Laser-irradiating infrared attenuated total reflection spectroscopy of articular cartilage: Potential and challenges for diagnosing osteoarthritis

Objective

A prototype infrared attenuated total reflection (IR-ATR) laser spectroscopic system designed for in vivo classification of human cartilage tissue according to its histological health status during arthroscopic surgery is presented. Prior to real-world in vivo applications, this so-called osteoarthritis (OA) scanner has been tested at in vitro conditions revealing the challenges associated with complex sample matrices and the accordingly obtained sparse spectral datasets.

Methods

In vitro studies on human knee cartilage samples at different contact pressures (i.e., 0.2-0.5 ​MPa) allowed recording cartilage degeneration characteristic IR signatures comparable to in vivo conditions with high temporal resolution. Afterwards, the cartilage samples were assessed based on the clinically acknowledged osteoarthritis cartilage histopathology assessment (OARSI) system and correlated with the obtained sparse IR data.

Results

Amide and carbohydrate signal behavior was observed to be almost identical between the obtained sparse IR data and previously measured FTIR data used for sparse partial least squares discriminant analysis (SPLSDA) to identify the spectral regions relevant to cartilage condition. Contact pressures between 0.3 and 0.4 ​MPa seem to provide the best sparse IR spectra for cylindrical (d ​= ​3 ​mm) probe tips.

Conclusion

Laser-irradiating IR-ATR spectroscopy is a promising analytical technique for future arthroscopic applications to differentiate healthy and osteoarthritic cartilage tissue. However, this study also revealed that the flexible connection between the laser-based analyzer and the arthroscopic ATR-probe via IR-transparent fiberoptic cables may affect the robustness of the obtained IR data and requires further improvements.

'It's a nightmare': informed consent in paediatric genome-wide sequencing. A qualitative expert interview study from Germany and Switzerland

The use of genome-wide sequencing (GWS) in paediatrics has added complexity to informed consent (IC) and pretest counselling because of the vast number and interpretation of potential findings, and their implications. However, empirical data from continental Europe on these issues remains limited. This study therefore aimed to explore the experiences and views of medical geneticists working with children in Germany and Switzerland regarding the challenges of obtaining valid IC in paediatric GWS. Qualitative interviews with 20 medical geneticists were analysed employing reflexive thematic analysis. In the interviews, many medical geneticists questioned the validity of parents' IC due to the enormous amount of relevant information given and the variety and complexity of the possible test outcomes. Key barriers identified included familial implications, administrative challenges and struggles with non-directiveness. Medical geneticists' suggestions for improvement included increasing the number of genetics professionals and better information material, which is crucial as GWS becomes a diagnostic standard in the early care pathways of children. An adjustment of aspirations from still existing ideal of traditional fully IC to appropriate IC seems to be needed. Such a more realistic and ethically sound adaptation of the requirements for IC can lead to better 'informedness' and improve the validity of the consent. This might also help reduce the moral distress for the medical geneticists involved.

Newspaper coverage on solidarity and personal responsibility in the COVID-19 pandemic: A content analysis from Germany and German-speaking Switzerland

Solidarity and personal responsibility have been repeatedly called upon during the COVID-19 pandemic. This study quantifies and contextualizes the use of these terms in newspaper coverage in Germany and German-speaking Switzerland based on n = 640 articles from six functionally equivalent newspapers. The term solidarity in the context of the COVID-19 pandemic was mentioned in 541/640 articles (84.5%) and was primarily used during phases with high death rates and comparatively stringent policies in place, supporting the idea that solidarity was used to explain restrictive measures to the population and motivate people to comply with these measures. German newspapers published more articles on solidarity than Swiss-German newspapers, consistent with more stringent COVID-19 policies in Germany. Personal responsibility was mentioned in 133/640 articles (20.8%), meaning that the term was less frequently discussed than solidarity. Articles covering personal responsibility included more negative evaluations during phases of high infection rates as compared to phases of low infection rates. Findings indicate that the two terms were, at least to some extent, used in newspaper reporting to contextualize and justify COVID-19 policy during phases of high infection rates. Moreover, the term solidarity was used in a high variety of different contexts and the inherent limits of solidarity were rarely mentioned. Policymakers and journalists need to take this into account for future crises to not jeopardize the positive effects of solidarity.

