Abstract:
BACKGROUND:Analyses of Expressed Sequence Tags (ESTs) databases suggest that most human genes have multiple alternative splice variants. The alternative splicing of pre-mRNA is tightly regulated during development and in different tissue types. Changes in splicing patterns have been described in disease states. Recently, we used whole-transcriptome shotgun pryrosequencing to characterize 4 malignant pleural mesothelioma (MPM) tumors, 1 lung adenocarcinoma and 1 normal lung. We hypothesized that alternative splicing profiles might be detected in the sequencing data for the expressed genes in these samples. METHODS:We developed a software pipeline to map the transcriptome read sequences of the 4 MPM samples and 1 normal lung sample onto known exon junction sequences in the comprehensive AceView database of expressed sequences and to count how many reads map to each junction. 13,274,187 transcriptome reads generated by the Roche/454 sequencing platform for 5 samples were compared with 151,486 exon junctions from the AceView database. The exon junction expression index (EJEI) was calculated for each exon junction in each sample to measure the differential expression of alternative splicing events. Top ten exon junctions with the largest EJEI difference between the 4 mesothelioma and the normal lung sample were then examined for differential expression using Quantitative Real Time PCR (qRT-PCR) in the 5 sequenced samples. Two of the differentially expressed exon junctions (ACTG2.aAug05 and CDK4.aAug05) were further examined with qRT-PCR in additional 18 MPM and 18 normal lung specimens. RESULTS:We found 70,953 exon junctions covered by at least one sequence read in at least one of the 5 samples. All 10 identified most differentially expressed exon junctions were validated as present by RT-PCR, and 8 were differentially expressed exactly as predicted by the sequence analysis. The differential expression of the AceView exon junctions for the ACTG2 and CDK4 genes were also observed to be statistically significant in an additional 18 MPM and 18 normal lung samples examined using qRT-PCR. The differential expression of these two junctions was shown to successfully classify these mesothelioma and normal lung specimens with high sensitivity (89% and 78%, respectively). CONCLUSION:Whole-transcriptome shotgun sequencing, combined with a downstream bioinformatics pipeline, provides powerful tools for the identification of differentially expressed exon junctions resulting from alternative splice variants. The alternatively spliced genes discovered in the study could serve as useful diagnostic markers as well as potential therapeutic targets for MPM.
journal_name
BMC Med Genetjournal_title
BMC medical geneticsauthors
Dong L,Jensen RV,De Rienzo A,Gordon GJ,Xu Y,Sugarbaker DJ,Bueno Rdoi
10.1186/1471-2350-10-149subject
Has Abstractpub_date
2009-12-31 00:00:00pages
149issn
1471-2350pii
1471-2350-10-149journal_volume
10pub_type
杂志文章abstract:BACKGROUND:The presence of the Y-chromosome or Y chromosome-derived material is seen in 4-60% of Turner syndrome patients (Chromosomal Disorders of Sex Development (DSD)). DSD patients with specific Y-chromosomal material in their karyotype, the GonadoBlastoma on the Y-chromosome (GBY) region, have an increased risk of...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-13-108
更新日期:2012-11-16 00:00:00
abstract:BACKGROUND:Progressive familial intrahepatic cholestasis (PFIC) type 3 is an autosomal recessive disorder arising from mutations in the ATP-binding cassette subfamily B member 4 (ABCB4) gene. This gene encodes multidrug resistance protein-3 (MDR3) that acts as a hepatocanalicular floppase that transports phosphatidylch...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-020-01173-0
更新日期:2020-11-30 00:00:00
abstract:BACKGROUND:Chronic hyperglycemia confers increased risk for long-term diabetes-associated complications and repeated hemoglobin A1c (HbA1c) measures are a widely used marker for glycemic control in diabetes treatment and follow-up. A recent genome-wide association study revealed four genetic loci, which were associated...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-12-20
更新日期:2011-02-04 00:00:00
abstract:BACKGROUND:In X-linked dilated cardiomyopathy due to dystrophin mutations which abolish the expression of the M isoform (5'-XLDC), the skeletal muscle is spared through the up-regulation of the Brain (B) isoform, a compensatory mechanism that does not appear to occur in the heart of affected individuals. METHODS:We qu...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-13-20
更新日期:2012-03-28 00:00:00
abstract:BACKGROUND:Prostate cancer is a heterogeneous disease, meaning patients would benefit from different treatment strategies based on their molecular stratification. In recent years, several genomic studies have identified prostate cancers with defects in DNA repair genes. It is known that the PARP inhibitor, olaparib, ha...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-018-0703-9
更新日期:2018-10-17 00:00:00
abstract:BACKGROUND:Recent investigations demonstrated many genetic contributions to the development of human age-related hearing impairment (ARHI), however, reports of factors associated with a reduction in the ARHI risk are rare. Folate metabolism is essential for cellular functioning. Despite the extensive investigations reg...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-12-35
