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Allelic Imbalance (1):
Recent article
Allelic Imbalance
Bipolar Disorders (12)4 2010
Abstract
We investigated whether, instead of affecting protein function, these risk variants might impact on gene regulation affecting expression.
We have done this by testing for allelic expression imbalance (AEI) to identify cis-acting regulatory polymorphisms.
We identified evidence of cis-acting variatio...
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PMID: 20636642
PDF is available here.
PDF is available here.
| < More recent | Older article > |
Abstract
We show that these elements are preferentially found in pathogenic deletions (enrichment ratio 3.6 vs. 0.5 in duplications), and that this association is not related with a higher content of genes. In contrast, pathogenic CNVs lacking UCEs showed almost a threefold higher content in genes.
We propos...
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PMID: 21092253
PDF is available here.
PDF is available here.
BMC Medical Genetics (11) 2010
Abstract
Our data provide evidence that SCN5A allelic expression imbalance occurs in African-Americans heterozygous for p.Ser1103Tyr, but this phenomenon alone does not appear to be a marker for risk of SIDS....
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PMID: 20470418
PDF is available here.
PDF is available here.
Oncology Reports (23)1 2010
Abstract
The biological properties and underlying genetics of gastric cancer and gastric intestinal metaplasia evolve with neoplastic progression from the genetics of the original gland cell. PCR assay with crypt isolation was used in tumors from 20 patients to examine microsatellite alterations (allelic imb...
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PMID: 19956861
PDF is available here.
PDF is available here.
Abstract
Pathological grade is routinely used to stratify breast cancer patients into favorable and less favorable outcome groups. Mechanisms by which genomic changes in breast tumors specifically contribute to the underlying components of tumor grade - tubule formation, nuclear pleomorphism,...
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PMID: 19194786
PDF is available here.
PDF is available here.
Acta Oto-Laryngologica (129)11 2009
Abstract
We found that the longer alleles (CA)17-20 had a very low frequency in BMD (2/160, 1.3%, OR=7.33 (1.77-30.37, 95% CI), corrected p=0.012), suggesting that it may confer some protection against BMD....
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PMID: 19863315
PDF is available here.
PDF is available here.
Annals of Surgical Oncology (16)10 2009
Abstract
Analysis for p53 AI and MSI might represent a clinically useful approach to predicting the response to neoadjuvant FP chemotherapy in gastric carcinoma....
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PMID: 19597886
PDF is available here.
PDF is available here.
Abstract
By focusing on the TYMS polymorphic variants in renal cancer, we here provide evidence, to our knowledge, for the first time showing loss of 18p11.32 and 18p11.31 in renal cell carcinomas. As allelic imbalances involving TYMS locus may be an important variable affecting 5-FU responsiveness, this stu...
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PMID: 19306093
PDF is available here.
PDF is available here.
Oncology Reports (22)3 2009
Abstract
We conducted a case-control study to determine the association of the MMP-1 genotype with susceptibility to prostate cancer involving 283 prostate cancer patients and 251 controls. Furthermore, AI, retention allele of the MMP-1 promoter, and MMP-1 protein expression were analyzed in 77 prostate canc...
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PMID: 19639194
PDF is available here.
PDF is available here.
Abstract
We focused on DUSP6, a pivotal negative feedback regulator of the RAS-ERK pathway. A dominant-negative DUSP6 mutant, however, failed to rescue KRAS/V12-induced growth suppression, but conferred a stronger anchorage-independent growth activity to the surviving subpopulation of cells generated from KR...
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PMID: 19608870
PDF is available here.
PDF is available here.
Journal of Pathology (217)5 2009
Abstract
We report the establishment of a permanent ILBC cell line, named IPH-926, which was derived from a patient with metastatic ILBC. The DNA fingerprint of IPH-926 verified genetic identity with the patient and had no match among the human cell line collections of several international biological resour...
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PMID: 19191266
PDF is available here.
PDF is available here.
Abstract
We performed genome-wide allelotyping analysis using 384 microsatellite markers spanning 22 autosomes together with comparative genomic hybridization (CGH) in 21 urothelial cancer. High frequency of allelic imbalance was observed in chromosome arm 1q (61.9%), 3p (61.9%), 4q (66.67%), 8p (57.14%), 9p...
