Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.

Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.

So many Nigerians: why is Nigeria overrepresented as the ancestral genetic homeland of Legacy African North Americans?

The genetics of African North Americans are complex amalgamations of various West and Central African peoples with modest gene flow from specific European and Amerindian peoples. A comprehensive understanding of African North American biohistory is a prerequisite for accurate interpretations of the ancestral genetics of this population. Too often, genetic interpretations falter with ahistorical reconstructions. The recently reported overrepresentation of Nigerian lineages in African North Americans reflects pronounced limitations in the African genomic database, the artificiality of the colonial maps of Africa, the contributions of multiple African empires and kingdoms into the transatlantic trade in enslaved Africans, and the overrepresentation of Yoruba peoples in the existing limited representation of West Africans in public genomic databases. This Matters Arising paper is in response to Micheletti et al. (2020), published in The American Journal of Human Genetics. See also the response by Micheletti et al. (2020), published in this issue.

RefXAS: an open access database of X-ray absorption spectra.

Under DAPHNE4NFDI, the X-ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user-friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server-side automatic authentication and (meta-) data storage via MongoDB, PostgreSQL and (data-) files via relevant APIs.

Environmental DNA: The next chapter.

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.

Supporting companies dealing with asbestos risk: Practical tools for occupational health services, risk prevention specialists, and companies.

Although asbestos has been officially banned in France for over two decades, it remains a major public health and occupational health issue. In 2012, French asbestos regulations became considerably more stringent and complex. Consequently, French Public Works and Building Trades Prevention Organisation (OPPBTP) and occupational health services have been working together for several years to support construction professionals. This support involves information, training and advice. This article presents the range of tools developed by OPPBTP and occupational health services to better understand the asbestos risk as it affects construction companies. These tools and this partnership have demonstrated positive results in confronting risk and in the implementation of suitable means of prevention. They serve the best interests of employees, companies and clients, by combining safeguards to employees' health and worksite performance.

East Asians' T-scores for the diagnosis of osteoporosis should be calculated using ethnicity- and gender-specific BMD reference ranges: justifications.

The 2013 ISCD consensus recommended a Caucasian female reference database for T-score calculation in men, which says "A uniform Caucasian (non-race adjusted) female reference database should be used to calculate T-scores for men of all ethnic groups." However, this statement was recommended for the US population, and no position was taken with respect to BMD reference data or ethnicity matching outside of the USA. In East Asia, currently, a Japanese BMD reference database is universally adopted in Japan for clinical DXA diagnosis, while both local BMD and Caucasian BMD reference databases are in use in Mainland China, South Korea, Taiwan, and Singapore. In this article, we argue that an ethnicity- and gender-specific BMD database should be used for T-score calculations for East Asians, and we list the justifications why we advocate so. Use of a Caucasian BMD reference database leads to systematically lower T-scores for East Asians and an overestimation of the prevalence of osteoporosis. Using a female BMD reference database to calculate T-scores for male patients leads to higher T-score values and an underestimation of the prevalence of osteoporosis. Epidemiological evidence does not support using a female BMD reference database to calculate T-scores for men. We also note that BMD reference databases collected in Asia should be critically evaluated for their quality.

The observation that older men suffer from hip fracture at DXA T-scores higher than older women and a proposal of a new low BMD category, osteofrailia, for predicting fracture risk in older men.

The clinical significance of osteoporosis lies in the occurrence of fragility fractures (FFx), and the most relevant fracture site is the hip. The T-score is defined as follows: (BMDpatient-BMDyoung adult mean)/SDyoung adult population, where BMD is bone mineral density and SD is the standard deviation. When the femoral neck (FN) is measured in adult Caucasian women, a cutpoint value of patient BMD of 2.5 SD below the young adult mean BMD results in a prevalence the same as the lifetime risk of hip FFx for Caucasian women. The FN T-score criterion for classifying osteoporosis in older Caucasian men has been provisionally recommended to be - 2.5, but debates remain. Based on a systematic literature review, we noted that older men suffer from hip FFx at a FN T-score approximately 0.5-0.6 higher than older women. While the mean hip FFx FN T-score of around - 2.9 for women lies below - 2.5, the mean hip FF FN T-score of around - 2.33 for men lies above - 2.5. This is likely associated with that older male populations have a higher mean T-score than older female populations. We propose a new category of low BMD status, osteofrailia, for older Caucasian men with T-score ≤ - 2 (T-score ≤ - 2.1 for older Chinese men) who are likely to suffer from hip FFx. The group with T-score ≤ - 2 for older Caucasian men is comparable in prevalence to the group with T-score ≤ - 2.5 for older Caucasian women. However, older men in such category on average have only half the FFx risk as that of older women with osteoporotic T-score.

Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.

BACKGROUND: The reliability of culture-independent pathogen detection in foods using metagenomics is contingent on the quality and composition of the reference database. The inclusion of microbial sequences from a diverse representation of taxonomies in universal reference databases is recommended to maximize classification precision for pathogen detection. However, these sizable databases have high memory requirements that may be out of reach for some users. In this study, we aimed to assess the performance of a foodborne pathogen (FBP)-specific reference database (taxon-specific) relative to a universal reference database (taxon-agnostic). We tested our FBP-specific reference database's performance for detecting Listeria monocytogenes in two complex food matrices-ready-to-eat (RTE) turkey deli meat and prepackaged spinach-using three popular read-based DNA-to-DNA metagenomic classifiers: Centrifuge, Kraken 2 and KrakenUniq. RESULTS: In silico host sequence removal led to substantially fewer false positive (FP) classifications and higher classification precision in RTE turkey deli meat datasets using the FBP-specific reference database. No considerable improvement in classification precision was observed following host filtering for prepackaged spinach datasets and was likely a consequence of a higher microbe-to-host sequence ratio. All datasets classified with Centrifuge using the FBP-specific reference database had the lowest classification precision compared to Kraken 2 or KrakenUniq. When a confidence-scoring threshold was applied, a nearly equivalent precision to the universal reference database was achieved for Kraken 2 and KrakenUniq. Recall was high for both reference databases across all datasets and classifiers. Substantially fewer computational resources were required for metagenomics-based detection of L. monocytogenes using the FBP-specific reference database, especially when combined with Kraken 2. CONCLUSIONS: A universal (taxon-agnostic) reference database is not essential for accurate and reliable metagenomics-based pathogen detection of L. monocytogenes in complex food matrices. Equivalent classification performance can be achieved using a taxon-specific reference database when the appropriate quality control measures, classification software, and analysis parameters are applied. This approach is less computationally demanding and more attainable for the broader scientific and food safety communities.

Reference population database for 24 STR loci of selected provinces of Argentina.

BACKGROUND: Argentinean population is the result of admixture between South Amerindians, Europeans and to a lesser degree, Africans. Since the advent of forensic molecular genetics, the construction of local reference databases became mandatory. Aiming to further extend the technical quality reference database of Argentina, we present herein the allele frequencies for 24 autosomal STRs, including D22S1045, and SE33 (not previously reported for Argentina in STRidER). CONCLUSIONS: Genotypes of 6454 unrelated individuals (3761 males and 2694 females) from 13 out of 23 provinces were analysed. Forensic parameters were calculated for each marker. The observed heterozygosity ranged from 0.661 (TPOX) to 0.941 (SE33). The locus SE33 was revealed to be the most informative marker showing the highest values for PIC (0.955), GD (0.952), TPI (8.455) and PE (0.879). On the other hand, TPOX turned out to be the least informative marker: PIC (0.618), GD (0.669), and PE (0.371). The high number of analyzed individuals allowed detecting low frequency alleles and microvariants in CSF1PO; D16S539 and D21S11 D18S51; PENTA D; PENTA E and at locus D6S1043. METHODS AND RESULTS: This study is the most extensive for Argentina and complements the already reported information concerning the autosomal STRs commonly used in forensic identification. The results were submitted passing STRidER quality control standards (QC), receiving the reference number STR000327 v.2.

Problems, principles and progress in computational annotation of NMR metabolomics data.

