame Acetylierer wiesen dagegen häufiger einen negativen Östrogenrezeptorstatus auf. Schlussfolgerung: Dem Polymorphismus des NAT2-Genotyps als unabhängigem Risikofaktor bei der Entstehung des Mammakarzinoms kommt keine mit den bekannten Risikofaktoren vergleichbare Bedeutung zu. Die Befunde in bezug auf die Tumorhistologie und auf den Hormonrezeptorstatus weisen möglicherweise auf Besonderheiten im Pathomechanismus bei der Entstehung des Mammakarzinoms hin, der derzeit unklar ist. Sie bedürfen weiterer Abklärung.<br>Genetically polymorphic xenobiotic metabolizing enzymes such as the polymorphic arylamine N-acetyltransferase (NAT2) are supposed to be a host factor for cancer susceptibility. A case-control study of a total of 248 patients with breast cancer and a matched reference group of 248 unrelated subjects without cancer was performed to explore the association between NAT2 genetic polymorphism and individual susceptibility to breast cancer. A structured questionnaire was used to collect relevant information regarding all known or suspected risk factors of breast cancer. Methods: The NAT2 genotype was determined using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The NAT2-genotype was characterized at nucleotide positions 191, 282, 341, 481, 590, 803, and 857. For evaluation of nucleotide 341, a 3’-mismatch primer was used. Homozygous wild type genotypes NAT2*4/*4 were confirmed by DNA sequencing. Results: Genotypes for rapid acetylation amounted to 44.4% among breast cancer and 41.5% among reference patients. There was no over-representation of specific NAT2-genotypes in the total of breast cancer patients compared with the reference group (odds ratio 1.12, 95%; confidence limits 0.03-1.60). Neither NAT2-status nor smoking status was independently associated with breast cancer risk. Logistic regression analysis, considering confounders such as age, body mass index (BMI), and smoking status (PJ) showed that the NAT2 rapid acetylator genotype was not associated with an increased cancer risk (odds ratio 1.05; 95%-CI: 0.67-1.67; P=0.82). Discrimination into homozygous and heterozygous carriers of allele NAT2*4 did not show any over-representation of NAT2*4/*4 genotypes among breast cancer patients (odds ratio 1.31; 95% confidence limits 0.59-2.91; p=0.50). Hence carriers of the NAT2*4/*4 genotypes, with its especially high acetylation capacity are not at significantly increased risk to breast cancer. Further stratification to different risk factors revealed a non-significant elevation in risk of breast cancer among patients with increasing cigarette smoking who represented the NAT2 rapid acetylator genotype, but lack of association to age, blood groups, menopause, period of menstruation, TNM-classification, tumor grading, and histology. However, evaluation of the role of estrogen receptor status and NAT2 showed that there was a significant association between positive receptor status and NAT2 rapid acetylator genotype (odds ratio 2.07; 95%-CI: 1.32-5.27; P=0.005). Interestingly, in patients with infiltrating lobular breast cancer (n = 33), NAT2 rapid acetylator genotypes were more frequent compared with other tumor subtypes (odds ratio 2.59; 95%-CI: 1.20-5.60; P=0.014). Logistic regression analysis, considering estrogen receptor status, and age showed that the rapid acetylator genotypes were associated with an increased cancer risk (odds ratio 2.4; 95%-CI: 1.04-5.61; P=0.04). Our findings suggest that NAT2-polymorphism is not an independent susceptibility factor for breast cancer. In particular the NAT2 slow acetylator genotype was not associated with an increased breast cancer risk. Striking results point out to a likely association between NAT2 rapid acetylator genotype and tumor histology especially infiltrating lobular breast cancer and positive hormone receptor status These findings refer to special features of pathogenesis in breast cancer requiring more and detailed clarification.
Books on the topic "Alu polymorphism"
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Morell-Ducos, Fausto. COMT and morphine use in cancer pain. Edited by Paul Farquhar-Smith, Pierre Beaulieu, and Sian Jagger. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198834359.003.0082.
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The landmark paper discussed in this chapter is ‘Genetic variation in the catechol-O-methyltransferase (COMT) gene and morphine requirements in cancer patients with pain’, published by Rakvåg et al. in 2008. Genetic variation contributes to differences in pain sensitivity and response to analgesics. Catecholamines are involved in the modulation of pain and are metabolized by catchol-O-methyltransferase (COMT). Genetic variability in the COMT gene may therefore contribute to differences in pain sensitivity and response to analgesics. It has been shown that a polymorphism in the COMT gene, Rs4680 (val158met), influences pain sensitivity and efficacy for morphine in cancer pain treatment. This study investigated whether the variability in other regions in the COMT gene also contributes to the inter-individual variability of morphine efficacy by mapping 11 single nucleotide polymorphisms, constructing haplotypes from them, and then comparing genotypes and haplotypes against pharmacological, demographic, and patient symptom measurements in patients receiving morphine for cancer pain.
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Cascorbi, Ingolf. Polymorphic cytochrome P450 2D6 as the responsible enzyme of activation. Edited by Paul Farquhar-Smith, Pierre Beaulieu, and Sian Jagger. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198834359.003.0079.
