Biomedical subjects

Ali Naderi

Publications and source records attributed to Ali Naderi.

9 recordsLinked to original sources

PubMed2006

A consensus prognostic gene expression classifier for ER positive breast cancer.

BACKGROUND: A consensus prognostic gene expression classifier is still elusive in heterogeneous diseases such as breast cancer. RESULTS: Here we perform a combined analysis of three major breast cancer microarray data sets to hone in on a universally valid prognostic molecular classifier in estrogen receptor (ER) positive tumors. Using a recently developed robust measure of prognostic separation, we further validate the prognostic classifier in three external independent cohorts, confirming the validity of our molecular classifier in a total of 877 ER positive samples. Furthermore, we find that molecular classifiers may not outperform classical prognostic indices but that they can be used in hybrid molecular-pathological classification schemes to improve prognostic separation. CONCLUSION: The prognostic molecular classifier presented here is the first to be valid in over 877 ER positive breast cancer samples and across three different microarray platforms. Larger multi-institutional studies will be needed to fully determine the added prognostic value of molecular classifiers when combined with standard prognostic factors.

Breast Neoplasms↗

PubMed2006

Adsorption properties of polyelectrolyte-surfactant complexes on hydrophobic surfaces studied by QCM-D.

Adsorption and deposition from turbid solutions are common in many industrial processes but notoriously difficult to investigate using standard optical techniques such as ellipsometry and reflectometry. In this report, we have addressed this problem by employing a quartz crystal microbalance with dissipation monitoring ability, QCM-D. The system under investigation consisted of a cationic polyelectrolyte, poly(vinylamine), PVAm, and an anionic surfactant, sodium dodecyl sulfate, SDS, which were mixed together in 10 mM NaCl solution. The polyelectrolyte and the surfactant readily associate in bulk solution, resulting in increased solution turbidity once large aggregates are formed. The solutions were placed in contact with a polystyrene surface, and the adsorption process was monitored by following the changes in the resonance frequency and dissipation factor. The results obtained can in most cases be evaluated using the Sauerbrey relation, but in some cases a more elaborate analysis is necessary. It is found that PVAm adsorbs to polystyrene in the absence of SDS. In the turbid region, deposition is observed, and the sensed mass exceeds the sum of that obtained for each of the components alone. On the other hand, at high SDS concentrations, the surfactant dominates in the adsorbed layer. Adsorption equilibrium is in most cases established within 1-2 h, the exception being found around the solution composition that results in the formation of charge-neutralized aggregates. In this case, a slow deposition of aggregates persists over prolonged times.

Journal Article↗

PubMed2006

PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer.

MOTIVATION: Elucidating the molecular taxonomy of cancers and finding biological and clinical markers from microarray experiments is problematic due to the large number of variables being measured. Feature selection methods that can identify relevant classifiers or that can remove likely false positives prior to supervised analysis are therefore desirable. RESULTS: We present a novel feature selection procedure based on a mixture model and a non-gaussianity measure of a gene's expression profile. The method can be used to find genes that define either small outlier subgroups or major subdivisions, depending on the sign of kurtosis. The method can also be used as a filtering step, prior to supervised analysis, in order to reduce the false discovery rate. We validate our methodology using six independent datasets by rediscovering major classifiers in ER negative and ER positive breast cancer and in prostate cancer. Furthermore, our method finds two novel subtypes within the basal subgroup of ER negative breast tumours, associated with apoptotic and immune response functions respectively, and with statistically different clinical outcome. AVAILABILITY: An R-function pack that implements the methods used here has been added to vabayelMix, available from (www.cran.r-project.org). CONTACT: aet21@cam.ac.uk SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

Algorithms↗

PubMed2005

A 1 Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes.

Amplification of 8p11-12 is a well-known alteration in human breast cancers but the driving oncogene has not been identified. We have developed a high-resolution comparative genomic hybridization array covering 8p11-12 and analysed 33 primary breast tumors, 20 primary ovarian tumors and 27 breast cancer cell lines. Expression analysis of the genes in the region was carried out by using real-time quantitative PCR and/or oligo-microarray profiling. In all, 24% (8/33) of the breast tumors, 5% (1/20) of the ovary tumors and 15% (4/27) of the cell lines showed 8p11-12 amplification. We identified a 1 Mb segment of common amplification that excludes previously proposed candidate genes. Some of the amplified genes did not show overexpression, whereas for others, overexpression was not specifically attributable to amplification. The genes FLJ14299, C8orf2, BRF2 and RAB11FIP, map within the 8p11-12 minimal amplicon, two have a putative function consistent with an oncogenic role, these four genes showed a strong correlation between amplification and overexpression and are therefore the best candidate driver oncogenes at 8p12.