BACKGROUND: Compound identification remains a critical bottleneck in the process of exploiting Nuclear Magnetic Resonance (NMR) metabolomics data, especially for 1H 1-dimensional (1H 1D) data. As databases of reference compound spectra have grown, workflows have evolved to rely heavily on their search functions to facilitate this process by generating lists of potential metabolites found in complex mixture data, facilitating annotation and identification. However, approaches for validating and communicating annotations are most often guided by expert knowledge, and therefore are highly variable despite repeated efforts to align practices and define community standards. AIM OF REVIEW: This review is aimed at broadening the application of automated annotation tools by discussing the key ideas of spectral matching and beginning to describe a set of terms to classify this information, thus advancing standards for communicating annotation confidence. Additionally, we hope that this review will facilitate the growing collaboration between chemical data scientists, software developers and the NMR metabolomics community aiding development of long-term software solutions. KEY SCIENTIFIC CONCEPTS OF REVIEW: We begin with a brief discussion of the typical untargeted NMR identification workflow. We differentiate between annotation (hypothesis generation, filtering), and identification (hypothesis testing, verification), and note the utility of different NMR data features for annotation. We then touch on three parts of annotation: (1) generation of queries, (2) matching queries to reference data, and (3) scoring and confidence estimation of potential matches for verification. In doing so, we highlight existing approaches to automated and semi-automated annotation from the perspective of the structural information they utilize, as well as how this information can be represented computationally.

Influence of 16S rRNA reference databases in amplicon-based environmental microbiome research.

PURPOSE: The reference databases play a pivotal role in amplicon microbiome research, however these databases differ in the sequence content and taxonomic information available. Studies on mock community and human health microbiome have revealed the problems associated with the choice of reference database on the outcome. Nonetheless, the influence of reference databases in environmental microbiome studies is not explicitly illustrated. METHODS: This study analyzed the amplicon (V1V3, V3V4, V4V5 and V6V8) data of 128 soil samples and evaluated the impact of 16S rRNA databases, Genome Taxonomy Database (GTDB), Ribosomal Database Project (RDP), SILVA and Consensus Taxonomy (ConTax), on microbiome inference. RESULTS: The analyses showed that the distribution of observed amplicon sequence variants was significantly different (P-value < 2.647e-12) across four datasets, generated using different databases for each amplicon region. In addition, the beta diversity was also found to be altered by different databases. Further investigation revealed that the microbiome composition inferred by various databases differ significantly (P-value = 0.001), irrespective of amplicon regions. This study, found that the core-microbiome structure in environmental studies is influenced by the type of reference database used. CONCLUSION: In summary, this present study illustrates that the choice of reference database could influence the outcome of environmental microbiome research.

Reference Database of Inner Retinal Layer Thickness and Thickness Asymmetry in Healthy Thai Adults as Measured by the Spectralis Spectral-Domain Optical Coherence Tomography.

INTRODUCTION: The study aimed to determine a reference database of the thickness and intraocular thickness asymmetry of total retina, retinal nerve fiber layer (RNFL), ganglion cell layer (GCL), and inner plexiform layer (IPL) in healthy Thai subjects measured by the Spectralis spectral-domain optical coherence tomography. METHODS: This cross-sectional study recruited the healthy subjects age ≥18 years, having spherical refraction within ±6 diopters and cylindrical refraction ±3 diopters, from a hospital's personnel and the people visiting the ophthalmology department. Only 1 eye of each subject was randomly selected for an analysis. Macular images were obtained using posterior pole thickness scan protocol over a 24° × 24° area at the center of the fovea. The automated retinal thickness segmentation values of total retina and three inner retinal layers were calculated for the mean and the mean intraocular thickness difference between superior and inferior retinal hemispheres. The influence of age, gender, and axial length on thickness and thickness asymmetry of individualized retinal layer was evaluated. RESULTS: 252 subjects were included in study with a mean (SD) age of 46.7 (15.8) years, and 120 (47.6%) were males. According to the Early Treatment Diabetic Retinopathy Study map, the inner ring area was the thickest location of the total retina (range; 326.0-341.5 µm), GCL (range; 47.7-52.7 µm), and IPL (range; 39.9-42.1 µm), whereas the thickest location of RNFL was at the outer ring area (range; 18.8-47.5 µm). For posterior pole intraocular thickness asymmetry, the greatest mean ± SD difference was observed for total retina (9.0 ± 2.2 µm), followed by RNFL (9.9 ± 3.2 µm) and GCL (2.7 ± 0.6 µm), and the lowest mean difference was noted for IPL (2.4 ± 0.5 µm). The thickness and thickness asymmetry of each retinal layer were variably influenced by age, gender, and axial length; however, these factors had a minimal influence on the thickness asymmetry maps of GCL and RNFL. CONCLUSION: The reference database of the macular thickness and thickness asymmetry from this study would be beneficial in determining physiologic variations of the OCT parameters in the healthy Thai population.

