Biology subjects

Hastings, W.

Publications and source records attributed to Hastings, W..

2 recordsLinked to original sources

bioRxiv2022

Effects of DNA extraction, DNA integrity, and laboratory on the precision of qPCR-based telomere length measurement - a multi-lab impartial study

Measuring telomere length (TL) with high precision is challenging. Currently there is insufficient understanding of the causes of variation in measurement precision, particularly for qPCR-based measurement. To better understand how DNA extraction protocols and laboratory-specific analytical factors influence qPCR-based TL measurement precision, we conducted a multi-laboratory study involving four labs and six DNA extraction protocols assaying the same blinded human whole blood samples. DNA extraction protocols differed in underlying principles (magnetic beads, salting out, silica membrane) and commercial kits. A fifth lab performed Telomere Restriction Fragment (TRF) analysis using Southern Blot technique with one DNA extraction protocol. All labs performed TL measurement using their standard procedures on two sets of fifty double blinded samples. Data was sent to a central point for unblinding and statistical analyses. Precision was quantified using the Intraclass Correlation Coefficient (ICC). Correlations with TRF measurements were also calculated. Repeated qPCR-based measurements of the same DNA extraction yielded ICC values ranging from 0.24 to 0.94. ICC values calculated over measurements of repeated DNA extractions were on average 0.23 lower and ranged from 0.02 to 0.83. The latter ICC estimates more strongly predicted the association between qPCR- and Southern blot-based measurements across the protocol / lab combinations (R2=0.56 vs. R2=0.93). We conclude that ICC calculated over measurements on repeated DNA extractions reliably indicates measurement precision, while ICC calculated over multiple measurements of the same DNA extraction overestimates measurement precision. Variation in ICC was driven by variation between laboratories, with few consistent DNA extraction protocol effects. Values of DNA integrity and purity generally characterized as reflecting high sample quality, (e.g. OD 260/280 of 1.8 and OD 260/230 of 2.0) were associated with qPCR-based measurement precision, but did not always predict higher ICCs.

molecular biology↗

bioRxiv2022

Ventral temporal and posteromedial sulcal morphology in autism spectrum disorder

Two recent parallel research tracks link tertiary sulcal morphology--sulci that emerge last in gestation and continue to develop after birth--with functional features of the cerebral cortex and cognition, respectively. The first track identified a relationship between the mid-fusiform sulcus (MFS) in ventral temporal cortex (VTC) and cognition in individuals with Autism Spectrum Disorder (ASD). The second track identified a new tertiary sulcus, the inframarginal sulcus (IFRMS), that serves as a tripartite landmark within the posteromedial cortex (PMC). As VTC and PMC are structurally and functionally different in individuals with ASD compared to neurotypical controls (NTs), here, we integrated these two tracks with a twofold approach. First, we tested if there are morphological differences in VTC and PMC sulci between 50 NTs and 50 individuals with ASD. Second, we tested if tertiary sulcal morphology was linked to cognition in ASD individuals. Our twofold approach replicates and extends recent findings in five ways. First, in terms of replication, the standard deviation (STD) of MFS cortical thickness (CT) was increased in ASDs compared to NTs. Second, MFS length was shorter in ASDs compared to NTs. Third, the CT STD effect extended to other VTC and PMC sulci. Fourth, a subset of VTC and PMC morphological features were correlated between regions in ASD. Fifth, IFRMS depth was negatively associated with ADOS-GS score. These results empirically support a relationship between later-developing, tertiary sulci and ASD, providing a novel framework to study the relationship between brain structure and cognition in additional neurodevelopmental disorders in future studies. Lay SummaryWe observed that some, but not all, morphological features of later-developing tertiary indentations (sulci) in the cerebral cortex differed significantly between neurotypical controls and individuals with autism spectrum disorder (ASD). In ASD, a subset of sulcal morphological features also correlated between brain areas and one feature reflected differences in cognition. Thus, studying these structures provides insight into how individual variability in structure is related to individual variability in cognition in ASD.

neuroscience↗