Abstract:
:Since the turn of the century, researchers have sought to diagnose cancer based on gene expression signatures measured from the blood or biopsy as biomarkers. This task, known as classification, is typically solved using a suite of algorithms that learn a mathematical rule capable of discriminating one group ("cases") from another ("controls"). However, discriminatory methods can only identify cancerous samples that resemble those that the algorithm already saw during training. As such, discriminatory methods may be ill-suited for the classification of cancer: because the possibility space of cancer is definitively large, the existence of a one-of-a-kind gene expression signature is likely. Instead, we propose using an established surveillance method that detects anomalous samples based on their deviation from a learned normal steady-state structure. By transferring this method to transcriptomic data, we can create an anomaly detector for tissue transcriptomes, a "tissue detector," that is capable of identifying cancer without ever seeing a single cancer example. As a proof-of-concept, we train a "tissue detector" on normal GTEx samples that can classify TCGA samples with >90% AUC for 3 out of 6 tissues. Importantly, we find that the classification accuracy is improved simply by adding more healthy samples. We conclude this report by emphasizing the conceptual advantages of anomaly detection and by highlighting future directions for this field of study.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Quinn TP,Nguyen T,Lee SC,Venkatesh Sdoi
10.3389/fgene.2019.00599subject
Has Abstractpub_date
2019-07-02 00:00:00pages
599issn
1664-8021journal_volume
10pub_type
杂志文章abstract::Systemic sclerosis-associated with pulmonary arterial hypertension (SSc-PAH) is still a major cause of SSc related deaths. Early diagnosis and prompt treatment are crucial to reduce the mortality of patients with SSc-PAH. To screen the candidate biomarkers and potential therapeutic targets for SSc-PAH, we analyzed the...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00816
更新日期:2020-07-24 00:00:00
abstract::In the last decade, several studies have been focused on revealing the microRNA (miRNA) repertoire and determining their functions in farm animals such as poultry, pigs, cattle, and fish. These small non-protein coding RNA molecules (18-25 nucleotides) are capable of controlling gene expression by binding to messenger...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2018.00088
更新日期:2018-03-19 00:00:00
abstract::Telomeres are essential nucleoprotein structures at linear chromosomes that maintain genome integrity by protecting chromosome ends from being recognized and processed as damaged DNA. In addition, they limit the cell's proliferative capacity, as progressive loss of telomeric DNA during successive rounds of cell divisi...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2017.00067
更新日期:2017-05-23 00:00:00
abstract::Known as the "fifth RNA nucleotide", pseudouridine (Ψ or psi) is the first-discovered and most abundant RNA modification occurring at the Uridine site, and it plays a prominent role in a number of biological processes. Thousands of Ψ sites have been identified within different biological contexts thanks to the advance...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00088
更新日期:2020-03-12 00:00:00
abstract::Previous efforts to characterize conservation between the human and mouse genomes focused largely on sequence comparisons. These studies are inherently limited because they don't account for gene structure differences, which may exist despite genomic sequence conservation. Recent high-throughput transcriptome studies ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00183
更新日期:2013-09-26 00:00:00
abstract::Simple sequence repeats (SSRs) of short nucleotide motifs occur very frequently in the 5' untranslated coding region (5'-UTR) of genes and have been implicated in the regulation of gene expression. In this study, we identified an SSR with a variable number of CT repeats in the 5'-UTR of the Litopenaeus vannamei IRF (L...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01257
更新日期:2019-12-06 00:00:00
abstract::Hematopoiesis results in the correct formation of all the different blood cell types. In mammals, it starts from specific hematopoietic stem and precursor cells residing in the bone marrow. Mature blood cells are responsible for supplying oxygen to every cell of the organism and for the protection against pathogens. T...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2018.00348
更新日期:2018-08-31 00:00:00
abstract::Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to the characterization of the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality foll...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00299
更新日期:2019-04-16 00:00:00
abstract::Leaf rust, caused by Puccinia triticina (Pt), is one of the most devastating diseases of wheat, affecting production in nearly all wheat-growing regions worldwide. Despite its economic importance, genomic resources for Pt are very limited. In the present study, we have used long-read sequencing (LRS) and the pipeline ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00521
更新日期:2020-06-04 00:00:00
abstract::Recently, an increasing number of studies sequence multiple biopsies of primary tumors, and even paired metastatic tumors to understand heterogeneity and the evolutionary trajectory of cancer progression. Although several algorithms are available to infer the phylogeny, most tools rely on accurate measurements of muta...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01371
更新日期:2020-02-07 00:00:00
abstract::Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor with the ability to bind to a CCAAT box in nearly all eukaryotes. However, the function of NF-Y in the life-history traits of insects is unclear. Here, we identified three NF-Y subunits, NlNF-YA, NlNF-YB, and NlNF-YC, in the wing-dimorphic brown planthop...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.585320
更新日期:2020-11-03 00:00:00
abstract::Chemicals, toxicants, and environmental stressors mediate their biologic effect through specific modes of action (MOAs). These encompass key molecular events that lead to changes in the expression of genes within regulatory pathways. Elucidating shared biologic processes and overlapping gene networks will help to bett...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2017.00157
更新日期:2017-10-24 00:00:00
abstract::Glioblastoma, also called glioblastoma multiform (GBM), is the most aggressive cancer that initiates within the brain. GBM is produced in the central nervous system. Cancer cells in GBM are similar to stem cells. Several different schemes for GBM stratification exist. These schemes are based on intertumoral molecular ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.604336