The COVID-19 Vaccine: Trust, doubt, and hope for a future beyond the pandemic in Germany

Public perceptions of COVID-19 vaccines are critical in reaching protective levels of herd immunity. Vaccine skepticism has always been relatively high in Germany, and surveys suggest that over the course of the pandemic, enthusiasm for the COVID-19 vaccine has dropped. Looking at the period just prior to the approval of the Pfizer/BioNTech and Moderna vaccines in Germany in the latter half of 2020, this paper aims to assess the reasons for and against COVID-19 vaccine uptake among residents of Germany, and to provide in-depth qualitative data to better understand and address concerns surrounding the safety and efficacy of a COVID-19 vaccine. Our findings indicate that there is widespread trust in German institutions and health experts to provide a safe vaccine for those who need it most. However, interviewees also point to the need for more information and the centrality of support from trusted medical authorities in making individual vaccination decisions. We also present the complexity of individual positions on vaccination, and suggest that vaccine hesitancy in relation to COVID-19 needs to be understood as a nuanced, and socially malleable, territory. This indicates that the goal of a vaccination campaign is not only achieving ‘herd immunity,’ but also a social endorsement of the collaborative effort that is required for a vaccine to be successful.

The second pandemic: Examining structural inequality through reverberations of COVID-19 in Europe

While everyone has been impacted directly or indirectly by the COVID-19 pandemic and the measures to contain it, not everyone has been impacted in the same way and certainly not to the same degree. Media coverage in early 2020 emphasized the “unprecedented” nature of the pandemic, and some even predicted that the virus could be a global “equalizer.” Ensuing debates over how the pandemic should be handled have often hinged on oppositions between protecting health and healthcare systems versus saving livelihoods and the economy, a dichotomy that we argue is false. Drawing on 482 interviews conducted in Germany, Italy, Ireland, Austria, German-speaking Switzerland and the UK over two points in a 6-month period as part of the ‘Solidarity in times of Pandemics Research Consortium’ (SolPan), we illustrate the ways that oppositions posed between saving lives or saving livelihoods fail to capture the entangled, long-standing nature of structural inequalities that have been revealed through the pandemic. Health- and wealth-related inequalities intersect to produce the “second pandemic,” a term used by a research participant to explain the other forms of devastation that run in parallel with virus. Our findings thus complicate such dichotomies through a qualitative understanding of the pandemic as a lived experience. The pandemic emerges as a critical juncture which, in exacerbating these existing structural inequalities, also poses an opportunity to work to better resolve them.

The full spectrum of ethical issues in pediatric genome-wide sequencing: a systematic qualitative review

Background

The use of genome-wide sequencing in pediatric medicine and research is growing exponentially. While this has many potential benefits, the normative and empirical literature has highlighted various ethical issues. There have not been, however, any systematic reviews of these issues. The aim of this systematic review is to determine systematically the spectrum of ethical issues that is raised for stakeholders in in pediatric genome-wide sequencing.

Methods

A systematic review in PubMed and Google Books (publications in English or German between 2004 and 2021) was conducted. Further references were identified via reference screening. Data were analyzed and synthesized using qualitative content analysis. Ethical issues were defined as arising when a relevant normative principle is not adequately considered or when two principles come into conflict.

Results

Our literature search retrieved 3175 publications of which 143 were included in the analysis. Together these mentioned 106 ethical issues in pediatric genome-wide sequencing, categorized into five themes along the pediatric genome-wide sequencing lifecycle. Most ethical issues identified in relation to genome-wide sequencing typically reflect ethical issues that arise in general genetic testing, but they are often amplified by the increased quantity of data obtained, and associated uncertainties. The most frequently discussed ethical aspects concern the issue of unsolicited findings.