更新日期:2011-03-07 00:00:00
abstract:BACKGROUND:Acute myeloid leukemia (AML) is a biologically and clinically heterogeneous cancer of the bone marrow that is characterized by the rapid growth of abnormal myeloid cells. METHODS:We performed a mutational analysis to identify AML somatic mutations using the whole-exome sequencing data of 36 tumor-normal sam...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-017-0382-y
更新日期:2017-03-01 00:00:00
abstract:BACKGROUND:Celiac disease has a strong genetic association with HLA. However, this association only explains approximately half of the sibling risk for celiac disease. Therefore, other genes must be involved in susceptibility to celiac disease. We tested for linkage to genes or loci that could play a role in pathogenes...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-2-12
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:Jervell and Lange-Nielsen syndrome (JLNS) isa recessive model of long QT syndrome which might also be related to possible hearing loss. Although the syndrome has been demonstrated to be originated from homozygous or compound heterozygous mutations in either the KCNQ1 or KCNE1 genes, additional mutations in o...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-017-0474-8
更新日期:2017-10-16 00:00:00
abstract:BACKGROUND:Recent genome-wide association (GWA) studies have identified several unsuspected genes associated with type 2 diabetes (T2D) with previously unknown functions. In this investigation, we have examined the role of 9 most significant SNPs reported in GWA studies: [peroxisome proliferator-activated receptor gamm...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-9-59
更新日期:2008-07-03 00:00:00
abstract:BACKGROUND:Mandibulofacial dysostosis with microcephaly (MFDM) is a rare autosomal dominant genetic disease characterized by intellectual and growth retardations, as well as major microcephaly, induced by missense and splice site variants or microdeletions in the EFTUD2 gene. CASE PRESENTATION:Here, we investigate the...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-020-01121-y
更新日期:2020-09-17 00:00:00
abstract:BACKGROUND:Waardenburg syndrome type I (WS1), an auditory-pigmentary genetic disorder, is caused by heterozygous loss-of-function mutations in PAX3. Abnormal physical signs such as dystopia canthorum, patchy hypopigmentation and sensorineural hearing loss are common, but short stature is not associated with WS1. CASE ...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-015-0165-2
更新日期:2015-04-11 00:00:00
abstract:BACKGROUND:To determine association of nine single nucleotide polymorphisms (SNPs) in ADP ribosyltransferase-1 (ADPRT1), aldo-keto reductase family 1 member B1 (AKR1B1), receptor for advanced glycation end-products (RAGE), glutamine:fructose-6-phosphate amidotransferase-2 (GFPT2), and plasminogen activator inhibitor-1 ...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-11-52
更新日期:2010-03-31 00:00:00
abstract:BACKGROUND:Crohn's disease (CD) has the highest prevalence among individuals of Ashkenazi Jewish (AJ) descent compared to non-Jewish Caucasian populations (NJ). We evaluated a set of well-established CD-susceptibility variants to determine if they can explain the increased CD risk in the AJ population. METHODS:We recr...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-12-63
更新日期:2011-05-06 00:00:00
abstract:BACKGROUND:E-selectin is implicated in various inflammatory processes and related disorders. We aimed to investigate the role of SELE-gene genotypes/haplotypes on plasma levels of MMP9 and sE-selectin in Taiwanese individuals. METHODS:Five hundred twenty individuals were enrolled. Seven tagging SELE single nucleotide ...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-13-115
更新日期:2012-11-29 00:00:00
abstract:BACKGROUND:Elastogenesis of elastic extracellular matrix (ECM) which was recognized as a major component of blood vessels has been believed for a long time to play only a passive role in the dynamic vascular changes of typical hypertension. Emilin1 gene participated in the transcription of ECM's formation and was recog...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-10-118
更新日期:2009-11-18 00:00:00
abstract:BACKGROUND:Inflammation is a response of body tissues to injury or irritation. Small RNAs, such as miR-146a and miR-499, participate in various processes of tumorigenesis. A recent study indicates that inflammation and abnormal immune responses may promote malignant progression in cancer development, indicating that in...
journal_title:BMC medical genetics
pub_type: 杂志文章,meta分析
doi:10.1186/s12881-014-0092-7
更新日期:2014-08-10 00:00:00
abstract:BACKGROUND:The Krüppel-like factor (KLF) family consists of transcription factors that can activate or repress different genes implicated in processes such as differentiation, development, and cell cycle progression. Moreover, several of these proteins have been implicated in glucose homeostasis, making them candidate ...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-8-53
更新日期:2007-08-09 00:00:00
abstract:BACKGROUND:Urolithiasis is a worldwide urological problem with significant contribution of genetic factors. Pakistan, which resides within the Afro-Asian stone belt, has a high reported prevalence (12%) of urolithiasis. Osteopontin (SPP1) is a urinary macromolecule with a suggested critical role in modulating renal sto...
