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There have been lots of efforts on the construction of quasi-cyclic (QC) low-density parity-check (LDPC) codes with large girth. However, most of them focus on protographs with single edges and little research has been done for the construction of QC LDPC codes lifted from protographs with multiple (i.e., parallel) edges. Compared to single-edge protographs, multiple-edge protographs have benefits such that QC LDPC codes lifted from them can potentially have larger minimum Hamming distance. In this paper, all subgraph patterns of multiple-edge protographs, which prevent QC LDPC codes from having large girth by inducing inevitable cycles, are fully investigated based on a graph-theoretic approach. By using combinatorial designs, a systematic construction method of multiple-edge protographs is proposed for regular QC LDPC codes with girth at least 12 and another method is proposed for regular QC LDPC codes with girth at least 14. Moreover, a construction algorithm of QC LDPC codes based on certain liftings of multiple-edge protographs is proposed and it is shown that the resulting QC LDPC codes have larger upper bounds on the minimum Hamming distance than those lifted from single-edge protographs. Simulation results are provided to compare the performance of the proposed QC LDPC codes with progressive edge-growth (PEG) LDPC codes and with PEG QC LDPC codes.