Return of non-ACMG recommended incidental genetic findings to pediatric patients: Considerations and opportunities from experiences in genomic sequencing

BACKGROUND: The uptake of exome/genome sequencing has introduced unexpected testing results (incidental findings) that have become a major challenge for both testing laboratories and providers. While the American College of Medical Genetics and Genomics has outlined guidelines for laboratory management of clinically actionable secondary findings, debate remains as to whether incidental findings should be returned to patients, especially those representing pediatric populations. METHODS: The Sequencing Analysis and Diagnostic Yield working group in the Clinical Sequencing Evidence-Generating Research Consortium has collected a cohort of pediatric patients found to harbor a genomic sequencing-identified non-ACMG-recommended incidental finding. The incidental variants were not thought to be associated with the indication for testing and were disclosed to patients and families. RESULTS: In total, 23 non-ACMG-recommended incidental findings were identified in 21 pediatric patients included in the study. These findings span four different research studies/laboratories and demonstrate differences in incidental finding return rate across study sites. We summarize specific cases to highlight core considerations that surround identification and return of incidental findings (uncertainty of disease onset, disease severity, age of onset, clinical actionability, and personal utility), and suggest that interpretation of incidental findings in pediatric patients can be difficult given evolving phenotypes. Furthermore, return of incidental findings can benefit patients and providers, but do present challenges. CONCLUSIONS: While there may be considerable benefit to return of incidental genetic findings, these findings can be burdensome to providers and present risk to patients. It is important that laboratories conducting genomic testing establish internal guidelines in anticipation of detection. Moreover, cross-laboratory guidelines may aid in reducing the potential for policy heterogeneity across laboratories as it relates to incidental finding detection and return. However, future discussion is required to determine whether cohesive guidelines or policy statements are warranted

Emissions of ozone-depleting halocarbons from China

National emission inventories of ozone-depleting substances (ODS) play a key role in the control mechanisms of the Montreal Protocol's emission reduction plans. New quasi-continuous ground-based atmospheric measurements allow us to estimate China's current emissions of the most effective ODS. This serves as an independent validation of China's ODS consumption data reported to the United Nations Environment Programme (UNEP). Emissions of most first-generation ODS have declined in recent years, suggesting compliance with the regulations of China's advanced phase-out program. In contrast the emissions of some second-generation ODS have increased. Because China is currently one of the largest consumers of first generation ODS, the country's upcoming complete phase-out will be crucial for the rate of decline of atmospheric ODS hence the eventual recovery of the stratospheric ozone. Citation: Vollmer, M. K., et al. (2009), Emissions of ozone-depleting halocarbons from China, Geophys. Res. Lett., 36, L15823, doi:10.1029/2009GL038659

HFC-23 (CHF3) emission trend response to HCFC-22 (CHClF2) production and recent HFC-23 emission abatement measures