Conclusion

Concentration of the debate on unsolicited findings risks overlooking other ethical challenges. An overarching difficulty presents the terminological confusion: both with regard to both the test procedure/ the scope of analysis, as well as with the topic of unsolicited findings. It is important that the genetics and ethics communities together with other medical professions involved work jointly on specific case related guidelines to grant the maximum benefit for the care of the children, while preventing patient harm and disproportionate overload of clinicians and the healthcare system by the wealth of available options and economic incentives to increase testing.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-021-02830-w.

Genetic and phylogeographic evidence for Jewish Holocaust victims at the Sobibór death camp

Six million Jews were killed by Nazi Germany and its collaborators during World War II. Archaeological excavations in the area of the death camp in Sobibór, Poland, revealed ten sets of human skeletal remains presumptively assigned to Polish victims of the totalitarian regimes. However, their genetic analyses indicate that the remains are of Ashkenazi Jews murdered as part of the mass extermination of European Jews by the Nazi regime and not of otherwise hypothesised non-Jewish partisan combatants. In accordance with traditional Jewish rite, the remains were reburied in the presence of a Rabbi at the place of their discovery.

Acute and transitional care or rehabilitation? Retrospective analysis of discharge planning from a municipal hospital in Switzerland

Background

Due to rising health care costs, in 2012 Switzerland introduced SwissDRG, a reimbursement system for hospitals based on lump sum per case. To circumvent possible negative consequences like reduction in length of stay, acute and transitional care (ATC) was anchored into the law (Federal act on health insurance) in 2011. ATC as a discharge option is applicable to patients who physicians deem will not fulfill rehabilitation criteria, but are unable to return home and are in need of temporary professional nursing care. ATC is associated with higher out of pocket costs to the patient than rehabilitation. Since social service workers are responsible for organizing discharge for patients with ongoing care needs after hospitalization, the aim of this study was to investigate how social service workers manage patient discharge in light of the new discharge option ATC.

Methods

Data was collected from 423 medical records of inpatients from Zurich’s municipal hospital, Triemli, discharged to ATC or rehabilitation, in 2016. We compared the two groups using inferential statistics and qualitatively analyzed written statements from social service workers.

Results

Our results showed that patients discharged to rehabilitation had a higher total number of discussions, but a shorter duration of discussions. Patients discharged to rehabilitation faced more delays, mainly due to unavailability of beds in rehabilitation centers. Conflicts concerning discharge arose mainly because of costs, discharge placement and too early discharge.

Conclusions

Our findings demonstrate how important social service workers are in providing information to patients about different discharge options. The newness of SwissDRG and ATC is still likely to cause longer discussion times and, consequently, more workload for social service workers. Only a small fraction of patients disagreed with their place of discharge, mostly due to financial reasons.

Media Coverage of Ethical Issues in Predictive Genetic Testing: A Qualitative Analysis

Background: Predictive genetic testing (PGT) raises many ethical issues and is of increasing interest to the general population. Mass media, especially newspapers, are the public's main source of information on this topic. Methods: We conducted a content analysis of British newspaper reporting, assessing which ethical issues were mentioned. The analysis was qualitative with semi-quantitative aspects. All articles about PGT published in The Guardian and the Daily Telegraph from 2011 to 2016 were included. Results: Most ethical issues discussed in the scientific and ethical literature are implicitly or explicitly covered in newspapers, but there was no discussion of incidental findings and the possibility of false reassurance of a negative test result was mentioned only once. There are also important gaps regarding the multidimensional nature and complexity of many issues. The Guardian mentioned ethical issues more frequently than the Daily Telegraph. Most ethical issues were portrayed as first-person narratives. Conclusions: Ethical issues concern potential test users and society more than scientific background knowledge about such tests; therefore, more efforts should be taken to address these complex issues in a manner that is comprehensible for the lay public.

Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel

The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.