The mitochondrial DNA HVI and HVII sequences and haplogroup distribution in a population sample from Vietnam.

BACKGROUND: Mitochondrial DNA (mtDNA) analysis has been used in forensics and requires well-established population databases for statistical interpretations. However, high-quality mtDNA data from Vietnamese population samples have been limited. AIM: To examine the mtDNA sequences and haplogroup compositions of a Vietnamese population to provide an mtDNA dataset that can further be used to construct a Vietnamese-specific reference database. SUBJECTS AND METHODS: A total of 173 Vietnamese individuals were analysed for two hypervariable regions (HVI and HVII) of mtDNA. Forensic parameters were calculated and haplogroup assignment was performed based on the resulting mtDNA haplotypes. Genetic relationships between the Vietnamese and other Asian populations were investigated through principal component analysis (PCA) and pairwise Fst. RESULTS: The Vietnamese population sample consisted of 145 different haplotypes with a random match probability of 0.96%, a power of discrimination of 0.9904, and a haplotype diversity of 0.9962. The samples were assigned to 83 haplogroups that were commonly reported in Asia. PCA and pairwise Fst revealed close relationships of the Vietnamese population with other Asian populations, especially with populations in proximity. CONCLUSION: The results from this study can contribute to the current genetic information content as a supplementary mtDNA reference dataset for forensic investigations and phylogenetic research.

Genetic characteristics and forensic features of Xibe ethnic group revealed via extended set of Y-STRs.

BACKGROUND: Xibe is the fifth largest minority population of Liaoning province. Predominately they live in Liaoning province (69.52%), followed by Xinjiang (18.06%), Heilongjiang (3.99%), Jilin (1.63%) and Inner Mongolia provinces (1.57%). AIM: To provide an updated and precise population database on an extended set of Y STRs not available before and explore the forensic characteristics of 26 Y chromosomal STRs. SUBJECTS & METHODS: In this study, we genotyped 406 unrelated Xibe male individuals from Liaoning province using Goldeneye® 26Y System kit and calculated the forensic parameters of these 26 Y STRs loci. RESULTS: All haplotypes generated for 406 Xibe samples using Goldeneye® 26Y kit were unique with a discrimination capacity (DC) of 1. On restricting the haplotypes to the Y-filer® set of 17 Y-STRs, we observed 392 haplotypes. Among them 93.53% (380) were unique with a DC of 0.9655 and haplotype diversity (HD) of 0.9998, showing high discrimination power of the extended set of markers in this population. Allelic frequencies ranged from 0.0024 to 0.7684 across 26 Y STRs loci. DYS385 showed the highest gene diversity (0.9691) among all markers. CONCLUSION: According to pairwise RST genetic distances among Xibe populations from China, the Liaoning Xibe population showed the closest genetic distance (0.0035) followed by Xinjiang Xibe population (0.0218). Multidimensional scaling (MDS) analysis among Xibe and 29 other Chinese populations showed that local populations such as Manchu from Liaoning and Han from Beijing had a close affinity while Tibetans from Aba, China, were most distant from Xibe populations. Moreover, 12 individuals showed a null allele at DYS448 in Xibe population samples. We submitted Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.

Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases.

