Efficient sequencing data compression and FPGA acceleration based on a two-step framework.

With the increasing throughput of modern sequencing instruments, the cost of storing and transmitting sequencing data has also increased dramatically. Although many tools have been developed to compress sequencing data, there is still a need to develop a compressor with a higher compression ratio. We present a two-step framework for compressing sequencing data in this paper. The first step is to repack original data into a binary stream, while the second step is to compress the stream with a LZMA encoder. We develop a new strategy to encode the original file into a LZMA highly compressed stream. In addition an FPGA-accelerated of LZMA was implemented to speedup the second step. As a demonstration, we present repaq as a lossless non-reference compressor of FASTQ format files. We introduced a multifile redundancy elimination method, which is very useful for compressing paired-end sequencing data. According to our test results, the compression ratio of repaq is much higher than other FASTQ compressors. For some deep sequencing data, the compression ratio of repaq can be higher than 25, almost four times of Gzip. The framework presented in this paper can also be applied to develop new tools for compressing other sequencing data. The open-source code of repaq is available at: https://github.com/OpenGene/repaq.

Celiac disease associated with aplastic anemia in a 6-year-old girl: a case report and review of the literature.

BACKGROUND: Celiac disease may present with hematological abnormalities including long-standing anemia. Both aplastic anemia and celiac disease have a similar underlying autoimmune process but an association between the two is seldom reported. There have only been three pediatric cases reporting this association and this case is the first reported in a female pediatric patient. CASE PRESENTATION: We report a case of 6-year-old South Asian girl presenting with bruises, petechiae, and recent history of loose stools. On evaluation, she was diagnosed as having celiac disease and was put on a gluten-free diet and further investigations including bone marrow biopsy revealed pancytopenia. She was managed with packed red cells, platelets, and diet restrictions and had improving platelet counts over yearly follow ups. Her parents were counseled regarding the need for bone marrow transplant. CONCLUSIONS: This is the fourth case report suggesting an association between celiac disease and aplastic anemia in the pediatric population and this association could be more common than expected. Timely intervention of either celiac disease through strict gluten-free diet or aplastic anemia through immunosuppressive therapy could potentially reduce the risk for other autoimmune conditions. We can see that all four pediatric cases reported with this potential association are from South East Asia and hence larger studies would be prudent to explore this association.