Deubiquitinase USP10 regulates Notch signaling in the endothelium

Notch signaling is a core patterning module for vascular morphogenesis that codetermines the sprouting behavior of endothelial cells (ECs). Tight quantitative and temporal control of Notch activity is essential for vascular development, yet the details of Notch regulation in ECs are incompletely understood. We found that ubiquitin-specific peptidase 10 (USP10) interacted with the NOTCH1 intracellular domain (NICD1) to slow the ubiquitin-dependent turnover of this short-lived form of the activated NOTCH1 receptor. Accordingly, inactivation of USP10 reduced NICD1 abundance and stability and diminished Notch-induced target gene expression in ECs. In mice, the loss of endothelial Usp10 increased vessel sprouting and partially restored the patterning defects caused by ectopic expression of NICD1. Thus, USP10 functions as an NICD1 deubiquitinase that fine-tunes endothelial Notch responses during angiogenic sprouting.

Suitability of Wild Boar (Sus scrofa) as a Bioindicator for Environmental Pollution with Perfluorooctanoic Acid (PFOA) and Perfluorooctanesulfonic Acid (PFOS)

Wildlife species, such as roe deer, moose, brown hare, wild boar, etc., are known to accumulate persistent environmental contaminants and thus are useful as bioindicators for environmental pollution. Wild boars become exposed to perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) from flora, fauna, water, and soil. The main exposure pathway to PFOA and PFOS is assumed to be the oral intake. From studies in domestic pigs (belonging to the same species Sus scrofa), it has been established that the oral exposure results in the liver accumulation of PFOA and PFOS. Thus, we posit that wild boars can be quantitatively used as suitable bioindicators for the presence of these substances in the environment. After the environmental pollution case in the Hessian region Sauerland in 2006, monitoring programs of individual Federal States from 2007 to 2013 showed that almost all wild boar liver samples contained PFOA and PFOS. In 2014, the analyses of PFOA and PFOS in liver of wild boars hunted in the south, north, and west of Germany showed liver concentrations at the same level among regions. Overall, an average ratio of PFOS:PFOA concentration in liver of 20.5:1 was found. To estimate the actual ratio of PFOS:PFOA in the wild boars' dietary exposure, we performed toxicokinetic modeling. According to the model, the PFOS exposure is only 2.2 times that of PFOA (because PFOS has slower elimination kinetics and higher affinity for the liver than PFOA). Overall, the determination of PFOA and PFOS in liver of wild boars indicates that both substances are ubiquitously distributed in the environment. At the same time, higher exposures were found for animals living in closer proximity to dense human populations.

Observation of Mie ripples in the synchrotron Fourier transform infrared spectra of spheroidal pollen grains

Conceptually, biological cells are dielectric, photonic resonators that are expected to show a rich variety of shape resonances when exposed to electromagnetic radiation. For spheroidal cells, these shape resonances may be predicted and analyzed using the Mie theory of dielectric spheres, which predicts that a special class of resonances, i.e., whispering gallery modes (WGMs), causes ripples in the absorbance spectra of spheroidal cells. Indeed, the first tentative indication of the presence of Mie ripples in the synchrotron Fourier transform infrared (SFTIR) absorbance spectra of Juniperus chinensis pollen has already been reported [Analyst140, 3273 (2015)ANLYAG0365-488510.1039/C5AN00401B]. To show that this observation is no isolated incidence, but a generic spectral feature that can be expected to occur in all spheroidal biological cells, we measured and analyzed the SFTIR absorbance spectra of Cunninghamia lanceolata, Juniperus chinensis, Juniperus communis, and Juniperus excelsa. All four pollen species show Mie ripples. Since the WGMs causing the ripples are surface modes, we propose ripple spectroscopy as a powerful tool for studying the surface properties of spheroidal biological cells. In addition, our paper draws attention to the fact that shape resonances need to be taken into account when analyzing (S)FTIR spectra of isolated biological cells since shape resonances may distort the shape or mimic the presence of chemical absorption bands.

