scholarly journals Genetic characteristics of Korean Jeju Black cattle with high density SNP chips

2020 ◽  
Author(s):  
Zahangir M. Alam ◽  
Yun-Mi Lee ◽  
Hyo-Jung Son ◽  
Lauren H. Hanna ◽  
David G. Riley ◽  
...  
Keyword(s):  
High Density ◽  
Genetic Characteristics ◽  
Jeju Black Cattle

A High Density Polymorphism Analysis of Factors Correlated with Neurotoxicity to Bortezomib in Patients with Multiple Myeloma.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4816-4816
Author(s):  
Stephane Minvielle ◽  
Céline Keime ◽  
Florence Magrangeas ◽  
Julie Vendrell ◽  
Wilfried Gouraud ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Quality Control ◽  
Feature Selection ◽  
High Density ◽  
Support Vector ◽  
Polymorphism Analysis ◽  
Snp Analysis ◽  
Call Rate ◽  
Genetic Characteristics ◽  
Two Samples

Abstract Abstract 4816 Bortezomib, a proteasome inhibitor, has become an essential compound in the treatment of multiple myeloma (MM). Clinically relevant (i.e. grade 2 or greater) peripheral neurotoxicity is a significant side-effect of bortezomib. As the occurrence of neurotoxicity is unforeseeable and apparently dose independent, we think that it might be associated with individual genetic characteristics such as Single Nucleotide Polymorphisms (SNP) or Copy Number Variants (CNV). In order to identify the genetic characteristics (SNP and CNV) correlated with the occurrence of neurotoxicity induced by bortezomib, we performed high density SNP analysis in 300 patients using Affymetrix Genome-Wide Human SNP Arrays 6.0. All patients were included in the prospective randomized trial IFM 99-01 and had received bortezomib and dexamethasone as induction therapy for previously untreated MM. Neurotoxicity was graded as severe (ECOG score of 2 or greater) or non severe (ECOG score of 0 or 1). Quality controls included Contrast Quality Control (CQC), the call rate and the percentage of heterozygotes. CQC estimates the ability to separate the intensities corresponding to the different alleles into three clusters. In poor quality samples, CQC is excessively low and a large difference between CQC calculated on SNP that reside on Nsp and Sty fragments can indicate a single-enzyme target preparation failure. Only one sample was considered to have an excessively low CQC value (<0.4) and two samples were considered to have an excessive difference between CQC calculated on SNP that reside on Nsp and Sty fragments ( CQCSty − CQCNsp   > 2), according to Affymetrix recommendations for quality control on SNP6.0 chips. Then the birdseed algorithm (Korn et al., 2008) was used to genotype the samples.. The median call rate was 99.57%. Eight samples were excluded to a call rate < 97%. Percentage of heterozygotes is also evaluated as an excessive percentage can be a consequence of contamination. We thus excluded 3 additional samples for which the percentage of heterozygotes was greater than m + 3 sd (m: mean of heterozygotes in the entire series, sd: standard deviation). Further analysis was performed on 281 samples that meet these quality criteria and for which we know the neurotoxicity grade of the treatment. 833,192 SNP were considered on these samples. For the CNV analysis, the Median of the Absolute Values of all Pairwise Differences (MAPD) metric was considered for quality control. According to Affymetrix recommendations, 22 samples with a MAPD>0.35 were excluded. Further analysis was performed on 270 samples that meet this quality criterion and for which we know the neurotoxicity grade of the treatment. 1,720,978 CNV markers were considered on these samples. To identify the SNP and CNV most associated with neurotoxicity in patients receiving bortezomib, we use of two efficient and highly scalable feature selection techniques. The aim is to identify the relevant SNP and CNV markers that are strictly necessary to construct an efficient classifier of the bortezomib neurotoxicity from data alone. One is based on Support Vector Machines (SVM-RFE), a common and well-studied method in the Machine Learning community. The other uses a probabilistic feature selection technique based on recent Bayesian networks advances to identify a Markov Blanket of the target variable T, that is, a subset of the variables that renders the the remaining ones independent of T. Statistical significance of the selected SNP and CNV markers are evaluated using bootstrapping. Additional data will be presented during the meeting. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Exploring the Genetic Characteristics of Two Recombinant Inbred Line Populations via High-Density SNP Markers in Maize

PLoS ONE ◽  
2012 ◽  
Vol 7 (12) ◽  
pp. e52777 ◽  
Author(s):  
Qingchun Pan ◽  
Farhan Ali ◽  
Xiaohong Yang ◽  
Jiansheng Li ◽  
Jianbing Yan
Keyword(s):  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Snp Markers ◽  
High Density ◽  
Genetic Characteristics

scholarly journals Genomic Structure and Variation of Nuclear Factor (Erythroid-Derived 2)-Like 2

2013 ◽  
Vol 2013 ◽  
pp. 1-24 ◽  
Author(s):  
Hye-Youn Cho
Keyword(s):  
Complex Traits ◽  
Genomic Structure ◽  
Inbred Mouse ◽  
High Density ◽  
Mouse Strains ◽  
Sequencing Analysis ◽  
Nuclear Factor ◽  
Genetic Characteristics ◽  
Density Mapping ◽  
Wide Range

High-density mapping of mammalian genomes has enabled a wide range of genetic investigations including the mapping of polygenic traits, determination of quantitative trait loci, and phylogenetic comparison. Genome sequencing analysis of inbred mouse strains has identified high-density single nucleotide polymorphisms (SNPs) for investigation of complex traits, which has become a useful tool for biomedical research of human disease to alleviate ethical and practical problems of experimentation in humans. Nuclear factor (erythroid-derived 2)-like 2 (NRF2) encodes a key host defense transcription factor. This review describes genetic characteristics of humanNRF2and its homologs in other vertebrate species.NRF2is evolutionally conserved and shares sequence homology among species. Compilation of publically available SNPs and other genetic mutations shows that humanNRF2is highly polymorphic with a mutagenic frequency of 1 per every 72 bp. Functional at-risk alleles and haplotypes have been demonstrated in various human disorders. In addition, other pathogenic alterations including somatic mutations and misregulated epigenetic processes inNRF2have led to oncogenic cell survival. Comprehensive information from the current review addresses association ofNRF2variation and disease phenotypes and supports the new insights into therapeutic strategies.

Planar defects in ordered (Ga,In)P

1988 ◽  
Vol 46 ◽  
pp. 902-903
Author(s):  
S. McKernan ◽  
C. B. Carter ◽  
D. Bour ◽  
J. R. Shealy
Keyword(s):  
Electron Diffraction ◽  
Vapor Phase ◽  
Growth Direction ◽  
High Density ◽  
Ordered Structure ◽  
Planar Defects ◽  
Diffraction Patterns ◽  
Ternary Semiconductors ◽  
Anion Species ◽  
Metallic Vapor

The growth of ternary III-V semiconductors by organo-metallic vapor phase epitaxy (OMVPE) is widely practiced. It has been generally assumed that the resulting structure is the same as that of the corresponding binary semiconductors, but with the two different cation or anion species randomly distributed on their appropriate sublattice sites. Recently several different ternary semiconductors including AlxGa1-xAs, Gaxln-1-xAs and Gaxln1-xP1-6 have been observed in ordered states. A common feature of these ordered compounds is that they contain a relatively high density of defects. This is evident in electron diffraction patterns from these materials where streaks, which are typically parallel to the growth direction, are associated with the extra reflections arising from the ordering. However, where the (Ga,ln)P epilayer is reasonably well ordered the streaking is extremely faint, and the intensity of the ordered spot at 1/2(111) is much greater than that at 1/2(111). In these cases it is possible to image relatively clearly many of the defects found in the ordered structure.

Quantitative defect studies in semiconductor TEM samples prepared by low angle ion milling

1995 ◽  
Vol 53 ◽  
pp. 512-513
Author(s):  
L. Mulestagno ◽  
J.C. Holzer ◽  
P. Fraundorf
Keyword(s):  
Sample Preparation ◽  
Milling Time ◽  
High Density ◽  
Low Density ◽  
Ion Milling ◽  
High Quality ◽  
Variable Angle ◽  
Major Disadvantage ◽  
Induced Defects

Due to the wealth of information, both analytical and structural that can be obtained from it TEM always has been a favorite tool for the analysis of process-induced defects in semiconductor wafers. The only major disadvantage has always been, that the volume under study in the TEM is relatively small, making it difficult to locate low density defects, and sample preparation is a somewhat lengthy procedure. This problem has been somewhat alleviated by the availability of efficient low angle milling.Using a PIPS® variable angle ion -mill, manufactured by Gatan, we have been consistently obtaining planar specimens with a high quality thin area in excess of 5 × 104 μm2 in about half an hour (milling time), which has made it possible to locate defects at lower densities, or, for defects of relatively high density, obtain information which is statistically more significant (table 1).

