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https://www.readbyqxmd.com/read/28628900/evaluation-of-the-innotyper-%C3%A2-21-genotyping-kit-in-multi-ethnic-populations
#1
Peter Gustav Ristow, Nicole Barnes, Gina Pineda Murphy, Hiromi Brown, Kevin Wesley Cloete, Maria Eugenia D'Amato
We report the findings of the evaluation of the InnoTyper(®) 21 genotyping kit for the use of human identification (HID) and paternity testing in South Africa. This novel forensic kit evaluates 20 retrotransposable elements (AC4027, MLS26, ALU79712, NBC216, NBC106, RG148, NBC13, AC2265, MLS09, AC1141, TARBP, AC2305, HS4.69, NBC51, ACA1766, NBC120, NBC10, NBC102, SB19.12 and NBC148) and the Amelogenin locus for sex determination. The evaluation of the genotyping performance showed no significant spectral pull-up for peak heights between 100 and 30,000 RFUs...
June 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28624837/clinical-response-to-non-surgical-periodontal-treatment-in-patients-with-interleukin-6-and-interleukin-10-polymorphisms
#2
G-S Chatzopoulos, A-E Doufexi, A Kouvatsi
BACKGROUND: Genetic polymorphisms are commonly associated with altered transcriptional activity and possibly make individuals more susceptible to periodontal disease development, increased disease severity and poor treatment outcome. The study aimed to determine the effect of Interleukin-6 (IL-6) -572 G/C (rs1800796) and IL-10 -592 C/A (rs1800872) polymorphisms on the outcomes of non-surgical periodontal therapy in a Caucasian population. MATERIAL AND METHODS: Sixty-eight patients with chronic periodontal disease were grouped according to their genotype: IL-6, IL-10, IL-6 and IL-10 susceptible (SCP) and non-susceptible (NSCP)...
June 18, 2017: Medicina Oral, Patología Oral y Cirugía Bucal
https://www.readbyqxmd.com/read/28619083/on-marker-based-parentage-verification-via-non-linear-optimization
#3
Vinzent Boerner
BACKGROUND: Parentage verification by molecular markers is mainly based on short tandem repeat markers. Single nucleotide polymorphisms (SNPs) as bi-allelic markers have become the markers of choice for genotyping projects. Thus, the subsequent step is to use SNP genotypes for parentage verification as well. Recent developments of algorithms such as evaluating opposing homozygous SNP genotypes have drawbacks, for example the inability of rejecting all animals of a sample of potential parents...
June 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28613042/allele-frequencies-of-15-str-loci-in-bosnian-and-herzegovinian-population
#4
Amela Pilav, Naris Pojskić, Anesa Ahatović, Mirela Džehverović, Jasmina Čakar, Damir Marjanović
AIM: To determine newest the most accurate allele frequencies for 15 short tandem repeat (STR) loci in the Bosnian and Herzegovinian population, calculate statistical parameters, and compare them with the relevant data for seven neighboring populations. METHODS: Genomic DNA was obtained from buccal swabs of 1000 unrelated individuals from all regions of Bosnia and Herzegovina. Genotyping was performed using PowerPlex® 16 System to obtain allele frequencies for 15 polymorphic STR loci including D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX, and FGA...
June 14, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/28608987/smarca4-inactivating-mutations-cause-concomitant-coffin-siris-syndrome-microphthalmia-and-small-cell-carcinoma-of-the-ovary-hypercalcemic-type
#5
Edoardo Errichiello, Noor Mustafa, Annalisa Vetro, Lucia Dora Notarangelo, Hugo de Jonge, Berardo Rinaldi, Debora Vergani, Sabrina Rita Giglio, Patrizia Morbini, Orsetta Zuffardi
SMARCA4 chromatin remodeling factor is mutated in 11% of Coffin-Siris syndrome (CSS) patients and in almost all small cell carcinoma of the ovary hypercalcemic type (SCCOHT) tumors. Missense mutations with gain-of-function or dominant-negative effects are associated with CSS, whereas inactivating mutations, leading to loss of SMARCA4 expression, have been exclusively found in SCCOHT. We applied whole exome sequencing to study a 15-year-old patient with mild CSS who concomitantly developed SCCOHT at age 13 years...
