Alex ZelikovskyDepartment of Computer Science

Georgia State University

Joint work with Adrian Caciula (GSU), Serghei Mangul (UCLA) James Lindsay, Ion Mandoiu (UCONN)

Monte-Carlo Regression Algorithm for IsoformFrequency Estimation from RNA-Seq Data

IEEE ICCABS 2013, New Orleans, LA

• RNA-Seq: Introduction

• MCReg: Monte Carlo Regression based Algorithm

• Experimental Results

• Conclusions and Future Work

IEEE ICCABS 2013, New Orleans, LA

Outline

Genome-Guided RNA-Seq Protocol

RNA-Seq enables transcript-level resolution of gene expression

From RNA – through the process of hybridization-

Make cDNA & shatter into fragments

Sequence fragment ends

A B C D E

Map reads to genome

Gene Expression (GE)Isoform Expression (IE)

A B C

A C

D E

Isoform Discovery (ID)

[Nicolae, et. al., 11] IEEE ICCABS 2013, New Orleans, LA

• RNA-Seq: Introduction

• MCReg: Monte Carlo Regression based Algorithm- Observed Read Distribution- MC-Based Estimation of Expected Read Distribution- Regression-Based Estimation of Isoform Frequencies

• Experimental Results

• Conclusions and Future Work

IEEE ICCABS 2013, New Orleans, LA

Outline

MCReg: Monte-Carlo Regression

MCReg Motivation:•Reducing the error rate is critical for detecting similar transcripts especially in those cases when one is a subset of another:

Screenshot from Genome browse:

IEEE ICCABS 2013, New Orleans, LA

• Map paired-end reads onto the library of known isoforms using an ungapped aligner (e.g., Bowtie)

• B. Langmead, C. Trapnell, et. al., “Ultrafast and memory-efficient alignment of short DNA sequences to the human genome,” Genome Biology, vol. 10, no. 3, p. R25, 2009.

• Group reads that have been mapped to the same transcripts into classes

• Monte-Carlo-Based Estimation of Expected Read Distribution using e.g. Grinder simulator

• F.E. Angly et. al. Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic acids research, 2012

• Solve the regression:The least-square formulation can be solved with a constrained quadratic programming solver

• M. S. Andersen et. al. CVXOPT: A Python package for convex optimization,  Available at cvxopt.org, 2013.

General Method Overview

Observed Read Distribution

IEEE ICCABS 2013, New Orleans, LA

Monte-Carlo-Based Estimation of Expected Read Distribution

IEEE ICCABS 2013, New Orleans, LA

MC-Based Estimation of Expected Read Distribution

IEEE ICCABS 2013, New Orleans, LA

Regression-Based Estimation of Isoform Frequencies

IEEE ICCABS 2013, New Orleans, LA

Regression-Based Estimation of Isoform Frequencies

IEEE ICCABS 2013, New Orleans, LA

• RNA-Seq: Introduction

• MCReg: Monte Carlo Regression based Algorithm

• Experimental Results

• Conclusions and Future Work

IEEE ICCABS 2013, New Orleans, LA

Outline

Simulation Setup

IEEE ICCABS 2013, New Orleans, LA

Experimental Results• Frequency estimation accuracy was assessed using

the coefficient of determination r2.

• For IsoEM r2 = 0.92, while for MCReg r2 = 0.97.

• The results shows better correlation compared with IsoEM especially because of those cases of sub-transcripts where IsoEM skewed the estimated frequency toward super-transcripts.

IEEE ICCABS 2013, New Orleans, LA

Thanks!

IEEE ICCABS 2013, New Orleans, LA