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PMID: 19287953
PDF is available here.
PDF is available here.
Abstract
Bladder cancer remains one of the most common and expensive cancers to treat worldwide. Numerous molecular markers are being investigated as possible ways to decrease health care costs, increase patient survival and prognosis, and increase sensitivity in screening tests. Several genetic markers have...
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PMID: 19320188
PDF is available here.
PDF is available here.
Hepatology (49)2 2009
Abstract
We analyzed molecular karyotypes using oligonucleotide genotyping 50K arrays. First, 1q21.3-44 gain and loss of heterozygosity (LOH) on 1p36.21-36.32 and 17p13.1-13.3 were frequently observed in eHCC, but not in chronic liver diseases, suggesting that such chromosomal aberrations are early, possibly...
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PMID: 19105209
PDF is available here.
PDF is available here.
Abstract
We present a girl who developed adrenocortical adenoma at the age of 1 year and osteosarcoma at the age of 5 years. There was no history of cancer in her parents and their relatives. However, both tumors were typical for the Li-Fraumeni syndrome (LFS), and the patient met criteria for germline TP53...
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PMID: 19012332
PDF is available here.
PDF is available here.
Prenatal Diagnosis (29)1 2009
Abstract
We will focus on the molecular biological techniques that are currently in use in the most advanced centers for PGD for monogenic disorders, including multiplex polymerase chain reaction (PCR) and post-PCR diagnostic methods, whole genome amplification (WGA) and multiple displacement amplification (...
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PMID: 19101953
PDF is available here.
PDF is available here.
Genome Biology (10)11 2009
Abstract
We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance prof...
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PMID: 19903341
PDF is available here.
PDF is available here.
Cancer Research (68)24 2008
Abstract
We combined flow-sorting and single nucleotide polymorphism arrays. Cells derived from archival cervical and colon cancers were flow-sorted based on differential vimentin and keratin expression and DNA content and analyzed on single nucleotide polymorphism arrays. A new algorithm, the lesser allele...
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PMID: 19074902
PDF is available here.
PDF is available here.
Clinical Cancer Research (14)24 2008
Abstract
Urine samples with tumor showed allelic imbalance at 0.4% of all informative SNPs. In samples without tumors, 0.04% of these SNPs were affected (P = 0.07). In addition, Copy Number Analyser for GeneChip analysis showed more copy number changes in samples with a tumor (P = 0.001). Losses and gains of...
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PMID: 19088036
PDF is available here.
PDF is available here.
Abstract
We performed linkage and haplotype analysis in six Han Chinese families with TPTPS and/or SD4, and refined the disease locus to an interval of 646 kb containing ZRS. In all families, the affected individuals heterozygous at rs10254391 (a single nucleotide polymorphism within ZRS) revealed a remarkab...
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PMID: 18417549
PDF is available here.
PDF is available here.
Abstract
We focused on three genes from the Regulator of G protein Signaling family clustered on 1q25.3 within the HPC1 region. RGS16, RGSL2, and RGSL1 encode proteins interacting with G proteins and accelerating termination of the G protein signaling. To evaluate the implication of these genes in somatic br...
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PMID: 18521847
PDF is available here.
PDF is available here.
Abstract
We discuss this mechanism focusing on the EGF receptor as an example for regulators of progenitor cell growth in many tissues. Phylloides tumors serve as a putative model for embryonic differentiation stage ruled by EGFR signaling and give insights into the tumor-host-interaction. The inhibition of...
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PMID: 18690849
PDF is available here.
PDF is available here.
BJU International (102)2 2008
Microsatellite analysis of allelic imbalance in tumour and blood from patients with prostate cancer.
Abstract
Plasma-based MS analysis may have clinical value for the molecular staging of prostate cancer....
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PMID: 18336598
PDF is available here.
PDF is available here.
Pathology International (58)7 2008
Abstract
The criterion tumor volume (TV) for clinically insignificant prostate cancer has been reported, but it differs from study to study: some have reported TV < 200 mm(3); others, < 500 mm(3). The aim of the present study was to distinguish clinically insignificant cancers from significant ones using mol...
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PMID: 18577109
PDF is available here.
PDF is available here.
