Evaluation of saliva as a source of human DNA for population and association studies

Point-of-care isothermal nucleic acid amplification tests: progress and bottlenecks for extraction-free sample collection and preparation

INTRODUCTION

Suitable sample collection and preparation methods are essential to enable nucleic acid amplification testing at the point of care (POC). Strategies that allow direct isothermal nucleic acid amplification testing (iNAAT) of crude sample lysate without the need for nucleic acid extraction minimize time to result as well as the need for operator expertise and costly infrastructure.

AREAS COVERED

The authors review research to understand how sample matrix and preparation affect the design and performance of POC iNAATs. They focus on approaches where samples are directly combined with liquid reagents for preparation and amplification via iNAAT strategies. They review factors related to the type and method of sample collection, storage buffers, and lysis strategies. Finally, they discuss RNA targets and relevant regulatory considerations.

EXPERT OPINION

Limitations in sample preparation methods are a significant technical barrier preventing implementation of nucleic acid testing at the POC. The authors propose a framework for co-designing sample preparation and amplification steps for optimal performance with an extraction-free paradigm by considering a sample matrix and lytic strategy prior to an amplification assay and readout. In the next 5 years, the authors anticipate increasing priority on the co-design of sample preparation and iNAATs.

DNA methylation changes during a sprint interval exercise performed under normobaric hypoxia or with blood flow restriction: A pilot study in men

This crossover study evaluated DNA methylation changes in human salivary samples following single sprint interval training sessions performed in hypoxia, with blood flow restriction (BFR), or with gravity-induced BFR. Global DNA methylation levels were evaluated with an enzyme-linked immunosorbent assay. Methylation-sensitive restriction enzymes were used to determine the percentage methylation in a part of the promoter of the gene-inducible nitric oxide synthase (p-iNOS), as well as an enhancer (e-iNOS). Global methylation increased after exercise (p < 0.001; dz = 0.50). A tendency was observed for exercise × condition interaction (p = 0.070). Post hoc analyses revealed a significant increase in global methylation between pre- (7.2 ± 2.6%) and postexercise (10.7 ± 2.1%) with BFR (p = 0.025; dz = 0.69). Methylation of p-iNOS was unchanged (p > 0.05). Conversely, the methylation of e-iNOS increased from 0.6 ± 0.4% to 0.9 ± 0.8% after exercise (p = 0.025; dz = 0.41), independently of the condition (p > 0.05). Global methylation correlated with muscle oxygenation during exercise (r = 0.37, p = 0.042), while e-iNOS methylation showed an opposite association (r = -0.60, p = 0.025). Furthermore, p-iNOS methylation was linked to heart rate (r = 0.49, p = 0.028). Hence, a single sprint interval training increases global methylation in saliva, and adding BFR tends to increase it further. Lower muscle oxygenation is associated with augmented e-iNOS methylation. Finally, increased cardiovascular strain results in increased p-iNOS methylation.

Response of salivary microbiome to temporal, environmental, and surface characteristics under in vitro exposure

The microbiome of saliva stains deposited at crime scenes and in everyday settings is valuable for forensic investigations and environmental ecology. However, the dynamics and applications of microbial communities in these saliva stains have not been fully explored. In this study, we analyzed saliva samples that were exposed to indoor conditions for up to 1 year and to different carriers (cotton, sterile absorbent cotton swab, woolen, dacron) in both indoor and outdoor environments for 1 month using high-throughput sequencing. The analysis of microbial composition and Mfuzz clustering showed that the salivary flora, specifically Streptococcus (cluster7), which was associated with microbial contamination, remained stable over short periods of time. However, prolonged exposure led to significant differences due to the invasion of environmental bacteria such as Pseudomonas and Achromobacter. The growth and colonization of environmental flora were promoted by humidity. The neutral model predictions indicated that the assembly of salivary microbial communities in outdoor environments was significantly influenced by stochastic processes, with environmental characteristics having a greater impact on community change compared to surface characteristics. By incorporating data from previous studies on fecal and vaginal secretion microbiology, we developed RF and XGBoost classification models that achieved high accuracy (>98 %) and AUC (>0.8). Additionally, a RF regression model was created to determine the time since deposition (TsD) of the stains. Time inference models yielded a mean absolute error (MAE) of 7.1 days for stains exposed for 1 year and 14.2 h for stains exposed for 14 days. These findings enhance our understanding of the changes in the microbiome of saliva stains over time, in different environments, and on different surfaces. They also have potential applications in assessing potential microbial contamination, identifying body fluids, and inferring the time of deposition.

Codiversification of gut microbiota with humans

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.

Native American mitochondrial lineages in admixed populations from Chile: Detecting recent migrations during post-Columbian times using geographically restricted lineages

OBJECTIVES

To analyze the mitochondrial diversity in three admixed populations and evaluate the historical migration effect of native southern population movement to Santiago (capital of Chile). The intensity of migration was quantified using three mitochondrial lineages restricted to South-Central native groups.

METHODS

D-loop sequences were genotyped in 550 unrelated individuals from San Felipe-Los Andes (n = 108), Santiago (n = 217), and Concepción (n = 225). Sequence processing, alignment, and haplogroup inference were carried out, and different genetic structure analyses were performed for haplogroup frequencies and D-loop sequences.

RESULTS

The Native lineages B2i2, C1b13, and D1g were the most frequent haplogroups, especially in Santiago (71.8%). Despite the distance, this city showed a high-genetic affinity with southern populations, including Concepción (~500 km distant) and native groups, rather than with those from San Felipe-Los Andes (<100 km distant). In fact, there was a negative correlation between geographical and genetic distance among these cities (r corr = -0.5593, p value = 0.8387). Network analysis revealed shared haplotypes between Santiago, Concepción, and other southern populations. Finally, we found lineages from Concepción acting as ancestral nodes in the northern clade.

CONCLUSIONS

Considering the geographic distances from these cities, the results were not consistent with a model of genetic isolation by geographic distance, revealing the effects of a historical migration process from the south to the capital. We also show evidence of possible north-to-south migration during admixture onset in Concepción and in addition, we were able to identify previously unreported mitochondrial diversity in urban populations that became lost in Native groups post-European contact.