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The landmark paper discussed in this chapter is ‘Bioactivation of the narcotic drug codeine in human liver is mediated by the polymorphic monooxygenase catalyzing debrisoquine 4-hydroxylation (cytochrome P-450 dbl/bufI)’, published by Dayer et al. in 1988. Codeine is an old but frequently prescribed drug used for the treatment of mild-to-moderate pain. However, its use is nowadays restricted after observations of partly fatal respiratory repression in children. Codeine itself exhibits no analgesic effect, but is partly activated by O-demethylation to morphine by cytochrome P450 2D6 (CYP2D6). The identification of the polymorphic CYP2D6 as the enzyme responsible for activation was achieved by Dayer et al. in 1998 and was an important milestone contributing to the widely observed inter-individual differences of drug action and side effects of codeine. Translating the pharmacogenetics of codeine into clinical practice is currently underway in clinical trials, to identify ineffective analgesics and, in particular, avoid severe adverse events.
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Lappano, E. R. Morphological Study of Larval Development in Polymorphic All-Worker Broods of the Army Ant Eciton Burchelli. Creative Media Partners, LLC, 2021.
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Schwartz, Peter J., and Lia Crotti. Monogenic and oligogenic cardiovascular diseases: genetics of arrhythmias—catecholaminergic polymorphic ventricular tachycardia. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0152.
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Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a rare inherited disorder associated with syncope and sudden death manifesting in the young during sympathetic activation. The electrocardiogram is normal and the heart is structurally normal. The diagnosis is usually made with an exercise stress test that shows a typical pattern of onset and offset of adrenergically induced ventricular arrhythmias. Molecular screening of RyR2, the major CPVT gene, is recommended whenever the suspicion of CPVT is high. If a disease-causing mutation is identified, cascade screening allows pre-symptomatic diagnosis among family members. All affected subjects should be treated with beta blockers (nadolol or propranolol). Preliminary data support the association of beta blockers with flecainide. After a cardiac arrest, an implantable cardioverter defibrillator (ICD) should be implanted, but it is accompanied by a disquietingly high incidence of adverse effects. After syncope on beta blocker therapy, left cardiac sympathetic denervation is most effective, preserves quality of life, and does not preclude a subsequent ICD implantation.
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Hamilton, Matthew Lloyd. COMT genotypes in pain responses. Edited by Paul Farquhar-Smith, Pierre Beaulieu, and Sian Jagger. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198834359.003.0080.
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The landmark study discussed in this chapter is ‘COMT val158met genotype affects μ-opioid neurotransmitter responses to a pain stressor’, published by Zubieta et al. in 2003. Catechol-O-methyl-transferase (COMT) is a key modulator of dopaminergic and noradrenergic neurotransmission. This study focused on a single nucleotide polymorphism of the COMT gene encoding the substitution of valine (val) by methionine (met) at Codon 158 (val158met), resulting in a three- to fourfold reduction in its activity. Individuals with the val/val genotype have the highest activity of COMT, val/met genotypes have intermediate activity, and met/met genotypes have the lowest activity of COMT. Using a mixture of PET imaging of the binding of μ-opioid receptors and correlation with clinical outcomes, this groundbreaking study provided evidence that confirmed their hypothesis and established the COMT val158met SNP as one of the first gene modifications with direct ramifications on human pain.
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Sinha, Sanjib. Laravel 5. 7. * All Model Relations Explained: A Detailed Discussion of MVC Pattern, Composer, Migrations, One to One, One to Many, Many to Many, and Polymorphic Relationships. Independently Published, 2018.
Find full textBook chapters on the topic "Alu polymorphism"
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Abdullah, Azzura, Wan Nurhayati Wan Hanafi, and Farida Zuraina Mohd Yusof. "PV92, ACE, and TPA25 Alu insertion polymorphism in the kelantan malaysia sub-ethnic group." In Bioresources Technology in Sustainable Agriculture. Apple Academic Press, 2018. http://dx.doi.org/10.1201/9781315365961-7.
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Peskin, Leonardo. "Are we perhaps all queer?" In Polymorphisms. Routledge, 2025. https://doi.org/10.4324/9781003534341-9.
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Ye, Wenjia, and Bruno C. d. S. Oliveira. "Pragmatic Gradual Polymorphism with References." In Programming Languages and Systems. Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-30044-8_6.
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AbstractGradualizing System F has been widely discussed. A big challenge is to preserve relational parametricity and/or the gradual guarantee. Most past work has focused on the preservation of parametricity, but often without the gradual guarantee. A few recent works satisfy both properties by giving up System F syntax, or with some restrictions and the introduction of sophisticated mechanisms in the dynamic semantics.While parametricity is important for polymorphic languages, most mainstream languages typically do not satisfy it, for a variety of different reasons. In this paper, we explore the design space of polymorphic languages that satisfy the gradual guarantee, but do not preserve parametricity. When parametricity is not a goal, the design of polymorphic gradual languages can be considerably simplified. Moreover, it becomes easy to add features that are of practical importance, such as mutable references. We present a new gradually typed polymorphic calculus, called $$\lambda ^{G}_{gpr}$$ λ gpr G , with mutable references and with an easy proof of the gradual guarantee. In addition, compared to other gradual polymorphism work, $$\lambda ^{G}_{gpr}$$ λ gpr G is defined using a Type-Directed Operational Semantics (TDOS), which allows the dynamic semantics to be defined directly instead of elaborating to a target cast language. $$\lambda ^{G}_{gpr}$$ λ gpr G and all the proofs in this paper are formalized in Coq.