HFC-23 (also known as CHF3 [CHF subscript 3], fluoroform or trifluoromethane) is a potent greenhouse gas (GHG), with a global warming potential (GWP) of 14 800 for a 100-year time horizon. It is an unavoidable by-product of HCFC-22 (CHClF2 [CHCIF subscript 2], chlorodifluoromethane) production. HCFC-22, an ozone depleting substance (ODS), is used extensively in commercial refrigeration and air conditioning, in the extruded polystyrene (XPS) foam industries (dispersive applications) and also as a feedstock in fluoropolymer manufacture (a non-dispersive use). Aside from small markets in specialty uses, HFC-23 has historically been considered a waste gas that was, and often still is, simply vented to the atmosphere. Efforts have been made in the past two decades to reduce HFC-23 emissions, including destruction (incineration) in facilities in developing countries under the United Nations Framework Convention on Climate Change's (UNFCCC) Clean Development Mechanism (CDM), and by process optimization and/or voluntary incineration by most producers in developed countries. We present observations of lower-tropospheric mole fractions of HFC-23 measured by "Medusa" GC/MSD instruments from ambient air sampled in situ at the Advanced Global Atmospheric Gases Experiment (AGAGE) network of five remote sites (2007–2009) and in Cape Grim air archive (CGAA) samples (1978–2009) from Tasmania, Australia. These observations are used with the AGAGE 2-D atmospheric 12-box model and an inverse method to produce model mole fractions and a "top-down" HFC-23 emission history. The model 2009 annual mean global lower-tropospheric background abundance is 22.6 (±0.2) pmol mol−1 [mol superscript -1]. The derived HFC-23 emissions show a "plateau" during 1997–2003, followed by a rapid ~50% increase to a peak of 15.0 (+1.3/−1.2) Gg/yr in 2006. Following this peak, emissions of HFC-23 declined rapidly to 8.6 (+0.9/−1.0) Gg/yr in 2009, the lowest annual emission of the past 15 years. We derive a 1990–2008 "bottom-up" HFC-23 emission history using data from the United Nations Environment Programme and the UNFCCC. Comparison with the top-down HFC-23 emission history shows agreement within the stated uncertainties. In the 1990s, HFC-23 emissions from developed countries dominated all other sources, then began to decline and eventually became fairly constant during 2003–2008. By this point, with developed countries' emissions essentially at a plateau, the major factor controlling the annual dynamics of global HFC-23 emissions became the historical rise of developing countries' HCFC-22 dispersive use production, which peaked in 2007. Thereafter in 2007–2009, incineration through CDM projects became a larger factor, reducing global HFC-23 emissions despite rapidly rising HCFC-22 feedstock production in developing countries.NASA Upper Atmospheric Research Program (Grant NNX07AE89G)NASA Upper Atmospheric Research Program (Grant NNX07AF09G)NASA Upper Atmospheric Research Program (Grant NNX07AE87G

An analytical inversion method for determining regional and global emissions of greenhouse gases: Sensitivity studies and application to halocarbons

A new analytical inversion method has been developed to determine the regional and global emissions of long-lived atmospheric trace gases. It exploits in situ measurement data from three global networks and builds on backward simulations with a Lagrangian particle dispersion model. The emission information is extracted from the observed concentration increases over a baseline that is itself objectively determined by the inversion algorithm. The method was applied to two hydrofluorocarbons (HFC-134a, HFC-152a) and a hydrochlorofluorocarbon (HCFC-22) for the period January 2005 until March 2007. Detailed sensitivity studies with synthetic as well as with real measurement data were done to quantify the influence on the results of the a priori emissions and their uncertainties as well as of the observation and model errors. It was found that the global a posteriori emissions of HFC-134a, HFC-152a and HCFC-22 all increased from 2005 to 2006. Large increases (21%, 16%, 18%, respectively) from 2005 to 2006 were found for China, whereas the emission changes in North America (−9%, 23%, 17%, respectively) and Europe (11%, 11%, −4%, respectively) were mostly smaller and less systematic. For Europe, the a posteriori emissions of HFC-134a and HFC-152a were slightly higher than the a priori emissions reported to the United Nations Framework Convention on Climate Change (UNFCCC). For HCFC-22, the a posteriori emissions for Europe were substantially (by almost a factor 2) higher than the a priori emissions used, which were based on HCFC consumption data reported to the United Nations Environment Programme (UNEP). Combined with the reported strongly decreasing HCFC consumption in Europe, this suggests a substantial time lag between the reported time of the HCFC-22 consumption and the actual time of the HCFC-22 emission. Conversely, in China where HCFC consumption is increasing rapidly according to the UNEP data, the a posteriori emissions are only about 40% of the a priori emissions. This reveals a substantial storage of HCFC-22 and potential for future emissions in China. Deficiencies in the geographical distribution of stations measuring halocarbons in relation to estimating regional emissions are also discussed in the paper. Applications of the inversion algorithm to other greenhouse gases such as methane, nitrous oxide or carbon dioxide are foreseen for the future

