NGS compatible streamlined DNA recovery from 3D cell cultures in GrowDex®

Here, we describe a streamlined workflow for constructing an NGS whole exome sequencing (WES) from a low amount of PDCs grown as spheroids in GrowDex.Non peer reviewe

Does early drug use-related police contact predict premature mortality and morbidity : A population register-based study

Introduction The aim was to analyse whether age at first drug offense predicts premature mortality and morbidity due to substance use and violence among adolescents and young adults. Methods A prospective longitudinal register-linkage study based on a total population sample from Finland including individuals born between 1987 and 1992 and aged 15-25 years during follow-up in 2002-2017 (n = 386 435). Age-specific rates of deaths and health-care admissions (morbidity) during a 5-year follow-up were calculated from the first drug offense. Cox regression models were used to estimate differences in mortality and morbidity at ages 21-25. Results Of all 15- to 20-year-olds, 1.4% (n = 5540) have had a police contact. The 5-year mortality rates (per 1000 person-years) among those with first drug offense at ages 15-16 was 2.92 [95% confidence interval (CI) 1.56-6.18], and 5.26 (CI 4.00-7.07) and 5.05 (CI 4.06-6.38) at ages 17-18, and 19-20, respectively. The rates of morbidity varied between 61.20 (CI 52.43-71.76) and 87.51 (CI 82.11-93.33). Both mortality and morbidity rates were over 10 times higher than among the general population. In models adjusted for family background, first police contact at an early age (15-16) did not increase the risk of mortality at ages 21-25 compared with first police contact at ages 17-18 (hazard ratio 1.55, CI 0.77-3.09) or 19-20 (hazard ratio 1.52, CI 0.78-2.98). The results were similar for morbidity. Discussion and Conclusions Adolescents with drug-related police contacts have high risk of mortality and morbidity due to substance use and violence regardless of age of first contact.Peer reviewe

Genome-wide DNA methylation in saliva and body size of adolescent girls

Aim: We performed an epigenome-wide association study within the Finnish Health in Teens cohort to identify differential DNA methylation and its association with BMI in adolescents. Materials & methods: Differential DNA methylation analyses of 3.1 million CpG sites were performed in saliva samples from 50 lean and 50 heavy adolescent girls by genome-wide targeted bisulfite-sequencing. Results: We identified 100 CpG sites with p-values <0.000524, seven regions by 'bumphunting' and five CpG islands that differed significantly between the two groups. The ten CpG sites and regions most strongly associated with BMI substantially overlapped with obesity-and insulin-related genes, including MC2R, IGFBPL1, IP6K1 and IGF2BP1. Conclusion: Our findings suggest an association between the saliva methylome and BMI in adolescence.Peer reviewe

Examining Sanction Type and Drug Offender Recidivism : A Register-Based Study in Finland

Nordic countries incarcerate offenders at much lower rates in comparison with incarceration rates in the United States, and reincarcerate fewer people per capita. Non-custodial alternatives to sanctions, including fines and community service, are used extensively in Finland to reduce negative effects of institutionalization and subsequent disadvantage caused by incarceration. The nature of drug-involved offenders within the Finnish system is reviewed in light of current research about the effectiveness of incarceration and deterrence-based approaches for drug offenders. Employing a 2014 sample from register data (consisting of official government records) of drug offenders in Finland with a 3-year recidivism period, this study utilizes a genetic matching procedure to compare offenders who received fines, conditional sentences (probation), or incarceration. While recognizing that numerous confounding variables affect incarceration, we compare a matched sample of drug offenders and the sanctions they have received from the Finland judicial system to determine whether offenders who initially receive a fine or a conditional sentence reenter the correctional system at different rates than those who are incarcerated. After matching, results found no significant differences between offenders receiving incarceration sentences or those who received noncustodial sentences (fine, or conditional sentence) for general and drug-related recidivism. These results are presented within the context of the Finnish corrections system in order to inform the criminal justice community about culture, incarceration, and process differences that could positively affect working with drug offenders in other localities.Nordic countries incarcerate offenders at much lower rates in comparison with incarceration rates in the United States, and reincarcerate fewer people per capita. Non-custodial alternatives to sanctions, including fines and community service, are used extensively in Finland to reduce negative effects of institutionalization and subsequent disadvantage caused by incarceration. The nature of drug-involved offenders within the Finnish system is reviewed in light of current research about the effectiveness of incarceration and deterrence-based approaches for drug offenders. Employing a 2014 sample from register data (consisting of official government records) of drug offenders in Finland with a 3-year recidivism period, this study utilizes a genetic matching procedure to compare offenders who received fines, conditional sentences (probation), or incarceration. While recognizing that numerous confounding variables affect incarceration, we compare a matched sample of drug offenders and the sanctions they have received from the Finland judicial system to determine whether offenders who initially receive a fine or a conditional sentence reenter the correctional system at different rates than those who are incarcerated. After matching, results found no significant differences between offenders receiving incarceration sentences or those who received noncustodial sentences (fine, or conditional sentence) for general and drug-related recidivism. These results are presented within the context of the Finnish corrections system in order to inform the criminal justice community about culture, incarceration, and process differences that could positively affect working with drug offenders in other localities.Peer reviewe

IDH1 Expression via the R132H Mutation-Specific Antibody in Adrenocortical Neoplasias-Prognostic Impact in Carcinomas