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Heinisch, Cornelia, Frank Müller, and Joachim Goll. "Vererbung und Polymorphie." In Java als erste Programmiersprache. Vieweg+Teubner Verlag, 2005. http://dx.doi.org/10.1007/978-3-322-94078-0_11.
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Goll, Joachim, Cornelia Weiß, and Frank Müller. "Vererbung und Polymorphie." In Java als erste Programmiersprache. Vieweg+Teubner Verlag, 2001. http://dx.doi.org/10.1007/978-3-322-94124-4_10.
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Heinisch, Cornelia, Frank Müller-Hofmann, and Joachim Goll. "Vererbung und Polymorphie." In Java als erste Programmiersprache. Vieweg+Teubner, 2011. http://dx.doi.org/10.1007/978-3-8348-9854-8_11.
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Goll, Joachim, and Cornelia Heinisch. "Vererbung und Polymorphie." In Java als erste Programmiersprache. Springer Fachmedien Wiesbaden, 2016. http://dx.doi.org/10.1007/978-3-658-12118-1_11.
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Goll, Joachim, Cornelia Weiß, and Peter Rothländer. "Vererbung und Polymorphie." In Java als erste Programmiersprache. Vieweg+Teubner Verlag, 2000. http://dx.doi.org/10.1007/978-3-322-92753-8_11.
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Goll, Joachim, and Cornelia Heinisch. "Vererbung und Polymorphie." In Java als erste Programmiersprache. Springer Fachmedien Wiesbaden, 2013. http://dx.doi.org/10.1007/978-3-8348-2270-3_11.
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Murase, Yuito, Yuichi Nishiwaki, and Atsushi Igarashi. "Contextual Modal Type Theory with Polymorphic Contexts." In Programming Languages and Systems. Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-30044-8_11.
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AbstractModal types—types that are derived from proof systems of modal logic—have been studied as theoretical foundations of metaprogramming, where program code is manipulated as first-class values. In modal type systems, modality corresponds to a type constructor for code types and controls free variables and their types in code values. Nanevski et al. have proposed contextual modal type theory, which has modal types with fine-grained information on free variables: modal types are explicitly indexed by contexts—the types of all free variables in code values.This paper presents $$\lambda _{\forall []}$$ λ ∀ [ ] , a novel extension of contextual modal type theory with parametric polymorphism over contexts. Such an extension has been studied in the literature but, unlike earlier proposals, $$\lambda _{\forall []}$$ λ ∀ [ ] is more general in that it allows multiple occurrence of context variables in a single context. We formalize $$\lambda _{\forall []}$$ λ ∀ [ ] with its type system and operational semantics given by $$\beta $$ β -reduction and prove its basic properties including subject reduction, strong normalization, and confluence. Moreover, to demonstrate the expressive power of polymorphic contexts, we show a type-preserving embedding from a two-level fragment of Davies’ $$\lambda _{\bigcirc }$$ λ ◯ , which is based on linear-time temporal logic, to $$\lambda _{\forall []}$$ λ ∀ [ ] .
Conference papers on the topic "Alu polymorphism"
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Flaten, Ellen Marie, Xiaoguang Ma, Marion Seiersten, Charlotte Aanonsen, Ralf Beck, and Jens-Petter Andreassen. "Impact of Monoethylene Glycol and Fe2+ on Crystal Growth of CaCO3." In CORROSION 2015. NACE International, 2015. https://doi.org/10.5006/c2015-05770.
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Abstract Calcium carbonate is one of the most abundant minerals precipitating during gas production. This work is focused on precipitation of CaCO3 in presence of Monoethylene glycol (MEG), used as hydrate inhibitor. MEG is known to affect the thermodynamics of calcium carbonate and this study shows that it has a large impact on the precipitation kinetics. The whole precipitation process has been investigated including polymorphism, induction times, nucleation rates and growth rates. Growth rate is emphasized as it has a large impact on both induction time and transformation rate from metastable polymorphs to stable calcite. The experiments were performed at 25-80°C with MEG concentration up to 90 wt%. MEG prolongs the induction period for precipitation as its presence decreases both nucleation rates and growth rates. The growth rates of all three polymorphs are reduced in presence of MEG, but calcite is most inhibited. The slow growth of calcite at high MEG concentrations result in a very slow transformation from initially mixed metastable polymorphs. Ferrous ions (Fe2+) affect the polymorphism of CaCO3. The growth of vaterite and aragonite is retarded to different extent. Vaterite growth is most inhibited resulting in aragonite being the most abundant polymorph in a larger MEG and temperature range. The effect depends strongly on Fe2+ concentration relative to solid surface area.
