Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

CONSERVATION OF PERIPHERAL PLANT POPULATIONS IN CALIFORNIA

Volume: 53Start Page: 264End Page: 27

Impacts of Surface Water Diversions for Marijuana Cultivation on Aquatic Habitat in Four Northwestern California Watersheds

<div><p>Marijuana (<i>Cannabis sativa</i> L.) cultivation has proliferated in northwestern California since at least the mid-1990s. The environmental impacts associated with marijuana cultivation appear substantial, yet have been difficult to quantify, in part because cultivation is clandestine and often occurs on private property. To evaluate the impacts of water diversions at a watershed scale, we interpreted high-resolution aerial imagery to estimate the number of marijuana plants being cultivated in four watersheds in northwestern California, USA. Low-altitude aircraft flights and search warrants executed with law enforcement at cultivation sites in the region helped to validate assumptions used in aerial imagery interpretation. We estimated the water demand of marijuana irrigation and the potential effects water diversions could have on stream flow in the study watersheds. Our results indicate that water demand for marijuana cultivation has the potential to divert substantial portions of streamflow in the study watersheds, with an estimated flow reduction of up to 23% of the annual seven-day low flow in the least impacted of the study watersheds. Estimates from the other study watersheds indicate that water demand for marijuana cultivation exceeds streamflow during the low-flow period. In the most impacted study watersheds, diminished streamflow is likely to have lethal or sub-lethal effects on state-and federally-listed salmon and steelhead trout and to cause further decline of sensitive amphibian species.</p></div

Salmon Creek and Redwood Creek South Watersheds.

<p>Outdoor marijuana plantings are marked in red and greenhouses are marked in light green.</p

Frequency distribution of the water demand for marijuana cultivation as a percentage of seven-day low flow by year in each study watershed.

<p>Water demand data are from a remote sensing exercise using aerial imagery from 2011–2012 and are compared with each year’s annual seven-day low flow value for the period of record in each study watershed: (a) Upper Redwood Creek watershed (USGS gage near Blue Lake, CA, coverage from water year (WY) 1954–1958 and 1973–2014), (b) Salmon Creek watershed (data modeled using USGS gage on Elder Creek, CA, coverage from WY 1968–2014), (c) Redwood Creek South (data modeled using USGS gage on Elder Creek, CA, coverage from WY 1968–2014), and (d) Outlet Creek (USGS gage near Longvale, CA, coverage from WY 1957–1994). Data from WYs 1977, 1981, 1987–1989, and 1991–1994 are excluded from Outlet Creek watershed due to seven-day low flow values of zero at the gage. Water demand as a percentage of seven-day low flow would be >100% in these years, but we cannot determine by how much.</p

Sensitive aquatic species with ranges that overlap the four study watersheds: Upper Redwood Creek (URC), Redwood Creek South (RCS), Salmon Creek (SC), and Outlet Creek (OC).

<p>¹The California Department of Fish and Wildlife designates certain vertebrate species as Species of Special Concern (SSC) because declining population levels, limited ranges, and/or continuing threats have made them vulnerable to extinction. Though not listed pursuant to the Federal Endangered Species Act or the California Endangered Species Act, the goal of designating taxa as SSC is to halt or reverse these species’ decline by calling attention to their plight and addressing the issues of conservation concern early enough to secure their long-term viability.</p><p>² The California Natural Diversity Database (CNDDB) designates conservation status rank based on a one to five scale, one being “Critically Imperiled”, five being “Secure”. Uncertainty about a rank is expressed by a range of values, thus a status of S1S2 indicates that there is uncertainty about whether <i>Margaritifera falcata</i> ranks as state “Critically Imperiled” (S1) or state “Imperiled” (S2) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120016#pone.0120016.ref041" target="_blank">41</a>].</p><p>Sensitive aquatic species with ranges that overlap the four study watersheds: Upper Redwood Creek (URC), Redwood Creek South (RCS), Salmon Creek (SC), and Outlet Creek (OC).</p

Marijuana mapping summary of four watersheds.

<p>Marijuana mapping summary of four watersheds.</p

Upper Redwood Creek Watershed.

<p>Outdoor marijuana plantings are marked in red and greenhouses are marked in light green.</p