Slow speed of the Next-Generation sequencing data analysis, compared to the latest high throughput sequencers such as HiSeq X system, using the current industry standard genome analysis pipeline, has been the major factor of data backlog which limits the real-time use of genomic data for precision medicine. This study demonstrates the DRAGEN Bio-IT Processor as a potential candidate to remove the "Big Data Bottleneck". DRAGEN TM accomplished the variant calling, for ~40× coverage WGS data in as low as ~30 minutes using a single command, achieving the over 50-fold data analysis speed while maintaining the similar or better variant calling accuracy than the standard GATK Best Practices workflow. This systematic comparison provides the faster and efficient NGS data analysis alternative to NGS-based healthcare industries and research institutes to meet the requirement for precision medicine based healthcare.

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Objective: To improve the detecting accuracy of chromosomal aneuploidy of fetus by non-invasive prenatal testing (NIPT) using next generation sequencing data of pregnant women's cell-free DNA. Methods: We proposed the multi-Z method which uses 21 z-scores for each autosomal chromosome to detect aneuploidy of the chromosome, while the conventional NIPT method uses only one z-score. To do this, mapped read numbers of a certain chromosome were normalized by those of the other 21 chromosomes. Average and standard deviation (SD), which are used for calculating z-score of each sample, were obtained with normalized values between all autosomal chromosomes of control samples. In this way, multiple z-scores can be calculated for 21 autosomal chromosomes except oneself. Results: Multi-Z method showed 100% sensitivity and specificity for 187 samples sequenced to 3 M reads while the conventional NIPT method showed 95.1% specificity. Similarly, for 216 samples sequenced to 1 M reads, Multi-Z method showed 100% sensitivity and 95.6% specificity and the conventional NIPT method showed a result of 75.1% specificity. Conclusion: Multi-Z method showed higher accuracy and robust results than the conventional method even at low coverage reads.

Photodynamic therapy (PDT) is a non‐invasive and highly selective therapeutic approach. Photosensitizers (PSs) are an essential ingredient in PDT. However, many PSs are hydrophobic and insoluble, seriously restraining their clinical use. In this study, we prepared biocompatible PSs using water‐soluble organic nanoparticles (WSONs) with a chlorin derivative, pyropheophorbide a (PPa), and polyethylene glycol (PEG) to overcome the limited clinical applications of PDT. Among the PEGylated WSONs (WSON‐PEGs), WSON‐PEG 3400 and 2000 exhibited good water solubility and stability, with no aggregation in aqueous media, a high photoactivity, and low dark toxicity in vitro against A549 and HeLa cells. An in vivo application of WSON‐PEG 3400 using A549 tumour‐bearing BALB/c nude mice demonstrated a three‐fold higher PDT efficacy compared with the control and drug only groups, without treatment‐induced toxicity or toxic side effects. These results demonstrate that WSON‐PEG (3400) is a biocompatible PS with a high PDT efficacy and reduced dark toxicity, suitable for use in clinical trials.

PurposeTransition to next generation sequencing (NGS) for BRCA1/BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1/2.Materials and MethodsThe results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1/BRCA2. Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite.ResultsFifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both false-positive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant.ConclusionIon PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.