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Flaten, Ellen Marie, Marion Seiersten, Ralf Beck, Charlotte Aanonsen, and Jens-Petter Andreassen. "Precipitation of Calcium Carbonate in Monoethylene Glycol and Water." In CORROSION 2014. NACE International, 2014. https://doi.org/10.5006/c2014-4047.
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Abstract Calcium carbonate is one of the most abundant minerals precipitating during gas production. This work is focused on precipitation of CaCO3 in presence of Monoethylene glycol (MEG), used as hydrate inhibitor. MEG is known to affect the thermodynamics of calcium carbonate and the results show that it also has a large impact on the precipitation kinetics. The whole precipitation process has been investigated including polymorphism, induction times, nucleation rates and growth rates. Emphasize has been on growth rate as it is most important and has a large impact on both induction time and transformation rate from metastable polymorphs to stable calcite. The experiments were performed at 25-80°C with MEG concentration up to 90 wt%. The growth rates of all the polymorphs are reduced in presence of MEG, but calcite is most inhibited. The slow growth of calcite at high MEG concentrations result in a very slow transformation from initially mixed metastable polymorphs. It prolongs the induction periods and makes it difficult to determine nucleation rates, too. However, it is possible to give a rough estimate of nucleation rates when the impact of the growth rate is taken account. Nucleation rates decrease with increasing MEG concentrations.
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Tjelta, M., and J. Kvarekvål. "Electrochemistry of Iron Sulfide and Its Galvanic Coupling to Carbon Steel in Sour Aqueous Solutions." In CORROSION 2016. NACE International, 2016. https://doi.org/10.5006/c2016-07478.
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Abstract Iron sulfide, frequently found on carbon steel under sour conditions, is under certain circumstances expected to act as a (large area) cathode thereby increasing the corrosion rate of the underlying steel through galvanic coupling. In the present work electrochemical reactions taking place at electrodes of different iron sulfide polymorphs (namely troilite, pyrrhotite and pyrite) in sour aqueous solutions have been studied using electrochemical techniques. Also, the effect of galvanic coupling between different iron sulfides and steel electrodes has been investigated. The results show that for the conditions studied in this work, all polymorphs act as cathodes when coupled to steel electrodes, with pyrrhotite having the largest effect of the polymorphs studied.
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Koutsoukos, Peter G., Panagiota D. Natsi, and Zahid Amjad. "Nucleation and Crystal Growth of Calcium Carbonate in the Presence of Zn." In CONFERENCE 2022. AMPP, 2022. https://doi.org/10.5006/c2022-17700.
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Abstract The effect of the presence of Zn is solutions supersaturated with respect to calcium carbonate was investigated at 25°C, pH 8.50. The stability domain of the calcium carbonate solutions was measured in the supersaturation ratio (SRcalcite) values between 20.89-32.36. Below the least SRcalcite value the solutions were stable. Above it, precipitation was spontaneous past induction time, inversely proportional to SRcalcite according to the classical nucleation theory (CNT). In the presence of 1.3 ppm of Zn in the supersaturated solutions, the stability domain was shifted to higher SRcalcite values (47.86&lt;SRcalcite&lt;112.2). The presence of Zn stabilized all three calcium carbonate polymorphs. In the absence of Zn only vaterite and calcite were identified in the precipitated. In all cases no Zn oxides were formed. The rate of spontaneous precipitation of calcium carbonate in the presence of Zn, was reduced by as much as 98% at the least SRcalcite values tested. Adsorption of Zn at the active sites of the supercritical nuclei of vaterite is responsible for the reduction of the rates of CaCO3 precipitation and for the delay of conversion of unstable polymorphs. Finally, induction times in the presence of Zn were significantly longer for the same SRcalcite values without Zn, suggesting that Zn is a nucleation inhibitor as well.
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Kvarekvål, J., and M. Tjelta. "Sour Under-Deposit Corrosion with Different Iron Sulfides." In CORROSION 2021. AMPP, 2021. https://doi.org/10.5006/c2021-16703.
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Abstract Under-deposit corrosion experiments were performed to study the corrosive effects of different types/polymorphs of iron sulfides; Pyrite, pyrrhotite and a troilite/pyrrhotite mixture, which were all commercially available, and mackinawite synthesized in-house by corrosion of steel shavings. Prior to testing the commercial iron sulfides were ground in a ball mill under oxygen-free atmosphere to ensure active particle surfaces. The H2S and CO2 partial pressures were 10 bar each, the temperature was 25 °C, and the test solutions consisted of high-salinity brine (100 g/L NaCl, 150 ppm bicarbonate). The duration of the tests was around 14 days. Both weight loss corrosion and localized corrosion data were obtained. The entire surfaces of the exposed coupons were scanned with a 3D profilometer, obtaining detailed data on localized corrosion morphology and pit depths. The different iron sulfide deposits exhibited different effects on both weight loss and localized corrosion. The experimental results, and various properties of iron sulfide deposits affecting the corrosion behavior, are discussed on the background of available literature.
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Gao, Shujun, Bruce Brown, David Young, Srdjan Nesic, and Marc Singer. "A Modified Thermodynamic Model for the Prediction of Mild Steel Corrosion Product Formation at High Temperature in an Aqueous H2S Environment." In CORROSION 2019. NACE International, 2019. https://doi.org/10.5006/c2019-12869.
