| 1. |
- Bohlin, Pernilla, et al.
(författare)
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Evaluation and guidelines for using polyurethane foam (PUF) passive air samplers in double-dome chambers to assess semi-volatile organic compounds (SVOCs) in non-industrial indoor environments
- 2014
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Ingår i: Environmental Science. - : Royal Society of Chemistry. - 2050-7887 .- 2050-7895. ; 16:11, s. 2617-2626
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Tidskriftsartikel (refereegranskat)abstract
- Indoor air pollution has been recognized as an important risk factor for human health, especially in areas where people tend to spend most of their time indoors. Many semi-volatile organic compounds (SVOCs) have primarily indoor sources and are present in orders of magnitude higher concentrations indoors than outdoors. Despite this, awareness of SVOCs in indoor air and assessment of the link between indoor concentrations and human health have tagged behind those of outdoor air. This is partially related to challenges associated with indoor sampling of SVOCs. Passive air samplers (PASs), which are widely accepted in established outdoor air monitoring networks, have been used to fill the knowledge gaps on indoor SVOCs distribution. However, their applicability for indoor environments and the assessment of human health risks lack sufficient experimental data. To address this issue, we performed an indoor calibration study of polyurethane foam (PUF) PAS deployed in a double-dome chamber, covering both legacy and new SVOC classes. PUF-PAS and a continuous low-volume active air sampler (AAS) were co-deployed for a calibration period of twelve weeks. Based on the results from this evaluation, PUF-PAS in a double-bowl chamber is recommended for indoor sampling and health risk assessment of gas phase SVOCs, including novel brominated flame retardants (nBFR) providing sufficient exposure time is applied. Data for particle associated SVOCs suffered from significant uncertainties caused by low level of detection and low precision in this study. A more open chamber design for indoor studies may allow for higher sampling rates (R-s) and better performance for the particle associated SVOCs.
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| 2. |
- Bohlin, P., et al.
(författare)
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Outdoor passive air monitoring of semi volatile organic compounds (SVOCs) : a critical evaluation of performance and limitations of polyurethane foam (PUF) disks
- 2014
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Ingår i: Environmental Science. - : Royal Society of Chemistry (RSC). - 2050-7887 .- 2050-7895. ; 16:3, s. 433-444
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Tidskriftsartikel (refereegranskat)abstract
- The most commonly used passive air sampler (PAS) (i.e. polyurethane foam (PUF) disk) is cheap, versatile, and capable of accumulating compounds present both in gas and particle phases. Its performance for particle associated compounds is however disputable. In this study, twelve sets of triplicate PUF-PAS were deployed outdoors for exposure periods of 1-12 weeks together with continuously operated active samplers, to characterize sampling efficiency and derive sampling rates (R-S) for compounds belonging to 7 SVOC classes (including particle associated compounds). PUF-PAS efficiently and consistently sampled polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), polycyclic aromatic hydrocarbons (PAHs), and eight novel brominated flame retardant (nBFR) compounds. Low accuracy and lack of sensitivity was observed for most polychlorinated dibenzo-p-dioxins/furans PCDD/Fs and polybrominated diphenyl ethers (PBDEs) (under the conditions of this study), with the exception of some congeners which may be used as qualitative markers for their respective classes. Application of compound specific R-S was found crucial for all compounds except PCBs. Sampling efficiency of the particle associated compounds was often low.
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| 3. |
- Čechová, Eliška, et al.
(författare)
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An effective clean-up technique for GC/EI-HRMS determination of developmental neurotoxicants in human breast milk
- 2017
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Ingår i: Analytical and Bioanalytical Chemistry. - Heidelberg, Germany : Springer Berlin/Heidelberg. - 1618-2642 .- 1618-2650. ; 409:5, s. 1311-1322
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Tidskriftsartikel (refereegranskat)abstract
- The increasing number of children suffering from developmental disorders has raised questions regarding their association with the presence of environmental contaminants in mothers and children. We therefore developed a new method for the determination of 78 proven and potential developmental neurotoxicants, including polychlorinated biphenyls, legacy pesticides, pyrethroids, and old and new halogenated flame retardants in breast milk. The essential part of sample preparation was dialysis as a non-destructive clean-up step which was newly used at 10 °C and showed more efficient lipid removal (up to 96%) than the conventional methods such as gel permeation chromatography or freezing-lipid filtration and thus ensured low limits of detection (LOD) by reducing the sample volume prior to injection. Next advantages were significant solvent reduction and no risk of sample cross-contamination. Gas chromatography coupled with high resolution mass spectrometry (GC-HRMS) was subsequently used for the separation and compound quantification. The method was validated using breast milk samples fortified with the analyzed compounds. Recoveries for most of the compounds ranged from 63 to 121% with a relative standard deviation of 2-25%, and LODs ranged between 0.001 and 0.87 ng g(-1) lipid weight. The method was applied to breast milk samples from a Dutch birth cohort where 35 out of the 78 compounds were quantified in more than 60% of the samples. For novel flame retardants, the method provides unique results regarding their occurrence in human matrices in Europe. Overall, the analysis of a complex mixture of developmental neurotoxicants could be useful for the assessment of the influence of the studied compounds to child health and development. Graphical abstract Flow diagram of the method and levels of the developmental neurotoxicants in Dutch human milk samples.
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| 4. |
- Fang, Li Tai, et al.
(författare)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Tidskriftsartikel (refereegranskat)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 5. |
- Okonski, Krzysztof, et al.
(författare)
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Particle size distribution of halogenated flame retardants and implications for atmospheric deposition and transport
- 2014
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 48:24, s. 14426-14434
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Tidskriftsartikel (refereegranskat)abstract
- This study investigates the distribution of polybrominated diphenyl ethers (PBDEs), hexabromocyclododecane (HBCD) and a group of novel flame retardants (NFRs) on atmospheric aerosols. Two high volume cascade impactors were used to collect particulate fractions of ambient air over a one year period at urban and rural sites. The majority of FRs were found on the finest aerosols (<0.95 mu m). Concentrations of HBCD were higher than those of SPBDEs. Moreover, we noted seasonality and spatial differences in particle size distributions, yet a large portion of the observed differences were due to differences in particulate matter (PM) itself. When normalized by PM, the size distributions of the FRs exhibited much greater heterogeneity. Differences existed between the FR distributions by molecular weight, with the higher molecular weight FRs (e.g., BDE-209, Dechlorane Plus) distributed more uniformly across all particulate size fractions. The seasonal, spatial, and compound-specific differences are of crucial importance when estimating dry and wet deposition of FRs as smaller aerosols have longer atmospheric residence times. Estimated wet and dry deposition of four representative FRs (BDE-47, BDE-209, HBCD, and Dechlorane Plus) using size-segregated aerosol data resulted in lower deposition estimates than when bulk aerosol data were used. This has implications for estimates of long-range atmospheric transport and atmospheric residence times, as it suggests that without size-specific distributions, these parameters could be underestimated for FRs.
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| 6. |
- Xiao, Wenming, et al.
(författare)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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| 7. |
- Zhao, Yongmei, et al.
(författare)
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Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study
- 2021
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- With the rapid advancement of sequencing technologies, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best practices in cancer mutation detection using NGS and the need for standard reference data sets for systematically measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples and generated whole-genome (WGS) and whole-exome sequencing (WES) data using sixteen library protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.
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