Breast Neoplasms↗

PubMed2005

Optimal amounts of fluorescent dye improve expression microarray results in tumor specimens.

Expression microarrays have great potential for clinical use but variability of the results represents a challenge for reliable practical application. The amount of fluorescent dye used in microarray experiments is a significant source of variability that has not been systematically studied. Here we demonstrate that the quantity of Cy3 dye affects microarray results performed on tumor specimens. Signal-to-noise ratios and coefficients of variation are significantly improved by increasing Cy3 to 150-180 pmol, but any further increase does not improve the data. In conclusion, optimal amounts of dye reduce variability and improve reliability of expression microarray experiments.

Carbocyanines↗

PubMed2004

Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling.

BACKGROUND: Expression microarrays have evolved into a powerful tool with great potential for clinical application and therefore reliability of data is essential. RNA amplification is used when the amount of starting material is scarce, as is frequently the case with clinical samples. Purification steps are critical in RNA amplification and labelling protocols, and there is a lack of sufficient data to validate and optimise the process. RESULTS: Here the purification steps involved in the protocol for indirect labelling of amplified RNA are evaluated and the experimentally determined best method for each step with respect to yield, purity, size distribution of the transcripts, and dye coupling is used to generate targets tested in replicate hybridisations. DNase treatment of diluted total RNA samples followed by phenol extraction is the optimal way to remove genomic DNA contamination. Purification of double-stranded cDNA is best achieved by phenol extraction followed by isopropanol precipitation at room temperature. Extraction with guanidinium-phenol and Lithium Chloride precipitation are the optimal methods for purification of amplified RNA and labelled aRNA respectively. CONCLUSION: This protocol provides targets that generate highly reproducible microarray data with good representation of transcripts across the size spectrum and a coefficient of repeatability significantly better than that reported previously.

Carbocyanines↗

PubMed2003

The 17q23 amplicon and breast cancer.

A novel region of amplification in breast tumors was recently identified on chromosome 17q23. Extensive mapping of the amplicon by Southern blotting and fluorescence in situ hybridization (FISH) in breast cancer cell lines determined that the amplicon can be up to 4 Mbp in size and may contain 50 genes. Copy number analysis at 50-75 kb resolution in breast cancer cell lines and breast tumors identified several independently amplified regions within the amplicon, suggesting that a number of genes are selected for amplification because they independently contribute to tumor formation and progression. Support for this hypothesis comes from studies demonstrating that many of the amplified genes are over-expressed in breast cancer cell lines and tumors, and that the RPS6KB1, TBX2, and PPM1D genes from the region, that are amplified and over-expressed in breast tumors and cell lines, contribute to tumor formation and/or tumor progression. In this review we summarize the structural studies of the amplicon that have been carried out, we outline the evidence implicating the RPS6KB1, TBX2, and PPM1D genes as oncogenes, and we describe some of the other candidate oncogenes from the region.

Breast Neoplasms↗

PubMed2002

TBX2 is preferentially amplified in BRCA1- and BRCA2-related breast tumors.

The chromosome 17q23 region is frequently amplified in breast tumors. Gain of the region is present in 50% of BRCA1-associated breast tumors and 87% of BRCA2-associated breast tumors. The amplification frequency of the RPS6KB1 and TBX2 oncogenes from this amplicon was compared in 27 BRCA1 and BRCA2 mutant breast tumors, 15 breast tumors from high-risk patients with no BRCA1 or BRCA2 mutations, and 62 matched sporadic breast tumor controls. TBX2 was determined to be preferentially amplified and overexpressed in BRCA1 and BRCA2 mutant tumors, whereas RPS6KB1 was not, suggesting a role for TBX2 amplification in the development of BRCA1- and BRCA2-associated breast tumors.

Adult↗

PubMed2002

BRCA2 and pancreatic cancer.

Many factors, including a family history of cancer, have been implicated in the development of pancreatic cancer. Among these factors, germline BRCA2 mutations have been clearly associated with the development of this disease, while mutations in BRCA1 appear to have a limited role. Patients with pancreatic cancer and germline BRCA2 mutations tend to be Ashkenazi Jewish, have a younger than average age of onset, and in many cases, lack family history for breast, ovarian, or pancreatic cancers. In addition, somatic mutations of BRCA2 appear to be rare in tumors of the pancreas. The mechanism by which mutant BRCA2 contributes to development of pancreatic cancers is not well understood. However, it appears that inactivation of several independent functions of BRCA2 including regulation of gene transcription, chromatin remodeling, cell growth, DNA damage repair, and chromosomal instability may provide a pathophysiological basis for the association of BRCA2 mutations and pancreatic cancer.

BRCA2 Protein↗