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Abstract The prediction of phase identity and characteristics of corrosion products formed on the corroding metal surface is of prime importance to understanding the corrosion mechanisms and the protectiveness conferred by the formed layers. Pourbaix diagrams, developed for CO2 environments, are typically successful in predicting (depending on pH, steel potential, temperature, pCO2, etc) the most stable forms of corrosion products. In H2S environments, however, it is more difficult to build a representative thermodynamic model (Pourbaix diagram) due to the formation of various iron sulfide polymorphs and phases which is a strongly kinetically controlled phenomenon. In addition, high temperature studies have also shown that a thermodynamically less stable but kinetically favored inner Fe3O4 layer developed under the iron sulfide layer and greatly affected the corrosion rate. In this paper, experiments performed at high temperature at different partial pressures of H2S (pH2S=0.10~2.0 bar) were conducted to investigate polymorphous iron sulfide formation and determine if the inner Fe3O4 corrosion product layer would fully convert to iron sulfide if the right conditions were met. The results show that the Fe3O4 layer is not a transient corrosion product layer, as previously thought, since it was always present in all the experimental conditions tested. A modified thermodynamic model was proposed by reconsidering the Fe3O4 stability zone in the Pourbaix diagram. The current model shows better agreement with the experimental results because of these changes.
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Chan, Vivian, V. W. S. Liu, A. C. K. Wong, and T. K. Chan. "DNA POLYMORPHISMS IN OR LINKED TO THE FACTOR VIII GENE IN CHINESE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644049.
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78 unrelated X chromosomes from Southern Chinese (56 normal and 22 haemophiliac) were studied. DNA was restricted by Bel I, Bgl I or Taq I and hybridized to 3' factor VIII:C cDNA probe (5 kb, Chiron) or St 14.1 probe(3 kb, Oberle &Mandel) by standard techniques. The intragenic Bel I polymorphic site was positive in 82%, while Bgl I polymorphic site was positive in all. Thus, 29.5%(2 x×0.82 × 0.18) of Chinese females carried the Bel I polymorphism. Asto the Taq I polymorphism in the closely linked DXS52 DNA segment, the incidences for the various alleles were :System I - allele (3) 10.2%, (4) 2.6%, (5) 2.6%,(6) 17.9%, (7) 21.8% and (8) 44.9% System II - α a allele 56%, 6 allele 44%. Approximately 80% of females were heterozygous for two different alleles. Hence the Bel I and Taq I polymorphisms can be used to track the defective factor VIII gene for carrier detection and prenatal diagnosis. Furthermore, their frequencies in the Chinese are different from those previously reported in other ethnic groups.
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Karasev, E. P., E. E. Andronov, E. P. Chizevskaya, and N. A. Provorov. "Comparative analysis of nucleotide polymorphism of chromosomal and symbiotic genes in symbionts of eastern and medical goat’s rue from a population of the North Caucasus." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.112.
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The analysis of the nucleotide polymorphism in two goatfish rhizobia biovars showed that the diversity of all gene groups corresponds to the diversity of the host plant, and the general polymorphism of chromosomal genes is higher than the symbiotic gene polymorphysm in both biovars.
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MAXIMCIUC, Victoria. "Particulars of the drawing for the child with autistic spectrum disorders." In Probleme ale ştiinţelor socioumanistice şi ale modernizării învăţământului. "Ion Creanga" State Pedagogical University, 2022. http://dx.doi.org/10.46728/c.v1.25-03-2022.p151-155.
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The article addresses the issue of research into the particularities of the plastic activity of children with autism spectrum disorders (ASD). Plastic activity with children with ASD is especially important for those with level 3 and 2 severities after DSM-V and contains several purposes. We can see few scientific papers in this field. This phenomenon is explained by the polymorphic impairment of mental processes, personality traits, diversity and inhomogeneity of this type of disability, the impossibility of applying projective tests that are traditionally used in traditional psychology. The research formulates the purpose and objectives of the research, presents two very different cases with the analysis of children's work and highlights specific features of the plastic activity of children with ASD.
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Stigler, William S., Lin Li, Xihong Lin, Yang Zhao, Mark M. Wurfel, and David C. Christiani. "MicroRNA Single Nucleotide Polymorphisms And Risk Of ARDS And ALI." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2120.
Full textReports on the topic "Alu polymorphism"
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Zou, Chenghui, Weng Zhang, Mao Li, Dan He, Yujie Han, and Mao Lu. A meta-analysis of association between CCL5、CCL11、CCL17 polymorphisms and AD. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, 2022. http://dx.doi.org/10.37766/inplasy2022.11.0148.
