performance+of+protein+microarrays+using+SEREX+derived+antigens+paper

paper found here C:\kurt\storage\CIM Research Folder\DR\2012\12-14-12\serex paper and here paper found here: "C:\kurt\storage\CIM Research Folder\DR\2013\1-26-13\some_serex_papers\Tumour auto-antibody screening performance of protein microarrays using SEREX derived antigens.pdf" PMID: 21078204

first started reading 12-14-12

notes Tumour auto-antibody screening: performance of protein microarrays using SEREX derived antigens BMC Cancer 2010 from Austrian Institute of Technology

people often do gene expression profiling

they make protein microarrays. However, the proteins included on their array are derived from the standard SEREX approach where clones are lysed directly on the membrane and working with the large membranes is a cumbersome process.

They produced his tagged protiens

they detected high levels of antibodies against e coli proteins in the sera of all donors and patients

they had better detection limit/signal intensity with the microarray than the macroarray

they used the limma R software package

they had good correlation between samples

they could distinguish between brain and lung cancer sera samples based on their reactivity for certain clones

SEREX arrays for screening several thousand expression clones

q Drawbacks of membrane based screening are low reproducibility, low dynamic range of signal intensities, and difficulties in handling membranes.

q We have found during optimization (data not shown) of protein microarray production that proteins concentrations of up to 0.5 mg/mL are well suited for spotting using a contact spotter.

they could screen 20000 different spots on the microarray

? I wonder why they didn't compare cancer with normal as well. Instead, they compared lung cancer with brain cancer.

notes from when I accidentally started reading the paper a 2nd time 1-27-13

microarrays have advantages over macroarrays

q Mutated, modified and aberrantly expressed proteins evoke an immunological response leading to the production of auto-antibodies [5,6].

q However, protein microarrays have great potential to characterize auto-antibodies [9].

q Over recent years most approaches have used so called macroarrays for autoantigen-profiling.

q Handling membranes and processing sera is cumbersome, and sensitivity and reproducibility of these macroarrays are limiting.

q 16 bit (0-216) dynamic range of standard microarrays.

q The bacterial wet biomass (30 mg/mL culture) obtained by autoinduction was twice when compared to that of obtained from IPTG cultures.

q Positive control spots of E. coli crude protein extracts showed high signals indicating the presence of high levels of antibodies against E. coli proteins in the sera of all donors and patients, whereas buffer spots serve as controls were clearly negative.

q This might be due to the smaller reaction surfaces and better distribution of the serum-sample over the array (Figure 1)

^explaining why the microarray gave a greater detection limit/signal intensity than the macroarray

high reproducibility q correlation coefficients ranging from 0.92 to 0.96