The problem of low species-level identification rates in plants by DNA barcoding is exacerbated by the fact that reference databases are far from being comprehensive. We investigate the impact of increased sampling depth on identification success by analyzing the efficacy of established plant barcode marker sequences (rbcL, matK, trnL-trnF, psbA-trnH, ITS). Adding sequences of the same species to the reference database led to an increase in correct species assignment of +10.9% for rbcL and +19.0% for ITS. Simultaneously, erroneous identification dropped from ∼40% to ∼12.5%. Despite its evolutionary constraints, ITS showed the highest identification rate and identification gain by increased sampling effort, which makes it a very suitable marker in the planning phase of a barcode study. The limited sequence availability of trnL-trnF is problematic for an otherwise very promising plastid plant barcoding marker. Future developments in machine learning algorithms have the potential to give new impetus to plant barcoding, but are dependent on extensive reference databases. We expect that our results will be incorporated into future plans for the development of DNA barcoding reference databases and will lead to these being developed with greater depth and taxonomic coverage.

Measurement of macular thickness with optical coherence tomography: impact of using a paediatric reference database and analysis of interocular symmetry.

PURPOSE: Optical coherence tomography (OCT) software is used to classify abnormality of macular thickness by colour category based on reference data from adult series. We assessed the impact of using paediatric reference thickness values for macular thickness instead of adult reference values. METHODS: Cross-sectional study. Primary and tertiary healthcare setting. Out of 140 healthy participants aged 5 to 18 years, 126 were eligible, 83% from European origin. Following a dilated eye examination and cycloplegic refraction, participants underwent macular scanning with OCT (Topcon 3D OCT-2000). Macular thickness paediatric reference values were recorded by spherical equivalent (SE) and sex, and the specific agreement between paediatric and adult reference values below or equal to percentile 5 and above percentile 95 was estimated. The absolute interocular differences for all macular parameters were determined. RESULTS: Multivariate regression analysis confirmed statistically independent positive associations between SE and average thickness, total volume, and temporal and inferior outer quadrants (all p values ≤ 0.003). The analysis also revealed higher values in males for average thickness, central thickness, and all inner macula quadrants (all p values ≤ 0.039). The use of the adult database only detected 49% of the extreme values (≤ p5 and > p95) in our paediatric sample. The 95th percentile limits for absolute interocular differences for all macular parameters ranged from 12 to 17 µm. CONCLUSIONS: OCT-based macular reference values for paediatric SE and sex improve detection of children with abnormal macular thicknesses. Interocular differences exceeding standard references for macular parameters should be considered for further examinations.

The use of taxon-specific reference databases compromises metagenomic classification.

A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the identification of a range of fungal species in the vast majority of samples. In the HumanMycobiomeScan pipeline, sequence reads are mapped against a reference database containing fungal genome sequences only. We argue that using reference databases comprised of a single taxonomic group leads to an unacceptably high number of false-positives due to: (i) mapping to conserved genetic regions in reference genomes, and (ii) sequence contamination in the assembled reference genomes. To demonstrate this, we replaced the HumanMycobiomeScan's fungal reference database with one containing genome sequences of amphibians and reptiles and re-analysed their case study. The classification pipeline recovered all species present in the reference database, revealing turtles (Geoemydidae), bull frogs (Pyxicephalidae) and snakes (Colubridae) as the most abundant herpetological taxa in the human gut. We also re-analysed their case study using a kingdom-agnostic pipeline. This revealed that while the gut of hunter-gatherers and Western subjects may be colonized by a range of microbial eukaryotes, only three fungal families were retrieved. These results highlight the pitfalls of using taxon-specific reference databases for metagenome classification, even when they are comprised of curated whole genome data. We propose that databases containing all domains of life provide the most suitable option for metagenomic species profiling, especially when targeting microbial eukaryotes.

Interobserver reproducibility and interocular symmetry of the macular ganglion cell complex: assessment in healthy children using optical coherence tomography.