The Oral, Gut Microbiota and Cardiometabolic Health of Indigenous Orang Asli Communities

The Orang Asli (OA) of Malaysia have been relatively understudied where little is known about their oral and gut microbiomes. As human health is closely intertwined with the human microbiome, this study first assessed the cardiometabolic health in four OA communities ranging from urban, rural to semi-nomadic hunter-gatherers. The urban Temuan suffered from poorer cardiometabolic health while rural OA communities were undergoing epidemiological transition. The oral microbiota of the OA were characterised by sequencing the V4 region of the 16S rRNA gene. The OA oral microbiota were unexpectedly homogenous, with comparably low alpha diversity across all four communities. The rural Jehai and Temiar PP oral microbiota were enriched for uncharacterised bacteria, exhibiting potential for discoveries. This finding also highlights the importance of including under-represented populations in large cohort studies. The Temuan oral microbiota were also elevated in opportunistic pathogens such as Corynebacterium, Prevotella, and Mogibacterium, suggesting possible oral dysbiosis in these urban settlers. The semi-nomadic Jehai gut microbiota had the highest alpha diversity, while urban Temuan exhibited the lowest. Rural OA gut microbiota were distinct from urban-like microbiota and were elevated in bacteria genera such as Prevotella 2, Prevotella 9, Lachnospiraceae ND3007, and Solobacterium. Urban Temuan microbiota were enriched in Odoribacter, Blautia, Parabacetroides, Bacteroides and Ruminococcacecae UCG-013. This study brings to light the current health trend of these indigenous people who have minimal access to healthcare and lays the groundwork for future, in-depth studies in these populations.

Novel use of menstrual blood for monitoring glycaemic control in patients with diabetes: a proof-of-concept study

BACKGROUND

Glycated haemoglobin (HbA1c) is the diagnostic and prognostic standard for clinical management of diabetes mellitus (DM). Unfortunately, patient adherence to guidelines for routine testing can be poor and there are significant gender-based disparities in DM management and outcomes. Recent evidence suggests that menstrual blood may be comparable to systemic blood for monitoring of common biomarkers. The objective of the present study was to assess the concordance of HbA1c levels between menstrual and systemic blood in healthy women and women with diabetes of reproductive age.

METHODS

In this prospective, observational cohort study, we enrolled healthy and diabetic (type 1 and type 2 DM) reproductive-age women (aged ≥18 and ≤45 years). Menstrual blood and venous systemic blood specimens were simultaneously obtained at time of menstruation, and analysed for HbA1c levels. Participants self-collected menstrual blood using a QPad, a novel, modified menstrual pad with an embedded dried blood spot strip.

RESULTS

Among 172 participants, 57.6% were healthy and 42.4% had a diagnosis of either type 1 or type 2 DM. There were no significant differences in mean HbA1c values in menstrual and systemic blood across the overall cohort or within the diabetic subgroup. Furthermore, HbA1c levels between blood sources were robustly correlated and demonstrated a significant linear relationship.

CONCLUSIONS

There is a strong concordance in HbA1c levels between menstrual and systemic blood. Empowered by self-collection technologies, these findings suggest that menstrual blood may serve as a reliable, non-invasive and potentially cost-effective alternative to serum for HbA1c monitoring among reproductive-age women with DM.

Influence of Pre-treatment Saliva Microbial Diversity and Composition on Nasopharyngeal Carcinoma Prognosis

Background

The human microbiome has been reported to mediate the response to anticancer therapies. However, research about the influence of the oral microbiome on nasopharyngeal carcinoma (NPC) survival is lacking. We aimed to explore the effect of oral microbiota on NPC prognosis.

Methods

Four hundred eighty-two population-based NPC cases in southern China between 2010 and 2013 were followed for survival, and their saliva samples were profiled using 16s rRNA sequencing. We analyzed associations of the oral microbiome diversity with mortality from all causes and NPC.

Results

Within- and between-community diversities of saliva were associated with mortality with an average of 5.29 years follow-up. Lower Faith’s phylogenetic diversity was related to higher all-cause mortality [adjusted hazard ratio (aHR), 1.52 (95% confidence interval (CI), 1.06–2.17)] and NPC-specific mortality [aHR, 1.57 (95% CI, 1.07–2.29)], compared with medium diversity, but higher phylogenetic diversity was not protective. The third principal coordinate (PC3) identified from principal coordinates analysis (PCoA) on Bray–Curtis distance was marginally associated with reduced all-cause mortality [aHR, 0.85 (95% CI, 0.73–1.00)], as was the first principal coordinate (PC1) from PCoA on weighted UniFrac [aHR, 0.86 (95% CI, 0.74–1.00)], but neither was associated with NPC-specific mortality. PC3 from robust principal components analysis was associated with lower all-cause and NPC-specific mortalities, with HRs of 0.72 (95% CI, 0.61–0.85) and 0.71 (95% CI, 0.60–0.85), respectively.

Conclusions

Oral microbiome may be an explanatory factor for NPC prognosis. Lower within-community diversity was associated with higher mortality, and certain measures of between-community diversity were related to mortality. Specifically, candidate bacteria were not related to mortality, suggesting that observed associations may be due to global patterns rather than particular pathogens.

Genetic analysis of four consanguineous multiplex families with inflammatory bowel disease

BACKGROUND

Family studies support a genetic predisposition to inflammatory bowel diseases (IBD), but known genetic variants only partially explain the disease heritability. Families with multiple affected individuals potentially harbour rare and high-impact causal variants. Long regions of homozygosity due to recent inbreeding may increase the risk of individuals bearing homozygous loss-of-function variants. This study aimed to identify rare and homozygous genetic variants contributing to IBD.

METHODS

Four families with known consanguinity and multiple cases of IBD were recruited. In a family-specific analysis, we utilised homozygosity mapping complemented by whole-exome sequencing.

RESULTS

We detected a single region of homozygosity shared by Crohn's disease cases from a family of Druze ancestry, spanning 2.6 Mb containing the NOD2 gene. Whole-exome sequencing did not identify any potentially damaging variants within the region, suggesting that non-coding variation may be involved. In addition, affected individuals in the families harboured several rare and potentially damaging homozygous variants in genes with a role in autophagy and innate immunity including LRRK1, WHAMM, DENND3, and C5.