Using the scanning electron microscope for failure analysis of high density magnetic media

1987 ◽  
Vol 45 ◽  
pp. 392-393
Author(s):  
Evelyn R. Ackerman ◽  
Gary D. Burnett
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
Failure Analysis ◽  
High Density ◽  
Magnetic Media ◽  
Specific Data ◽  
Retrieval Systems ◽  
Operating Environments ◽  
The Media ◽  
Scanning Electron

Advancements in state of the art high density Head/Disk retrieval systems has increased the demand for sophisticated failure analysis methods. From 1968 to 1974 the emphasis was on the number of tracks per inch. (TPI) ranging from 100 to 400 as summarized in Table 1. This emphasis shifted with the increase in densities to include the number of bits per inch (BPI). A bit is formed by magnetizing the Fe203 particles of the media in one direction and allowing magnetic heads to recognize specific data patterns. From 1977 to 1986 the tracks per inch increased from 470 to 1400 corresponding to an increase from 6300 to 10,800 bits per inch respectively. Due to the reduction in the bit and track sizes, build and operating environments of systems have become critical factors in media reliability.Using the Ferrofluid pattern developing technique, the scanning electron microscope can be a valuable diagnostic tool in the examination of failure sites on disks.

Triglyceride to high density lipoprotein cholesterol ratio, total cholesterol to high density lipoprotein cholesterol ratio and low ankle brachial index in an elderly population

VASA ◽  
2014 ◽  
Vol 43 (3) ◽  
pp. 189-197 ◽  
Author(s):  
Yiqiang Zhan ◽  
Jinming Yu ◽  
Rongjing Ding ◽  
Yihong Sun ◽  
Dayi Hu
Keyword(s):  
High Density Lipoprotein ◽  
Total Cholesterol ◽  
High Density Lipoprotein Cholesterol ◽  
Ankle Brachial Index ◽  
Density Lipoprotein ◽  
High Density ◽  
Lipoprotein Cholesterol ◽  
Lipid Lowering ◽  
Cholesterol Ratio ◽  
Potential Biomarker

Background: The associations of triglyceride (TG) to high-density lipoprotein cholesterol ratio (HDL‑C) and total cholesterol (TC) to HDL‑C ratio and low ankle brachial index (ABI) were seldom investigated. Patients and methods: A population based cross-sectional survey was conducted and 2982 participants 60 years and over were recruited. TG, TC, HDL‑C, and low-density lipoprotein cholesterol (LDL-C) were assessed in all participants. Low ABI was defined as ABI ≤ 0.9 in either leg. Multiple logistic regression models were applied to study the association between TG/HDL‑C ratio, TC/HDL‑C ratio and low ABI. Results: The TG/HDL‑C ratios for those with ABI > 0.9 and ABI ≤ 0.9 were 1.28 ± 1.20 and 1.48 ± 1.13 (P < 0.0001), while the TC/HDL‑C ratios were 3.96 ± 1.09 and 4.32 ± 1.15 (P < 0.0001), respectively. After adjusting for age, gender, body mass index, obesity, current drinking, physical activity, hypertension, diabetes, lipid-lowering drugs, and cardiovascular disease history, the odds ratios (ORs) with 95 % confidence intervals (CIs) of low ABI for TG/HDL‑C ratio and TC/HDL‑C ratio were 1.10 (0.96, 1.26) and 1.34 (1.14, 1.59) in non-smokers. When TC was further adjusted, the ORs (95 % CIs) were 1.40 (0.79, 2.52) and 1.53 (1.21, 1.93) for TG/HDL‑C ratio and TC/HDL‑C ratio, respectively. Non-linear relationships were detected between TG/HDL‑C ratio and TC/HDL‑C ratio and low ABI in both smokers and non-smokers. Conclusions: TC/HDL‑C ratio was significantly associated with low ABI in non-smokers and the association was independent of TC, TG, HDL‑C, and LDL-C. TC/HDL‑C might be considered as a potential biomarker for early peripheral arterial disease screening.

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