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Review question / Objective: At present, many studies on the association between CCL5、CCL11、CCL17 polymorphisms and atopic dermatitis（AD）are inconsistent. We conducted this meta-analysis of Case control trial to evaluate the association between CCL5、CCL11、CCL17 polymorphisms and atopic dermatitis（AD). Condition being studied: Since the discovery of cytokines, and in particular the role of chemokines in the progression of AD, many clinical studies have been carried out around the world to explore the association of AD with chemokine polymorphism. However, the quality, type and conclusions of studies on the correlation between chemokine polymorphism and AD are inconsistent. Foreign studies have shown that chemokine polymorphism is statistically significant in relation to AD. Studies by Menzies-Gow A et al have shown that a new therapeutic strategy targeting to block CCL11 signal has been proven to significantly improve patients with moderate to severe AD. However, some foreign studies have also reported that chemokine polymorphism is unrelated to AD.
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Torrungruang, Kitti, Soranun Chantarangsu, and Thanyachai Sura. Association between vitamin D receptor gene polymorphisms and chronic periodontitis in Thais. Chulalongkorn University, 2015. https://doi.org/10.58837/chula.res.2015.18.
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Polymorphisms of the vitamin D receptor (VDR) gene have been implicated in the susceptibility to infections and bone-related diseases. However, their relationship with periodontal disease remains unclear. This cross-sectional study investigated whether the susceptibility to chronic periodontitis in a Thai population is associated with VDR polymorphisms. Genomic DNA was obtained from 1,460 subjects, aged 39-65 years. Genotyping of VDR polymorphisms (FokI, BsmI, ApaI, and TaqI) was performed using real-time polymerase chain reaction. Subjects were categorized into three groups; no/mild, moderate, and severe periodontitis. Multinomial logistic regression analysis was used to determine the degree of association between VDR polymorphisms and periodontal status adjusted for age, gender, education, smoking, and diabetes. The CC+CT genotypes of FokI polymorphism were associated with moderate and severe periodontitis with odds ratios (OR) of 1.4 (95% CI 1.0-1.9) and 2.0 (95% CI 1.3-2.9), respectively. There was no significant relationship between the other VDR polymorphisms or BsmI-ApaI-TaqI haplotypes and periodontitis. To examine gene-smoking interaction, non-smokers with the TT genotype of FokI polymorphism were used as the reference group for all comparisons. Current smokers who had the CC+CT genotypes presented the highest risk of severe periodontitis with an OR of 10.4 (95% CI 4.9-22.1), whereas their counterparts with the TT genotype and non-smokers bearing the CC+CT genotypes had an increased risk by 2.7 (95% CI 1.1-6.7) and 2.0 folds (95% CI 1.2-3.4), respectively. The combined effect of FokI polymorphism and current smoking was 3.5 times (95% CI 1.3-9.9) greater than what would be expected from the sum of their individual effects, indicating a significant additive interaction. In conclusion, our data indicate that FokI polymorphism of VDR gene was significantly associated with periodontal disease severity in this study group. We are also the first to demonstrate that FokI polymorphism and smoking synergistically interacted in increasing the risk of chronic periodontitis.
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Avihingsanon, Yingyos, Jongkonnee Wongpiyabovorn, and Nattiya Hirankarn. Biomarker discovery in systemic lupus erythematosus: genome-methylation approaches : Research report. Chulalongkorn University, 2010. https://doi.org/10.58837/chula.res.2010.15.
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Discovery of novel biomarkers in lupus nephritis Biomarkers are needed for making diagnosis and prognosis. In lupus nephritis, conventional tests like urinalysis or serum creatinine remain inadequate for patient care. In this proposal, we focused on non-invasive tools like blood and urine mRNAs or proteins. We chose candidate genes involving regulatory T-cell, B-lymphocyte signatures or vascular protective factors. Expression of regulatory cell signature (FOXP3) in peripheral blood mononuclear cells is associated with activity of lupus nephritis. We found FOXP3 mRNA levels in PBMCs from patients with active lupus nephritis were significantly lower than inactive lupus nephritis. Expression levels of FOXP3 mRNA were associated with pathological activity index, cellular crescent and fibrinoid necrosis. BLyS and APRIL are B-lymphocyte related cytokines that play an important role in generating and maintaining the mature B-cell pool. In this study, we found blood APRIL correlated with activity of lupus nephritis. Blood APRIL levels could precisely predict failure of standard treatment treatment. APRIL is a potential biomarker for predicting treatment failure. Lastly, we found an expression of VEGF in renal tissue may serve as a molecular marker of renal damage from LN and may be a predictive factor for short-term loss of kidney function in lupus nephritis patients. We proposed that reduction of intra-renal VEGF level caused by losses of podocyte cells. Genetic polymorphism of drug toxicity or pharmacokinetics in SLE patients We began to explore the pharmacokinetics and pharmacogenomics of two important immunosuppressants, azathioprine and mycophenolate. In this study, we report TPMT polymorphisms and TPMT enzyme activity were important predictors of AZA-induced myelosuppression. The tests are available for routine care. Mycophenolic acid (MPA) is active metabolite of mycophenalate. We found MPA levels is important predictor of therapeutic response. The therapeutic drug monitoring is now an important issue of patient care. We found UGT1A9 polymorphism may play a pivotal role in drug metabolisms. Methylation study We examined and compared the methylation levels of long terminal repeats (LTRs) and non-LTR retroelements in normal and SLE CD4+ T lymphocytes, CD8+ T lymphocytes and B lymphocytes. Hypomethylation of LINE-1 but not Alu was found in CD4+ T lymphocytes, CD8+ T lymphocytes, and B lymphocytes of SLE patient. Moreover, when the SLE patients were divided into active and inactive groups, LINE-1 hypomethylation was more significantly distinguished in both CD4+ and CD8+ T lymphocytes of patients from the active SLE group when compared to the controls. Genome-wide scanning using SNP microarrays In this study, we applied case-control association study including pooling genome wide association (GWA) and candidate gene association studies to search for SNPs associated with SLE susceptibility and/or severity. We could not identify any SNPs with distinct p-value or odds ratio from our pooling GWA result due to limited power. We selected IFIX for further study in candidate gene’s part. Besides IFIX, we also focus on MNDA, IFI16 and AIM2 genes which located in the same region and are all IFN-inducible genes. They are important SLE susceptibility genes due to several reasons including 1) genetic mapping from lupus murine model and 2) an upregulated IFN-inducible genes in patients with SLE from microarray studies and 3) IFI16 was identified as new autoantigen for patients with SLE. We genotyped 10 SNPs from these 4 genes and found that SNP within IFIX and IFI16 are independently important.
