Abstract:
:Traditionally, somatic mutations are detected by examining DNA sequence. The maturity of sequencing technology has allowed researchers to screen for somatic mutations in the whole genome. Increasingly, researchers have become interested in identifying somatic mutations through RNAseq data. With this motivation, we evaluated the practicability of detecting somatic mutations from RNAseq data. Current somatic mutation calling tools were designed for DNA sequencing data. To increase performance on RNAseq data, we developed a somatic mutation caller GLMVC based on bias reduced generalized linear model for both DNA and RNA sequencing data. Through comparison with MuTect and Varscan we showed that GLMVC performed better for somatic mutation detection using exome sequencing or RNAseq data. GLMVC is freely available for download at the following website: https://github.com/shengqh/GLMVC/wiki.
journal_name
Genomicsjournal_title
Genomicsauthors
Sheng Q,Zhao S,Li CI,Shyr Y,Guo Ydoi
10.1016/j.ygeno.2016.03.006subject
Has Abstractpub_date
2016-05-01 00:00:00pages
163-9issue
5eissn
0888-7543issn
1089-8646pii
S0888-7543(16)30021-0journal_volume
107pub_type
杂志文章相关文献
GENOMICS文献大全abstract::Madin-Darby canine kidney(MDCK) cells can be used to prepare cell-based influenza vaccines; however, little is known regarding the effect of lncRNA regulatorson tumorigenicity. In the present study, two cell lines with low tumorigenicity were screened from highly tumorigenic MDCK cell lines using monoclonal cell techn...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2019.08.002
更新日期:2020-03-01 00:00:00
abstract::Understanding patterns of linkage disequilibrium (LD) across genomes may facilitate association mapping studies to localize genetic variants influencing complex diseases, a recognition that led to the International Haplotype Mapping Project (HapMap). Divergent patterns of haplotype frequency and LD across global popul...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2006.03.003
更新日期:2006-11-01 00:00:00
abstract::Primary pulmonary hypertension (PPH), an often fatal disorder, is characterized by sustained elevation of pulmonary artery pressure of unknown cause. In its familial form (FPPH), the disorder segregates as an autosomal dominant and displays markedly reduced penetrance. A gene for FPPH was previously localized to a 25-...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.2000.6291
更新日期:2000-09-01 00:00:00
abstract::The chromosomal locations and the tissue expression patterns of the human transcriptional adaptors TADA2L and GCN5L2 have been determined. Northern blot analysis across a range of human tissues revealed that both the TADA2L and the GCN5L2 mRNAs are expressed to varying degrees in all tissue types. Furthermore, in most...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1996.4605
更新日期:1997-03-15 00:00:00
abstract::In response to nutrient deprivation, the ubiquitous Gram-negative soil bacterium Myxococcus xanthus undergoes a well-characterized developmental response, resulting in the formation of a multicellular fruiting body. The center of the fruiting body consists of myxospores; surrounding this structure are rod-shaped perip...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2019.09.008
更新日期:2020-03-01 00:00:00
abstract::Chromosome 11p13 is frequently rearranged in individuals with the WAGR syndrome (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) or parts of this syndrome. To map the cytogenetic aberrations molecularly, we screened DNA from cell lines with known WAGR-related chromosome abnormalities for rearra...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(88)90141-3
更新日期:1988-08-01 00:00:00
abstract::Specific probes derived from the human genes that complement the mutations of two independent temperature-sensitive (ts) mutants of the BHK-21 hamster cell line were used to determine the chromosomal locations of the loci in the human genome. The ts11 gene, which complements a mutation that blocks progression through ...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(89)90326-1
更新日期:1989-04-01 00:00:00
abstract::Creating transgenic mice is an important technology for genetic studies and is currently performed by pronuclear microinjection of plasmid DNA into fertilized eggs. Since survival of injected embryos and integration of plasmid DNA are not efficient, total efficiency is only around 3% with a standard protocol. To circu...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2010.02.006
更新日期:2010-05-01 00:00:00
abstract::We have isolated cDNA clones for the gene, termed GPX1, encoding the major human selenoprotein, glutathione peroxidase. Sequence analysis confirmed previous findings that the unusual amino acid seleno-cysteine is encoded by the opal terminator codon UGA. Southern blot analysis of human genomic DNA with the GPX1 cDNA s...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(90)90566-d
更新日期:1990-02-01 00:00:00
abstract::A significant fraction of the human genome is composed of various types of transposable elements, which are divided into two broad classes based on their mehcanism of transposition: via an RNA intermediate (retroelements) or via a DNA intermediate (DNA transposons). The retroelements, which include endogenous retrovir...