Abstract
Higher frequencies of AI at chromosome 8q24 in patients with positive lymph nodes suggest that genetic changes in this region are important to the process of metastasis. Because overexpression of c-MYC has been associated with cellular dissemination as well as development of the premetastatic niche,...
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PMID: 18401664
PDF is available here.
PDF is available here.
Trends in Genetics (24)6 2008
Abstract
Monoallelic gene expression exposes an organism to the risks associated with the unmasking of recessive mutations. A recent study by Gimelbrant and colleagues, supported by results from two methodologically different studies, demonstrated that random monoallelic expression is surprisingly widespread...
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PMID: 18450315
PDF is available here.
PDF is available here.
Human Molecular Genetics (17)9 2008
Abstract
We investigated whether allelic imbalance (AI) of BRCA1 or BRCA2 expression was associated with an increased risk of developing breast cancer. By developing a quantitative approach utilizing allele-specific real-time PCR, we first evaluated AI caused by nonsense-mediated mRNA decay in patients with...
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PMID: 18204050
PDF is available here.
PDF is available here.
Modern Pathology (21)4 2008
Abstract
Large-cell neuroendocrine and small-cell lung carcinomas are highly aggressive neuroendocrine tumors that can be associated in a variant of 'small-cell lung carcinoma combined with large-cell neuroendocrine carcinoma'. Little is known about this rare tumor type with biphenotypic neuroendocrine diffe...
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PMID: 18204434
PDF is available here.
PDF is available here.
Abstract
Submicroscopic genomic imbalances affecting the 1q21.1, 17q12, 22q11.21, and Xq21.31 chromosome regions were detected in four probands. Presence of the alterations in the normal mother of one patient suggests incomplete penetrance and/or variable expressivity. CONCLUSION: 4 of the 14 patients (29%)...
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PMID: 18039948
PDF is available here.
PDF is available here.
Abstract
The extent of genomic heterogeneity in axillary lymph node metastases differs markedly among individual patients. Genomic diversity may be associated with response to adjuvant therapy, recurrence, and survival, and thus may be important in improving clinical management of breast cancer patients....
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PMID: 18246400
PDF is available here.
PDF is available here.
Genome Research (18)4 2008
Abstract
We can directly test for allelic imbalance (AI), which must be due to cis-acting variants in the parental strains. We tested over one hundred genes for AI between C57Bl/6J and A/J alleles in F1 mice, including a validation set of 23 genes enriched for cis-acting variants and a second set of 92 genes...
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PMID: 18256236
PDF is available here.
PDF is available here.
Abstract
We screened 70 sporadic colorectal cancer cases (27 rectal, 43 intestinal) of different stages for promoter hypermethylation, allelic imbalance (AI) and somatic mutations. The presence of promoter hypermethylation was observed in 21 cases (30%). Fifteen of the examined tumors (21%) showed AI, and al...
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PMID: 18369740
PDF is available here.
PDF is available here.
Mayo Clinic Proceedings (83)2 2008
Abstract
Of 52 homozygous QQ patients, 39 (75%) had endothelial dysfunction vs 20 (43%) of the 47 RR/QR patients (P=.001), and this association remained significant after adjustment in a multivariable linear regression model (P=.005). In homozygous QQ vs RR/QR patients, epicardial arterial diameter decreased...
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PMID: 18241625
PDF is available here.
PDF is available here.
Abstract
We describe a robust and high-throughput method to directly measure differences in allelic expression for a large number of genes using the Illumina Allele-Specific Expression BeadArray platform and quantitative sequencing of RT-PCR products. We show that this approach allows reliable identification...
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PMID: 18454203
PDF is available here.
PDF is available here.
Journal of Immunology (180)2 2008
Abstract
We have addressed this question by adopting a combined genetic and functional approach. We analyzed TCRzeta protein expression using a FACS-based expression index and documented considerable, but longitudinally stable, variation in TCRzeta expression in healthy individuals. The variation in TCRzeta...
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PMID: 18178846
PDF is available here.
PDF is available here.
Abstract
Our data indicate that often there was loss of chromosomal material in the proximal to middle part of the chromosome followed by gains in distal RNO10. This suggested that there is a tumor suppressor gene(s) in the proximal to middle part of RNO10 and an oncogene(s) in the distal part of the chromos...
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PMID: 18497077
PDF is available here.
PDF is available here.