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Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu, and George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, 2015. http://dx.doi.org/10.32747/2015.7600017.bard.
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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.
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Weller, Joel I., Ignacy Misztal, and Micha Ron. Optimization of methodology for genomic selection of moderate and large dairy cattle populations. United States Department of Agriculture, 2015. http://dx.doi.org/10.32747/2015.7594404.bard.
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The main objectives of this research was to detect the specific polymorphisms responsible for observed quantitative trait loci and develop optimal strategies for genomic evaluations and selection for moderate (Israel) and large (US) dairy cattle populations. A joint evaluation using all phenotypic, pedigree, and genomic data is the optimal strategy. The specific objectives were: 1) to apply strategies for determination of the causative polymorphisms based on the “a posteriori granddaughter design” (APGD), 2) to develop methods to derive unbiased estimates of gene effects derived from SNP chips analyses, 3) to derive optimal single-stage methods to estimate breeding values of animals based on marker, phenotypic and pedigree data, 4) to extend these methods to multi-trait genetic evaluations and 5) to evaluate the results of long-term genomic selection, as compared to traditional selection. Nearly all of these objectives were met. The major achievements were: The APGD and the modified granddaughter designs were applied to the US Holstein population, and regions harboring segregating quantitative trait loci (QTL) were identified for all economic traits of interest. The APGD was able to find segregating QTL for all the economic traits analyzed, and confidence intervals for QTL location ranged from ~5 to 35 million base pairs. Genomic estimated breeding values (GEBV) for milk production traits in the Israeli Holstein population were computed by the single-step method and compared to results for the two-step method. The single-step method was extended to derive GEBV for multi-parity evaluation. Long-term analysis of genomic selection demonstrated that inclusion of pedigree data from previous generations may result in less accurate GEBV. Major conclusions are: Predictions using single-step genomic best linear unbiased prediction (GBLUP) were the least biased, and that method appears to be the best tool for genomic evaluation of a small population, as it automatically accounts for parental index and allows for inclusion of female genomic information without additional steps. None of the methods applied to the Israeli Holstein population were able to derive GEBV for young bulls that were significantly better than parent averages. Thus we confirm previous studies that the main limiting factor for the accuracy of GEBV is the number of bulls with genotypes and progeny tests. Although 36 of the grandsires included in the APGD were genotyped for the BovineHDBeadChip, which includes 777,000 SNPs, we were not able to determine the causative polymorphism for any of the detected QTL. The number of valid unique markers on the BovineHDBeadChip is not sufficient for a reasonable probability to find the causative polymorphisms. Complete resequencing of the genome of approximately 50 bulls will be required, but this could not be accomplished within the framework of the current project due to funding constraints. Inclusion of pedigree data from older generations in the derivation of GEBV may result is less accurate evaluations.
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Aziz, Md Abdul, Tahmina Akter, and Mohammad Safiqul Islam. Effect of miR-196a2 rs11614913 polymorphism on cancer susceptibility: evidence from an updated meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, 2022. http://dx.doi.org/10.37766/inplasy2022.5.0027.
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Review question / Objective: MiR-196a2 rs11614913 polymorphism has been studied in a wide range of cancers throughout the years. Despite a large number of epidemiological studies performed in almost all ethnic populations, the contribution of this polymorphism in cancer risk is still inconclusive. Therefore, this updated meta-analysis was performed to estimate a meticulous correlation between miR-196a2 rs11614913 variant and cancer susceptibility. Condition being studied: Different types of cancer patients and healthy controls were evaluated to detect the cancer risk in the individual case-control studies. We performed a meta analysis of these case control studies to get a pulled outcome risk.
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Kistler, Harold Corby, Talma Katan, and Dani Zamir. Molecular Karyotypes of Pathogeic Strains of Fusarium oxysporum. United States Department of Agriculture, 1995. http://dx.doi.org/10.32747/1995.7604927.bard.