BACKGROUND: Assessment of interobserver reproducibility and interocular symmetry using optical coherence tomography (OCT)-based measurements of the macular ganglion cell complex (GCC) in healthy children facilitates interpretation of OCT data. We assessed the interobserver reproducibility and interocular symmetry of GCC and evaluated candidate determinants. METHODS: This was a cross-sectional study performed in a primary and tertiary health-care setting. A total of 126 healthy participants aged 5 to 18 years were eligible. GCC scans were performed by 4 operators using the Topcon 3D OCT-2000 device. Intraclass correlation coefficients (ICCs) were used to estimate reproducibility and symmetry. Cut-off points for symmetry were defined as the 95th percentile of the absolute interocular difference for 6 GCC parameters. Percentile distributions of interocular difference were generated based on age and difference in absolute interocular spherical equivalent (SE). RESULTS: The reproducibility ICC ranged from 0.96 to 0.98 for all 6 GCC parameters. Cut-off points for interocular symmetry of the superior and inferior quadrants and total macular retinal nerve fibre layer thickness (mRNFL) and macular ganglion cell layer-inner plexiform layer thickness were 3.5, 4.5, 3.0, 3.0, 2.5, and 2.5 µm respectively. A positive association was observed between the absolute interocular difference of SE and superior and total mRNFL symmetry values (p = 0.047 and p = 0.040, respectively). CONCLUSIONS: OCT measurements of GCC in healthy children show excellent reproducibility. Interocular differences in SE should be assessed when mRNFL differences exceed the 95% cut-off. These findings can contribute to establish reference values for interocular symmetry in paediatric GCC parameters.

Demand for larger Y-STR reference databases in ethnic melting-pot countries: Argentina as a test case.

The Y chromosome behaves as a single locus. Its genetic information is useful in forensic casework, deficiency kinship testing, and population genetics studies. Continuous increases of loci number within commercial kits forced modification of worldwide reference databases. In Pan American countries, like Argentina, diverse parental ethnic groups contributed to the extant admixed urban populations. We report 509 additional haplotypes of 23 Y-STRs from donors inhabiting urban areas of six Argentinean provinces: Buenos Aires, Santiago del Estero, Santa Cruz, Rio Negro, Santa Fe, and Formosa. To better understand the demographic landscape of the admixed urban paternal lineages, structural analysis was performed using published data from other Argentinean provinces. AMOVA by Rst distance and inferred haplogroups by two predictive online software methods based on haplotypes yielded complementary results with respect to detected population structure, probably due to the different proportions of the Native American Q3-M3 haplogroup in the studied samples. This situation, which is common to most North, Meso, and South American countries, underscores the need for the additional step of typing specific SNPs for haplogroup diagnosis. We propose organizing Y-STR haplotype reference databases according to the most frequent haplogroups detected in a given admixed population.

Test-retest repeatability of the pattern electroretinogram and flicker electroretinogram.

PURPOSE: To evaluate the repeatability of the steady-state pattern electroretinogram (PERG) and full-field flicker electroretinogram (Flicker ERG) protocols, delivered by the office-based Neuro Optic Vision Assessment (NOVA)™ testing platform, in healthy subjects. METHODS: Healthy individuals underwent PERG (16° and 24°) and Flicker ERG [fixed luminance (FL) and multi-luminance (ML)] testing protocols. Test-retest repeatability of protocols was calculated using intra-class correlation coefficients (ICC). Reference values of the parameters of the aforementioned tests were also calculated. RESULTS: The ICCs for the PERG parameters ranged from 0.793 to 0.911 (p < 0.001). The ICCs for the Flicker ERG parameters ranged from 0.968 to 0.994 (p < 0.001). A linear regression analysis was applied to assess the impact of age on ERG responses. Age had a significant impact on all PERG parameters (16° or 24°). The phase response of the FL Flicker ERG significantly decreased with age (ß = - 0.837, p ≤ 0.001). The FL Flicker ERG Magnitude was also impacted with a significant quadratic effect of age (ß = - 0.0047, p = 0.0004). Similarly, the Phase Area Under the Curve (Phase AUC) of the ML Flicker ERG significantly declined with age (ß = - 0.007, p = 0.009), and the impact on the Magnitude AUC was significant as well, with a negative quadratic age effect. CONCLUSIONS: The PERG and Flicker ERG protocols, delivered by an office-based testing platform, were shown to have good-to-excellent test-retest repeatability when tests were performed in the same order and in immediate succession.