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PubMed2026

Hypoxia-Inducible Factor-1α Gene (HIF1A) rs11549465 (1772 C>T) Polymorphism, Body Mass Index, Smoking, and Cutaneous Melanoma: An Observational Case-Control Study.

BACKGROUND: Hypoxia and oxidative stress are central features of cutaneous melanoma biology. Body mass index (BMI) and smoking, both of which can influence systemic hypoxia, inflammation, and oxidative stress, have shown inconsistent associations with melanoma. We investigated the association of the hypoxia-inducible factor-1 alpha gene (HIF1A) rs11549465 (1772 C>T; Pro582Ser) polymorphism, alone and in combination with overweight/obesity or smoking habits, with cutaneous melanoma susceptibility and clinicopathological characteristics. METHODS: This observational case-control study included 132 Caucasian Italian patients with cutaneous melanoma and 312 healthy controls. The rs11549465 polymorphism was genotyped by genomic DNA restriction fragment analysis. Logistic regression provided age- and sex-adjusted and mutually adjusted estimates. RESULTS: Genotype and allele frequencies did not differ between patients and controls. Within the melanoma cohort, smoking for ≥20 years remained associated with metastatic disease after adjustment for BMI ≥ 25 kg/m2, age at diagnosis, and sex (aOR = 3.12, p = 0.006), whereas BMI did not (aOR = 1.23, p = 0.612). Compared with healthy controls, metastatic melanoma was independently associated with BMI ≥ 25 kg/m2 (aOR = 2.26, p = 0.010) and smoking for ≥20 years (aOR = 3.85, p < 0.001). Mean pack-years were higher in melanoma patients than controls (9.4 ± 16.7 vs. 5.1 ± 12.2; p = 0.002), and ≥10 and ≥20 pack-years remained associated after age- and sex-adjustment (aOR = 2.19, p = 0.001 and aOR = 3.31, p < 0.001, respectively). Mean pack-years were higher in MetM than NMetM (13.1 ± 21.0 vs. 5.9 ± 10.0; p = 0.013), and ≥20 pack-years was associated with MetM (OR = 3.05, p = 0.017). Adjusted associations with head/neck melanoma (n = 13) were observed for CC plus BMI ≥ 30 kg/m2 (aOR = 9.07, p < 0.001), ≥20 cigarette/day (aOR = 5.96, p = 0.004), ≥20 years smoking (aOR = 6.64, p = 0.003), and other smoking measures. CONCLUSIONS: To our knowledge, this is the first report on the interplay between the rs11549465 polymorphism and cutaneous melanoma. HIF1A rs11549465 was not independently associated with melanoma susceptibility. Associations involving smoking, BMI, joint genotype-lifestyle exposures, and anatomical localization had wide confidence intervals and were exploratory; small subgroups and multiple comparisons require cautious interpretation and independent validation.

cigarette smoke↗

PubMed2000

Genetic variants of myeloperoxidase and lung cancer risk.

The cytochrome P450 family of enzymes is responsible for many of the initial metabolic conversions of procarcinogenic compounds in tobacco smoke to reactive metabolites. However, other enzyme-based systems such as myeloperoxidase (MPO) may also be involved in this metabolic process. MPO is a phase I metabolic enzyme that has a polymorphic region upstream of the gene that appears to reduce transcriptional activity. The polymorphic G-->A nucleotide base shift negates the binding region for the general transcription factor SP1. Thus, individuals with the variant allele may be provided with a protective effect due to decreased metabolic conversion of carcinogenic compounds in tobacco smoke. This study has investigated the hypothesis that individuals with the variant allele may be at a reduced risk for lung cancer. Our results demonstrate that the protective effects of the MPO variant allele reduced overall lung cancer risk in Caucasians by 48% (OR = 0.52, 95% CI 0.30-0.90, P = 0.02). There was a 72% protective effect (OR = 0.28, 95% CI 0.12-0.61, P < 0.05) evident in men but not in women. Additionally, in younger individuals (<61 years) there was a statistically significant 72% reduction in risk (OR = 0.28, 95% CI 0. 11-0.69, P < 0.05) but not in older individuals. A protective effect was observed for current smokers (OR = 0.24, 95% CI 0.10-0.58, P < 0. 05) but not in former smokers and those who had never smoked. These data demonstrate that there is a reduction in lung cancer risk associated with a variant allele of MPO that is evident in men, younger individuals and current smokers.

Base Sequence↗

PubMed1999

An untranslated insertion variant in the uncoupling protein 2 gene is not related to body mass index and changes in body weight during a 26-year follow-up in Danish Caucasian men.

AIMS: Associations between a 45 bp 3'untranslated insertion polymorphism in the uncoupling protein 2 (UCP2) gene and both body mass index (BMI) and sleeping metabolic rate have previously been reported. We investigated the impact of this polymorphism on BMI and long-term body weight changes. METHODS: The allelic frequency of the UCP2 insertion variant was determined in a cohort of 744 obese Danish Caucasian men who had a BMI of at least 31 kg/m2 at the draft-board examinations and a randomly selected control cohort consisting of 872 draftees. Follow-up measurements of BMI were done on average 26 years after the draft-board examinations. RESULTS: The prevalence of the insertion allele was 30.4% (95% confidence interval: 28.0-32.8%) among the obese and 29.6% (27.4-31.8%) in the control group (p = 0.6). In a lean group selected as the 354 subjects with a BMI less than 25 kg/m2 at 46 years of age from the control group, the frequency of insertion allele was 29.0% (27.2-30.8%) (p = 0.5 compared with the obese cohort). The BMI at the ages of 20 and 46 years did not differ between genotypes either in the obese or the control group. Similarly, the changes in BMI/year between examinations at 20 and 46 years of age did not differ between genotypes in either group. CONCLUSION/INTERPRETATION: In a large group of Danish Caucasian men we found no association between a 3'untranslated insertion polymorphism in the UCP2 gene and obesity. Neither did we identify a relation between this variant and BMI changes during adult age.

3' Untranslated Regions↗

PubMed2006

Selected gene polymorphisms and their interaction with maternal smoking, as risk factors for gastroschisis.

BACKGROUND: Gastroschisis is a severe birth defect in which the infant is born with a portion of the intestines extruding through a small tear in the abdominal wall, usually to the right of the umbilical cord. Its etiology is unknown, but the prevailing hypothesis is that it results from a vascular accident at the time of involution of the right umbilical vein or of the development of the superior mesenteric artery. METHODS: In a case-control study of 57 cases of gastroschisis and 506 controls, we tested DNA for polymorphisms of 32 genes representing enzymes involved in angiogenesis, blood vessel integrity, inflammation, wound repair, and dermal or epidermal strength. RESULTS: In logistic regression, controlling for maternal ethnicity, and using the homozygote wild-type as referent, the following gene polymorphisms were associated with an increased risk for a gastroschisis for heterozygotes: ICAM1 gly241arg (odds ratio [OR], 1.9; 95% confidence interval [CI], 1.1 -3.4); NOS3 glu298asp (OR, 1.9; 95% CI, 1.1-3.4); NPPA 2238T > C (OR, 1.9; 95% CI, 1.0-3.4); and ADD1 gly460trp (OR, 1.5; 95% CI, 0.8-2.8). Additionally, for the NPPA and ADD1 single-nucleotide polymorphisms (SNPs), the homozygote variants had a significantly higher risk than the heterozygotes (OR, 7.5; 95% CI, 1.7-33.5 and OR, 4.9; 95% CI, 1.9-12.9, respectively). Three SNPs showed a strong interaction with maternal smoking. The risk for smokers with 1 or 2 variant alleles compared to nonsmokers with the wild-type allele were: NOS3 (OR, 5.2; 95% CI, 2.4-11.4); ICAM1 (OR, 5.2; 95% CI, 2.1-12.7); and NPPA (OR, 6.4; 95% CI, 2.8-14.6). CONCLUSIONS: These results support the hypothesis of a vascular compromise as part of a multifactorial etiology of gastroschisis involving both genes and environmental factors.

Female↗

PubMed2005

Thrombophilic risk factors for symptomatic peripheral arterial disease.

OBJECTIVE: Peripheral arterial disease (PAD) is a common manifestation of systemic atherosclerosis. Over the last years, several novel mediators relevant to the process of atherogenesis have been identified, but few and conflicting data are available on the possible association with PAD symptoms. The aim of this study was to determine an extended thrombophilic risk profile of patients with symptomatic PAD. METHODS: Two hundred eighty patients with symptomatic PAD admitted to the Department of Vascular Surgery of the University of Florence were compared with 280 control subjects without PAD, matched for age and gender. The following metabolic and genetic risk factors were evaluated: lipoprotein(a), homocysteine, antiphospholipid antibodies, plasminogen activator inhibitor-1, factor V Leiden mutation, prothrombin variant, and 5,10-methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism. RESULTS: Multivariate logistic regression analysis, adjusted for traditional cardiovascular risk factors, showed a significant association between PAD symptoms and prothrombin variant, altered levels of homocysteine, lipoprotein(a), plasminogen activator inhibitor-1, and antiphospholipid antibodies. Moreover, the presence of high levels of lipoprotein(a) and another metabolic risk factor raised the likelihood of PAD symptoms (dyslipidemia and elevated lipoprotein[a]: odds ratio [OR], 29; 95% confidence interval [CI], 6.2 to 136.2; P <.0001; hyperhomocysteinemia and elevated lipoprotein[a]: OR, 37.7; 95% CI, 3.7 to 381.5; P <.0001). A significant correlation between the number of altered thrombophilic parameters and the Fontaine stage was observed ( R = 0.16; P = .006). CONCLUSION: There is an independent association between altered levels of important thrombophilic risk factors and PAD symptoms. The clinical significance of this association needs to be tested in prospective population-based trials.

Adult↗

PubMed2003

Polymorphisms of the TAP1 and TAP2 genes in human alveolar echinococcosis.

We postulated that TAP genes may influence the susceptibility of some individuals to Echinococcus multilocularis infection. Six coding region variants (codons 333 and 637 in TAP1, and 379, 565, 651 and 665 in TAP2) were typed in 94 patients and 100 controls. Thr/Thr homozygosity at TAP2/665 was more prevalent in patients than in controls [64% vs. 45%, respectively; odds ratio (OR) = 2.1 (95% confidence interval (CI) 1.1; 2.7)] and Thr/Ala heterozygozity was less prevalent (32% vs. 50%, respectively) (P = 0.014). Of the 38 patients with progressive lesions, 76% were Thr/Thr, as compared with 55% of patients without progressive lesions and 45% of controls (P = 0.058 and 0.02, respectively), independent of HLA status. To determine whether this association is functionally relevant, functional analyses and/or confirmation in distinct populations of patients with alveolar echinococcosis would be required.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1988

Estimation of allele frequencies at isoloci.

In some polyploid animals and plants, pairs of duplicated loci occur that share alleles encoding proteins with identical electrophoretic mobilities. Except in cases where these "isoloci" are known to be inherited tetrasomically, individual genotypes cannot be determined unambiguously, and there is no direct way to assign observed variation to a particular locus of the pair. For a pair of diallelic isoloci, nine genotypes are possible but only five phenotypes can be identified, corresponding to individuals with 0-4 doses of the variant allele. A maximum likelihood (ML) approach is used here to identify the set of allele frequencies (p, q) at the individual gene loci with the highest probability of producing the observed phenotypic distribution. A likelihood ratio test is used to generate the asymmetrical confidence intervals around ML estimates. Simulations indicate that the standard error of p is typically about twice the binomial sampling error associated with single locus allele frequency estimates. ML estimates can be used in standard indices of genetic diversity and differentiation and in goodness-of-fit tests of genetic hypotheses. The noncentral chi 2 distribution is used to evaluate the power of a test of apparent heterozygote deficiency that results from attributing all variation to one locus when both loci are polymorphic.

Alleles↗

PubMed2007

Papillary thyroid cancer and polymorphic variants in TSHR- and RET-related genes: a nested case-control study within a cohort of U.S. radiologic technologists.

Several variants in the TSHR and RET signaling pathways genes have been reported to be related to cancer risk. We hypothesized that polymorphic variants in these genes are associated with the risk of papillary thyroid cancer. A nested case-control study was conducted within the U.S. Radiologic Technologists cohort. Eligible validated papillary thyroid cancer cases (n = 167) and frequency-matched (by sex and birth year) controls (n = 491) donated blood for analysis. There were no statistically significant associations between papillary thyroid cancer and 10 selected polymorphic variants in analyses of men and women combined. A borderline significant increasing risk was found for RET G691S (P(trend) = 0.05) and was especially pronounced among young women. For women under 38 years (the median age at diagnosis), the odds ratios were 2.1 (95% confidence interval, 1.2-3.7) for those heterozygous for the RET G691S polymorphism and 3.7 (95% confidence interval, 1.1-11.8) for those who were homozygous (P(trend) = 0.001). Our data provide limited evidence that TSHR- and RET-related genes are related to papillary thyroid cancer risk.

Adult↗

PubMed2006

A prospective assessment of the Y402H variant in complement factor H, genetic variants in C-reactive protein, and risk of age-related macular degeneration.

PURPOSE: Two biologically related factors, complement factor H (CFH) and C-reactive protein (CRP), have been associated with AMD. The Y402H variant of CFH is located within the binding site of CFH for CRP. Although plasma CRP levels have been related to AMD and plasma CRP levels are partly determined by genetic variation, there is no information on whether genetic variants in CRP are associated with AMD. METHODS: A prospective analysis was performed of 111 men who eventually developed AMD and 401 men who remained free of AMD, all participants in the Physicians' Health Study. Genotypes were determined for the common T-->C single nucleotide polymorphism (SNP) in exon 9 of CFH (rs1061170; protein Y402H), as well as seven previously described CRP SNPs (rs3093059, rs2794521, rs3091244, rs1417938, rs1800947, rs1130864, and rs1205). Logistic regression analysis was used to evaluate individual SNPs, as well as six CRP haplotypes for association with AMD. RESULTS: The high-risk C allele of CFH was present in 45% of cases and 34% of controls. An odds ratio (OR) of 1.46 was observed for AMD (95% confidence interval [CI]: 1.05-2.04) for TC heterozygotes and an OR of 2.13 (95% CI: 1.10-4.16) for CC homozygotes, assuming a multiplicative (log-additive) model and attributable fraction of 25% (95% CI: 1% to 44%) was calculated. For CRP, single-marker or haplotype-based analysis failed to reveal any significant associations with a risk of AMD. CONCLUSIONS: These prospective data confirmed an association between the Y402H variant of CFH and a risk of AMD. In contrast, although a biologically plausible, genetic variation in CRP does not appear to be associated with a risk of AMD. Further prospective studies of a larger number of subjects are needed to substantiate available information on the genetic epidemiology of AMD.

Aged↗

PubMed2005

Combined genetic assessment of transforming growth factor-beta signaling pathway variants may predict breast cancer risk.

There is growing evidence that common variants of the transforming growth factor-beta (TGF-beta) signaling pathway may modify breast cancer risk. In vitro studies have shown that some variants increase TGF-beta signaling, whereas others have an opposite effect. We tested the hypothesis that a combined genetic assessment of two well-characterized variants may predict breast cancer risk. Consecutive patients (n = 660) with breast cancer from the Memorial Sloan-Kettering Cancer Center (New York, NY) and healthy females (n = 880) from New York City were genotyped for the hypomorphic TGFBR1*6A allele and for the TGFB1 T29C variant that results in increased TGF-beta circulating levels. Cases and controls were of similar ethnicity and geographic location. Thirty percent of cases were identified as high or low TGF-beta signalers based on TGFB1 and TGFBR1 genotypes. There was a significantly higher proportion of high signalers (TGFBR1/TGFBR1 and TGFB1*CC) among controls (21.6%) than cases (15.7%; P = 0.003). The odds ratio [OR; 95% confidence interval (95% CI)] for individuals with the lowest expected TGF-beta signaling level (TGFB1*TT or TGFB1*TC and TGFBR1*6A) was 1.69 (1.08-2.66) when compared with individuals with the highest expected TGF-signaling levels. Breast cancer risk incurred by low signalers was most pronounced among women after age 50 years (OR, 2.05; 95% CI, 1.01-4.16). TGFBR1*6A was associated with a significantly increased risk for breast cancer (OR, 1.46; 95% CI, 1.04-2.06), but the TGFB1*CC genotype was not associated with any appreciable risk (OR, 0.89; 95% CI, 0.63-1.21). TGFBR1*6A effect was most pronounced among women diagnosed after age 50 years (OR, 2.20; 95% CI, 1.25-3.87). This is the first study assessing the TGF-beta signaling pathway through two common and functionally relevant TGFBR1 and TGFB1 variants. This approach may predict breast cancer risk in a large subset of the population.

Activin Receptors, Type I↗

PubMed2004

Is the Addenbrooke's cognitive examination effective to detect frontotemporal dementia?

We evaluated the Addenbrooke's cognitive examination (ACE), a simple instrument to differentiate frontotemporal dementia (FTD) from Alzheimer's disease (AD), in our dementia patients clinic population. The Verbal-Language/Orientation-Memory (VLOM) ratio, which compares its language and memory scores, determines whether FTD or AD is more likely. The ACE was translated into French with adaptation maintaining the number of words in the name and address learning and delayed recall test, and with cultural adaptation for the semantic memory. The 85 included subjects had no evidence of two or more organic pathologies, after at least six months of follow-up, and an MMSE score>or=20/30. Patients with cognitive impairment due to alcohol intake were excluded. The diagnosis of a specific dementing illness was based on the consensus of the neurologist and neuropsychologists in the team. Thereafter, another neurologist expert in dementia, blinded to the ACE result and to the diagnosis and treatment, reviewed all cases files and proposed a diagnosis. A diagnostic agreement was reached for 79 cases (92.9%) with 40 (50.6%) dementia: 25 AD (62.5 %), 9 FTD (22.5 %). We estimated that the sensitivity for detecting dementia of an ACE score 3.2 was 72%,with a specificity of 69.4%. We conclude that, when used as originally proposed, ACE is very accurate for the detection of dementia, but much less effective in discriminating the most common frontal variant of FTD.

Aged↗

PubMed2005

A novel CYP2A6*20 allele found in African-American population produces a truncated protein lacking enzymatic activity.

Human CYP2A6 is a cytochrome P450 (CYP) isoform responsible for the metabolism of nicotine, coumarin, tegafur, and valproic acid, and metabolic activation of nitrosamines. Genetic polymorphisms of the CYP2A6 gene are a major causal factor of the large interindividual differences in nicotine metabolism. In the present study, we identified a novel allele, termed CYP2A6*20, in an African-American population. The allele possesses the deletion of two nucleotides in exon 4 resulting in a frame-shift from codon 196 and an early stop codon at 220 (exon 5) as well as three synonymous SNPs of G51A (G51A in cDNA), T5684C (T1191C), and C6692G (C1546G, 3'-untranslated region). The allele frequency in the African-American population (n=96) was 1.6% (95% confidence interval, 0.6-4.5%). In contrast, the CYP2A6*20 allele was not found in Caucasians (European-American) (n=185), Japanese (n=184) and Korean (n=209) populations. To investigate the effects of the polymorphism on the enzymatic activities, we expressed a wild type or variant (deletion of two nucleotides) CYP2A6 together with NADPH-CYP reductase in Escherichia coli. SDS-PAGE and immunoblot analyses demonstrated that truncated CYP2A6 protein was produced from the variant allele, although detected mRNA was the predicted size by reverse transcriptional-polymerase chain reaction. Coumarin 7-hydroxylation and nicotine C-oxidation, which are typical CYP2A6 activities, were completely abolished in the E. coli membrane expressing the variant allele. In vivo nicotine metabolism was evaluated using the cotinine/nicotine ratio 2 h after the chewing of one piece of nicotine gum. Two CYP2A6*1/CYP2A6*20 heterozygotes and a single CYP2A6*17/CYP2A6*20 heterozygote revealed lower cotinine/nicotine ratios compared with CYP2A6*1/CYP2A6*1 subjects (1.6 and 4.5, and 1.8 versus 9.5+/-5.4, n=52, respectively). We found a novel CYP2A6*20 allele in African-American subjects which codes a truncated protein lacking enzymatic activity.

Black or African American↗

PubMed2026

Multiregion profiling of genomic and transcriptional heterogeneity in head and neck squamous-cell carcinoma.

BACKGROUND: Intratumoral heterogeneity (ITH) is thought to contribute to tumour evolution and treatment resistance but its biological and clinical significance in localised head and neck squamous-cell carcinoma (HNSCC) remains incompletely understood. PATIENTS AND METHODS: In the prospective SCANDARE study, we analysed 87 patients with resectable HNSCC treated with upfront surgery. Two to five spatially distinct tumour regions per patient underwent pathological evaluation, targeted DNA sequencing, and bulk RNA sequencing. Genomic ITH (gITH) was quantified using clonal deconvolution and Shannon diversity indices, whereas transcriptional heterogeneity (tITH) was assessed using the intratumour expression distance metric. Associations between ITH, molecular features, tumour microenvironment composition, and clinical outcomes were explored using multivariable statistical models. RESULTS: Pathology-based spatial heterogeneity showed limited prognostic value. gITH was common, with 37% of tumours displaying regionally heterogeneous pathogenic variants, including spatially actionable alterations in 10% of patients. In an initial multivariable Cox model, higher gITH was associated with shorter disease-free survival. However, after Ridge-penalised modelling and bootstrap internal validation, the effect size was attenuated [corrected hazard ratio 1.42, 95% confidence interval (CI) 0.91-2.75]. The overall model retained moderate discriminative performance (optimism-corrected C-index 0.69, 95% CI 0.59-0.79). gITH was associated with tumour cellularity, reduced estimated endothelial cell infiltration, and alterations in KMT2C and PIK3CA. tITH differed according to human papillomavirus (HPV) status, with lower tITH in HPV-positive tumours, and was associated with distinct biological pathways and genomic alterations. Genomic and tITH were not correlated. CONCLUSIONS: This prospective multiregion study provides a comprehensive characterisation of genomic and tITH in localised HNSCC. Our findings highlight substantial spatial molecular diversity within primary tumours and suggest potential associations between heterogeneity, tumour biology, and clinical outcome that warrant validation in independent cohorts.

head and neck squamous-cell carcinoma (HNSCC)↗

PubMed2005

Rapid detection methods and prevalence estimation for Borrelia lonestari glpQ in Amblyomma americanum (Acari: Ixodidae) pools of unequal size.

DNA was extracted from pools of Amblyomma americanum ticks collected from vegetation at two sites in Fort Leonard Wood, Missouri and tested for the presence of Borrelia spp. Two new methods were developed to detect Borrelia lonestari DNA by targeting the glycerophosphodiester phosphodiesterase (glpQ) gene. The first method detected B. lonestari DNA using a SYBR green I melting curve analysis of the PCR product obtained with glpQ gene primers. The second method, a glpQ TaqMan assay, detected and confirmed the presence of B. lonestari glpQ-specific sequences. Twenty-two of 95 tick pools collected at site A148 contained B. lonestari DNA. None of 19 pools from site A241 contained B. lonestari DNA. No B. burgdorferi sensu lato DNA was detected using a SYBR green I melting curve analysis of the PCR product obtained with outer surface protein A (ospA) primers. The overall B. lonestari infection prevalence (with 95% confidence interval) at site A148 was estimated using two algorithms: minimum infection rate 4.14% (2.45, 5.84) and maximum likelihood with correction 4.82% (3.11, 7.16). The merits of each are discussed. Sequencing of the entire B. lonestari glpQ and partial 16S rRNA genes revealed two genetic variants circulating in this population of A. americanum from Missouri.

Algorithms↗

PubMed2026

DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.

SUMMARY: We developed DirectASRM, a comprehensive database for the systematic identification, integration, and annotation of allele-specific RNA modifications (ASRMs) from direct RNA sequencing data. DirectASRM enables single-base, transcript-level detection of ASRMs across multiple RNA modification types, diverse organisms and condition-specific contexts. The database further evaluates the confidence of each ASRM-SNP pair association within isoform context by jointly considering statistical evidence of allelic modification imbalance and independent support from external next-generation sequencing (NGS) - based RNA modification resources. DirectASRM also provides extensive functional annotations for ASRMs and their associated variants, including intra-sample transcript-level allele-specific expression (ASE) and allele-specific splicing, as well as additional post-transcriptional regulatory features such as miRNA binding, circRNA, RNA-protein interactions, and disease relevance. Overall, DirectASRM serves as a comprehensive resource that supports systematic investigation of the potential functional impact of genetic variants in epitranscriptomic regulation. AVAILABILITY AND IMPLEMENTATION: DirectASRM database is freely accessible at http://modinfor.com/DirectASRM/. DirectASRM pipeline is available at GitHub (https://github.com/jiayin1101/DirectASRM_pipeline) and Zenodo (DOI: https://doi.org/10.5281/zenodo.19876077).

Alleles↗

PubMed2002

The neural basis of the blood-oxygen-level-dependent functional magnetic resonance imaging signal.

Magnetic resonance imaging (MRI) has rapidly become an important tool in clinical medicine and biological research. Its functional variant (functional magnetic resonance imaging; fMRI) is currently the most widely used method for brain mapping and studying the neural basis of human cognition. While the method is widespread, there is insufficient knowledge of the physiological basis of the fMRI signal to interpret the data confidently with respect to neural activity. This paper reviews the basic principles of MRI and fMRI, and subsequently discusses in some detail the relationship between the blood-oxygen-level-dependent (BOLD) fMRI signal and the neural activity elicited during sensory stimulation. To examine this relationship, we conducted the first simultaneous intracortical recordings of neural signals and BOLD responses. Depending on the temporal characteristics of the stimulus, a moderate to strong correlation was found between the neural activity measured with microelectrodes and the BOLD signal averaged over a small area around the microelectrode tips. However, the BOLD signal had significantly higher variability than the neural activity, indicating that human fMRI combined with traditional statistical methods underestimates the reliability of the neuronal activity. To understand the relative contribution of several types of neuronal signals to the haemodynamic response, we compared local field potentials (LFPs), single- and multi-unit activity (MUA) with high spatio-temporal fMRI responses recorded simultaneously in monkey visual cortex. At recording sites characterized by transient responses, only the LFP signal was significantly correlated with the haemodynamic response. Furthermore, the LFPs had the largest magnitude signal and linear systems analysis showed that the LFPs were better than the MUAs at predicting the fMRI responses. These findings, together with an analysis of the neural signals, indicate that the BOLD signal primarily measures the input and processing of neuronal information within a region and not the output signal transmitted to other brain regions.

