Biomedical subjects

Suhail Nasim

Publications and source records attributed to Suhail Nasim.

4 recordsLinked to original sources

PubMed2006

A prospective study of the natural history of transient leukemia (TL) in neonates with Down syndrome (DS): Children's Oncology Group (COG) study POG-9481.

A unique transient leukemia (TL) has been described in newborns with Down syndrome (DS; or trisomy 21 mosaics). This leukemia has a high incidence of spontaneous remission; however, early death and subsequent development of acute megakaryoblastic leukemia (AMKL) have been reported. We prospectively evaluated 48 infants with DS and TL to determine the natural history and biologic characteristics of this disease, identify the clinical characteristics associated with early death or subsequent leukemia, and assess the incidence of subsequent leukemia. Blast cells associated with TL in DS infants exhibited FAB M(7) morphology and phenotype. Most infants (74%) had trisomy 21 (or mosaicism) as the only cytogenetic abnormality in the blast cells. Most children were able to spontaneously clear peripheral blasts (89%), normalize blood counts (74%), and maintain a complete remission (64%). Early death occurred in 17% of infants and was significantly correlated with higher white blood cell count at diagnosis (P < .001), increased bilirubin and liver enzymes (P < .005), and a failure to normalize the blood count (P = .001). Recurrence of leukemia occurred in 19% of infants at a mean of 20 months. Development of leukemia was significantly correlated with karyotypic abnormalities in addition to trisomy 21 (P = .037). Ongoing collaborative clinical studies are needed to determine the optimal role of chemotherapy for infants at risk for increased mortality or disease recurrence and to further the knowledge of the unique biologic features of this TL.

Bilirubin↗

PubMed2004

Evaluation of quality-control criteria for microarray gene expression analysis.

BACKGROUND: Development of quality-control criteria to ensure reproducibility of microarray results for potential clinical application is still in its infancy. METHODS: In the present studies we developed quality-control criteria and evaluated their effect in microarray data analysis using total RNA from cell lines, frozen tumors, and a commercially available reference RNA. Quality-control criteria such as A(260)/A(280) ratios, percentage of rRNA, and median size of cDNA and cRNA synthesis products were evaluated for robustness in microarray analysis. Furthermore, precision studies using a reference material were performed on the Affymetrix HG-U133A high-density oligonucleotide microarrays. The same reference RNA sample was examined in 16 different chips run on 2 different days in the four different modules of the Affymetrix fluidics workstation. Fresh and frozen fragmented cRNAs were also compared. An ANOVA model was fit to identify the main sources of variation. RESULTS: Good-quality samples showed >30% rRNA in the electropherograms and cDNA and cRNA synthesis products with median sizes of 2.0 and 3.0 kb, respectively. Precision studies showed that the main source of variation was the day-to-day variability, minimally affecting hybridization exogenous control genes. Altogether, the results showed that the Affymetrix Genechip system is highly reproducible when RNA that meet the quality-control criteria are used (overall P >0.01). CONCLUSIONS: These results confirm the need to establish defined quality-control criteria for sample quality to distinguish between analytical and biological variability.

Analysis of Variance↗

PubMed2004

Evaluation of a linear amplification method for small samples used on high-density oligonucleotide microarray analysis.

High-density oligonucleotide microarray analysis has proven to be an excellent approach for gene expression profiling in human cancers. This technique assesses the expression of thousands of genes simultaneously, from at least 5 microg of total RNA per sample per experiment. This total RNA requirement poses a challenge when studying small, unique clinical samples, like biopsies. Recently, a new standardized protocol for small samples was released by Affymetrix, which includes a linear amplification step. To evaluate the impact of such amplification in the gene expression profiling of human ovarian cancer, we compared results obtained from 5 microg and 100 ng of total RNA from the same tumor sample, using the standard Affymetrix protocol and the new linear RNA amplification protocol, respectively. We identified a small bias in gene expression data caused by linear amplification, potentially due to shorter elongation products leading to misclassification of probe sets directed to the middle-5' region of the transcripts. Interestingly, the magnitude of the bias varied when different normalization and expression summary algorithms were used. However, this bias does not affect tumor gene expression profiling. Consequently, linear amplification may be of utility in cases of extremely low RNA recovery from critical and unique samples, such as small biopsies.

Cluster Analysis↗

PubMed2002

Normal, benign, preneoplastic, and malignant prostate cells have distinct protein expression profiles resolved by surface enhanced laser desorption/ionization mass spectrometry.

PURPOSE: The objective of this study was to discover protein biomarkers that differentiate malignant from nonmalignant cell populations, especially early protein alterations that signal the initiation of a developing cancer. We hypothesized that Surface Enhanced Laser Desorption/Ionization-time of flight-mass spectrometry-assisted protein profiling could detect these protein alterations. EXPERIMENTAL DESIGN: Epithelial cell populations [benign prostatic hyperplasia (BPH), prostate intraepithelial neoplasia (PIN), and prostate cancer (PCA)] were procured from nine prostatectomy specimens using laser capture microdissection. Surface Enhanced Laser Desorption/Ionization-time of flight-mass spectrometry analysis was performed on cell lysates, and the relative intensity levels of each protein or peptide in the mass spectra was calculated and compared for each cell type. RESULTS: Several small molecular mass peptides or proteins (3000-5000 Da) were found in greater abundance in PIN and PCA cell lysates. Another peak, with an average mass of 5666 Da, was observed to be up-regulated in 86% of the BPH cell lysates. Higher levels of this same peak were found in only 22% of the PIN lysates and none of the PCA lysates. Expression differences were also found for intracellular levels of prostate-specific antigen, which were reduced in PIN and PCA cells when compared with matched normals. Although no single protein alteration was observed in all PIN/PCA samples, combining two or more of the markers was effective in distinguishing the benign cell types (normal/BPH) from diseased cell types (PIN/PCA). Logistic regression analysis using seven differentially expressed proteins resulted in a predictive equation that correctly distinguished the diseased lysates with a sensitivity and specificity of 93.3 and 93.8%, respectively. CONCLUSIONS: We have shown that the protein profiles from prostate cells with different disease states have discriminating differences. These differentially regulated proteins are potential markers for early detection and/or risk factors for development of prostate cancer. Studies are under way to identify these protein/peptides, with the goal of developing a diagnostic test for the early detection of prostate cancer.

Adult↗