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Open Access Methodology article

A molecular inversion probe assay for detecting alternative splicing

Shengrong Lin12, Wenyi Wang13, Curtis Palm1, Ronald W Davis1 and Kara Juneau1*

Author Affiliations

1 Stanford Genome Technology Center, Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA USA

2 Illumina Inc. 9885 Towne Centre Dr. San Diego, CA 92121, USA

3 Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, 1400 Pressler St. Unit 1410, Houston, TX 77030, USA

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BMC Genomics 2010, 11:712  doi:10.1186/1471-2164-11-712

Published: 17 December 2010

Additional files

Additional file 1:

This figure shows the reproducibility of the asMIP assay using decreasing amounts of probe library (Figures A & B), and presents evidence that the linear dynamic range of the arrays used to quantify asMIPs is approximately 100-fold (Figure C).

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Additional file 2:

Data presented in this figure demonstrate that splice scores for alternatively spliced junctions are much larger than for constitutive junctions.

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Additional file 3:

The plots in this figure show the correlation between splice scores derived from asMIP assays compared to qPCR.

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Additional file 4:

This figure shows two Receiver Operating Characteristic (ROC) plots comparing qPCR splicing calls against asMIP splicing calls made at various cutoffs for either the positive (Figure A) or negative (Figure B) qPCR splicing calls.

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Additional file 5:

A detailed, step-by-step example calculation for M-score for one gene.

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