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1.
Alzheimers Dement ; 20(2): 1038-1049, 2024 Feb.
Article En | MEDLINE | ID: mdl-37855447

INTRODUCTION: This study aimed to investigate the influence of the overall Alzheimer's disease (AD) genetic architecture on Down syndrome (DS) status, cognitive measures, and cerebrospinal fluid (CSF) biomarkers. METHODS: AD polygenic risk scores (PRS) were tested for association with DS-related traits. RESULTS: The AD risk PRS was associated with disease status in several cohorts of sporadic late- and early-onset and familial late-onset AD, but not in familial early-onset AD or DS. On the other hand, lower DS Mental Status Examination memory scores were associated with higher PRS, independent of intellectual disability and APOE (PRS including APOE, PRSAPOE , p = 2.84 × 10-4 ; PRS excluding APOE, PRSnonAPOE , p = 1.60 × 10-2 ). PRSAPOE exhibited significant associations with Aß42, tTau, pTau, and Aß42/40 ratio in DS. DISCUSSION: These data indicate that the AD genetic architecture influences cognitive and CSF phenotypes in DS adults, supporting common pathways that influence memory decline in both traits. HIGHLIGHTS: Examination of the polygenic risk of AD in DS presented here is the first of its kind. AD PRS influences memory aspects in DS individuals, independently of APOE genotype. These results point to an overlap between the genes and pathways that leads to AD and those that influence dementia and memory decline in the DS population. APOE ε4 is linked to DS cognitive decline, expanding cognitive insights in adults.


Alzheimer Disease , Cognitive Dysfunction , Down Syndrome , Adult , Humans , Alzheimer Disease/diagnosis , Down Syndrome/genetics , Genetic Risk Score , Apolipoproteins E/genetics , Phenotype , Cognitive Dysfunction/diagnosis , Biomarkers/cerebrospinal fluid , Cognition , Memory Disorders , Amyloid beta-Peptides/cerebrospinal fluid
2.
Mol Psychiatry ; 28(10): 4451-4462, 2023 Oct.
Article En | MEDLINE | ID: mdl-37666928

The APOE 2/3/4 polymorphism is the greatest genetic risk factor for Alzheimer's disease (AD). This polymorphism is also associated with variation in plasma ApoE level; while APOE*4 lowers, APOE*2 increases ApoE level. Lower plasma ApoE level has also been suggested to be a risk factor for incident dementia. To our knowledge, no large genome-wide association study (GWAS) has been reported on plasma ApoE level. This study aimed to identify new genetic variants affecting plasma ApoE level as well as to test if baseline ApoE level is associated with cognitive function and incident dementia in a longitudinally followed cohort of the Ginkgo Evaluation of Memory (GEM) study. Baseline plasma ApoE concentration was measured in 3031 participants (95.4% European Americans (EAs)). GWAS analysis was performed on 2580 self-identified EAs where both genotype and plasma ApoE data were available. Lower ApoE concentration was associated with worse cognitive function, but not with incident dementia. As expected, the risk for AD increased from E2/2 through to E4/4 genotypes (P for trend = 4.8E-75). In addition to confirming the expected and opposite associations of APOE*2 (P = 4.73E-79) and APOE*4 (P = 8.73E-12) with ApoE level, GWAS analysis revealed nine additional independent signals in the APOE region, and together they explained about 22% of the variance in plasma ApoE level. We also identified seven new loci on chromosomes 1, 4, 5, 7, 11, 12 and 20 (P range = 5.49E-08 to 5.36E-10) that explained about 9% of the variance in ApoE level. Plasma ApoE level-associated independent variants, especially in the APOE region, were also associated with AD risk and amyloid deposition in the brain, indicating that genetically determined ApoE level variation may be a risk factor for developing AD. These results improve our understanding of the genetic determinants of plasma ApoE level and their potential value in affecting AD risk.


