de Vries, J. H. | bioRxiv Science

bioRxiv2021

Impact of SNP microarray analysis of compromised DNA on kinship classification success in the context of investigative genetic genealogy

Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relatively high input DNA quantity and quality, while SNP microarray data from compromised DNA typically obtainable from crime scene stains are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of SNP microarray analysis of deprecated DNA on kinship classification success, as relevant in IGG. Reference data from manufacturer-recommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 nanogram to 6.25 picogram led to decreased SNP call rates and increased genotyping errors, kinship classification success did not decrease down to 250 picogram for siblings and 1st cousins, 1 nanogram for 2nd cousins, while at 25 picogram and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800-200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false positive ones. Author SummaryInvestigative genetic genealogy (IGG), i.e., identifying unknown perpetrators of crime via genomic database-tracing of their relatives by means of microarray-based single nucleotide polymorphism (SNP) data, is a recently emerging field. However, SNP microarrays were developed for much higher DNA quantity and quality than typically available from crime scenes, while SNP microarray data on quality and quantity compromised DNA are largely missing. As first attempt to investigate how SNP microarray analysis of quantity and quality compromised DNA impacts kinship classification success in the context of IGG, we performed systematic SNP microarray analyses on DNA samples below the manufacturer-recommended quantity and quality as well as on mock casework samples and on skeletal remains. In addition to IGG, our results are also relevant for any SNP microarray analysis of compromised DNA, such as for the DNA prediction of appearance and biogeographic ancestry in forensics and anthropology and for other purposes.

genetics↗

bioRxiv2017

The effect of an 8-week mindful eating intervention on anticipatory reward responses in the midbrain

Obesity is a highly prevalent disease, usually resulting from chronic overeating. Accumulating evidence suggests that increased neural responses during the anticipation of high-calorie food play an important role in overeating. A promising method for counteracting enhanced food anticipation in overeating might be mindfulness-based interventions (MBIs). However, the neural mechanisms by which MBIs can affect food reward anticipation are unclear. In this randomized, actively controlled study, the primary objective was to investigate the effect of an 8-week mindful eating intervention on reward anticipation. On the neural level, we hypothesized that mindful eating would decrease striatal reward anticipation responses. Additionally, responses in the midbrain - from which the reward pathways originate - were explored. Using functional magnetic resonance imaging (fMRI), we tested 58 healthy participants with a wide body mass index range (BMI: 19-35 kg/m2), motivated to change their eating behavior. During scanning they performed an incentive delay task, measuring neural reward anticipation responses to caloric and monetary cues before and after 8 weeks of mindful eating or educational cooking (active control). Compared with the educational cooking intervention, mindful eating affected neural reward anticipation responses, with relatively reduced caloric versus monetary reward responses. This effect was, however, not seen in the striatum, but only in the midbrain. The secondary objective was to assess temporary and long-lasting (one year follow-up) intervention effects on self-reported eating behavior and anthropometric measures (BMI, waist circumference, waist-to-hip-ratio (WHR)). We did not observe effects of the mindful eating intervention on eating behavior. Instead, the control intervention showed temporary beneficial effects on BMI, waist circumference, and diet quality, but not on WHR or self-reported eating behavior, as well as long-lasting increases in knowledge about healthy eating. These results suggest that an 8-week mindful eating intervention may have decreased the relative salience of food cues by affecting midbrain but not striatal reward responses. However, these exploratory results should be verified in confirmatory research. The primary and secondary objectives of the study were registered in the Dutch Trial Register (NTR): NL4923 (NTR5025).

neuroscience↗