June 13, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28606620/efficacy-and-safety-of-lumacaftor-and-ivacaftor-in-patients-aged-6-11-years-with-cystic-fibrosis-homozygous-for-f508del-cftr-a-randomised-placebo-controlled-phase-3-trial
#6
Felix Ratjen, Christopher Hug, Gautham Marigowda, Simon Tian, Xiaohong Huang, Sanja Stanojevic, Carlos E Milla, Paul D Robinson, David Waltz, Jane C Davies
BACKGROUND: Lumacaftor and ivacaftor combination treatment showed efficacy in patients aged 12 years or older with cystic fibrosis homozygous for F508del-cystic fibrosis transmembrane conductance regulator (CFTR) in placebo-controlled studies and patients aged 6-11 years with cystic fibrosis homozygous for F508del-CFTR in an open-label study. We report efficacy and safety of lumacaftor and ivacaftor in patients with cystic fibrosis aged 6-11 years homozygous for F508del-CFTR. METHODS: In this phase 3, randomised, double-blind, placebo-controlled, multicentre study, patients were enrolled at 54 hospitals and medical centres in nine countries (the USA, Australia, Belgium, Canada, Denmark, France, Germany, Sweden, and the UK)...
June 8, 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28600722/genetic-dissection-of-plant-growth-habit-in-chickpea
#7
Hari D Upadhyaya, Deepak Bajaj, Rishi Srivastava, Anurag Daware, Udita Basu, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs...
June 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28600642/characterization-and-comparison-of-genetic-variation-in-cotesia-flavipes-hymenoptera-braconidae-mass-reared-for-biological-pest-control-using-microsatellite-markers
#8
F C Freitas, A C Morales-Corrêa E Castro, N C C P Barbosa, O A Fernandes
The larval parasitoid Cotesia flavipes (Cameron) (Hymenoptera: Braconidae) is an important biological control agent of the sugarcane borer, Diatraea saccharalis (Fabricius) (Lepidoptera: Crambidae). This exotic parasitoid has been mass reared for field release since its introduction in the 1970s. Insects are exchanged between labs or introduced from the field, but without basic studies or criteria. Thus, the objective of this study was to evaluate the genetic variability of insects from six Brazilian States (São Paulo, Minas Gerais, Paraná, Goiás, Maranhão, and Alagoas) using microsatellites...
June 9, 2017: Neotropical Entomology
https://www.readbyqxmd.com/read/28600257/search-for-more-effective-microsatellite-markers-for-forensics-with-next-generation-sequencing
#9
Bowen Tan, Zicheng Zhao, Zhe Zhang, Shengbin Li, Shuai Cheng Li
Published by the Combined DNA Index System (CODIS) program of the Federal Bureau of Investigation (FBI) in 1997, the 13 core short tandem repeat (STR) loci are widely adopted as genetic markers in forensic applications, e.g., identity testing and paternity testing. However, these loci may be biased and suffer from reduced sensitivities towards specific population groups. In addition, the rapid growth of entries in forensic databases raises the chance of random hits, which can cause false recognitions of criminal suspects...
June 7, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28589897/phylogenic-analysis-and-forensic-genetic-characterization-of-chinese-uyghur-group-via-autosomal-multi-str-markers
#10
Xiaoye Jin, Yuanyuan Wei, Jiangang Chen, Tingting Kong, Yuling Mu, Yuxin Guo, Qian Dong, Tong Xie, Haotian Meng, Meng Zhang, Jianfei Li, Xiaopeng Li, Bofeng Zhu
We investigated the allelic frequencies and forensic descriptive parameters of 23 autosomal short tandem repeat loci in a randomly selected sample of 1218 unrelated healthy Uyghur individuals residing in the Xinjiang Uyghur Autonomous Region, northwest China. A total of 281 alleles at these loci were identified and their corresponding allelic frequencies ranged from 0.0004 to 0.5390. The combined match probability and combined probability of exclusion of all loci were 5.192 × 10-29 and 0.9999999996594, respectively...
May 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28587495/allele-specific-interaction-between-glutathione-peroxidase-1-and-manganese-superoxide-dismutase-affects-the-levels-of-bcl-2-sirt3-and-e-cadherin
#11
Dede N Ekoue, Soumen Bera, Emmanuel Ansong, Peter C Hart, Sofia Zaichick, Frederick E Domann, Marcelo G Bonini, Alan M Diamond
Manganese superoxide dismutase (MnSOD) is a mitochondrial resident enzyme that reduces superoxide to hydrogen peroxide (H2O2), which can be further reduced to water by glutathione peroxidase (GPX1). Data from human studies has indicated that common polymorphisms in both of these proteins are associated with the risk of several cancers, including breast cancer. Moreover, polymorphisms in MnSOD and GPX1 were shown to interact to increase the risk of breast cancer. To gain an understanding of the molecular mechanisms behind these observations, we engineered human MCF-7 breast cancer cells to exclusively express GPX1 and/or MnSOD alleles and investigated the consequences on the expression of several proteins associated with cancer etiology...
