"I'm trying to figure out who the hell I am": Examining the psychosocial and mental health experience of individuals learning "Not Parent Expected" news from a direct-to-consumer DNA ancestry test.

Background: According to recent estimates, around 30 million people have taken Direct-to-Consumer DNA ancestry tests, typically marketed as a fun, harmless and exciting process of discovery. These tests estimate a user's ethnic ancestry, also matching users with biological relations on their database. This matching can produce a surprising 'not parent expected' discovery, where a user learns that an assumed parent (typically the father) is not a biological parent.

Toward 3D facial analysis for recognizing Mendelian causes of autism spectrum disorder.

Recognizing Mendelian causes is crucial in molecular diagnostics and counseling for patients with autism spectrum disorder (ASD). We explored facial dysmorphism and facial asymmetry in relation to genetic causes in ASD patients and studied the potential of objective facial phenotyping in discriminating between Mendelian and multifactorial ASD. In a cohort of 152 ASD patients, 3D facial images were used to calculate three metrics: a computational dysmorphism score, a computational asymmetry score, and an expert dysmorphism score.

A Guide to Measuring Heart and Respiratory Rates Based on Off-the-Shelf Photoplethysmographic Hardware and Open-Source Software.

The remote monitoring of vital signs via wearable devices holds significant potential for alleviating the strain on hospital resources and elder-care facilities. Among the various techniques available, photoplethysmography stands out as particularly promising for assessing vital signs such as heart rate, respiratory rate, oxygen saturation, and blood pressure. Despite the efficacy of this method, many commercially available wearables, bearing Conformité Européenne marks and the approval of the Food and Drug Administration, are often integrated within proprietary, closed data ecosystems and are very expensive.

Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders.

The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry.

Whole Slide Imaging-Based Prediction of TP53 Mutations Identifies an Aggressive Disease Phenotype in Prostate Cancer.

Unlabelled: In prostate cancer, there is an urgent need for objective prognostic biomarkers that identify the metastatic potential of a tumor at an early stage. While recent analyses indicated TP53 mutations as candidate biomarkers, molecular profiling in a clinical setting is complicated by tumor heterogeneity. Deep learning models that predict the spatial presence of TP53 mutations in whole slide images (WSI) offer the potential to mitigate this issue.

MEMOR: A database of archeological human remains collections from Flanders, Belgium.

The aim of this article is to describe a newly created open access database of archeological human remains collections from Flanders, Belgium. The MEMOR database (www.memor.

Genomic analyses of hair from Ludwig van Beethoven.

Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public.

From collected stamps to hair locks: ethical and legal implications of testing DNA found on privately owned family artifacts.

Biological samples containing DNA that is attributed to deceased relatives, can now undergo genetic testing at a reasonable cost due to revolutionary improvements in sampling, sequencing, and analytical techniques. This artifact DNA testing, or 'artDNA', includes genetic analysis of hair locks, stamps, envelopes with saliva traces or teeth. ArtDNA can reveal valuable information about a deceased relative or one's genetic background, but it also presents novel ethical dilemmas and legal uncertainties for genetic researchers and commercial testing services.

Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition.

The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.

Extracting functional insights from loss-of-function screens using deep link prediction.

We present deep link prediction (DLP), a method for the interpretation of loss-of-function screens. Our approach uses representation-based link prediction to reprioritize phenotypic readouts by integrating screening experiments with gene-gene interaction networks. We validate on 2 different loss-of-function technologies, RNAi and CRISPR, using datasets obtained from DepMap.

Halvade somatic: Somatic variant calling with Apache Spark.

Background: The accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the detection of low-frequency variants is also desired. In turn, this leads to large volumes of raw sequencing data to process and hence, large computational requirements.

Network-Based Analysis to Identify Drivers of Metastatic Prostate Cancer Using GoNetic.

Most known driver genes of metastatic prostate cancer are frequently mutated. To dig into the long tail of rarely mutated drivers, we performed network-based driver identification on the Hartwig Medical Foundation metastatic prostate cancer data set (HMF cohort). Hereto, we developed GoNetic, a method based on probabilistic pathfinding, to identify recurrently mutated subnetworks.

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics.

Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification.

3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies.

The analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height).

Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples.

Background: Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artefacts might obfuscate the variant calling.

Identification and characterization of novel rapidly mutating Y-chromosomal short tandem repeat markers.

Short tandem repeat polymorphisms on the male-specific part of the human Y-chromosome (Y-STRs) are valuable tools in many areas of human genetics. Although their paternal inheritance and moderate mutation rate (~10 mutations per marker per meiosis) allow detecting paternal relationships, they typically fail to separate male relatives. Previously, we identified 13 Y-STR markers with untypically high mutation rates (>10 ), termed rapidly mutating (RM) Y-STRs, and showed that they improved male relative differentiation over standard Y-STRs.

Review of policies of companies and databases regarding access to customers' genealogy data for law enforcement purposes.

The rapidly evolving popularity of direct-to-consumer genetic genealogy companies has made it possible to retrieve genomic information for unintended reasons by third parties, including the emerging use for law enforcement purposes. The question remains whether users of direct-to-consumer genetic genealogy companies and genealogical databases are aware that their genetic and/or genealogical data could be used as means to solving forensic cases. Our review of 22 companies' and databases' policies showed that only four companies have provided additional information on how law enforcement agencies should request permission to use their services for law enforcement purposes.

Ysurnames? The patrilineal Y-chromosome and surname correlation for DNA kinship research.

The Y-chromosome is a widely studied and useful small part of the genome providing different applications for interdisciplinary research. In many (Western) societies, the Y-chromosome and surnames are paternally co-inherited, suggesting a corresponding Y-haplotype for every namesake. While it has already been observed that this correlation may be disrupted by a false-paternity event, adoption, anonymous sperm donor or the co-founding of surnames, extensive information on the strength of the surname match frequency (SMF) with the Y-chromosome remains rather unknown.

A Historical-Genetic Reconstruction of Human Extra-Pair Paternity.

Paternity testing using genetic markers has shown that extra-pair paternity (EPP) is common in many pair-bonded species [1, 2]. Evolutionary theory and empirical data show that extra-pair copulations can increase the fitness of males as well as females [3, 4]. This can carry a significant fitness cost for the social father, who then invests in rearing offspring that biologically are not his own [5].

Correction to: The Dutch Y-chromosomal landscape.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.