ALBERT

Description: Abstract 4849 Introduction: Current diagnostic screening strategies for copy number variations (CNVs) in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) include fluorescence in situ hybridization (FISH) or karyotyping, both of which are time-consuming, costly, laborious, and lacking in resolution. Multiplex ligation-dependent probe amplification (MLPA) can be used to detect copy number changes in multiple loci simultaneously in a single PCR reaction, and boasts a resolution down to single exons. To adapt MLPA for use in routine clinical diagnostics, we have developed and validated a protocol for automatic data analysis and interpretation of common chromosomal abnormalities in MDS/AML. Patients and Methods: The study used a training set of 45 healthy subjects to establish a normal reference range for each individual probe. Using these ranges we built an automated Excel spreadsheet-based analysis system, which included multiple quality checks, and flagged samples failing these quality controls. Each probe was given a call of “no mutation detected,” “deletion,” or “gain,” based on whether the normalized ratio fell within or outside of the empirically-determined normal range for that probe. We then analyzed over 100 leukemia cases tested by FISH, including both suspected myeloid leukemia samples and suspected chronic lymphocytic leukemia (CLL) samples. Documented chromosomal abnormalities in CLL include 11q-, 17p- (loss of TP53), and trisomy 12, all of which had the potential to be detected by the probes in the MDS MLPA probemix. The greater prevalence of CLL and its associated CNVs provided additional positive controls for the validation of the MDS MLPA probemix and our analysis method. Results: The empirically-determined normal ranges demonstrated that some probes varied widely (3 standard deviation [3SD] normal range of 0.46–1.54), while others were extremely reliable (3SD normal range of 0.84–1.16). The MLPA assay demonstrated excellent overall accuracy (〉90%) and specificity (〉93%) for both suspected myeloid and CLL samples when compared to FISH. The sensitivity of the MLPA assay is somewhat lower than that of FISH, requiring a probe-dependent 20–40% positivity for a given CNV to be detected. However in several cases, the MDS MLPA assay was able to detect additional lesions too small to be seen by FISH. Conclusions: For MLPA, the total process-to-report time, including data analysis, is 2–3 days, versus the 7–10 days required for FISH analysis. In addition, the MLPA assay is substantially cheaper and considerably less labor-intensive than FISH. Our improved MLPA assay protocol and analysis method provides a clinically robust, multiplexed, high-throughput, high-resolution, and low-cost solution for detection of copy number changes in MDS/AML, and can therefore be used as a first-line screening test in a clinical laboratory. Disclosures: Donahue: Quest Diagnostics Inc.: Employment. Abdool: Quest Diagnostics Inc.: Employment. Wohlgemuth: Quest Diagnostics Inc.: Employment. Yeh: Quest Diagnostics Inc.: Employment.

Description: Abstract 2716 Background: Current strategies based on karyotyping or fluorescent in situ hybridization (FISH) for detection of chromosomal abnormalities in chronic lymphocytic leukemia (CLL) are laborious, time-consuming, and costly and have limitations in resolution. Multiplex ligation-dependent probe amplification (MLPA) can simultaneously detect copy number changes of multiple loci in a single PCR, making it an attractive alternative. We developed and validated an MLPA protocol for comprehensive, automated data analysis and interpretation of chromosome abnormalities associated with CLL. Patients and Methods: Reference ranges for individual MLPA probes were established from a group of 50 healthy control subjects. Using these ranges we built an automated spreadsheet-based analysis system that includes multiple quality checks; samples that fail these checks are flagged and not reported. Each target was given a call of “deletion,” “normal,” or “amplification,” depending on whether the normalized ratio fell within or outside of the established normal range (mean ± 2SD or mean ± 3SD). After establishing the normal references ranges for each probe, we used the MLPA assay to characterize chromosome abnormalities in blood samples from 100 patients with suspected CLL that had been previously tested with FISH. Results: The maximum normal ranges were distributed between 0.82 and 1.18 for the mean ± 2SD values (ie, 95% CI, P = 0.05), and between 0.73 and 1.27 for the mean ± 3SD values (ie, 99.7% CI, P = 0.01). MLPA showed good concordance with FISH results in the 100 clinically suspected CLL cases. In 6 of these cases, abnormalities detected by MLPA were in regions not covered by FISH, including additional copy number gains on chromosomes 18q21.1 and 19, and novel micro-deletions at 19q13.43 and 19p13.2 loci. Excluding these cases, MLPA showed 94% sensitivity, 94% concordance, and 93% specificity relative to FISH. MLPA detected abnormalities in 3 FISH-negative cases and failed to detect abnormalities in three 13q- cases with low percentages of leukemic cells (7%, 12% and 19%). The limit of detection of the CLL MLPA assay was about 20% leukemic clones. Conclusions: This MLPA-based assay for chromosome abnormalities in CLL showed excellent concordance with FISH. This multiplex assay represents a fast (roughly 2–3 days total process to report time vs 7–10 days for FISH), high-throughput, accurate, and user-friendly process for that has potential for use as a first-line screening test for detection of chromosome abnormalities associated with CLL in the clinical laboratory. Disclosures: No relevant conflicts of interest to declare.

Description: Omega-3 (n-3) treatment may lower cardiovascular risk, yet its effects on the circulating lipidome and relation to cardiovascular risk biomarkers are unclear. We hypothesized that n-3 treatment is associated with favorable changes in downstream fatty acids (FAs), oxylipins, bioactive lipids, clinical lipid and inflammatory biomarkers. We examined these VITAL200, a nested substudy of 200 subjects balanced on demographics and treatment and randomly selected from the Vitamin D and Omega-3 Trial (VITAL). VITAL is a randomized double-blind trial of 840 mg/d eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA) vs. placebo among 25,871 individuals. Small polar bioactive lipid features, oxylipins and FAs from plasma and red blood cells were measured using three independent assaying techniques at baseline and one year. The Women’s Health Study (WHS) was used for replication with dietary n-3 intake. Randomized n-3 treatment led to changes in 143 FAs, oxylipins and bioactive lipids (False Discovery Rate (FDR) 〈 0.05 in VITAL200, validated (p-values 〈 0.05)) in WHS with increases in 95 including EPA, DHA, n-3 docosapentaenoic acid (DPA-n3), and decreases in 48 including DPA-n6, dihomo gamma linolenic (DGLA), adrenic and arachidonic acids. N-3 related changes in the bioactive lipidome were heterogeneously associated with changes in clinical lipid and inflammatory biomarkers. N-3 treatment significantly modulates the bioactive lipidome, which may contribute to its clinical benefits.