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes

BACKGROUND: DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their genomic targeting. However, whether this role of DNA methylation is important in the context of transcriptional regulation is unclear. RESULTS: By genome-wide mapping of the Polycomb Repressive Complex 2-signature histone mark, H3K27me3, in severely DNA hypomethylated mouse somatic cells, we show that hypomethylation leads to widespread H3K27me3 redistribution, in a manner that reflects the local DNA methylation status in wild-type cells. Unexpectedly, we observe striking loss of H3K27me3 and Polycomb Repressive Complex 2 from Polycomb target gene promoters in DNA hypomethylated cells, including Hox gene clusters. Importantly, we show that many of these genes become ectopically expressed in DNA hypomethylated cells, consistent with loss of Polycomb-mediated repression. CONCLUSIONS: An intact DNA methylome is required for appropriate Polycomb-mediated gene repression by constraining Polycomb Repressive Complex 2 targeting. These observations identify a previously unappreciated role for DNA methylation in gene regulation and therefore influence our understanding of how this epigenetic mechanism contributes to normal development and disease

Peroxisome Proliferator-Activated Receptor alpha (PPAR alpha) down-regulation in cystic fibrosis lymphocytes

Background: PPARs exhibit anti-inflammatory capacities and are potential modulators of the inflammatory response. We hypothesized that their expression and/or function may be altered in cystic fibrosis (CF), a disorder characterized by an excessive host inflammatory response. Methods: PPARα, β and γ mRNA levels were measured in peripheral blood cells of CF patients and healthy subjects via RT-PCR. PPARα protein expression and subcellular localization was determined via western blot and immunofluorescence, respectively. The activity of PPARα was analyzed by gel shift assay. Results: In lymphocytes, the expression of PPARα mRNA, but not of PPARβ, was reduced (-37%; p < 0.002) in CF patients compared with healthy persons and was therefore further analyzed. A similar reduction of PPARα was observed at protein level (-26%; p < 0.05). The transcription factor was mainly expressed in the cytosol of lymphocytes, with low expression in the nucleus. Moreover, DNA binding activity of the transcription factor was 36% less in lymphocytes of patients (p < 0.01). For PPARα and PPARβ mRNA expression in monocytes and neutrophils, no significant differences were observed between CF patients and healthy persons. In all cells, PPARγ mRNA levels were below the detection limit. Conclusion: Lymphocytes are important regulators of the inflammatory response by releasing cytokines and antibodies. The diminished lymphocytic expression and activity of PPARα may therefore contribute to the inflammatory processes that are observed in CF

Optimal estimation of the surface fluxes of methyl chloride using a 3-D global chemical transport model

Methyl chloride (CH3Cl) [CH subscript 3 Cl] is a chlorine-containing trace gas in the atmosphere contributing significantly to stratospheric ozone depletion. Large uncertainties in estimates of its source and sink magnitudes and temporal and spatial variations currently exist. GEIA inventories and other bottom-up emission estimates are used to construct a priori maps of the surface fluxes of CH3Cl [CH subscript 3 Cl]. The Model of Atmospheric Transport and Chemistry (MATCH), driven by NCEP interannually varying meteorological data, is then used to simulate CH3Cl [CH subscript 3 Cl] mole fractions and quantify the time series of sensitivities of the mole fractions at each measurement site to the surface fluxes of various regional and global sources and sinks. We then implement the Kalman filter (with the unit pulse response method) to estimate the surface fluxes on regional/global scales with monthly resolution from January 2000 to December 2004. High frequency observations from the AGAGE, SOGE, NIES, and NOAA/ESRL HATS in situ networks and low frequency observations from the NOAA/ESRL HATS flask network are used to constrain the source and sink magnitudes. The inversion results indicate global total emissions around 4100 ± 470 Gg yr−1 [yr superscript -1] with very large emissions of 2200 ± 390 Gg yr−1 [yr superscript -1] from tropical plants, which turn out to be the largest single source in the CH3Cl [CH subscript 3 Cl] budget. Relative to their a priori annual estimates, the inversion increases global annual fungal and tropical emissions, and reduces the global oceanic source. The inversion implies greater seasonal and interannual oscillations of the natural sources and sink of CH3Cl [CH subscript 3 Cl] compared to the a priori. The inversion also reflects the strong effects of the 2002/2003 globally widespread heat waves and droughts on global emissions from tropical plants, biomass burning and salt marshes, and on the soil sink.United States. National Aeronautics and Space Administration (Grant NNX07AE89G)United States. National Aeronautics and Space Administration (Grant NAG5-12669)United States. National Aeronautics and Space Administration (Grant NNX07AF09G)United States. National Aeronautics and Space Administration (Grant NNX07AE87G)National Science Foundation (U.S.) (Grant ATM-0120468)United States. National Aeronautics and Space Administration (Grant NAG5-12099