CONCLUSION

This study examined the potential contribution of rare, high-impact homozygous variants in consanguineous families with IBD. While the analysis was not designed to achieve statistical significance, our findings highlight genes or loci that warrant further research. Non-coding variants affecting NOD2 may be of importance in Druze patients with Crohn's disease.

A proof of concept pilot trial of probiotics in symptomatic oral lichen planus (CABRIO)

OBJECTIVE

To preliminary evaluate the clinical effects of probiotics in individuals with symptomatic oral lichen planus and the possible mechanisms of action.

SUBJECTS AND METHODS

A group of 30 individuals with symptomatic oral lichen planus were recruited in a randomised double-blind parallel group controlled (1:1) proof-of-concept pilot trial of probiotic VSL#3 vs placebo. Efficacy outcomes included changes in pain numeric rating scale, oral disease severity score and the chronic oral mucosal disease questionnaire. Adverse effects, home diary and withdrawals were assessed as feasibility outcomes. Mechanistic outcomes included changes in salivary and serum levels of CXCL10 and IFN-γ and in oral microbial composition.

RESULTS

The probiotic VSL#3 was safe and well tolerated. We observed no statistically significant change in pain, disease activity, quality of life, serum/salivary CXCL10 or oral microbial composition with respect to placebo. Salivary IFN-γ levels demonstrate a trend for a reduced level in the active group (p = 0.082) after 30 days of probiotic consumption.

CONCLUSIONS

The present proof-of-concept study provides some weak not convincing indication of biological and clinical effects of probiotic VSL#3 in individuals with painful oral lichen planus. Further research in this field is needed, with the current study providing useful information to the design of future clinical trials.

An analysis of the demographic history of the risk allele R4810K in RNF213 of moyamoya disease

BACKGROUND

Ring finger protein 213 (RNF213) is a susceptibility gene of moyamoya disease (MMD). A previous case-control study and a family analysis demonstrated a strong association of the East Asian-specific variant, R4810K (rs112735431), with MMD. Our aim is to uncover evolutionary history of R4810K in East Asian populations.

METHODS

The RNF213 locus of 24 MMD patients in Japan were sequenced using targeted-capture sequencing. Based on the sequence data, we conducted population genetic analysis and estimated the age of R4810K using coalescent simulation.

RESULTS

The diversity of the RNF213 gene was higher in Africans than non-Africans, which can be explained by bottleneck effect of the out-of-Africa migration. Coalescent simulation showed that the risk variant was born in East Asia 14,500-5100 years ago and came to the Japanese archipelago afterward, probably in the period when the known migration based on archaeological evidences occurred.

CONCLUSIONS

Although clinical data show that the symptoms varies, all sequences harboring the risk allele are almost identical with a small number of exceptions, suggesting the MMD phenotypes are unaffected by the variants of this gene and rather would be more affected by environmental factors.

Evaluation of saliva as a source of accurate whole-genome and microbiome sequencing data

This study sets out to establish the suitability of saliva-based whole-genome sequencing (WGS) through a comparison against blood-based WGS. To fully appraise the observed differences, we developed a novel technique of pseudo-replication. We also investigated the potential of characterizing individual salivary microbiomes from non-human DNA fragments found in saliva. We observed that the majority of discordant genotype calls between blood and saliva fell into known regions of the human genome that are typically sequenced with low confidence; and could be identified by quality control measures. Pseudo-replication demonstrated that the levels of discordance between blood- and saliva-derived WGS data were entirely similar to what one would expect between technical replicates if an individual's blood or saliva had been sequenced twice. Finally, we successfully sequenced salivary microbiomes in parallel to human genomes as demonstrated by a comparison against the Human Microbiome Project.

Salivary Raman Spectroscopy: Standardization of Sampling Protocols and Stratification of Healthy and Oral Cancer Subjects

Minimally invasive cancer detection using bio-fluids has been actively pursued due to practical limitations, though there are better suited noninvasive and online in vivo methods. Saliva is one such clinically informative bio-fluid that offers the advantages of easy and multiple sample collection. Despite its potential in cancer diagnostics, saliva analysis is challenging due to its heterogeneous composition. Recently, there has been an upsurge in saliva exploration using optical techniques. Forms of saliva such as precipitate and supernatant have been monitored, but this sampling method needs to be standardized due to the obvious loss of analytes in processing. In that context, present work details the comparison of four different saliva sampling methodologies, i.e., air-dried, lyophilized, pellet, and supernatant using Raman spectroscopy collected from 10 healthy samples. Composition-driven spectral features of all forms were compared and classified using principal component analysis and linear discriminant analysis. Analysis was carried out on all four groups in the first step. In the second step, groups of pellet and supernatant , and air-dried and lyophilized were analyzed. Findings suggest that pellet and supernatant exhibit discrete spectroscopic features and demonstrate high classification efficiency, which is indicative of their distinctive biochemical composition. On the other hand, air-dried and lyophilized forms showed overlapping spectral features and low classification, suggesting these forms retain majority spectroscopic features of whole saliva and are less prone to sampling losses. Thus, this study indicates air-dried and lyophilized forms may be more appropriate for saliva sampling using Raman spectroscopy providing the comprehensive information required for cancer diagnosis. Furthermore, the method was also tested for the classification of oral cancer and healthy subjects (n = 27) which yielded 90% stratification. The findings of the study indicate the utility of minimally invasive salivary Raman-based diagnostics in oral cancers.

An effective method for saliva stabilization and magnetic nanoparticles based DNA extraction for genomic applications

Introduction of magnetisable solid phase extraction procedures have provided various advantages over spin-column based extraction techniques. Although certain methods for magnetic bead based extraction of DNA from human saliva already exist, there is still a need to address the inadequate purity profile and low yield which occur due to the inefficiency of extraction methods. Hence, an improved method for DNA extraction from human saliva using uncoated magnetic nanoparticles (MNPs) intended to resolve the issues mentioned above is described here. The uncoated magnetic nanoparticles used in this study facilitate reversible binding of DNA and due to the absence of surface coating the particle size remains small thereby providing higher surface area to volume ratio for binding DNA. Another objective of this study was to develop a saliva preservation buffer (SPB) to solve the major challenges associated with storage and easy transportation of saliva sample at room temperature. Human saliva samples stored in the saliva preservation buffer were stable up to 160 days at room temperature without any bacterial or fungal growth and the quality of genomic DNA was intact.