Context: Mutations to isocitrate dehydrogenase (IDH) appear to play a prognostic or predictive role in several neoplasias. Immunohistochemical staining designed to detect a specific R132H mutation to IDH1 showed expression in the normal adrenal cortex, raising interest to study the potential role of IDH1 in the pathogenesis of adrenocortical tumors. Objective: The objective of this work is to study the role of IDH1 and its mutations in adrenocortical tumors. Design and patients: IDH1 R132H immunohistological staining was performed on a cohort of 197 adrenocortical tumors. The exon of the IDH1 gene was sequenced in 16 tumors. Results: Positive IDH1 R132H immunohistochemical staining correlated with a better prognosis among patients with a malignant adrenocortical tumor. However, IDH1 R132H immunohistochemistry did not distinguish between local and metastasized tumors. We were unable to identify IDH1 mutations among our adrenocortical tumors using a targeted next-generation sequencing panel or via exon sequencing. Conclusions: Among adrenocortical carcinomas, IDH1 R132H immunopositivity correlated with a better prognosis. Thus, IDH1 R132H immunohistochemical staining could serve as a prognostic or as a potential predictive marker in adrenocortical carcinomas. Further research is needed to identify the possible alterations in IDH1 that could explain our findings, because we identified no known mutations to the IDH1 gene. (C) Endocrine Society 2020.Peer reviewe

Socioeconomic differences in children’s victimization to maternal and paternal violence : a register-based study

Aims: To explore the potential of administrative data in assessment of the association between parental socioeconomic position (SEP) and children’s violent victimization by biological parents. Methods: A longitudinal register-linkage study based on child–mother and child–father data, including all children born in Finland between 1991 and 2017. The data included 1,535,428 children, 796,335 biological mothers, and 775,966 fathers. We used logistic regression with person-years as observations and cluster-robust standard errors to predict children’s violent victimization in 2009–2018 and assessed effect modification by child’s age and gender. Results: For the SEP indicators, lower maternal education (adjusted odds ratio (OR) 2.90, secondary education OR 1.99) and lower paternal education (OR 2.24, secondary education OR 1.59) were risk factors for violent victimization. Parental social assistance receipt (OR 2.4) and non-employment (OR 1.8–1.9) increased the risk of victimization to maternal and paternal violence. Income was associated with victimization in a gradient-like manner, with ORs ranging from 1.14 to 1.98 among mothers and from 1.29 to 2.56 among fathers. Children with low parental SEP were at the highest risk of parental violence, particularly paternal violence, at ages 3−8 years. Conclusions: All indicators of low SEP increased the risk of children experiencing both maternal and paternal physical violence, especially at ages 3–8 years. Longitudinal register data—because of large samples, no nonresponse or self-report bias, and the possibility to analyze violence committed by mother and father and age-groups separately—have great potential for comprehensive research on the risk factors of parental violence that are difficult to reliably assess with other types of data.Peer reviewe

A novel class of somatic mutations in blood detected preferentially in CD8+cells

Somatic mutations have a central role in cancer but their role in other diseases such as autoimmune disorders is poorly understood. Earlier work has provided indirect evidence of rare somatic mutations in autoreactive T-lymphocytes in multiple sclerosis (MS) patients but such mutations have not been identified thus far. We analysed somatic mutations in blood in 16 patients with relapsing MS and 4 with other neurological autoimmune disease. To facilitate the detection of somatic mutations CD4 +, CD8 +, CD19 + and CD4-/CD8-/CD19- cell subpopulations were separated. We performed next-generation DNA sequencing targeting 986 immune related genes. Somatic mutations were called by comparing the sequence data of each cell subpopulation to other subpopulations of the same patient and validated by amplicon sequencing. We found non-synonymous somatic mutations in 12 (60%) patients (10 MS, 1 myasthenia gravis, 1 narcolepsy). There were 27 mutations, all different and mostly novel (67%). They were discovered at subpopulation-wise allelic fractions of 0.2%-4.6% (median 0.95%). Multiple mutations were found in 8 patients. The mutations were enriched in CD8 + cells (85% of mutations). In follow-up after a median time of 2.3 years, 96% of the mutations were still detectable. These results unravel a novel class of persistent somatic mutations, many of which were in genes that may play a role in autoimmunity (ATM, BTK, CD46, CD180, CLIP2, HMMR, IKEF3, ITGB3, KIR3DL2, MAPK10, CD56/NCAM1, RBM6, RORA, RPM and STAT3). Whether some of this class of mutations plays a role in disease is currently unclear, but these results define an interesting hitherto unknown research target for future studies. (C) 2016 The Authors. Published by Elsevier Inc.Peer reviewe

Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling

Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 +/- 0.097 and 13.56 +/- 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.Peer reviewe

Clonal hematopoiesis in patients with rheumatoid arthritis

Peer reviewe

Gender-Specific Associations Between Saliva Microbiota and Body Size

Objective: The human intestinal microbiota likely play an important role in the development of overweight and obesity. However, the associations between saliva microbiota and body mass index (BMI) have been sparsely studied. The aim of this study was to identify the associations between saliva microbiota and body size in Finnish children. Methods: The saliva microbiota of 900 Finnish children, aged 11-14 years with measured height and weight, was characterized using 16S rRNA (V3-V4) sequencing. Results: The core saliva microbiota consisted of 14 genera that were present in more than 95% of the Finnish children. The saliva microbiota profiles were gender-specific with higher alpha-diversity in boys than girls and significant differences between the genders in community composition and abundances. Alpha-diversity differed between normal weight and overweight girls and between normal weight and obese boys. The composition was dissimilar between normal weight and obese girls, but not in boys. The relative abundance profiles differed according to body size. Decrease in commensal saliva bacteria were observed in all the body sizes when compared to normal weight children. Notably, the relative abundance of bacteria related to, Veillonella, Prevotella, Selenomonas, and Streptococcus was reduced in obese children. Conclusion: Saliva microbiota diversity and composition were significantly associated with body size and gender in Finnish children. Body size-specific saliva microbiota profiles open new avenues for studying the potential roles of microbiota in weight development and management.Peer reviewe