De novo intrachromosomal gene conversion from OPN1MW to OPN1LW in the male germline results in Blue Cone Monochromacy

X-linked cone dysfunction disorders such as Blue Cone Monochromacy and X-linked Cone Dystrophy are characterized by complete loss (of) or reduced L- and M- cone function due to defects in the OPN1LW/OPN1MW gene cluster. Here we investigated 24 affected males from 16 families with either a structurally intact gene cluster or at least one intact single (hybrid) gene but harbouring rare combinations of common SNPs in exon 3 in single or multiple OPN1LW and OPN1MW gene copies. We assessed twelve different OPN1LW/MW exon 3 haplotypes by semi-quantitative minigene splicing assay. Nine haplotypes resulted in aberrant splicing of ≥20% of transcripts including the known pathogenic haplotypes (i.e. ‘LIAVA’, ‘LVAVA’) with absent or minute amounts of correctly spliced transcripts, respectively. De novo formation of the ‘LIAVA’ haplotype derived from an ancestral less deleterious ‘LIAVS’ haplotype was observed in one family with strikingly different phenotypes among affected family members. We could establish intrachromosomal gene conversion in the male germline as underlying mechanism. Gene conversion in the OPN1LW/OPN1MW genes has been postulated, however, we are first to demonstrate a de novo gene conversion within the lineage of a pedigree

The Drosophila homolog of the mammalian imprint regulator, CTCF, maintains the maternal genomic imprint in Drosophila melanogaster

<p>Abstract</p> <p>Background</p> <p>CTCF is a versatile zinc finger DNA-binding protein that functions as a highly conserved epigenetic transcriptional regulator. CTCF is known to act as a chromosomal insulator, bind promoter regions, and facilitate long-range chromatin interactions. In mammals, CTCF is active in the regulatory regions of some genes that exhibit genomic imprinting, acting as insulator on only one parental allele to facilitate parent-specific expression. In <it>Drosophila</it>, CTCF acts as a chromatin insulator and is thought to be actively involved in the global organization of the genome.</p> <p>Results</p> <p>To determine whether CTCF regulates imprinting in <it>Drosophila</it>, we generated <it>CTCF </it>mutant alleles and assayed gene expression from the imprinted <it>Dp(1;f)LJ9 </it>mini-X chromosome in the presence of reduced <it>CTCF </it>expression. We observed disruption of the maternal imprint when <it>CTCF </it>levels were reduced, but no effect was observed on the paternal imprint. The effect was restricted to maintenance of the imprint and was specific for the <it>Dp(1;f)LJ9 </it>mini-X chromosome.</p> <p>Conclusions</p> <p>CTCF in <it>Drosophila </it>functions in maintaining parent-specific expression from an imprinted domain as it does in mammals. We propose that <it>Drosophila </it>CTCF maintains an insulator boundary on the maternal X chromosome, shielding genes from the imprint-induced silencing that occurs on the paternally inherited X chromosome.</p> <p>See commentary: <url>http://www.biomedcentral.com/1741-7007/8/104</url></p

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

The “arms race” relationship between transposable elements (TEs) and their host has promoted a series of epigenetic silencing mechanisms directed against TEs. Retrotransposons, a class of TEs, are often located in repressed regions and are thought to induce heterochromatin formation and spreading. However, direct evidence for TE–induced local heterochromatin in mammals is surprisingly scarce. To examine this phenomenon, we chose two mouse embryonic stem (ES) cell lines that possess insertionally polymorphic retrotransposons (IAP, ETn/MusD, and LINE elements) at specific loci in one cell line but not the other. Employing ChIP-seq data for these cell lines, we show that IAP elements robustly induce H3K9me3 and H4K20me3 marks in flanking genomic DNA. In contrast, such heterochromatin is not induced by LINE copies and only by a minority of polymorphic ETn/MusD copies. DNA methylation is independent of the presence of IAP copies, since it is present in flanking regions of both full and empty sites. Finally, such spreading into genes appears to be rare, since the transcriptional start sites of very few genes are less than one Kb from an IAP. However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness