Detection of Mosaic Absence of Heterozygosity (AOH) Using Low-Pass Whole Genome Sequencing in Prenatal Diagnosis: A Preliminary Report.

Objective: Mosaicism is a common biological phenomenon in organisms and has been reported in many types of chromosome abnormalities, including the absence of heterozygosity (AOH). Due to the detection limitations of the sequencing approach, mosaic AOH events are rarely assessed in clinical cases. Herein, we report the performance of mosaic AOH identification using a low-pass (5~8-fold) WGS method (termed 'CMA-seq', an abbreviation for 'Chromosome Analysis by Sequencing') in fetal genetic diagnosis. Methods: Thirty AOH-negative, eleven constitutional AOH, and three mosaic AOH samples were collected as training data sets to develop the algorithm and evaluate the suitable thresholds for distinguishing mosaic AOH. Twenty-four new chromosomal aberrant cases, along with sixteen constitutional AOH samples, which were previously ascertained via the SNP-array-based method, were used as a validation data set to measure the performance in terms of sensitivity and specificity of this algorithm. Results: A new statistic, 'D-value', was implemented to identify and distinguish constitutional and mosaic AOH events. The reporting thresholds for constitutional and mosaic AOH were also established. In the validation set consisting of 24 new cases, seven constitutional AOH cases and 1 mosaic AOH case were successfully identified, indicating that the results were consistent with those of the SNP-array-based method. The results of all sixteen constitutional AOH validation samples also met the threshold requirements. Conclusions: In this study, we developed a new bioinformatic algorithm to accurately distinguish mosaic AOH from constitutional AOH by low-pass WGS. However, due to the small sample size of the training data set, the algorithm proposed in this manuscript still needs further refinements.

A Game Theory Approach for Strategic Partnerships in Academic Medicine.

Forming strategic partnerships is vital to academic health centers to further their missions of patient care, education, research, and community engagement. Formulating a strategy for such partnerships can be daunting due to the complexities of the health care landscape. The authors propose a game theory approach to partnership formation with the players being gatekeepers, facilitators, organizational employees, and economic buyers. Forming an academic partnership is not a game that is typically won or lost but is rather an ongoing engagement. Consistent with our game theory approach, the authors propose six basic rules to assist in successful strategic partnership formation for academic health centers.

Evaluation and Analysis of Absence of Homozygosity (AOH) Using Chromosome Analysis by Medium Coverage Whole Genome Sequencing (CMA-seq) in Prenatal Diagnosis.

OBJECTIVE: Absence of homozygosity (AOH) is a genetic characteristic known to cause human diseases mainly through autosomal recessive or imprinting mechanisms. The importance and necessity of accurate AOH detection has become more clinically significant in recent years. However, it remains a challenging task for sequencing-based methods thus far. METHODS: In this study, we developed and optimized a new bioinformatic algorithm based on the assessment of minimum sequencing coverage, optimal bin size, the Z-score threshold of four types of allele count and the frequency for accurate genotyping using 28 AOH negative samples, and redefined the AOH detection cutoff value. We showed the performance of chromosome analysis by five-fold coverage whole genome sequencing (CMA-seq) for AOH identification in 27 typical prenatal/postnatal AOH positive samples, which were previously confirmed by chromosomal microarray analysis with single nucleotide polymorphism array (CMA/SNP array). RESULTS: The blinded study indicated that for all three forms of AOH, including whole genomic AOH, single chromosomal AOH and segmental AOH, and all kinds of sample types, including chorionic villus sampling, amniotic fluid, cord blood, peripheral blood and abortive tissue, CMA-seq showed equivalent detection power to that of routine CMA/SNP arrays (750K). The subtle difference between the two methods is that CMA-seq is prone to detect small inconsecutive AOHs, while CMA/SNP array reports it as a whole. CONCLUSION: Based on our newly developed bioinformatic algorithm, it is feasible to detect clinically significant AOH using CMA-seq in prenatal diagnosis.

[A consensus recommendation for the interpretation and reporting of exome sequencing in prenatal genetic diagnosis].

With the rapid development and adaptation of high-throughput sequencing in clinical settings, application of exome sequencing (ES) has been gradually expanded from pediatric to prenatal diagnosis in recent years. There is an urgent need to establish criteria for clinical grade ES in order to facilitate such a complex testing. The standardization of pre- and post-test consultation, quality control for sample processing process and validation of bioinformatics data analysis, and more importantly data interpretation and reporting, as well as appropriate reporting scope, is of great importance for health care stakeholders. To achieve this, a committee composed of a wide range of healthcare professionals has proposed an ES standard for prenatal diagnosis. This has provided expert opinion on the genetic counseling and reporting standards of prenatal ES for the purpose of applying ES technology in prenatal setting.

Ammonia, thiocyanate, and cyanate removal in an aerobic up-flow submerged attached growth reactor treating gold mine wastewater.

The objective of the study was to investigate the nitrification process, as well as the bio-chemical removal of cyanate and thiocyanate, while treating gold mining wastewater using an aerobic up-flow SAGR. A total of six SAGRs, each packed with locally sourced pea gravel (estimated specific surface area of 297 m-2 m-3), were operated at various HRTs and tested on both low- and high-strength gold mining wastewaters. The two sets of three SAGRs were operated at HRTs of 0.45 days, 1.20 days, and 2.40 days. Nitrification was successfully achieved in all six SAGRs regardless of the wastewater strength or HRT examined. The steady-state, 20 °C surface area loading rate was determined to be 1.2 g-TAN m-2 d-1 in order to comply with an effluent discharge limit at 10 mg-TAN L-1 (i.e., with the wastewater sources examined). At all ammonia loading rates, thiocyanate was successfully removed, and residual concentrations were below 2 mg-SCN-N L-1. Cyanate appeared to be hydrolyzed and subsequently nitrified. Acute toxicity tests conducted on both daphnia and trout revealed the effluent to be safe for direct discharge.

Electrocoagulation of wastewater using aluminum, iron, and magnesium electrodes.

Primary influent from a municipal wastewater treatment plant was electrochemically treated with sacrificial aluminum, iron, and magnesium electrodes. The influence of sacrificial anodes on the removal of chemical oxygen demand, total nitrogen, total phosphorus, and orthophosphate during sedimentation was investigated. Nitrification kinetics were assessed on treated supernatant and biogas production was monitored on settled solids. Changes in alkalinity, conductivity, and pH were also recorded. Aluminum and iron electrodes provided high rates of orthophosphate removal (i.e., 6.8 mg-P/mmol-e). Aluminum and iron electrodes also provided similar treatment to equivalent doses of alum and ferric salts (i.e., 38-68% chemical oxygen demand, 10-13% total nitrogen, and 67-93% total phosphorus). The estimated stochiometric ratio of aluminum and iron dosed to orthophosphate removed was approximately 1.3:1 and 4.1:1, respectively. Magnesium electrodes, on the other hand, removed orthophosphate at rates 8-9 times slower than aluminum and iron (i.e., 0.9 mg-P/mmol-e). Magnesium had to be dosed at a ratio of 13.5:1 orthophosphate for phosphorus removal. Orthophosphate removal by magnesium electrodes was most likely limited by electrolysis reactions responsible for increases in pH (i.e., 0.52 pH units/mmol-e). Magnesium electrodes removed 49% chemical oxygen demand and 21% total nitrogen at the high molar ratios required for orthophosphate removal.