Serious limitations of the QTL/Microarray approach for QTL gene discovery

<p>Abstract</p> <p>Background</p> <p>It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL). However, the effectiveness of this approach has not been assessed.</p> <p>Results</p> <p>Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons<b/> between congenic and background strains. Three studies led to the identification of an underlying <it>QTL </it>gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD) regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of <it>QTL </it>regulated in <it>cis </it>(<it>cis </it>eQTL) showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP).</p> <p>Conclusions</p> <p>The literature shows limited successes from the QTL/microarray approach to identify <it>QTL </it>genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select <it>cis-</it>eQTL over <it>trans-</it>eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false <it>cis-</it>eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes that were not tested. Together, our results explain the tendency to report QTL candidates as differentially expressed and indicate that the utility of the QTL/microarray as currently implemented is limited. Alternatives are proposed that make use of microarray data from multiple experiments to overcome the outlined limitations.</p

Functional polymorphisms in the P2X7 receptor gene are associated with stress fracture injury

Context: Military recruits and elite athletes are susceptible to stress fracture injuries. Genetic predisposition has been postulated to have a role in their development. The P2X7 receptor (P2X7R) gene, a key regulator of bone remodelling, is a genetic candidate that may contribute to stress fracture predisposition. Objective: To evaluate the putative contribution of P2X7R to stress fracture injury in two separate cohorts, military personnel and elite athletes. Methods: In 210 Israeli Defence Forces (IDF) military conscripts, stress fracture injury was diagnosed (n=43) based on symptoms and a positive bone scan. In a separate cohort of 518 elite athletes, self-reported medical imaging scan-certified stress fracture injuries were recorded (n=125). Non-stress fracture controls were identified from these cohorts who had a normal bone scan or no history or symptoms of stress fracture injury. Study participants were genotyped for functional SNPs within the P2X7R gene using proprietary fluorescence-based competitive allele-specific PCR assay. Pearson Chi-square (χ2) tests, corrected for multiple comparisons, were used to assess associations in genotype frequencies. Results: The variant allele of P2X7R SNP rs3751143 (Glu496Ala- loss of function) was associated with stress fracture injury, while the variant allele of rs1718119 (Ala348Thr- gain of function) was associated with a reduced occurrence of stress fracture injury in military conscripts (P<0.05). The association of the variant allele of rs3751143 with stress fractures was replicated in elite athletes (P<0.05), whereas the variant allele of rs1718119 was also associated with reduced multiple stress fracture cases in elite athletes (P<0.05). Conclusions: The association between independent P2X7R polymorphisms with stress fracture prevalence supports the role of a genetic predisposition in the development of stress fracture injury

The effect of postexercise carbohydrate and protein ingestion on bone metabolism

Purpose To investigate the effect of feeding carbohydrate and protein (CHO+PRO), immediately or 2 h after an exhaustive run, on the bone turnover response in endurance runners. Methods 10 men (age 28±5 y, height 1.74±0.05 m, body mass 69.7±6.3 kg) performed treadmill running at 75%VO2max, until exhaustion, on three occasions. Blood was collected before and immediately, 1, 2, 3, 4 and 24 h post-exercise, for measurement of β-CTX, P1NP, PTH, PO4, ACa and Ca2+. This was a randomised, counterbalanced, placebo-controlled, single-blinded, cross-over study. The three trials were; i) placebo (PLA), PLA solution was ingested immediately and 2 h post-exercise, ii) immediate feeding (IF), CHO+PRO (1.5 g.kgBM-1 dextrose and 0.5 g.kgBM-1 whey) were ingested immediately post-exercise and PLA 2 h post-exercise, and iii) delayed feeding (DF), PLA was ingested immediately post-exercise and CHO+PRO solution 2 h post-exercise. Data were analysed using repeated measures ANOVA and post-hoc Tukey’s HSD. Results At 1 and 2 h post-exercise, β-CTX concentrations were lower in the IF trial than the DF and PLA trials (P≤0.001). At 3 h post-exercise, β-CTX concentrations were higher in the PLA trial than the IF (P≤0.001) and DF trials (P=0.026). At 4 h post-exercise, β-CTX concentrations were lower in the DF trial than the IF (P=0.003) and PLA trials (P≤0.001). At 4 h post-exercise, P1NP was higher in the IF trial than in DF (P=0.026) and PLA trials (P=0.001). At 3 h post-exercise, PTH was higher in the IF trial than the DF trial (P≤0.001). Conclusions Following exhaustive running, immediate ingestion of CHO+PRO may be beneficial, as it decreases bone resorption marker concentrations and increases bone formation marker concentrations; creating a more positive bone turnover balance