Gene Expression of Quaking in Sporadic Alzheimer's Disease Patients is Both Upregulated and Related to Expression Levels of Genes Involved in Amyloid Plaque and Neurofibrillary Tangle Formation

Quaking (QKI) is a gene exclusively expressed within glial cells. QKI has previously been implicated in various neurological disorders and diseases, including Alzheimer’s disease (AD), a condition for which increasing evidence suggests a central role of glia cells. The objective of the present study was to investigate the expression levels of QKI and three QKI isoforms (QKI5, QKI6, and QKI7) in AD. Genes that have previously been related to the ontogeny and progression of AD, specifically APP, PSEN1, PSEN2, and MAPT, were also investigated. A real-time PCR assay of 123 samples from human postmortem sporadic AD patients and control brains was performed. The expression values were analyzed with an analysis of covariance model and subsequent multiple regressions to explore the possibility of related expression values between QKI, QKI isoforms, and AD-related genes. Further, the sequences of AD-related genes were analyzed for the presence of QKI binding domains. QKI and all measured QKI isoforms were found to be significantly upregulated in AD samples, relative to control samples. However, APP, PSEN1, PSEN2, and MAPT were not found to be significantly different. QKI and QKI isoforms were found to be predictive for the variance of APP, PSEN1, PSEN2, and MAPT, and putative QKI binding sites suggests an interaction with QKI. Overall, these results implicate a possible role of QKI in AD, although the exact mechanism by which this occurs remains to be uncovered.

Hospital discharge of patients with ongoing care needs: a cross-sectional study using data from a city hospital under SwissDRG

AIM OF THE STUDY

Switzerland introduced the SwissDRG in 2012. The goal of this reimbursement system was to promote cost containment and efficiency in hospital care. To ensure that patients with care needs are not released prematurely because of constraints under the new hospital financing system, the Swiss law on Acute and Transitional Care (ATC) was introduced one year earlier. The objective of the present study was to investigate the impact of ATC and its effects on discharge of patients with persisting care needs after hospitalisation.

METHODS

Social service workers, nurses and palliative care team members at a Swiss municipal hospital were asked to complete a four-page closed-ended questionnaire about patients who require care after their hospital discharge. This included questions on discharge management, their perceptions of the appropriateness of discharge timing and details about conflicts regarding discharge. Information on length of stay, discharge location, age and sex was extracted from hospital records and matched to the information from the questionnaires. Demographic data are presented descriptively, differences between patients released to ATC and patients released elsewhere (home, nursing home, rehabilitation, etc.) were evaluated with chi-square tests. Logistic regression analyses were performed to evaluate differences between those sent to ATC and rehabilitation with age, length of stay and sex as predictors.

RESULTS

A total 1410 of valid questionnaires were collected, comprised of 746 female patients (52.9%) and 664 male patients (47.1%). The mean age of our patient cohort was 73.2 years (SD 15.1), and the mean hospital stay was 12.8 days (SD 9.1). After their hospital stay, 553 patients (39.2%) returned home either alone, or with the help of family members or Spitex. More than a quarter of the sample, 387 (27.4%) patients, was sent to rehabilitation. Less than a fifth, 199 (14.1%) patients, received ATC in an inpatient institution (e.g., nursing home). Compared with patients released elsewhere, significantly more problems/conflicts with regard to hospital discharge were reported for ATC patients (28.6 vs 20.6%, p = 0.01) and their relatives (12.6 vs 7.2%, p = 0.01). Women had a higher probability of being discharged to ATC (OR 1.522, p = 0.014) and a lower chance of receiving rehabilitation upon discharge (OR 0.733, p = 0.014).

CONCLUSION

The study identified important concerns related to receiving ATC after a hospital stay, that is, more problems/conflicts occur with patients discharged to ATC and that the introduction of ATC might particularly disadvantage female patients, who are less likely to receive rehabilitation care.