Salivary Microbiome Variation in Early Childhood Caries of Children 3-6 Years of Age and Its Association With Iron Deficiency Anemia and Extrinsic Black Stain

ECC is a common clinical manifestation of the oral cavity in childhood and Iron deficiency-anemia (IDA) is a high-risk factor but extrinsic black stain on the tooth surface is a protective factor for caries. There is limited information about oral microecological change in early children who suffer from ECC with IDA and extrinsic black stain (BS). This study enrolled 136 children aged 3-6 years. Dental caries and teeth BS were examined. Saliva was collected for 16S rRNA gene and fingertip blood were for Hemoglobin test. There are 93 ECC including 13 with IDA (IDA ECC) and 80 without IDA (NIDA ECC) and 43 caries free (CF) including 17 with BS (BSCF) and 26 without BS (NBS CF). Statistical analysis of microbiota data showed differences of the oral flora in different groups. The oral flora of the IDA ECC group had a high diversity, while the BSCF group had a low diversity. The bacterial genera Bacillus, Moraxella, and Rhodococcus were enriched in the IDA ECC while Neisseria was enriched in the NIDA ECC. Neisseria only exhibited high abundance in the BSCF, and the remaining genera exhibited high abundance in the NBSCF. Interestingly, the BSCF had the same trend as the NIDA ECC, and the opposite trend was observed with IDA ECC. We established random forest classifier using these biomarkers to predict disease outcomes. The random forest classifier achieved the best accuracy in predicting the outcome of caries, anemia and black stain using seven, one and eight biomarkers, respectively; and the accuracies of the classifiers were 93.35%, 94.62% and 95.23%, respectively. Our selected biomarkers can achieve good prediction, suggesting their potential clinical implications.

Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that is becoming a significant global health care problem. Several studies have shown that people with diabetes are more susceptible to oral problems, such as periodontitis and, although the causes are still inconclusive, oral microbiota is considered to play a major role in oral health. This study aimed to characterize the oral microbiome of a sample representing T2DM patients from Portugal and exploit potential associations between some microorganisms and variables like teeth brushing, smoking habits, average blood sugar levels, medication and nutrient intake. By sequencing the hypervariable regions V3-V4 of the 16S rRNA gene in 50 individuals belonging to a group of diabetes patients and a control group, we found a total of 232 taxa, from which only 65% were shared between both groups. No differences were found in terms of alpha and beta diversity between categories. We did not find significant differences in the oral microbiome profiles of control and diabetes patients. Only the class Synergistia and the genus TG5, which are related to periodontitis, were statistically more frequent in the control group. The similar microbiome profiles of medicated diabetics and the control group indicates that the relationship between the T2DM and the oral microbiome might be more related to either the lifestyle/diet rather than diabetes per se. Moreover, this study provides, for the first time, insights into the oral microbiome of a population with a high prevalence of diabetes.

The correlation of salivary telomere length and single nucleotide polymorphisms of the ADIPOQ, SIRT1 and FOXO3A genes with lifestyle-related diseases in a Japanese population

Background

It has been reported that genetic factors are associated with risk factors and onset of lifestyle-related diseases, but this finding is still the subject of much debate.

Objective

The aim of the present study was to investigate the correlation of genetic factors, including salivary telomere length and three single nucleotide polymorphisms (SNPs) that may influence lifestyle-related diseases, with lifestyle-related diseases themselves.

Methods

In one year at a single facility, relative telomere length and SNPs were determined by using monochrome multiplex quantitative polymerase chain reaction and TaqMan SNP Genotyping Assays, respectively, and were compared with lifestyle-related diseases in 120 Japanese individuals near our university.

Results

In men and all participants, age was inversely correlated with relative telomere length with respective p values of 0.049 and 0.034. In men, the frequency of hypertension was significantly higher in the short relative telomere length group than in the long group with unadjusted p value of 0.039, and the difference in the frequency of hypertension between the two groups was of borderline statistical significance after adjustment for age (p = 0.057). Furthermore, in men and all participants, the sum of the number of affected lifestyle-related diseases, including hypertension, was significantly higher in the short relative telomere length group than in the long group, with p values of 0.004 and 0.029, respectively. For ADIPOQ rs1501299, men’s ankle brachial index was higher in the T/T genotype than in the G/G and G/T genotypes, with p values of 0.001 and 0.000, respectively. For SIRT1 rs7895833, men’s body mass index and waist circumference and all participants’ brachial-ankle pulse wave velocity were higher in the A/G genotype than in the G/G genotype, with respective p values of 0.048, 0.032 and 0.035. For FOXO3A rs2802292, women’s body temperature and all participants’ saturation of peripheral oxygen were lower in the G/T genotype than in the T/T genotype, with respective p values of 0.039 and 0.032. However, relative telomere length was not associated with physiological or anthropometric measurements except for height in men (p = 0.016). ADIPOQ rs1501299 in men, but not the other two SNPs, was significantly associated with the sum of the number of affected lifestyle-related diseases (p = 0.013), by genotype. For each SNPs, there was no significant difference in the frequency of hypertension or relative telomere length by genotype.

Conclusion

Relative telomere length and the three types of SNPs determined using saliva have been shown to be differentially associated with onset of and measured risk factors for lifestyle-related diseases consisting mainly of cardiovascular diseases and cancer.

Contaminating DNA in human saliva alters the detection of variants from whole genome sequencing

Cells obtained from human saliva are commonly used as an alternative DNA source when blood is difficult or less convenient to collect. Although DNA extracted from saliva is considered to be of comparable quality to that derived from blood, recent studies have shown that non-human contaminating DNA derived from saliva can confound whole genome sequencing results. The most concerning complication is that non-human reads align to the human reference genome using standard methodology, which can critically affect the resulting variant genotypes identified in a genome. We identified clusters of anomalous variants in saliva DNA derived reads which aligned in an atypical manner. These reads had only short regions of identity to the human reference sequence, flanked by soft clipped sequence. Sequence comparisons of atypically aligning reads from eight human saliva-derived samples to RefSeq genomes revealed the majority to be of bacterial origin (63.46%). To partition the non-human reads during the alignment step, a decoy of the most prevalent bacterial genome sequences was designed and utilised. This reduced the number of atypically aligning reads when trialled on the eight saliva-derived samples by 44% and most importantly prevented the associated anomalous genotype calls. Saliva derived DNA is often contaminated by DNA from other species. This can lead to non-human reads aligning to the human reference genome using current alignment best-practices, impacting variant identification. This problem can be diminished by using a bacterial decoy in the alignment process.