journal_title:BMC medical genetics
pub_type: 杂志文章,meta分析
doi:10.1186/s12881-020-01101-2
更新日期:2020-08-25 00:00:00
abstract:BACKGROUND:Previous studies indicated a strong association between hyperkalemia and lung squamous cell carcinomas (LSCC). However, the underlying mechanism is not fully understood so far. METHODS:Literature-based data mining was conducted to identify genes, molecule, and cell processes linked to both hyperkalemia and ...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-020-01099-7
更新日期:2020-10-22 00:00:00
abstract:BACKGROUND:PMM2-CDG, is the most common N-linked glycosylation disorder and subtype among all CDG syndromes, which are a series of genetic disorders involving the synthesis and attachment of glycoproteins and glycolipid glycans. The mutations of PMM2-CDG might lead to the loss of PMM2, which is responsible for the conv...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-019-0902-z
更新日期:2019-11-14 00:00:00
abstract:BACKGROUND:The variant rs11085226 (G) within the gene encoding polypyrimidine tract binding protein 1 (PTBP1) was reported to associate with reduced insulin release determined by an oral glucose tolerance test (OGTT) as well as an intravenous glucose tolerance test (IVGTT). The aim of the present study was to validate ...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-015-0160-7
更新日期:2015-03-20 00:00:00
abstract:BACKGROUND:CHARGE syndrome is an autosomal dominant disorder, characterized by ocular Coloboma, congenital Heart defects, choanal Atresia, Retardation, Genital anomalies and Ear anomalies. Over 90 % of typical CHARGE patients are mutated in the CHD7 gene, 65 %-70 % of the cases for all typical and suspected cases combi...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-015-0225-7
更新日期:2015-09-03 00:00:00
abstract:BACKGROUND:L. braziliensis causes cutaneous (CL) and mucosal (ML) leishmaniasis. Wound healing neutrophil (PMN) and macrophage responses made following the bite of the vector sand fly contribute to disease progression in mice. To look at the interplay between PMN and macrophages in disease progression in humans we aske...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-11-10
更新日期:2010-01-20 00:00:00
abstract:BACKGROUND:The lectin-like oxidized LDL receptor LOX-1 (encoded by OLR1) is believed to play a key role in atherogenesis and some reports suggest an association of OLR1 polymorphisms with myocardial infarction (MI). We tested whether single nucleotide polymorphisms (SNPs) in OLR1 are associated with clinically signific...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-9-23
更新日期:2008-04-02 00:00:00
abstract:BACKGROUND:Probably the best example of the rise and maintenance of balancing selection as an evolutionary trend is the role of S-haemoglobin (HbS - rs334) in protecting from malaria. Yet, the dynamics of such a process remains poorly understood, particularly in relation to different malaria transmission rates and the ...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-11-21
更新日期:2010-02-03 00:00:00
abstract:BACKGROUND:Pulmonary capillary hemangiomatosis (PCH) is an uncommon pulmonary disorder, with variable clinical features depending on which lung structure is affected, and it is usually linked to pulmonary arterial hypertension. Congenital PCH has been very rarely described and, so far, the only causative gene identifie...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-015-0241-7
更新日期:2015-10-13 00:00:00
abstract:BACKGROUND:Observational studies and randomized trials have suggested that estrogens and/or progesterone may lower the risk for colorectal cancer. Inherited variation in the sex-hormone genes may be one mechanism by which sex hormones affect colorectal cancer, although data are limited. METHOD:We conducted a comprehen...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-12-78
更新日期:2011-05-31 00:00:00
abstract:BACKGROUND:Low-frequency nonsyndromic hearing loss (LF-NSHL) is a rare, inherited disorder. Here, we report a family with LF-NSHL in whom a missense mutation was found in the Wolfram syndrome 1 (WFS1) gene. CASE PRESENTATION:Family members underwent audiological and imaging evaluations, including pure tone audiometry ...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/s12881-017-0511-7
更新日期:2017-12-19 00:00:00
abstract:BACKGROUND:Autism is a complex, heterogeneous, behaviorally-defined disorder characterized by disruptions of the nervous system and of other systems such as the pituitary-hypothalamic axis. In a previous genome wide screen, we reported linkage of autism with a 1.2 Megabase interval on chromosome 5q31. For the current s...
journal_title:BMC medical genetics
pub_type: 杂志文章
doi:10.1186/1471-2350-8-74
更新日期:2007-12-06 00:00:00