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Genetic diversity of pathogenic strains of the fungus Fusarium oxysporum was determied by analysis of electrophoretic karyotype, as well as by DNA variation detected by Restriction Fragment Length Polymorphisms (RFLPs) and Random Amplified Polymorphic DNAs (RAPDs). The electrophoretic karyotypes for 130 isolates of the fungus pathogenic to tomato, melon, and banana were analyzed. Electrophoretic karyotype variation, reflected in differences in apparent chromosome number and genome size, was observed even among isolates from the same host and sub specific category. Sub specific categories studied were forma specialis, vegetative compatibility group (VCG) and race. Chromosome number and genome size variation was less for isolates within the same VCG than for the collection of isolates as a whole. RFLP and RAPD analysis were performed on 62 isolates of F. oxysporum from tomato and melon. Polygenetic trees were constructed from genetic diversity data. The results support the hypothesis that isolates belonging to the same VCG originate from a single ancestor compared to other isolates. The results do not support the hypothesis that all isolates belonging to the same forma specialis originate from a common ancestor. These conclusions have profound implication for breeding resistance to diseases caused by particular formae speciales of F. oxysporum.
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Wu, Ling, Tao Zhang, Yao Wang, et al. Polymorphisms and premature ovarian insufficiency and failure: A comprehensive meta-analysis update, subgroup, ranking, and network analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, 2022. http://dx.doi.org/10.37766/inplasy2022.1.0052.
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Review question / Objective: Early identification of women potentially who develop POI and POF is essential for early screening and treatment to improve clinical outcomes. We aim to conduct a comprehensive meta-analysis update, subgroup, ranking and network analysis for all available genetic polymorphism and associated with the POI and POF risk. Information sources: Six electronic databases will be included such as PubMed, Web of Science, Embase, MEDLINE, WANFANG DATA, CNKI. Will contact with authors by emails when necessary.
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Veilleux, Richard E., Jossi Hillel, A. Raymond Miller, and David Levy. Molecular Analysis by SSR of Genes Associated with Alkaloid Synthesis in a Segregating Monoploid Potato Family. United States Department of Agriculture, 1994. http://dx.doi.org/10.32747/1994.7570550.bard.
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More than 15,000 anthers of an interspecific hybrid (CP2) between two diploid (2n=2x=24) potato species, Solanum chacoense (weedy) and S. phureja (cultivated), were cultured to generate a family of monoploid (haploid, 2n-1x=12) plants. Of 260 regenerated plants, 34 were monoploid, 210 diploid and 16 tetraploid. SSR analysis revealed that six monoploids were genetically identical and 14 diploids were homozygous, thus limiting the population to 42 (28 monoploids and 14 homozygous diploids). New microsatellite loci were developed for potato from database sequences (15), a conventional genomic library (6), an enriched library (18) and tomato (11). Of these, 13 were polymorphic in the CP2 family and 11 were used to study genetic segregatin. Four of 11 exhibited skewed segregation in the monoploid family. Seven of 18 microsatellite markers were polymorphic and informative on a set of 12 tetraploid potato cultivars. Acetylleptinidine (ALD) is the aglycone of leptines, a natural defense against insects, especially the highly destructuve Colorado potato beetle. ALD is absend in S. phureja but highly expressed in the S. chacoense parent of CP2. A backcross population between CP2 and tis S. phureja parent was used to examine segregation for ALD. Bulks of 10 backcross individuals that expressed ALD and 10 that did not were used to identify putative RAPD markers associatd with the trait. Of 80 primers tested, one putative marker amplified by OPQ02 was present in eight of ten individuals comprising the high bulk and absent in all 10 individuals comprising the low bulk. This is a putative marker for ALD expression in potato.
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Cao, Xianling, Xuanyou Zhou, Naixin Xu, Songchang Chang, and Chenming Xu. Association of IL-4 and IL-10 Polymorphisms with Preterm Birth Susceptibility: A Systematic Review and Meta-Analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, 2022. http://dx.doi.org/10.37766/inplasy2022.4.0044.
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Review question / Objective: The aim of our systematic review and meta-analysis was to summarize the effects of IL-4 and IL-10 gene polymorphism and clarify their possible association with PTB. Condition being studied: World Health Organization (WHO) defines preterm birth (PTB) as babies born alive before 37 weeks of pregnancy are completed. The new estimates show that the prevalence of PTB during 2014 ranged from 8.7% to13.4% of all live births, about 15 million preterm babies born each year. Besides, PTB is the leading cause of death worldwide for children below 5 years of age. Babies born preterm are at an increased risk of short-term and long-term complications attributed to immaturity of multiple organ systems, such as cerebral palsy, intellectual disabilities, vision and hearing impairments, and impaired cognitive development. PTB has become a worldwide public health problem, but its etiology remains unclear. Accumulating evidence shows that PTB is a syndrome that can be attributed to a variety of pathological processes(5). Inflammatory diseases and genetic background are known risk factors for PTB, many studies had shown that genetic variations in proinflammatory cytokines such as tumor necrosis factor-α (TNF-α) and interleukin-1 α (IL-1 α) are associated with increased risk of PTB, but the relationship between genetic polymorphism in anti-inflammatory cytokines and risk of PTB remains controversial.