June 6, 2017: Free Radical Research
https://www.readbyqxmd.com/read/28583085/intricacies-in-arrangement-of-snp-haplotypes-suggest-great-admixture-that-created-modern-humans
#12
Rajib Dutta, Joseph Mainsah, Yuriy Yatskiv, Sharmistha Chakrabortty, Patrick Brennan, Basil Khuder, Shuhao Qiu, Larisa Fedorova, Alexei Fedorov
BACKGROUND: Inferring history from genomic sequences is challenging and problematic because chromosomes are mosaics of thousands of small Identicalby-descent (IBD) fragments, each of them having their own unique story. However, the main events in recent evolution might be deciphered from comparative analysis of numerous loci. A paradox of why humans, whose effective population size is only 10(4), have nearly three million frequent SNPs is formulated and examined. RESULTS: We studied 5398 loci evenly covering all human autosomes...
June 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28549550/forensic-efficiency-parameters-of-the-investigator-argus-x-12-kit-in-women-from-two-mestizo-and-seven-amerindian-populations-from-mexico
#13
I Cortés-Trujillo, B Ramos-González, O Salas-Salas, F Zuñiga-Chiquette, A Zetina Hernández, G Martínez-Cortés, M Ruiz-Hernández, A González-Martín, J F Ferragut, H Rangel-Villalobos
Allele frequency distribution and statistical parameters of forensic efficiency concerning the Investigator Argus X-12 kit (Qiagen, Hilden, Germany) were determined in a total sample of 641 unrelated Mexican females, including two Mestizo-admixed- populations (n=309) and seven Amerindian groups (n=332) from the main regions of the country. Most of the 12 X-STRs were in agreement with Hardy-Weinberg expectations in all nine Mexican populations. The power of discrimination in females (PD) and Median exclusion chance for trios (MECT) and duos (MECD) of this genetic system based on X-STRs were >99...
May 2017: Legal Medicine
https://www.readbyqxmd.com/read/28549546/population-genetic-analysis-of-xiamen-han-population-on-21-short-tandem-repeat-loci
#14
Lili Wu, Bin Pei, Peng Ran, Xiuyu Song
GlobalFiler™ Express amplification kit incorporates 21 commonly used autosomal short tandem repeat (STR) loci and three gender determination loci. In this study, we analyzed GlobalFiler STR loci on 1006 unrelated individuals sampled of the Han population from Xiamen city, Fujian province, China. No deviations from Hardy-Weinberg equilibrium were observed. The combined probability of exclusion (CPE) for all 21 STR loci were >0.99999999771. A comparison of the allele frequencies in the population under study has been performed with other published from East Asian population for the same loci...
May 2017: Legal Medicine
https://www.readbyqxmd.com/read/28543872/pai-1-gain-of-function-genotype-factors-increasing-pai-1-levels-and-airway-obstruction-the-gala-ii-cohort
#15
Michael G Sherenian, Seong H Cho, Albert Levin, Jin-Young Min, Sam S Oh, Donglei Hu, Joshua Galanter, Saunak Sen, Scott Huntsman, Celeste Eng, Jose R Rodriguez-Santana, Denise Serebrisky, Pedro C Avila, Ravi Kalhan, Lewis J Smith, Luisa N Borrell, Max A Seibold, L Keoki Williams, Esteban G Burchard, Rajesh Kumar
BACKGROUND: PAI-1 gain of function variants promote airway fibrosis, and are associated with asthma and with worse lung function in subjects with asthma. OBJECTIVE: We sought to determine if the association of a gain-of-function polymorphism in Plasminogen Activator Inhibitor -1 (PAI-1) with airway obstruction is modified by asthma status, and whether any genotype effect persists after accounting for common exposures that increase PAI-1 level. METHODS: We studied 2070 Latino children (8-21y) with genotypic and pulmonary function data from the GALA II cohort...
May 24, 2017: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28537274/characterization-of-pathogenic-sorl1-genetic-variants-for-association-with-alzheimer-s-disease-a-clinical-interpretation-strategy
#16
Henne Holstege, Sven J van der Lee, Marc Hulsman, Tsz Hang Wong, Jeroen Gj van Rooij, Marjan Weiss, Eva Louwersheimer, Frank J Wolters, Najaf Amin, André G Uitterlinden, Albert Hofman, M Arfan Ikram, John C van Swieten, Hanne Meijers-Heijboer, Wiesje M van der Flier, Marcel Jt Reinders, Cornelia M van Duijn, Philip Scheltens
Accumulating evidence suggests that genetic variants in the SORL1 gene are associated with Alzheimer disease (AD), but a strategy to identify which variants are pathogenic is lacking. In a discovery sample of 115 SORL1 variants detected in 1908 Dutch AD cases and controls, we identified the variant characteristics associated with SORL1 variant pathogenicity. Findings were replicated in an independent sample of 103 SORL1 variants detected in 3193 AD cases and controls. In a combined sample of the discovery and replication samples, comprising 181 unique SORL1 variants, we developed a strategy to classify SORL1 variants into five subtypes ranging from pathogenic to benign...
May 24, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28523558/epigenome-editing-in-the-brain
#17
Pavel Bashtrykov, Albert Jeltsch
Epigenome editing aims for an introduction or removal of chromatin marks at a defined genomic region using artificial EpiEffectors resulting in a modulation of the activity of the targeted functional DNA elements. Rationally designed EpiEffectors consist of a targeting DNA-binding module (such as a zinc finger protein, TAL effector, or CRISPR/Cas complex) and usually, but not exclusively, a catalytic domain of a chromatin-modifying enzyme. Epigenome editing opens a completely new strategy for basic research of the central nervous system and causal treatment of psychiatric and neurological diseases, because rewriting of epigenetic information can lead to the direct and durable control of the expression of disease-associated genes...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28520715/geographical-distribution-of-complement-receptor-type-1-variants-and-their-associated-disease-risk
#18
Thaisa Lucas Sandri, Selorme Adukpo, Dao Phuong Giang, Christian N Nguetse, Fabiana Antunes Andrade, Hoang van Tong, Nguyen Linh Toan, Le Huu Song, Preetham Elumalai, Kumarasamy Thangaraj, Vijaya Lakshmi Valluri, Francine Ntoumi, Christian G Meyer, Iara Jose de Messias Reason, Peter G Kremsner, Thirumalaisamy P Velavan
BACKGROUND: Pathogens exert selective pressure which may lead to substantial changes in host immune responses. The human complement receptor type 1 (CR1) is an innate immune recognition glycoprotein that regulates the activation of the complement pathway and removes opsonized immune complexes. CR1 genetic variants in exon 29 have been associated with expression levels, C1q or C3b binding and increased susceptibility to several infectious diseases. Five distinct CR1 nucleotide substitutions determine the Knops blood group phenotypes, namely Kna/b, McCa/b, Sl1/Sl2, Sl4/Sl5 and KCAM+/-...
2017: PloS One
https://www.readbyqxmd.com/read/28508289/somatic-mosaicism-with-reversion-to-normality-of-a-mutated-transthyretin-allele-related-to-a-familial-amyloidotic-polyneuropathy
#19
Concetta Federico, Ketty Dugo, Francesca Bruno, Anna Maria Longo, Agata Grillo, Salvatore Saccone
Familial amyloidotic polyneuropathy (FAP) is a progressive neuropathy, with onset in adulthood and high mortality. It is related to an altered transthyretin (TTR) plasma protein, mainly produced by the liver and responsible for amyloid deposit in the peripheral nervous system. SNPs in the TTR gene were associated with FAP, and the G>C substitution (NM_000371.3:c.325G>C) in the 109th codon (GAG vs CAG; NP_362.1:p.E109Q) was previously described in Sicily (Italy). Here, we report on a Sicilian family with several patients affected by FAP related to the E109Q mutation, which displayed a somatic mosaicism with the reversion to normality of the c...
May 15, 2017: Human Genetics
https://www.readbyqxmd.com/read/28500993/nonsynonymous-changes-of-equine-lentivirus-receptor-1-elr1-gene-in-amino-acids-involved-in-the-interaction-with-equine-infectious-anemia-virus-eiav
#20
C M Corbi-Botto, S A Sadaba, M E Zappa, P Peral-García, S Díaz
Equine lentivirus receptor-1 (ELR1) has been characterized as the specific functional receptor that mediates equine infectious anemia virus (EIAV) entrance to horse macrophages. This receptor is tumor necrosis factor receptor superfamily member 14 (TNFRSF14). The aim of this study was to investigate the occurrence of allelic variants in the coding sequence of equine TNFRSF14 gene by screening for single-nucleotide polymorphisms (SNPs) in different equine populations. Forty seven horse samples were randomly selected from a reservoir of EIAV-seropositive and seronegative samples collected from different outbreaks and regions of Argentina...
May 2, 2017: Research in Veterinary Science
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