Auditory brainstem measures and genotyping boost the prediction of literacy: A longitudinal study on early markers of dyslexia

•

Multi-domain profiles advance retrospective prediction of emergent literacy.

•

DCDC2 and KIAA0319 risk variants influence emergent spelling skills.

•

Combined DYX2 and auditory brainstem measures enhance predictive model fits.

•

Additional benefit of preliterate phonological awareness on predictive power.

Literacy acquisition is impaired in children with developmental dyslexia resulting in lifelong struggle to read and spell. Proper diagnosis is usually late and commonly achieved after structured schooling started, which causes delayed interventions. Legascreen set out to develop a preclinical screening to identify children at risk of developmental dyslexia. To this end we examined 93 preliterate German children, half of them with a family history of dyslexia and half of them without a family history. We assessed standard demographic and behavioral precursors of literacy, acquired saliva samples for genotyping, and recorded speech-evoked brainstem responses to add an objective physiological measure. Reading and spelling was assessed after two years of structured literacy instruction. Multifactorial regression analyses considering demographic information, genotypes, and auditory brainstem encoding, predicted children’s literacy skills to varying degrees. These predictions were improved by adding the standard psychometrics with a slightly higher impact on spelling compared to reading comprehension. Our findings suggest that gene-brain-behavior profiling has the potential to determine the risk of developmental dyslexia. At the same time our results imply the need for a more sophisticated assessment to fully account for the disparate cognitive profiles and the multifactorial basis of developmental dyslexia.

Neurobiological origins of individual differences in mathematical ability

Mathematical ability is heritable and related to several genes expressing proteins in the brain. It is unknown, however, which intermediate neural phenotypes could explain how these genes relate to mathematical ability. Here, we examined genetic effects on cerebral cortical volume of 3-6-year-old children without mathematical training to predict mathematical ability in school at 7-9 years of age. To this end, we followed an exploration sample (n = 101) and an independent replication sample (n = 77). We found that ROBO1, a gene known to regulate prenatal growth of cerebral cortical layers, is associated with the volume of the right parietal cortex, a key region for quantity representation. Individual volume differences in this region predicted up to a fifth of the behavioral variance in mathematical ability. Our findings indicate that a fundamental genetic component of the quantity processing system is rooted in the early development of the parietal cortex.

Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases

Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.

Response of the human gut and saliva microbiome to urbanization in Cameroon

Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. To unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. To do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in Cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. Interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. Finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors.

STR technique for the detection of contamination by exogenous DNA in paraffin blocks and histological slides

Gastrointestinal Stromal Tumors (GIST) present different types of mutations that may or may not be sensitive to specific target therapy. The laboratory procedure required to prepare histological sections traditionally demands multiple steps, making the process prone to contamination by exogenous genetic material (DNA). An eventual contamination of the biological sample with exogenous DNA may jeopardize subsequent analysis of mutations. The Short Tandem Repeat (STR) technique is frequently used in forensic science fields and presents a potential application in surgical pathology, especially in situations of suspected sample exchange. In the present study, the objective is to verify the possible contamination by exogenous DNA in gastric GIST samples and to evaluate if the presence of contamination can interfere in the detection of the mutations of interest. We assessed eight gastric GISTs by the Sanger sequencing and STR sequence analyses. Seven samples presented more than one profile, a result interpreted as contamination. Our results indicate that exogenous DNA contamination occurred in most of the samples studied and that this was more frequent in samples obtained from the slides than those obtained from the block. The presence of contamination did not inhibit the detection of the mutations of interest for a specific target therapy. Furthermore, the histologic block revealed to be more advantageously when compared to the slide for molecular pathology diagnosis.

Genetic structure of Mataco-Guaycurú speakers from Argentina and the extent of their genetic admixture with neighbouring urban populations

Argentina hosts more than 30 Native American groups, who are widely distributed throughout the country. Mataco-Guaycurú speakers settled in the ecoregion of Gran Chaco and represent 26.7% of the extant aboriginal population of the country. To further investigate the genetic attributes of these speakers, we focused our attention on four aboriginal groups, namely, Wichí, Toba, Pilagá and Mocoví, belonging to the Mataco-Guaycurú linguistic group. Our main goal was to evaluate the interrelationships among the groups and the relationships of these groups with admixed urban populations and to assess correspondences between molecular analysis and historical information. A total of 890 samples (282 Native Americans and 608 inhabitants of admixed urban areas) were analysed. Genetic information was gathered from 15 autosomal STRs, 17 Y-STRs, entire mtDNA control region sequences, 24 AIM-SNPs and 46 AIM-DIPs. Native American signatures were detected in 97.9% of mtDNA lineages, 89.1% of Y-haplotypes and 90.3% to 96.9% of autosomal markers. Wichí exhibited the genetic composition with the largest Native American contribution among the groups and a weak signal of gene flow. This work provides extended genetic information of potential interest in the fields of molecular anthropology and forensic genetics.

DNA Methylation Changes Are Associated With an Incremental Ascent to High Altitude

Genetic and nongenetic factors are involved in the individual ability to physiologically acclimatize to high-altitude hypoxia through processes that include increased heart rate and ventilation. High-altitude acclimatization is thought to have a genetic component, yet it is unclear if other factors, such as epigenetic gene regulation, are involved in acclimatization to high-altitude hypoxia in nonacclimatized individuals. We collected saliva samples from a group of healthy adults of European ancestry (n = 21) in Kathmandu (1,400 m; baseline) and three altitudes during a trek to the Everest Base Camp: Namche (3,440 m; day 3), Pheriche (4,240 m; day 7), and Gorak Shep (5,160 m; day 10). We used quantitative bisulfite pyrosequencing to determine changes in DNA methylation, a well-studied epigenetic marker, in LINE-1, EPAS1, EPO, PPARa, and RXRa. We found significantly lower DNA methylation between baseline (1,400 m) and high altitudes in LINE-1, EPO (at 4,240 m only), and RXRa. We found increased methylation in EPAS1 (at 4,240 m only) and PPARa. We also found positive associations between EPO methylation and systolic blood pressure and RXRa methylation and hemoglobin. Our results show that incremental exposure to hypoxia can affect the epigenome. Changes to the epigenome, in turn, could underlie the process of altitude acclimatization.

From matrimonial practices to genetic diversity in Southeast Asian populations: the signature of the matrilineal puzzle

In matrilineal populations, the descent group affiliation is transmitted by women whereas the socio-political power frequently remains in the hands of men. This situation, named the 'matrilineal puzzle', is expected to promote local endogamy as a coping mechanism allowing men to maintain their decision-making power over their natal descent group. In this paper, we revisit this 'matrilineal puzzle' from a population genetics' point of view. Indeed, such tendency for local endogamy in matrilineal populations is expected to increase their genetic inbreeding and generate isolation-by-distance patterns between villages. To test this hypothesis, we collected ethno-demographic data for 3261 couples and high-density genetic data for 675 individuals from 11 Southeast Asian populations with a wide range of social organizations: matrilineal and matrilocal populations (M), patrilineal and patrilocal populations (P) or cognatic populations with predominant matrilocal residence (C). We observed that M and C populations have higher levels of village endogamy than P populations, and that such higher village endogamy leads to higher genetic inbreeding. M populations also exhibit isolation-by-distance patterns between villages. We interpret such genetic patterns as the signature of the 'matrilineal puzzle'. Notably, our results suggest that any form of matrilocal marriage (whatever the descent rule is) increases village endogamy. These findings suggest that male dominance, when combined with matrilocality, constrains inter-village migrations, and constitutes an underexplored cultural process shaping genetic patterns in human populations. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.

Comparing DNA quantity and quality using saliva collection following food and beverage consumption

Objective

With the democratization of genetic testing, researchers, clinicians, and educators must consider the varying degree of field conditions when collecting samples for genetic analyses. For genotyping or sequencing studies, study designers have multiple options from which to choose, including cheek swabs and saliva sampling. One significant benefit of saliva collection is that it can be done remotely, in the privacy of one’s home. This same benefit adds a risk of compliance. Therefore, our goal with this study was to see if the quality and quantity of the saliva collection by a saliva DNA collection kit would be affected by not following the manufacturer’s directions, i.e., drinking or eating right before collection.

Results

We asked five participants to collect saliva samples according to the manufacturer’s guidance and also after consuming five food items or beverages. We evaluated DNA quantity and quality post-purification using spectroscopy, electrophoresis, and polymerase chain reaction genotyping. Consistent with our hypothesis, we did not see a difference in quantity or quality of the isolated DNA. From our results, we conclude that the manufacturer’s instructions serve as an ideal guideline, but the collection devices are robust enough to permit flexibility in sampling at home or in the field.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4211-6) contains supplementary material, which is available to authorized users.

Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia

Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods:  Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R.   Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of Bifidobacterium was increased in men whereas Prevotella, Capnocytophaga, Leptotrichia, Neisseria and Streptococcus were increased in women. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI scores, abdominal obesity and smoking status.

Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia

Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods:  Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R.   Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of Bifidobacterium, bacteria commonly found in dairy products, was increased in men. Prevotella, associated with consumption of plant-rich diets, was increased in women. Mogibacteriacea and Mycoplasma levels were significantly elevated in overweight individuals. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI scores and abdominal obesity and smoking status.

Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia

Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods:  Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R.   Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of the genus Bifidobacterium was increased in men whereas the genera  Prevotella, Capnocytophaga, Leptotrichia, Neisseria and Streptococcus were increased in women. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI, abdominal obesity and smoking status.

Rare coding variant analysis in a large cohort of Ashkenazi Jewish families with inflammatory bowel disease

Rare variants are thought to contribute to the genetics of inflammatory bowel disease (IBD), which is more common amongst the Ashkenazi Jewish (AJ) population. A family-based approach using exome sequencing of AJ individuals with IBD was employed with a view to identify novel rare genetic variants for this disease. Exome sequencing was performed on 960 Jewish individuals including 513 from 199 multiplex families with up to eight cases. Rare, damaging variants in loci prioritized by linkage analysis and those shared by multiple affected individuals within the same family were identified. Independent evidence of association of each variant with disease was assessed. A number of candidate variants were identified, including in genes involved in the immune system. The ability to achieve statistical significance in independent case/control replication data was limited by power and was only achieved for variants in the well-established Crohn's disease gene, NOD2. This work demonstrates the challenges of identifying disease-associated rare damaging variants from exome data, even amongst a favorable cohort of familial cases from a genetic isolate. Further research of the prioritized rare candidate variants is required to confirm their association with the disease.

Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy

This study examined the microbial diversity and community assembly of oral microbiota in periodontal health and disease and after nonsurgical periodontal treatment. The V4 region of 16S rRNA gene from DNA of 238 saliva and subgingival samples of 21 healthy and 48 diseased subjects was amplified and sequenced. Among 1979 OTUs identified, 28 were overabundant in diseased plaque. Six of these taxa were also overabundant in diseased saliva. Twelve OTUs were overabundant in healthy plaque. There was a trend for disease-associated taxa to decrease and health-associated taxa to increase after treatment with notable variations among individual sites. Network analysis revealed modularity of the microbial communities and identified several health- and disease-specific modules. Ecological drift was a major factor that governed community turnovers in both plaque and saliva. Dispersal limitation and homogeneous selection affected the community assembly in plaque, with the additional contribution of homogenizing dispersal for plaque within individuals. Homogeneous selection and dispersal limitation played important roles, respectively, in healthy saliva and diseased pre-treatment saliva between individuals. Our results revealed distinctions in both taxa and assembly processes of oral microbiota between periodontal health and disease. Furthermore, the community assembly analysis has identified potentially effective approaches for managing periodontitis.

