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We address joint design of optimum generalized partial response (GPR) target and equalizer for perpendicular recording channels with jitter noise. We develop a new cost function which accounts for the data-dependent nature of jitter noise based on the minimum mean square error (MMSE) criterion. Using the step-response-based channel model, we derive expressions for the statistics required to compute the optimum equalizer and target in the presence of jitter noise. We also derive a bit-response-based model for the jitter noise channel. We present an approach for doing simulations as well as analytical computations for the jitter noise channel without resorting to the widely used Taylor series approximations. Our computational and simulation results show that, while the targets designed without accounting for the jitter lead to error-floor effect in the bit-error-rate performance, the targets designed by our approach give significant performance improvement under high jitter conditions, with no sign of error-floor effect for the range of signal-to-noise ratios considered.