QKI6B mRNA levels are upregulated in schizophrenia and predict GFAP expression

Schizophrenia is a highly heritable disorder with a heterogeneous symptomatology. Research increasingly indicates the importance of the crucial and often overlooked glial perturbations within schizophrenia. Within this study, we examined an isoform of quaking (a gene encoding an RNA-binding protein that is exclusively expressed in glial cells), known as QKI6B, and a prototypical astrocyte marker, glial fibrillary acidic protein (GFAP), postulated to be under the regulation of QKI. The expression levels of these genes were quantified across post-mortem brain samples from 55 schizophrenic individuals, and 55 healthy controls, using real-time PCR. We report, through an analysis of covariance (ANCOVA) model, an upregulation of both QKI6B, and GFAP in the prefrontal cortex of brain samples of schizophrenic individuals, as compared to control samples. Previous research has suggested that the QKI protein directly regulates the expression of several genes through interaction with a motif in the target's sequence, termed the Quaking Response Element (QRE). We therefore examined if QKI6B expression can predict the outcome of GFAP, and several oligodendrocyte-related genes, using a multiple linear regression approach. We found that QKI6B significantly predicts the expression of GFAP, but does not predict oligodendrocyte-related gene outcome, as previously seen with other QKI isoforms.

Lack of gene-language correlation due to reciprocal female but directional male admixture in Austronesians and non-Austronesians of East Timor

Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene-language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene-language correlation in this region. Aiming to investigate gene-language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN- and NAN-speaking groups. Y-SNP (single-nucleotide polymorphism) data were newly generated for 273 samples and combined with previously established Y-STR (short tandem repeat) data of the same samples, and with previously established mtDNA data of 290 different samples with, however, very similar representation of geographic and linguistic coverage of the country. We found NRY and mtDNA haplogroups of previously described putative East/Southeast Asian (E/SEA) and Near Oceanian (NO) origins in both AN and NAN speakers of East Timor, albeit in different proportions, suggesting reciprocal genetic admixture between both linguistic groups for females, but directional admixture for males. Our data underline the dual genetic origin of East Timorese in E/SEA and NO, and highlight that substantial genetic admixture between the two major linguistic groups had occurred, more so via women than men. Our study therefore provides another example where languages and genes do not conform due to sex-biased genetic admixture across major linguistic groups.

Testing Hadronic Interactions at Ultrahigh Energies with Air Showers Measured by the Pierre Auger Observatory

Ultrahigh energy cosmic ray air showers probe particle physics at energies beyond the reach of accelerators. Here we introduce a new method to test hadronic interaction models without relying on the absolute energy calibration, and apply it to events with primary energy 6-16 EeV (E_{CM}=110-170  TeV), whose longitudinal development and lateral distribution were simultaneously measured by the Pierre Auger Observatory. The average hadronic shower is 1.33±0.16 (1.61±0.21) times larger than predicted using the leading LHC-tuned models EPOS-LHC (QGSJetII-04), with a corresponding excess of muons.

Measurement of the Radiation Energy in the Radio Signal of Extensive Air Showers as a Universal Estimator of Cosmic-Ray Energy

We measure the energy emitted by extensive air showers in the form of radio emission in the frequency range from 30 to 80 MHz. Exploiting the accurate energy scale of the Pierre Auger Observatory, we obtain a radiation energy of 15.8±0.7(stat)±6.7(syst)  MeV for cosmic rays with an energy of 1 EeV arriving perpendicularly to a geomagnetic field of 0.24 G, scaling quadratically with the cosmic-ray energy. A comparison with predictions from state-of-the-art first-principles calculations shows agreement with our measurement. The radiation energy provides direct access to the calorimetric energy in the electromagnetic cascade of extensive air showers. Comparison with our result thus allows the direct calibration of any cosmic-ray radio detector against the well-established energy scale of the Pierre Auger Observatory.

Detection of ubiquitous and heterogeneous mutations in cell-free DNA from patients with early-stage non-small-cell lung cancer

BACKGROUND

The aim of this pilot study was to assess whether both ubiquitous and heterogeneous somatic mutations could be detected in cell-free DNA (cfDNA) from patients with early-stage non-small-cell lung cancer (NSCLC).

PATIENTS AND METHODS

Three stage I and one stage II primary NSCLC tumors were subjected to multiregion whole-exome sequencing (WES) and validated with AmpliSeq. A subset of ubiquitous and heterogeneous single-nucleotide variants (SNVs) were chosen. Multiplexed PCR using custom-designed primers, coupled with next-generation sequencing (mPCR-NGS), was used to detect these SNVs in both tumor DNA and cfDNA isolated from plasma obtained before surgical resection of the tumors. The limit of detection for each assay was determined using cfDNA from 48 presumed-normal healthy volunteers.