Responsive Operations for Key Services (ROKS): A Modular, Low SWaP Quantum Communications Payload

Quantum key distribution (QKD) is a theoretically proven future-proof secure encryption method that inherits its security from fundamental physical principles. With a proof-of-concept QKD payload having flown on the Micius satellite since 2016, efforts have intensified globally. Craft Prospect, working with a number of UK organisations, has been focused on miniaturising the technologies that enable QKD so that they may be used in smaller platforms including nanosatellites. The significant reduction of size, and therefore the cost of launching quantum communication technologies either on a dedicated platform or hosted as part of a larger optical communications will improve potential access to quantum encryption on a relatively quick timescale. The Responsive Operations for Key Services (ROKS) mission seeks to be among the first to send a QKD payload on a CubeSat into low Earth orbit, demonstrating the capabilities of newly developed modular quantum technologies. The ROKS payload comprises a quantum source module that supplies photons randomly in any of four linear polarisation states fed from a quantum random number generator; an acquisition, pointing, and tracking system to fine-tune alignment of the quantum source beam with an optical ground station; an imager that will detect cloud cover autonomously; and an onboard computer that controls and monitors the other modules, which manages the payload and assures the overall performance and security of the system. Each of these modules have been developed with low Size, Weight and Power (SWaP) for CubeSats, but with interoperability in mind for other satellite form factors. We present each of the listed components, together with the initial test results from our test bench and the performance of our protoflight models prior to initial integration with the 6U CubeSat platform systems. The completed ROKS payload will be ready for flight at the end of 2022, with various modular components already being baselined for flight and integrated into third party communication missions

Evidence of maternal QTL affecting growth and obesity in adult mice

Most quantitative trait loci (QTL) studies fail to account for the effect that the maternal genotype may have on an individual’s phenotypes, even though maternal effect QTL have been shown to account for considerable variation in growth and obesity traits in mouse models. Moreover, the fetal programming theory suggests that maternal effects influence an offspring’s adult fitness, although the genetic nature of fetal programming remains unclear. Within this context, our study focused on mapping genomic regions associated with maternal effect QTL by analyzing the phenotypes of chromosomes 2 and 7 subcongenic mice from genetically distinct dams. We analyzed 12 chromosome 2 subcongenic strains that spanned from 70 to 180 Mb with CAST/EiJ donor regions on the background of C57BL/6 J, and 14 chromosome 7 subcongenic strains that spanned from 81 to 111 Mb with BALB/cByJ donor regions on C57BL/6ByJ background. Maternal QTL analyses were performed on the basis of overlapping donor regions between subcongenic strains. We identified several highly significant (P < 5 × 10−4) maternal QTL influencing total body weight, organ weight, and fat pad weights in both sets of subcongenics. These QTL accounted for 1.9-11.7% of the phenotypic variance for growth and obesity and greatly narrowed the genomic regions associated with the maternal genetic effects. These maternal effect QTL controlled phenotypic traits in adult mice, suggesting that maternal influences at early stages of development may permanently affect offspring performance. Identification of maternal effects in our survey of two sets of subcongenic strains, representing approximately 5% of the mouse genome, supports the hypothesis that maternal effects represent significant sources of genetic variation that are largely ignored in genetic studies

Mendelian adult-onset leukodystrophy genes in Alzheimer´s disease. Critical influence of CSF1R and NOTCH3

Mendelian adult-onset leukodystrophies are a spectrum of rare inherited progressive neurodegenerative disorders affecting the white matter of the central nervous system. Among these, Cerebral Autosomal Dominant and Recessive Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL and CARASIL), Cerebroretinal vasculopathy (CRV), Metachromatic leukodystrophy (MLD), Hereditary diffuse Leukoencephalopathy with spheroids (HDLS), Vanishing white matter disease (VWM) present with rapidly progressive dementia as dominant feature and are caused by mutations in NOTCH3, HTRA1, TREX1, ARSA, CSF1R, EIF2B1, EIF2B2, EIF2B3, EIF2B4, EIF2B5, respectively. Given the rare incidence of these disorders and the lack of unequivocally diagnostic features, leukodystrophies are frequently misdiagnosed with common sporadic dementing diseases such as Alzheimer’s disease (AD), raising the question of whether these overlapping phenotypes may be explained by shared genetic risk factors. To investigate this intriguing hypothesis, we have combined gene expression analysis 1) in 6 different AD mouse strains (APPPS1, HOTASTPM, HETASTPM, TPM, TAS10 and TAU), at 5 different developmental stages (Embryo [E15], 2 months, 4 months, 8 months and 18 months), 2) in APPPS1 primary cortical neurons under stress conditions (oxygen-glucose deprivation) and single-variant and single-gene (c-alpha and SKAT tests) based genetic screening in a cohort composed of 332 Caucasian late-onset AD patients and 676 Caucasian elderly controls. Csf1r was significantly overexpressed (Log2FC>1, adj. p-val<0.05) in the cortex and hippocampus of aged HOTASTPM mice with extensive Aβ core dense plaque pathology. We identified 3 likely pathogenic mutations in CSF1R TK domain (p.L868R, p.Q691H and p.H703Y) in our discovery and validation cohort, composed of 465 AD and MCI Caucasian patients from the UK. Moreover, NOTCH3 was a significant hit in the c-alpha test (adj p-val = 0.01). Adult onset Mendelian leukodystrophy genes are not common factors implicated in AD. Nevertheless, our study suggests a potential pathogenic link between NOTCH3, CSF1R and sporadic LOAD, that warrants further investigation

ABCA7 p.G215S as potential protective factor for Alzheimer’s disease

Genome-wide association studies (GWASs) have been effective approaches to dissect common genetic variability underlying complex diseases in a systematic and unbiased way. Recently, GWASs have led to the discovery of over 20 susceptibility loci for Alzheimer’s disease (AD). Despite the evidence showing the contribution of these loci to AD pathogenesis, their genetic architecture has not been extensively investigated, leaving the possibility that low frequency and rare coding variants may also occur and contribute to the risk of disease. We have used exome and genome sequencing data to analyse the single independent and joint effect of rare and low frequency protein coding variants in 9 AD GWAS loci with the strongest effect sizes after APOE (BIN1, CLU, CR1, PICALM, MS4A6A, ABCA7, EPHA1, CD33, CD2AP) in a cohort of 332 sporadic AD cases and 676 elderly controls of British and North American ancestry. We identified coding variability in ABCA7 as contributing to AD risk. This locus harbors a low frequency coding variant (p.G215S, rs72973581, MAF=4.3%) conferring a modest but statistically significant protection against AD (p-value= 6x10-4, OR=0.57, 95% CI 0.41-0.80). Notably, our results are not driven by an enrichment of loss of function variants in ABCA7, recently reported as main pathogenic factor underlying AD risk at this locus. In summary, our study confirms the role of ABCA7 in AD and provide new insights that should address functional studies

The case for strategic international alliances to harness nutritional genomics for public and personal health

Nutrigenomics is the study of how constituents of the diet interact with genes, and their products, to alter phenotype and, conversely, how genes and their products metabolise these constituents into nutrients, antinutrients, and bioactive compounds. Results from molecular and genetic epidemiological studies indicate that dietary unbalance can alter gene-nutrient interactions in ways that increase the risk of developing chronic disease. The interplay of human genetic variation and environmental factors will make identifying causative genes and nutrients a formidable, but not intractable, challenge. We provide specific recommendations for how to best meet this challenge and discuss the need for new methodologies and the use of comprehensive analyses of nutrient-genotype interactions involving large and diverse populations. The objective of the present paper is to stimulate discourse and collaboration among nutrigenomic researchers and stakeholders, a process that will lead to an increase in global health and wellness by reducing health disparities in developed and developing countrie