journal_title:Genomics
pub_type: 杂志文章
doi:
更新日期:2002-11-01 00:00:00
abstract::Palmitoyl-protein thioesterase (PPT) is a small glycoprotein that removes palmitate groups from cysteine residues in lipid-modified proteins. We recently reported mutations in PPT in patients with infantile neuronal ceroid lipofuscinosis (INCL), a severe neurodegenerative disorder (J. Vesa et al., 1995, Nature 376: 58...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1996.0292
更新日期:1996-06-15 00:00:00
abstract::Differences in the methylation status of certain cytosine residues between active and inactive X chromosomes can be used to determine X-inactivation in females heterozygous for X-linked restriction fragment length polymorphisms. We have studied methylation patterns in 105 females heterozygous at the DXS255 locus by So...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/s0888-7543(05)80285-x
更新日期:1992-09-01 00:00:00
abstract::One of the important goals in systems biology is to infer transcription network based on gene expression data. Validation of the reconstructed network often requires benchmark datasets, e.g. gene expression data, which are usually unattainable. Synthetic datasets are therefore often needed to test the structure learni...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2009.08.009
更新日期:2009-11-01 00:00:00
abstract::Mapping of 33 anonymous DNA probes and 12 genes to the long arm of chromosome 16 was achieved by the use of 14 mouse/human hybrid cell lines and the fragile site FRA16B. Two of the hybrid cell lines contained overlapping interstitial deletions in bands q21 and q22.1. The localization of the 12 genes has been refined. ...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(91)90313-4
更新日期:1991-06-01 00:00:00
abstract::Mutations in the FBN1 gene, encoding the extracellular matrix protein fibrillin-1, result in the dominant connective tissue disease Marfan syndrome. Marfan syndrome has a variable phenotype, even within families carrying the same FBN1 mutation. Differences in gene expression resulting from sequence differences in the ...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2009.06.005
更新日期:2009-10-01 00:00:00
abstract::Data from family studies demonstrating RH:MYCL linkage (zeta = 4.07 at theta = 0.09) in paternal meioses are presented. Although positive, MYCL:PGM1 lods are not of the magnitude of those for RH:MYCL. Taken together, these results are consistent with the physical assignment of MYCL to 1p32. Furthermore, evidence to su...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(88)90097-3
更新日期:1988-02-01 00:00:00
abstract::Transport proteins have essential functions in the uptake of neurotransmitters and neuromodulators. We have mapped the gene encoding the taurine transporter, Taut, to the central region of mouse chromosome 6. Analysis of a cross segregating the neurological mutant mnd2 excluded Taut as a candidate gene for this closel...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(95)80146-d
更新日期:1995-01-01 00:00:00
abstract::FAT, a new member of the human cadherin super-family, has been isolated from the T-leukemia cell line J6. The predicted protein closely resembles the Drosophila tumor suppressor fat, which is essential for controlling cell proliferation during Drosophila development. The gene has the potential to encode a large transm...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1995.9884
更新日期:1995-11-20 00:00:00
abstract::The behaviors of autism overlap with a diverse array of other neurological disorders, suggesting common molecular mechanisms. We conducted a large comparative analysis of the network of genes linked to autism with those of 432 other neurological diseases to circumscribe a multi-disorder subcomponent of autism. We leve...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2008.09.015
更新日期:2009-02-01 00:00:00
abstract::Immunoblotting of isoelectric focusing gels of plasma and direct genomic DNA sequencing have been used to characterize a mutation in apolipoprotein A-I associated with the familial amyloidotic polyneuropathy originally described by Van Allen in an Iowa kindred. An arginine for glycine substitution in apolipoprotein A-...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(90)90288-6