High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups

Because of its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only two gene families (RBMY and TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of a male could not be predicted based on his ampliconic gene copy numbers. Finally, we did not find significant correlations either between copy number variation and individual's height, or between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

Saliva samples as a source of DNA for high throughput genotyping: an acceptable and sufficient means in improvement of risk estimation throughout mammographic diagnostics

Background

Breast cancer screening programs seem to be an insufficient tool for women at high genetic risk for breast cancer. These women are not adequately monitored yet. Genetic testing may improve clearly the quality of breast cancer prevention programs. At present, blood samples are favored for obtaining high-quality DNA; however, DNA can also be obtained by collecting saliva. The aim of this study was, on the one hand, to determine whether saliva sampling is a practicable means to obtain sufficient quantity and quality of DNA and, on the other hand, whether it is accepted by patients throughout mammographic diagnostics.

Methods

67 consecutive women with diagnostic need for mammography with or without a family history for breast cancer were asked for their basic willingness to undergo a genetic testing by saliva sample in addition to standard diagnostics. Saliva samples were analyzed in terms of DNA quantity and quality.

Results

64 (95.6%) women agreed to provide a saliva sample; 3 of them denied participation. And even 63 out of 64 (98.4%) were interested in their specific results. 45 out of 64 samples contained a DNA concentration above 50 ng/µl, 12 samples were between 25 and 50 ng/µl and only 7 of them were under 25 ng/µl with the standard extraction procedure.

Conclusion

A high number of patients seem to accept salvia samples as a risk assessment tool in breast diagnostics and are interested in their specific risk situation. At the same time, it could be demonstrated that it is an effective way to provide high-quality DNA for breast cancer gene analysis. However, it remains to be shown whether it would be possible to integrate it with the same acceptance in a nationwide breast cancer screening program.

Electronic supplementary material

The online version of this article (10.1186/s40001-018-0318-9) contains supplementary material, which is available to authorized users.

Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia

The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245. Through NETWORK and BATWING analyses, we found that the subclades of haplogroup Q continued to disperse from Central Asia and Southern Siberia during the past 10,000 years. Apart from its migration through the Beringia to the Americas, haplogroup Q also moved from Asia to the south and to the west during the Neolithic period, and subsequently to the whole of Eurasia and part of Africa.

Nasopharyngeal carcinoma risk prediction via salivary detection of host and Epstein-Barr virus genetic variants

Genetic susceptibility and Epstein-Barr virus (EBV) infection are important etiological factors in nasopharyngeal carcinoma (NPC). In this study, in southern China, where NPC is endemic, a single nucleotide polymorphism (SNP) in the EBV-encoded RPMS1 gene (locus 155391: G > A [G155391A]) and seven host SNPs (rs1412829, rs28421666, rs2860580, rs2894207, rs31489, rs6774494, and rs9510787) were confirmed to be significantly associated with NPC risk in 50 NPC cases versus 54 hospital-based controls with throat washing specimens and 1925 NPC cases versus 1947 hospital-based controls with buffy coat samples, respectively. We established a strategy to detect the NPC-associated EBV and host SNPs using saliva samples in a single test that is convenient, noninvasive, and cost-effective and displays good compliance. The potential utility of this strategy was tested by applying a risk prediction model integrating these EBV and host genetic variants to a population-based case-control study comprising 1026 incident NPC cases and 1148 controls. Receiver operating characteristic (ROC) curve analysis revealed an area under the curve of the NPC risk prediction model of 0.74 (95% CI: 0.71-0.76). Net reclassification improvement (NRI) analysis showed that inclusion of the EBV SNP significantly improved the discrimination ability of the model (NRI = 0.30, P < 0.001), suggesting the promising value of EBV characteristics for identifying high-risk NPC individuals in endemic areas. Taken together, we developed a promising NPC risk prediction model via noninvasive saliva sampling. This approach might serve as a convenient and effective method for screening the population with high-risk of NPC.

ATP2C2 and DYX1C1 are putative modulators of dyslexia-related MMR

BACKGROUND

Dyslexia is a specific learning disorder affecting reading and spelling abilities. Its prevalence is ~5% in German-speaking individuals. Although the etiology of dyslexia largely remains to be determined, comprehensive evidence supports deficient phonological processing as a major contributing factor. An important prerequisite for phonological processing is auditory discrimination and, thus, essential for acquiring reading and spelling skills. The event-related potential Mismatch Response (MMR) is an indicator for auditory discrimination capabilities with dyslexics showing an altered late component of MMR in response to auditory input.

METHODS

In this study, we comprehensively analyzed associations of dyslexia-specific late MMRs with genetic variants previously reported to be associated with dyslexia-related phenotypes in multiple studies comprising 25 independent single-nucleotide polymorphisms (SNPs) within 10 genes.

RESULTS

First, we demonstrated validity of these SNPs for dyslexia in our sample by showing that additional inclusion of a polygenic risk score improved prediction of impaired writing compared with a model that used MMR alone. Secondly, a multifactorial regression analysis was conducted to uncover the subset of the 25 SNPs that is associated with the dyslexia-specific late component of MMR. In total, four independent SNPs within DYX1C1 and ATP2C2 were found to be associated with MMR stronger than expected from multiple testing. To explore potential pathomechanisms, we annotated these variants with functional data including tissue-specific expression analysis and eQTLs.

CONCLUSION

Our findings corroborate the late component of MMR as a potential endophenotype for dyslexia and support tripartite relationships between dyslexia-related SNPs, the late component of MMR and dyslexia.

Development of a population-based cancer case-control study in southern china

With its population of over 1.3 billion persons, China offers abundant opportunities to discover causes of disease. However, few rigorous population-based case-control studies have as yet been conducted in mainland China. We conducted a population-based case-control study of nasopharyngeal carcinoma in Guangdong Province and Guangxi Autonomous Region. We collected questionnaires and biospecimens from incident cases recruited between March 2010 and December 2013, and population-based controls between November 2010 and November 2014. Preparatory activities prior to subject enrollment required approximately 18 months. We enrolled a total of 2554 NPC cases and 2648 controls. Among all identified cases, 83.8% participated. For the participating cases, the median time between diagnosis and interview was 2 days. Among all contacted controls, 82.7% participated. From the enrolled cases, we collected 2518 blood specimens (provided by 98.6% of eligible cases), 2350 saliva specimens (92.0%), 2514 hair specimens (98.4%), and 2507 toenail/fingernail specimens (98.2%). From the enrolled controls, we collected 2416 blood specimens (91.2%), 2505 saliva specimens (94.6%), 2517 hair specimens (95.1%), and 2514 toenail/fingernail specimens (94.9%). We demonstrate that population-based epidemiologic research can successfully be conducted in southern China. The study protocols, databases, and biobank will serve as an extraordinarily valuable resource for testing future etiologic hypotheses.

