Journal: BMC Microbiology

Article Title: Rapid identification of bacterial pathogens using a PCR- and microarray-based assay

doi: 10.1186/1471-2180-9-161

Figure Lengend Snippet: Oligonucleotide probes included in the final microarray layout.

Article Snippet: In total, 22 species-specific probes for 12 bacteria, 2 CNS-specific, and 4 mecA resistance marker specific probes (Metabion, Germany) were chosen for spotting on the microarray (Table ).

Techniques: Microarray, Bacteria, Sequencing

Journal: BMC Microbiology

Article Title: Rapid identification of bacterial pathogens using a PCR- and microarray-based assay

doi: 10.1186/1471-2180-9-161

Figure Lengend Snippet: The species coverage of Staphylococcus probe panel.

Article Snippet: In total, 22 species-specific probes for 12 bacteria, 2 CNS-specific, and 4 mecA resistance marker specific probes (Metabion, Germany) were chosen for spotting on the microarray (Table ).

Techniques: Microarray

Journal: BMC Microbiology

Article Title: Rapid identification of bacterial pathogens using a PCR- and microarray-based assay

doi: 10.1186/1471-2180-9-161

Figure Lengend Snippet: Pathogens identified from the blood culture samples using PCR- and microarray-based analysis.

Article Snippet: In total, 22 species-specific probes for 12 bacteria, 2 CNS-specific, and 4 mecA resistance marker specific probes (Metabion, Germany) were chosen for spotting on the microarray (Table ).

Techniques: Microarray, Bacteria, Marker

Journal: PLoS ONE

Article Title: Amplified Loci on Chromosomes 8 and 17 Predict Early Relapse in ER-Positive Breast Cancers

doi: 10.1371/journal.pone.0038575

Figure Lengend Snippet: Over-expressed genes in chromosomal regions 17q12, 17q21.33-q25.1, 8p11.2 and 8q24.3 associated with early relapse in ER+ breast cancers treated with tamoxifen.

Article Snippet: Competing Interests: SG is a consultant for Ibris Inc. SG, EB and GB are co-inventors on a patent entitled “GENETIC MARKERS AND DIAGNOSTIC METHODS FOR RESISTANCE OF BREAST CANCER TO HORMONAL THERAPIES” United States Patent Application Serial No. 13/220,434.

Techniques:

Journal: PLoS ONE

Article Title: Amplified Loci on Chromosomes 8 and 17 Predict Early Relapse in ER-Positive Breast Cancers

doi: 10.1371/journal.pone.0038575

Figure Lengend Snippet: A) Kaplan-Meier curves of the samples in the primary dataset (GSE6532) enriched for over-expressed cell cycle genes versus the rest of samples that don’t show this feature. Patients with cell cycle activated genes show a significant decrease in distant metastasis free survival rate (HR = 9.71, 95% CI = 3.3–28.6; P<0.0001). B) Kaplan-Meier curves of the ER+ samples in the primary dataset (GSE6532) stratified by presence of putative amplicons in 17q12, 17q21.33-q25.1, 8p11.2 and 8q24.3. Patients that show any one of the chromosomal amplifications have significantly higher relapse rates when compared to samples without any amplifications: 17q12 (HR = 4.09, 95% CI = 3.84–21.99; P = 6.3e−07), 17q21.33– q25.1 (HR = 3.14, 95% CI = 2.17–13.62; P = 3.0e−04), 8p11.2 (HR = 3.75, 95% CI = 3.18–18.31; P = 5.7e−06), and 8q24.3 (HR = 4.29, 95% CI = 4.32–34.08; P = 2.2e−06). C) Analysis of combined gene expression data of 624 ER+ breast cancers from multiple published data sets. Outlier analysis was performed to identify cases with evidence of amplification at 17q12, 17q22, 8p11.2, and 8q24.3 and those without evidence of any amplification. Kaplan-Meier curves of relapse free survival for ER+ samples with each of the four amplicons, and samples containing no amplicon are plotted: 17q12 (HR = 2.30, 95% CI = 1.45–3.64; P = 4.0e−04), 17q22 (HR = 3.07, 95% CI = 1.99–4.73; P<1.0e−04), 8p11.2 (HR = 1.96, 95% CI = 1.23–3.13; P = 4.9e−3), 8q24.3 (HR = 2.38, 95% CI = 1.60–3.55; P<1.0e−04) D) Kaplan-Meier curves of overall survival for the ER+ samples in the test CGH dataset (GSE22133) with each of the 4 amplicons, as well as samples that don’t have any of the chromosomal amplifications. Analysis of the CGH data identified amplification peaks at each of the four regions that overlap with the previously identified loci. Patients that show any one of the chromosomal amplifications have significantly higher event rates than those without any of the amplifications: 17q12 (HR = 2.61, 95% CI = 1.51–5.51; P = 6.8e−04), 17q22 (HR = 3.02, 95% CI = 1.76–5.18; P = 7.3e−05), 8p11.2 (HR = 2.65, 95% CI = 1.48–4.74; P = 1.3e−03), and 8q24.3 (HR = 2.12, 95% CI = 1.24–3.65; P = 6.7e−03). Log-rank tests were used to calculate all the P values.

Article Snippet: Competing Interests: SG is a consultant for Ibris Inc. SG, EB and GB are co-inventors on a patent entitled “GENETIC MARKERS AND DIAGNOSTIC METHODS FOR RESISTANCE OF BREAST CANCER TO HORMONAL THERAPIES” United States Patent Application Serial No. 13/220,434.

Techniques: Gene Expression, Amplification

Journal: PLoS ONE

Article Title: Amplified Loci on Chromosomes 8 and 17 Predict Early Relapse in ER-Positive Breast Cancers

doi: 10.1371/journal.pone.0038575

Figure Lengend Snippet: FISH scores for ER+/HER2- breast cancer tissue samples.

Article Snippet: Competing Interests: SG is a consultant for Ibris Inc. SG, EB and GB are co-inventors on a patent entitled “GENETIC MARKERS AND DIAGNOSTIC METHODS FOR RESISTANCE OF BREAST CANCER TO HORMONAL THERAPIES” United States Patent Application Serial No. 13/220,434.

Techniques: Amplification

Journal: PLoS ONE

Article Title: Amplified Loci on Chromosomes 8 and 17 Predict Early Relapse in ER-Positive Breast Cancers

doi: 10.1371/journal.pone.0038575

Figure Lengend Snippet: ER+/HER2- samples with systemic relapse events were probed for the amplification of 8p11.2, 17q22 and 8q24.3 by multiplexed FISH assay as described in Methods. A) Out of 36 samples, 15 had at least one region amplified. Kaplan-Meier curves for relapse free survival is shown for cancers having at least one amplicon vs cancer having no amplicons (HR = 2.31, 95% CI = 0.66–8.06; P = 0.1041 (Gehan-Willcoxon) or P = 0.1886 (Mantel-Cox)). B) A typical image of multicolor FISH in a breast cancer specimen. This cell has evidence of amplification of both 17q23.1 and 8p11 loci, but normal 8q24 loci.

Article Snippet: Competing Interests: SG is a consultant for Ibris Inc. SG, EB and GB are co-inventors on a patent entitled “GENETIC MARKERS AND DIAGNOSTIC METHODS FOR RESISTANCE OF BREAST CANCER TO HORMONAL THERAPIES” United States Patent Application Serial No. 13/220,434.

Techniques: Amplification