Animals↗

PubMed2002

Disease transmission by blood products: past, present and future.

Transfusion of blood and blood products has been associated with transmission of infectious agents. However, it is probable that blood products are currently very safe and that pooled virus-inactivated products from remunerated donors are now safer than untreated single voluntary donor components. Although the transmission events of the past and the present are reasonably well understood, reliance on a linear approach to predict safety in the future is open to criticism. Indeed, it was not possible to predict the extent or consequences of the AIDS epidemic or of hepatitis C transmission. Moreover, although variant Creutzfeldt-Jakob disease (vCJD) may not be transmitted to any large extent by transfusion of manufactured blood products, this will be due more to good fortune than good judgement - this agent could have escaped the screening, testing and eradication methods on which current confidence in blood product safety depends. Similarly, the emergence of a highly resistant non-enveloped virus, or even of another previously unrecognised disease-causing agent, could result in new threats from transfusion of blood components and products. The ecology of blood transfusion is exquisitely sensitive to variations in starting conditions, a situation typical of a chaotic rather than a linear system. Seemingly trivial events, often apparently unrelated to blood transfusion, have had enormous consequences in this field. Whatever the events that introduced simian immunodeficiency virus to humans or scrapie to cattle, they were a long way from those involved in the manufacture of blood products. In such a setting, reliance on methods that deal effectively with known threats (such as encapsulated viruses and bacteria) without adequate investigation and management of the intrinsic sensitivity to unpredictable events, leaves open the possibility of further infections emerging in the future. It is this reality that will ultimately result in the eradication of the transfusion of donor-derived blood and blood products in the developed world. In addition, all infections with a long disease-free incubation period in the host that can be transmitted in blood will eventually be over-expressed in groups that are exposed to blood either recreationally or professionally. As in the past, this could have occurred before testing or decontamination processes have been developed for emerging pathogens. Failure to be able to rely on completely risk-free donors, in both the voluntary and non-voluntary sides of the blood industry, continues to offer the potential for the transmission of infectious diseases in the future.

Blood Donors↗

PubMed2004

Toxicological considerations in the application and interpretation of susceptibility biomarkers in epidemiological studies.

With major advances in genotyping technology, it has become practical and affordable to screen biological samples for multiple polymorphisms for which there is more or less knowledge about their functional relevance in relation to toxicological agents or disease. This situation creates some unique epidemiological challenges in which careful consideration of the mechanisms underlying genotype-disease and genotype-exposure-disease relationships, or the lack of knowledge thereof, may help to prevent false-positive results or misinterpretation of data that could mislead future research. Coordination and linkage of data resources on toxicological exposures, genes and disease would be useful as an integrated source of information to devise study design, analysis and interpretation. Such a database could be useful in collating information from which to determine relevant exposures for the disease and to guide the selection of susceptibility markers for study. Further information on toxicological mechanisms and functional relevance of gene variants in relation to disease could be accounted for in statistical analyses and interpretation. Statistical methods that can incorporate this prior information on mechanism, such as hierarchical regression modelling, may help to mitigate some of the problems inherent to these studies by adjusting estimates and confidence limits according to this prior information. Even in the situation where little information on etiological mechanisms is available, application of a less informed prior can be beneficial in improving the accuracy and precision for an ensemble of estimates. The changing paradigm of epidemiological research with regard to increasing detail of underlying mechanisms and the sheer amount of data being evaluated necessitates access to sources of information and analytic methods that can integrate this complexity.

Biomarkers↗