Health and well-being management in the military: a systematic review of genetic studies

BACKGROUND

Genetic research may have therapeutic value for mental and physical disorders and could have an indicative or preventative capacity. Little is known about the extent, form and utility of military-specific genetic research.

METHOD

A systematic review was conducted to evaluate existing genetic well-being studies of service personnel. The review specifically aimed to ascertain the current state of knowledge and feasibility of using genetics to aid recruitment and health management within military populations. Databases searched included MEDLINE, Embase, PsycINFO and Web of Science for relevant studies. Papers were rated using a genetics-specific quality assessment framework.

RESULTS

Ten papers were included within the final review, with seven mental-health-focused and three physical-health-focused genetic studies found within military populations. Eight papers considered candidate genes, one gene expression and one study was an outline of a future study of significant interest. Genetic commonalties were derived to yield shared physiological pathways. The 10 reviewed papers revealed moderate quality based on quality assessment.

CONCLUSIONS

Current genetic research within military populations is limited. Further studies on genetics, cost effectiveness, ethics and continual monitoring need to be explored before considering any movement toward clinical translation.

The Human Salivary Microbiome Is Shaped by Shared Environment Rather than Genetics: Evidence from a Large Family of Closely Related Individuals

The human microbiome is affected by multiple factors, including the environment and host genetics. In this study, we analyzed the salivary microbiomes of an extended family of Ashkenazi Jewish individuals living in several cities and investigated associations with both shared household and host genetic similarities. We found that environmental effects dominated over genetic effects. While there was weak evidence of geographical structuring at the level of cities, we observed a large and significant effect of shared household on microbiome composition, supporting the role of the immediate shared environment in dictating the presence or absence of taxa. This effect was also seen when including adults who had grown up in the same household but moved out prior to the time of sampling, suggesting that the establishment of the salivary microbiome earlier in life may affect its long-term composition. We found weak associations between host genetic relatedness and microbiome dissimilarity when using family pedigrees as proxies for genetic similarity. However, this association disappeared when using more-accurate measures of kinship based on genome-wide genetic markers, indicating that the environment rather than host genetics is the dominant factor affecting the composition of the salivary microbiome in closely related individuals. Our results support the concept that there is a consistent core microbiome conserved across global scales but that small-scale effects due to a shared living environment significantly affect microbial community composition.

Previous research shows that the salivary microbiomes of relatives are more similar than those of nonrelatives, but it remains difficult to distinguish the effects of relatedness and shared household environment. Furthermore, pedigree measures may not accurately measure host genetic similarity. In this study, we include genetic relatedness based on genome-wide single nucleotide polymorphisms (SNPs) (rather than pedigree measures) and shared environment in the same analysis. We quantify the relative importance of these factors by studying the salivary microbiomes in members of a large extended Ashkenazi Jewish family living in different locations. We find that host genetics plays no significant role and that the dominant factor is the shared environment at the household level. We also find that this effect appears to persist in individuals who have moved out of the parental household, suggesting that aspects of salivary microbiome composition established during upbringing can persist over a time scale of years.

Unraveling the human salivary microbiome diversity in Indian populations

The importance of studying the salivary microbiome has been highlighted for its connection to health and disease and as a potential tool for supplementing human genetic diversity studies. While the salivary microbiome has been studied in various world populations, Indian populations have not been examined. We therefore analyzed microbiome diversity in saliva samples from 92 volunteers from eight different sampling locations in India by amplifying and sequencing variable regions (V1 and V2) of the bacterial 16S rRNA gene. The results showed immense bacterial richness in Indian populations; we identified 165 bacterial genera and 785 unique Operational Taxonomic Units (OTUs), with substantial sharing among the populations. There were small, but significant correlations in the abundance of bacterial genera in sampling locations from the same geographic region. Most of the core OTUs detected were also observed previously in other populations, but Solobacterium spp., Lachnoanaerobaculum spp. and Alloprevotella spp. were observed to be a component of the saliva microbiome unique to Indian populations. Importantly, nine bacterial genera were observed that were not listed in the Human Oral Microbiome Database (HOMD). These results highlight the importance of analyzing underrepresented populations like those of India.

Human DNA extraction from whole saliva that was fresh or stored for 3, 6 or 12 months using five different protocols

Objective and Material and Methods

This study aimed to compare the quantity and quality of human DNA extracted from saliva that was fresh or frozen for three, six and twelve months using five different DNA extraction protocols: protocol 1 - Oragene™ commercial kit, protocol 2 - QIAamp DNA mini kit, protocol 3 - DNA extraction using ammonium acetate, protocol 4 - Instagene™ Matrix and protocol 5 - Instagene™ Matrix diluted 1:1 using proteinase K and 1% SDS. Briefly, DNA was analyzed using spectrophotometry, electrophoresis and PCR.

Results

Results indicated that time spent in storage typically decreased the DNA quantity with the exception of protocol 1. The purity of DNA was generally not affected by storage times for the commercial based protocols, while the purity of the DNA samples extracted by the noncommercial protocols typically decreased when the saliva was stored longer. Only protocol 1 consistently extracted unfragmented DNA samples. In general, DNA samples extracted through protocols 1, 2, 3 and 4, regardless of storage time, were amplified by human specific primers whereas protocol 5 produced almost no samples that were able to be amplified by human specific primers. Depending on the protocol used, it was possible to extract DNA in high quantities and of good quality using whole saliva, and furthermore, for the purposes of DNA extraction, saliva can be reliably stored for relatively long time periods.

Conclusions

In summary, a complicated picture emerges when taking into account the extracted DNA's quantity, purity and quality; depending on a given researchers needs, one protocol's particular strengths and costs might be the deciding factor for its employment.

Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations

OBJECTIVES

Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups.

METHODS

We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups.

RESULTS

Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis.

CONCLUSIONS

This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure.