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We investigate the performance of the protograph low-density parity-check (LDPC) codes, which have been shown to possess simple structures and outstanding error performance over additive white Gaussian noise (AWGN) channels, over partial response (PR) channels using the finite-length extrinsic information transfer (EXIT) algorithm. Due to the intersymbol interference (ISI) caused by the PR channels, we observe that the conventional protograph LDPC codes do not perform well in terms of error rates. We further propose a new design scheme and construct three new types of protograph LDPC codes. Unlike conventional protograph LDPC codes in which the highest-degree variable nodes are punctured, the new protograph LDPC codes have their lowest-degree variable nodes punctured. Moreover, some edge re-connections are made in one of the proposed codes. The EXIT-chart analysis, the convergence analysis and the bit-error-rate simulation have shown that all three new codes outperform the conventional protograph LDPC codes. Moreover, two of the proposed codes are superior to the regular column-weight-3 LDPC code and thus they are good alternatives compared to other error-correction codes for use in data storage systems.