RESULTS

Tumor DNA and plasma-derived cfDNA was successfully amplified and sequenced for 37/50 (74%) SNVs using the mPCR-NGS method. Twenty-five (68%) were ubiquitous and 12 (32%) were heterogeneous SNVs. Variant detection by mPCR-NGS and WES-AmpliSeq in tumor tissue was well correlated (R(2) = 0.8722, P < 0.0001). Sixteen (43%) out of 37 SNVs were detected in cfDNA. Twelve of these were ubiquitous SNVs with a variant allele frequency (VAF) range of 0.15-23.25%, and four of these were heterogeneous SNVs with a VAF range of 0.28-1.71%. There was a statistically significant linear relationship between the VAFs for tumor and cfDNA (R(2) = 0.5144; P = 0.0018). For all four patients, at least two variants were detected in plasma. The estimated number of copies of variant DNA present in each sample ranged from 5 to 524. The average number of variant copies required for detection (VCRD) was 3.16 (range: 0.2-7.6 copies).

CONCLUSIONS

The mPCR-NGS method revealed intratumor heterogeneity in early-stage NSCLC tumors, and was able to detect both ubiquitous and heterogeneous SNVs in cfDNA. Further validation of mPCR-NGS in cfDNA is required to define its potential use in clinical practice.

Clinical experience with single-nucleotide polymorphism-based non-invasive prenatal screening for 22q11.2 deletion syndrome

OBJECTIVES

To evaluate the performance of a single-nucleotide polymorphism (SNP)-based non-invasive prenatal test (NIPT) for the detection of fetal 22q11.2 deletion syndrome in clinical practice, assess clinical follow-up and review patient choices for women with high-risk results.

METHODS

In this study, 21 948 samples were submitted for screening for 22q11.2 deletion syndrome using a SNP-based NIPT and subsequently evaluated. Follow-up was conducted for all cases with a high-risk result.

RESULTS

Ninety-five cases were reported as high risk for fetal 22q11.2 deletion. Diagnostic testing results were available for 61 (64.2%) cases, which confirmed 11 (18.0%) true positives and identified 50 (82.0%) false positives, resulting in a positive predictive value (PPV) of 18.0%. Information regarding invasive testing was available for 84 (88.4%) high-risk cases: 57.1% (48/84) had invasive testing and 42.9% (36/84) did not. Ultrasound anomalies were present in 81.8% of true-positive and 18.0% of false-positive cases. Two additional cases were high risk for a maternal 22q11.2 deletion; one was confirmed by diagnostic testing and one had a positive family history. There were three pregnancy terminations related to screening results of 22q11.2 deletion, two of which were confirmed as true positive by invasive testing.

CONCLUSIONS

Clinical experience with this SNP-based non-invasive screening test for 22q11.2 deletion syndrome indicates that these deletions have a frequency of approximately 1 in 1000 in the referral population with most identifiable through this test. Use of this screening method requires the availability of counseling and other management resources for high-risk pregnancies.

High-quality mtDNA control region sequences from 680 individuals sampled across the Netherlands to establish a national forensic mtDNA reference database

The use of mitochondrial DNA (mtDNA) for maternal lineage identification often marks the last resort when investigating forensic and missing-person cases involving highly degraded biological materials. As with all comparative DNA testing, a match between evidence and reference sample requires a statistical interpretation, for which high-quality mtDNA population frequency data are crucial. Here, we determined, under high quality standards, the complete mtDNA control-region sequences of 680 individuals from across the Netherlands sampled at 54 sites, covering the entire country with 10 geographic sub-regions. The complete mtDNA control region (nucleotide positions 16,024-16,569 and 1-576) was amplified with two PCR primers and sequenced with ten different sequencing primers using the EMPOP protocol. Haplotype diversity of the entire sample set was very high at 99.63% and, accordingly, the random-match probability was 0.37%. No population substructure within the Netherlands was detected with our dataset. Phylogenetic analyses were performed to determine mtDNA haplogroups. Inclusion of these high-quality data in the EMPOP database (accession number: EMP00666) will improve its overall data content and geographic coverage in the interest of all EMPOP users worldwide. Moreover, this dataset will serve as (the start of) a national reference database for mtDNA applications in forensic and missing person casework in the Netherlands.

Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity

BACKGROUND

Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice.

RESULTS

In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya.

CONCLUSIONS

The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.

A laboratory study of the performance of the handheld diffusion size classifier (DiSCmini) for various aerosols in the 15-400 nm range

In addition to chemical composition, particle concentration and size are among the main parameters used to characterize exposure to airborne ultrafine or nanoparticles. To assess occupational inhalation exposure, real-time instruments are recommended in recent strategies published. Among portable devices for personal exposure assessment in the workplace, DiSCmini (Matter Aerosol AG, Switzerland) has been identified as a potential candidate with its capacity to measure the airborne nanoparticle concentration and average particle size with good time-resolution. Monodisperse and polydisperse test nanoaerosols of varying compositions and morphologies were produced in the laboratory using the CAIMAN facility. These aerosols covered a range of particle sizes between 15 and 400 nm and number concentrations from 700 to 840,000 cm(-3). The aerosols were used to investigate the behavior of DiSCmini, comparing experimental data to reference data. In spite of a slight tendency to underestimate particle size, all particle diameters, number concentrations and surface area concentrations measured were in the same order of magnitude as reference data. Furthermore, no significant effect due to particle composition or morphology was noted.

Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia

A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks).

Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software

Aim

To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors.

Method

We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; www.empop.org) by means of two mtDNA data sets that were submitted for quality control.

Results

The quasi-median network torsi of the two data sets resulted in complex reticulations, suggesting ambiguous data. To check the corresponding raw data, accountable nodes and connecting branches of the network could be identified by highlighting induced subgraphs with concurrent dimming of their complements. This is achieved by accentuating the relevant substructures in the network: mouse clicking on a node displays a list of all mtDNA haplotypes included in that node; the selection of a branch specifies the mutation(s) connecting two nodes. It is indicated to evaluate these mutations by means of the raw data.

Conclusion

Inspection of the raw data confirmed the presence of phantom mutations due to suboptimal electrophoresis conditions and data misinterpretation. The network software proved to be a powerful tool to highlight problematic data and guide quality control of mtDNA data tables.

Development of forensic-quality full mtGenome haplotypes: success rates with low template specimens

Forensic mitochondrial DNA (mtDNA) testing requires appropriate, high quality reference population data for estimating the rarity of questioned haplotypes and, in turn, the strength of the mtDNA evidence. Available reference databases (SWGDAM, EMPOP) currently include information from the mtDNA control region; however, novel methods that quickly and easily recover mtDNA coding region data are becoming increasingly available. Though these assays promise to both facilitate the acquisition of mitochondrial genome (mtGenome) data and maximize the general utility of mtDNA testing in forensics, the appropriate reference data and database tools required for their routine application in forensic casework are lacking. To address this deficiency, we have undertaken an effort to: (1) increase the large-scale availability of high-quality entire mtGenome reference population data, and (2) improve the information technology infrastructure required to access/search mtGenome data and employ them in forensic casework. Here, we describe the application of a data generation and analysis workflow to the development of more than 400 complete, forensic-quality mtGenomes from low DNA quantity blood serum specimens as part of a U.S. National Institute of Justice funded reference population databasing initiative. We discuss the minor modifications made to a published mtGenome Sanger sequencing protocol to maintain a high rate of throughput while minimizing manual reprocessing with these low template samples. The successful use of this semi-automated strategy on forensic-like samples provides practical insight into the feasibility of producing complete mtGenome data in a routine casework environment, and demonstrates that large (>2kb) mtDNA fragments can regularly be recovered from high quality but very low DNA quantity specimens. Further, the detailed empirical data we provide on the amplification success rates across a range of DNA input quantities will be useful moving forward as PCR-based strategies for mtDNA enrichment are considered for targeted next-generation sequencing workflows.