更新日期:2020-11-24 00:00:00
abstract::Colon cancer has the third highest incidence and mortality among cancers in the United States. MicroRNA-21 (miR21) has been described as an oncomir that is highly overexpressed in tumor tissue from colorectal cancer. Recent studies showed that silencing of miR21 through use of a miR21 inhibitor (anti-miR21) affected v...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00301
更新日期:2014-01-02 00:00:00
abstract::Extracting inherent valuable knowledge from omics big data remains as a daunting problem in bioinformatics and computational biology. Deep learning, as an emerging branch from machine learning, has exhibited unprecedented performance in quite a few applications from academia and industry. We highlight the difference a...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00214
更新日期:2019-03-26 00:00:00
abstract::Vitamin D receptor (VDR) gene polymorphisms were reported to influence blood lead levels (BLL) and the response of subjects to the symptoms of lead toxicity. However, no studies have been conducted in the Saudi Arabian population which has unique ethnicity and socio-demographic features. This study examined the polymo...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00388
更新日期:2019-04-26 00:00:00
abstract::Mesopelagic fish are largely abundant poorly studied fish that are still intact, but which, due to their potentially great added value, will be imminently exploited by humans. Therefore, studies that provide information to anticipate the anthropogenic impact on this important resource are urgently needed. In particula...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2017.00195
更新日期:2017-11-28 00:00:00
abstract::Molecular epidemiological studies have identified several risk factors linking to the genes and external factors in the pathogenesis of breast cancer. In this sense, genetic instability caused by DNA damage and DNA repair inefficiencies are important molecular events for the diagnosis and prognosis of therapies. There...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2017.00236
更新日期:2018-02-16 00:00:00
abstract::Across species and tissues and especially in the mammalian brain, production of gene isoforms is widespread. While gene expression coordination has been previously described as a scale-free coexpression network, the properties of transcriptome-wide isoform production coordination have been less studied. Here we evalua...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00174
更新日期:2015-05-13 00:00:00
abstract::Human T-lymphotropic virus 1 (HTLV-1) was the first human retrovirus to be discovered and is the causative agent of adult T-cell leukemia/lymphoma (ATL) and the neurodegenerative disease HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The importance of microRNA (miRNA) in the replicative cycle of ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00295
更新日期:2012-12-17 00:00:00
abstract::There is a paradigm shift from the traditional focus on the "average" individual towards the definition and analysis of trait variation within individual life-history and among individuals in populations. This is a result of increasing availability of individual phenotypic data. The shift allows the use of genetic and...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00727
更新日期:2019-09-20 00:00:00
abstract::Lumbar disc degeneration (LDD) is age-related break-down in the fibrocartilaginous joints between lumbar vertebrae. It is a major cause of low back pain and is conventionally assessed by magnetic resonance imaging (MRI). Like most other complex traits, LDD is likely polygenic and influenced by both genetic and environ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00267
更新日期:2018-08-03 00:00:00
abstract::Few studies have been conducted to explore the influence of the catechol-o-methyltransferase (COMT) genotype on the severity of and treatment efficacy on auditory verbal hallucination (AVH) symptoms in healthy individuals with AVHs (Hi-AVHs). We hypothesized that the efficacy of dopamine antagonist treatment on AVHs i...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00092
更新日期:2019-03-06 00:00:00
abstract::Ethylmalonic encephalopathy (EE) is a very rare autosomal recessive metabolic disorder that primarily affects children. Less than one hundred EE patients have been diagnosed worldwide. The clinical manifestations include chronic diarrhea, petechiae, orthostatic acrocyanosis, psychomotor delay and regression, seizures,...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00341
更新日期:2020-04-17 00:00:00
abstract::The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is virtually capable of detecting any given RNA modification present in the molecule that is being s...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00211
更新日期:2020-03-17 00:00:00
abstract::Transcriptomics technologies such as next-generation sequencing and microarray platforms provide exciting opportunities for improving diagnosis and treatment of complex diseases. Transcriptomics studies often share similar hypotheses, but are carried out on different platforms, in different conditions, and with differ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00396
更新日期:2019-04-30 00:00:00
abstract::Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer's palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional pro...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00441
更新日期:2018-10-05 00:00:00
abstract::The phenotype of carcass traits in beef cattle are affected by random genetic and non-genetic effects, which both can be modulated by an environmental variable such as Temperature-Humidity Index (THI), a key environmental factor in cattle production. In this study, a multivariate reaction norm model (MRNM) was used to...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.576377
更新日期:2020-12-23 00:00:00
abstract::Several cyanobacterial species are dominant primary producers in hot spring microbial mats. To date, hot spring cyanobacterial taxonomy, as well as the evolution of their genomic adaptations to high temperatures, are poorly understood, with genomic information currently available for only a few dominant genera, includ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.568223
更新日期:2020-11-05 00:00:00
abstract::Eukaryotic protein kinases are well conserved through evolution. The genome of Schistosoma mansoni, which causes intestinal schistosomiasis, encodes over 250 putative protein kinases with all of the main eukaryotic groups represented. However, unraveling functional roles for these kinases is a considerable endeavor, p...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00229
更新日期:2014-07-31 00:00:00