Abstract
Pathological grade is a useful prognostic factor for stratifying breast cancer patients into favorable (well-differentiated tumors) and less favorable (poorly-differentiated tumors) outcome groups. The current system of tumor grading, however, is subjective and a large proportion of tumors are chara...
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PMID: 17351743
PDF is available here.
PDF is available here.
BMC Medical Genetics (9)1 2008
Abstract
No duplication at 8p23.1-p22 was observed in our patients. We detected complex rearrangements involving 2q in two patients with Kabuki-like features: 1) a de novo inverted duplication of 11 Mb with a 4.5 Mb terminal deletion, and 2) a de novo 7.2 Mb-terminal deletion in a patient with an additional...
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PMID: 18405349
PDF is available here.
PDF is available here.
Genome Biology (9)9 2008
Abstract
We present a strategy for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome single nucleotide polymorphism genotyping data. Using a dilution series of a tumor cell line mixed with its paired normal cell line and data generated on Affymetrix and Illumina plat...
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PMID: 18796136
PDF is available here.
PDF is available here.
BMC Bioinformatics (9)1 2008
Abstract
We demonstrate an asymmetry in the detection of the two alleles for each SNP, which deleteriously influences both allelic proportions and copy number estimates. The asymmetry is caused by a remaining bias between the two dyes used in the Infinium II assay after using the normalization method in Illu...
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PMID: 18831757
PDF is available here.
PDF is available here.
BMC Cancer (8)1 2008
Abstract
The frequency of AI was significantly higher (P<0.005) in HER2 amplified (27%) compared to HER2 negative tumors (19%). Samples with HER2 amplification showed significantly higher levels of AI (P<0.05) at chromosomes 11q23, 16q22-q24 and 18q21. Partial correlations including ER status and tumor grade...
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PMID: 18854030
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
We have utilized allelic ratios to detect patterns that are indicative of higher ploidy levels. An integrated analysis using allelic ratios, total signal and LOH indicates that many or most of the chromosomes from 24 glioblastoma tumors are in fact aneuploid. Some putative whole-chromosome losses ac...
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PMID: 18928532
PDF is available here.
PDF is available here.
Cytogenetic and Genome Research (122)3-4 2008
Genomic imbalances in key ion channel genes and telomere shortening in sudden cardiac death victims.
Abstract
We hypothesize that some patients may show genomic imbalances and changes in the gene copy number leading to genetic instability. To clarify this, we analysed DNA samples from SCD victims using comparative genomic hybridization (CGH), a molecular cytogenetic technique that permits the genome-wide sc...
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PMID: 19188705
PDF is available here.
PDF is available here.
Cancer Research (68)1 2008
Abstract
We genotyped a population-based series of 1,042 patients with CRC and 1,012 healthy controls for rs6983267 and determined the contribution of SNP to CRC in Finland, using germ line DNA, as well as the respective cancer DNA in heterozygous patients. The comprehensive clinical data available from the...
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PMID: 18172290
PDF is available here.
PDF is available here.
Abstract
We used genome-wide high-density single nucleotide polymorphism (SNP) array analysis to detect copy number alterations in 29 WDNTs, including seven lung, seven nonileal gastrointestinal, and 15 ileal tumors, and compared with allelic imbalances in 15 pancreatic endocrine tumors (PETs). Most frequent...
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PMID: 17943967
PDF is available here.
PDF is available here.
New England Journal of Medicine (357)25 2007
Abstract
Stroma-specific loss of heterozygosity or allelic imbalance is associated with somatic TP53 mutations and regional lymph-node metastases in sporadic breast cancer but not in hereditary breast cancer.
Copyright 2007 Massachusetts Medical Society....
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PMID: 18094375
PDF is available here.
PDF is available here.
Electrophoresis (28)23 2007
Abstract
We searched for mutations in a cohort of 38 patients and investigated the relationship between mutation type and allele-specific transcription from the wild-type versus mutant alleles. Quantification of relative mRNA transcript numbers was done by Pyrosequencing, a novel real-time sequencing method...
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PMID: 18041031
PDF is available here.
PDF is available here.
Abstract
We analyzed loci on 8p, 10q, and 13q14 in archival prostate tumors matched for Gleason grade, pre-operative prostate-specific antigen levels, and pathologic stage, and they were paired on the basis of relapse status after 3 years. AI was identified in 66% of patients without relapse and in 73% with...
