A deduplication storage system enables new input data to be deduplicated with data of synthetic backups already constructed, and for this purpose efficiently calculates deduplication digests for synthetic backups being constructed, based on already existing digests of data referenced by the synthetic backups. For each input data segment of the plurality of input data segments of a synthetic backup being constructed, a plurality of deduplication digests of stored data segments, referenced by the input data segment, is retrieved from an index. Each input data segment is partitioned into each of a plurality of fixed-sized data sub-segments. A calculation is performed producing a deduplication digest for a data sub-segment, where the calculation is based on the retrieved deduplication digests of the plurality of stored data sub-segments referenced by the input data sub-segment.