Large insertions and deletions (indels), including copy number variations (CNVs), are commonly seen in many diseases. Standard approaches for indel detection rely on well-established methods such as qPCR or short tandem repeat (STR) markers. Recently, a number of tools for CNV detection based on next-generation sequencing (NGS) data have also been developed; however, use of these methods is limited. Here, we used whole-exome sequencing (WES) in patients previously diagnosed with CMT1A or HNPP using STR markers to evaluate the ability of WES to improve the clinical diagnosis. Patients were evaluated utilizing three CNV detection tools including CONIFER, ExomeCNV and CEQer, and array comparative genomic hybridization (aCGH). We identified a breakpoint region at 17p11.2-p12 in patients with CMT1A and HNPP. CNV detection levels were similar in both 6 Gb (mean read depth = 80×) and 17 Gb (mean read depth = 190×) data. Taken together, these data suggest that 6 Gb WES data are sufficient to reveal the genetic causes of various diseases and can be used to estimate single mutations, indels, and CNVs simultaneously. Furthermore, our data strongly indicate that CNV detection by NGS is a rapid and cost-effective method for clinical diagnosis of genetically heterogeneous disorders such as CMT neuropathy. Conflict of interestThe authors report no conflict of interest. Structural variants including copy number variation (CNV) and insertions and deletions (indel) have been highlighted as the causes of genetic disorders. Recently, it has been reported that CNVs significantly contribute to various diseases such as neurodevelopmental disorders, intellectual disabilities and numerous cancers

This study investigated co‐occurrences of endocrine‐disrupting compounds (EDCs), and pharmaceuticals and personal care products (PPCPs) in order to develop effective monitoring strategies. EDCs/PPCPs were clustered on the basis of similarities in their occurrence in surface waters to reduce analytical complexity. Chemometric approaches were applied to three water bodies with different water systems and climate conditions: Lake Mead in Nevada, the Assabet River in Massachusetts, and the Santa Ana River in California. The results show that site‐specific co‐occurrences among EDCs/PPCPs exist, though these co‐occurrences do not translate well between sites. Therefore, the usefulness of this study is in demonstrating the approach of selecting indicator/surrogate compounds using chemometrics rather than providing a single list of recommended compounds for long‐term monitoring. This study offers a systematic and practical approach to selecting a suite of analytes when implementing a monitoring program for EDCs/PPCPs in surface waters.

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The study that is the basis for this article evaluated water quality trends in tributaries of a drinking water source to assist in developing effective management strategies. Nutrient and total organic carbon (TOC) trends from 1998 to 2012 were assessed in major tributaries of the Wachusett Reservoir in Massachusetts. In this period, solute concentrations generally declined—in seven of eight tributaries for nitrate (all statistically significant at p < 0.05), four of eight tributaries for total phosphorus (all significant), and six of eight tributaries for TOC (three significant). Despite these changes, increased flows resulted in increased or constant daily loads. Installation of municipal sewer systems in selected subbasins between 2002 and 2008 coincided with decreased concentration trends in their tributaries and decreased loads in the most sewered tributary. These results illustrate the dominance of flow in determining loads and have implications for water managers seeking to quantify and manage solute transport.

Many water utilities have recently initiated or are considering initiating monitoring programs to establish baseline contaminant concentrations of endocrine‐disrupting compounds (EDCs) and pharmaceuticals/personal care products (PPCPs) in their water supply. Unfortunately, monitoring sites and sampling frequency have often been conducted without regard to end use of the data, loading dynamics, and environmental behavior of trace contaminants. This article provides an a posteriori analysis of more than eight years of monitoring data from Lake Mead, Nev., including more than 80 EDCs/PPCPs to ascertain what effects sample location, sample frequency, and analyte reporting limits have on interpretation of the baseline dataset. The results of this study indicate that, for the Lake Mead dataset, the same general conclusions regarding the mean, median, maximum, and minimum concentrations can be drawn from the complete monthly sample dataset as can be drawn from a two‐year snapshot and/or even quarterly or bimonthly data alone. This finding points to the possible reduction of sampling, campaign frequency, and duration for utilities, although this type of analysis needs to be conducted in other watersheds to determine portability of results.