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PMID: 18036398
PDF is available here.
PDF is available here.
Abstract
Tumor ADC was significantly different from normal brain (P < 0.001). ADC in regions of highest Cho/Cr was greater than minimum ADC and did not correlate with the Cho/Cr ratio. ADC and ATC were not significantly different between oligodendroglial subtypes or grades. Tumors with intact 1p/19q had high...
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PMID: 17968881
PDF is available here.
PDF is available here.
Abstract
We have studied 119 low-risk MDS patients (refractory anemia [RA] = 22; refractory cytopenia with multilineage dysplasia [RCMD] = 51; refractory anemia with ringed sideroblasts [RARS] = 12; refractory cytopenia with multilineage dysplasia with ringed sideroblasts [RCMD-RS] = 12; 5q- syndrome = 16; r...
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PMID: 17634407
PDF is available here.
PDF is available here.
Annals of Surgical Oncology (14)11 2007
Abstract
The inability to discriminate DCIS at the genetic level suggests that grades 1 and 2 DCIS may represent a single, non-high-grade form of DCIS, whereas poorly differentiated DCIS seems to be a genetically more advanced disease that may represent a discrete disease entity, characterized by a unique sp...
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PMID: 17549568
PDF is available here.
PDF is available here.
Annals of Surgical Oncology (14)11 2007
Abstract
In metastatic LNs, levels of AI were not associated with tumor burden, suggesting that accumulation of genetic changes is not coincidental with tumor growth; rather the accumulation of specific genetic changes is a prerequisite to the transformation of disseminated breast cells into metastatic LN tu...
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PMID: 17653592
PDF is available here.
PDF is available here.
Nature Medicine (13)11 2007
Abstract
Abstract
In advanced breast cancers, TP53 mutation is highly predictive of complete response to high-dose epirubicin/cyclophosphamide chemotherapy. In these tumours with an altered control of genomic stability, accumulation of chemotherapy-induced genetic alterations may contribute to cell death and account...
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PMID: 17876337
PDF is available here.
PDF is available here.
Abstract
We have undertaken a pairwise comparison of the genomic imbalances occurring in primary and recurrent WDL from the same patient. In one of the cases, the patient's final recurrence, which was 17 years after the primary tumor and showed more pronounced nuclear atypia, had seven additional genomic cha...
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PMID: 17954275
PDF is available here.
PDF is available here.
Abstract
Traditional cytogenetic studies of ovarian stromal tumors are few, although trisomy 12 has been frequently documented with fluorescence in situ hybridization (FISH). In the current study, karyotypic analysis of four ovarian stromal tumors and a review of the literature suggest that numerical abnorma...
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PMID: 17954269
PDF is available here.
PDF is available here.
Oral Oncology (43)9 2007
Abstract
We utilise pyrosequencing techniques of quantitative methylation analysis to investigate the presence of CIMP in oral squamous cell carcinoma (OSCC) for the first time, and evaluate its correlation with allelic imbalance, pathology and clinical behaviour. Tumour tissue, control tissue and PBLs were...
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PMID: 17257884
PDF is available here.
PDF is available here.
Abstract
We evaluated allele-specific expression of DLX5 and DLX6 in mouse x human somatic cell hybrids, lymphoblastoid cell lines, and frontal cortex from controls and individuals with MECP2 mutations. We identified novel single-nucleotide polymorphisms in DLX5 and DLX6, enabling the first imprinting studie...
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PMID: 17701895
PDF is available here.
PDF is available here.
Human Molecular Genetics (16)16 2007
Abstract
We evaluate this assumption directly by examining the translation of in vitro results on allele-specific expression to an in vivo system using four genes that have been well documented through reporter assays to have promoter polymorphisms affecting transcription level: monoamine oxidase A (MAOA), n...
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PMID: 17566082
PDF is available here.
PDF is available here.
Clinical Cancer Research (13)16 2007
Abstract
These data suggest that novel cancer genes may be located within the other identified small regions of copy number alteration. Analysis of the number of copy number breakpoints and the distribution of the small regions of copy number change indicate high levels of structural chromosomal genetic inst...
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PMID: 17699850
PDF is available here.
PDF is available here.