更新日期:1990-10-01 00:00:00
abstract::The human ubiquitin-homology domain protein PIC1 interacts with the acute promyelocytic leukemia protein PML, and both proteins form part of the large, nuclear, multiprotein complexes known as PML nuclear bodies. The normal punctate immunohistochemical staining pattern of these complexes is disrupted by viral infectio...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1997.5091
更新日期:1998-01-01 00:00:00
abstract::We describe the isolation and characterization of a human gene (CLCN3) and its murine homologue (Clcn3) sharing significant sequence and structural similarities with all previously identified members of the voltage-gated chloride channel (ClC) family. This gene is expressed primarily in tissues derived from neuroectod...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1995.1015
更新日期:1995-05-01 00:00:00
abstract::The chromosomal locations of mouse DNA sequences homologous to a feline cDNA clone encoding glutamic acid decarboxylase (GAD) were determined. Although cats and humans are thought to have only one gene for GAD, GAD cDNA sequences hybridize to two distinct chromosomal loci in the mouse, chromosomes 2 and 10. The chromo...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(90)90455-4
更新日期:1990-01-01 00:00:00
abstract::Mammalian sex chromosomes are the remnants of an ancient autosomal pair present in the ancestral mammalian karyotype. As a consequence of random decay and chromosome rearrangements over evolutionary time, Y chromosome gene repertoires differ between eutherian lineages. To investigate the gene repertoire and transcript...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2008.06.012
更新日期:2008-11-01 00:00:00
abstract::A novel method for identifying DNA point mutations has been developed by using mismatch repair enzymes. The high specificity of the Escherichia coli MutY protein has permitted the development of a reliable and sensitive method for the detection and characterization of point mutations in the human genome. The MutY prot...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/s0888-7543(05)80213-7
更新日期:1992-10-01 00:00:00
abstract::The Long-Evans Cinnamon (LEC) rat has a spontaneous mutation, T helper immunodeficiency (thid), which causes a markedly reduced CD4(+) thymocyte population. Here we positionally clone the locus and identify a deletion in the gene encoding a receptor-like protein tyrosine phosphatase kappa (Ptprk) that led to complete ...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2007.03.001
更新日期:2007-06-01 00:00:00
abstract::Most members of the large family of rhodopsin-like G-protein-coupled receptors possess an evolutionarily conserved Asp-Arg-Tyr (DRY) motif in the C-terminal region of the third transmembrane domain. Mutations of residues within this motif usually abolish receptor function and, when they occur naturally, can even cause...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2006.02.009
更新日期:2006-06-01 00:00:00
abstract::Lymphocytes of mouse strains BALB/cHeA (BALB/c) and STS/A (STS) differ in the IL-2-induced proliferative response, STS being a high and BALB/c a low responder in the range of concentrations 125-2000 IE/ml. We analyzed the genetic basis of this strain difference using the recombinant congenic (RC) strains of the BALB/c...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1997.4694
更新日期:1997-05-15 00:00:00
abstract::Amaranth has been proposed as an exceptional alternative for food security and climate change mitigation. Information about the distribution, abundance, or specificity of miRNAs in amaranth species is scare. Here, small RNAs from seedlings under control, drought, heat, and cold stress conditions of the Amaranthus hypo...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2020.11.027
更新日期:2021-01-01 00:00:00
abstract::A cDNA clone encoding the major antigen (CDR62) associated with the antibody-induced paraneoplastic cerebellar degeneration has been used to identify the chromosomal location of the corresponding structural gene(s) by screening for its retention in a panel of rodent-human somatic cell hybrids. Having established the s...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(92)90063-x
更新日期:1992-08-01 00:00:00