Abstract:
:High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
journal_name
Int J Genomicsjournal_title
International journal of genomicsauthors
Zhang P,Lehmann BD,Shyr Y,Guo Ydoi
10.1155/2017/1926304subject
Has Abstractpub_date
2017-01-01 00:00:00pages
1926304eissn
2314-436Xissn
2314-4378journal_volume
2017pub_type
杂志文章,评审abstract::The purpose of this work was to study changes in the level of cell-free DNA (cfDNA) in the blood of young and old rats in the normal state and with induced benign prostatic hyperplasia (BPH). Male Wistar rats were divided into 4 groups-young (3 months), old (20 months), intact, or with testosterone-induced BPH. Groups...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2019/8173630
更新日期:2019-06-02 00:00:00
abstract:Background:Chronic kidney disease (CKD) is characterized by progressive renal function loss, which may finally lead to end-stage renal disease (ESRD). The study is aimed at identifying crucial genes related to CKD progressive and constructing a disease prediction model to investigate risk factors. Methods:GSE97709 and...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2020/7524057
更新日期:2020-11-12 00:00:00
abstract::The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire geno...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2017/1712530
更新日期:2017-01-01 00:00:00
abstract:Purpose:Next-generation sequencing (NGS) has become more accessible, leading to an increasing number of genetic studies of familial bradycardia being reported. However, most of the variants lack full evaluation. The relationship between genetic factors and bradycardia should be summarized and reevaluated. Methods:We s...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2020/2415850
更新日期:2020-02-25 00:00:00
abstract::Taxol is one of the most potent and effective anticancer drugs and is originally isolated from Taxus species. To investigate the specific regulatory mechanisms of taxol synthesis in Taxus wallichiana var. mairei, RNA-seq was conducted to reveal the differences in transcriptional levels between wild type (WT) and "Jinx...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2019/1596895
更新日期:2019-05-02 00:00:00
abstract::Calmodulin II (CALM2) gene polymorphism might be responsible for the variation in the left ventricular mass amongst healthy individuals. The aim was to evaluate the correlation between left ventricular mass (LVM) and g.474955027G>A (rs7565161) polymorphism adjacent to the CALM2 gene. Healthy Polish newborns (n = 206) ...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2013/410407
更新日期:2013-01-01 00:00:00
abstract::We characterized the male-specific region on the Y chromosome of rainbow trout, which contains both sdY (the sex-determining gene) and the male-specific genetic marker, OmyY1. Several clones containing the OmyY1 marker were screened from a BAC library from a YY clonal line and found to be part of an 800 kb BAC contig....
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2013/261730
更新日期:2013-01-01 00:00:00
abstract::Rett spectrum disorder is a progressive neurological disease and the most common genetic cause of intellectual disability in females. MECP2 is the major causative gene. In addition, CDKL5 and FOXG1 mutations have been reported in Rett patients, especially with the atypical presentation. Each gene and different mutatio...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2019/6956934
更新日期:2019-03-27 00:00:00
abstract::miRNAs are a class of noncoding RNAs important in posttranscriptional repressors and involved in the regulation of almost every biological process by base paring with target genes through sequence in their seed regions. Genetic variations in the seed regions have vital effects on gene expression, phenotypic variation,...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2018/2456076
更新日期:2018-03-06 00:00:00
abstract::Auxin response factors (ARFs) have been reported to play vital roles during plant growth and development. In order to reveal specific functions related to vegetative organs in grasses, an in-depth study of the ARF gene family was carried out in switchgrass (Panicum virgatum L.), a warm-season C4 perennial grass that i...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2018/7658910
更新日期:2018-04-29 00:00:00
abstract::Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, mil...
journal_title:International journal of genomics
pub_type: 杂志文章,评审
doi:10.1155/2020/5940205
更新日期:2020-08-18 00:00:00
abstract:Purpose:Airway epithelium acts as a protective barrier against the particles from the inhaled air. Damage to the epithelium may result in loss of the barrier function. Epithelial repair in response to injury requires complex mechanisms, such as microRNA, small noncoding molecules, to regulate the processes involved in ...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2018/9093785
更新日期:2018-09-05 00:00:00
abstract::Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9....
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2018/3057272
更新日期:2018-05-15 00:00:00
abstract::Rice grain shape and nutritional quality traits have high economic value for commercial production of rice and largely determine the market price, besides influencing the global food demand for high-quality rice. In order to understand the genetic components of grain appearance traits in paddy, brown, and head rice, 1...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2019/3160275
更新日期:2019-02-25 00:00:00
abstract::To better understand the molecular functions of the master stress-response regulator AtfA in Aspergillus nidulans, transcriptomic analyses of the atfA null mutant and the appropriate control strains exposed to menadione sodium bisulfite- (MSB-), t-butylhydroperoxide- and diamide-induced oxidative stresses were perform...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2017/6923849
更新日期:2017-01-01 00:00:00
abstract::Puberty is a transition period where a child transforms to an adult. Puberty can be affected by various genetic factors and environmental influences. In mammals, the regulation of puberty is enhanced by the hypothalamic-pituitary-gonadal axis (HPG axis). A number of genes such as GnRH, Kiss1, and GPR54 have been repor...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2020/1426761
更新日期:2020-05-22 00:00:00
abstract:Background:Breast cancer development and progression involve both germline and somatic mutations. High-throughput genotyping and next-generation sequencing technologies have enabled discovery of genetic risk variants and acquired somatic mutations driving the disease. However, the possible oncogenic interactions betwee...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2020/2641370
更新日期:2020-07-06 00:00:00
abstract::A population of 146 RILs (Recombinant Inbred Line) was derived from the cross between a cold-sensitive cultivated Solanum lycopersicum L. XF98-7 and a cold-tolerant wild Solanum pimpinellifolium LA2184. Relative germination ratio (RGR) and chilling index (CI) were used to evaluate the cold tolerance of the parental li...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2016/3219276
更新日期:2016-01-01 00:00:00
abstract::Insulin resistance has a central role in the pathogenesis of several metabolic diseases, including type 2 diabetes, obesity, glucose intolerance, metabolic syndrome, atherosclerosis, and cardiovascular diseases. Insulin resistance and related traits are likely to be caused by abnormalities in the genes encoding for pr...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2013/376454
更新日期:2013-01-01 00:00:00
abstract::Identifying differentially variable (DV) genomic probes is becoming a new approach to detect novel genomic risk factors for complex human diseases. The F test is the standard equal-variance test in statistics. For high-throughput genomic data, the probe-wise F test has been successfully used to detect biologically rel...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2018/6591634
更新日期:2018-07-12 00:00:00
abstract::Cancer is a multistep process characterized by various and different genetic lesions which cause the transformation of normal cells into tumor cells. To preserve the genomic integrity, eukaryotic cells need a complex DNA damage/repair response network of signaling pathways, involving many proteins, able to induce cell...
journal_title:International journal of genomics
pub_type: 杂志文章,评审
doi:10.1155/2014/820248
更新日期:2014-01-01 00:00:00
abstract::Pseudomonas aeruginosa PGPR2 is a mung bean rhizosphere strain that produces secondary metabolites and hydrolytic enzymes contributing to excellent antifungal activity against Macrophomina phaseolina, one of the prevalent fungal pathogens of mung bean. Genome sequencing was performed using the Ion Torrent Personal Gen...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2014/123058
更新日期:2014-01-01 00:00:00
abstract::TSEN54 encodes a subunit of the tRNA-splicing endonuclease complex, which catalyzes the identification and cleavage of introns from precursor tRNAs. Previously, we identified an AluSx-derived alternative transcript in TSEN54 of cynomolgus monkey. Reverse transcription-polymerase chain reaction (RT-PCR) amplification a...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2016/1679574
更新日期:2016-01-01 00:00:00
abstract::The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus ...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2015/198560
更新日期:2015-01-01 00:00:00
abstract::Cardiovascular disease is a leading cause of death in both humans and dogs. Dilated cardiomyopathy (DCM) accounts for a large number of these cases, reported to be the third most common form of cardiac disease in humans and the second most common in dogs. In human studies of DCM there are more than 50 genetic loci ass...
journal_title:International journal of genomics
pub_type: 杂志文章,评审
doi:10.1155/2015/204823
更新日期:2015-01-01 00:00:00
abstract::The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. cor...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2018/8084032
更新日期:2018-04-01 00:00:00
abstract::Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic backg...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2020/3236461
更新日期:2020-09-05 00:00:00
abstract::Background and Objectives. Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airflow limitation. Although airway inflammation and oxidative stress are known to be important in the pathogenesis of COPD, the mechanism underlying airflow obstruction is not fully understood. Gene expressio...
journal_title:International journal of genomics
pub_type: 杂志文章
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abstract::The threat of heat stress on crop production increased dramatically due to global warming leading to the rise on the demand of heat-tolerant crops and understanding their tolerance. The leguminous forage crop Guar [Cyamopsis tetragonoloba (L.) Taub] is a high-temperature tolerant plant with numerous works on its toler...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2020/3126592
更新日期:2020-06-19 00:00:00
abstract::Severe gastroenteritis and foodborne illness caused by Noroviruses (NoVs) during the winter are a worldwide phenomenon. Vulnerable populations including young children and elderly and immunocompromised people often require hospitalization and may die. However, no efficient vaccine for NoVs exists because of their vari...
journal_title:International journal of genomics
pub_type: 杂志文章
doi:10.1155/2013/456356
更新日期:2013-01-01 00:00:00