Alzheimer Disease , Humans , Alzheimer Disease/genetics , Genome-Wide Association Study , Apolipoproteins E/genetics , Genotype , Polymorphism, Genetic , Apolipoprotein E4/genetics
3.
Acta Neuropathol Commun ; 11(1): 68, 2023 04 26.
Article En | MEDLINE | ID: mdl-37101235

Amyloid PET imaging has been crucial for detecting the accumulation of amyloid beta (Aß) deposits in the brain and to study Alzheimer's disease (AD). We performed a genome-wide association study on the largest collection of amyloid imaging data (N = 13,409) to date, across multiple ethnicities from multicenter cohorts to identify variants associated with brain amyloidosis and AD risk. We found a strong APOE signal on chr19q.13.32 (top SNP: APOE ɛ4; rs429358; ß = 0.35, SE = 0.01, P = 6.2 × 10-311, MAF = 0.19), driven by APOE ɛ4, and five additional novel associations (APOE ε2/rs7412; rs73052335/rs5117, rs1081105, rs438811, and rs4420638) independent of APOE ɛ4. APOE ɛ4 and ε2 showed race specific effect with stronger association in Non-Hispanic Whites, with the lowest association in Asians. Besides the APOE, we also identified three other genome-wide loci: ABCA7 (rs12151021/chr19p.13.3; ß = 0.07, SE = 0.01, P = 9.2 × 10-09, MAF = 0.32), CR1 (rs6656401/chr1q.32.2; ß = 0.1, SE = 0.02, P = 2.4 × 10-10, MAF = 0.18) and FERMT2 locus (rs117834516/chr14q.22.1; ß = 0.16, SE = 0.03, P = 1.1 × 10-09, MAF = 0.06) that all colocalized with AD risk. Sex-stratified analyses identified two novel female-specific signals on chr5p.14.1 (rs529007143, ß = 0.79, SE = 0.14, P = 1.4 × 10-08, MAF = 0.006, sex-interaction P = 9.8 × 10-07) and chr11p.15.2 (rs192346166, ß = 0.94, SE = 0.17, P = 3.7 × 10-08, MAF = 0.004, sex-interaction P = 1.3 × 10-03). We also demonstrated that the overall genetic architecture of brain amyloidosis overlaps with that of AD, Frontotemporal Dementia, stroke, and brain structure-related complex human traits. Overall, our results have important implications when estimating the individual risk to a population level, as race and sex will needed to be taken into account. This may affect participant selection for future clinical trials and therapies.


Alzheimer Disease , Amyloidosis , Humans , Female , Alzheimer Disease/diagnostic imaging , Alzheimer Disease/genetics , Alzheimer Disease/complications , Amyloid beta-Peptides/genetics , Genome-Wide Association Study , Amyloidosis/diagnostic imaging , Amyloidosis/genetics , Amyloid , Apolipoproteins E/genetics
4.
Alzheimers Dement ; 19(11): 5010-5022, 2023 11.
Article En | MEDLINE | ID: mdl-37089073

INTRODUCTION: Cognitive abilities have substantial heritability throughout life, as shown by twin- and population-based studies. However, there is limited understanding of the genetic factors related to cognitive decline in aging across neurocognitive domains. METHODS: We conducted a meta-analysis on 3045 individuals aged ≥65, derived from three population-based cohorts, to identify genetic variants associated with the decline of five neurocognitive domains (attention, memory, executive function, language, visuospatial function) and global cognitive decline. We also conducted gene-based and functional bioinformatics analyses. RESULTS: Apolipoprotein E (APOE)4 was significantly associated with decline of memory (p = 5.58E-09) and global cognitive function (p = 1.84E-08). We identified a novel association with attention decline on chromosome 9, rs6559700 (p = 2.69E-08), near RASEF. Gene-based analysis also identified a novel gene, TMPRSS11D, involved in the activation of SARS-CoV-2, to be associated with the decline in global cognitive function (p = 4.28E-07). DISCUSSION: Domain-specific genetic studies can aid in the identification of novel genes and pathways associated with decline across neurocognitive domains. HIGHLIGHTS: rs6559700 was associated with decline of attention. APOE4 was associated with decline of memory and global cognitive decline. TMPRSS11D, a gene involved in the activation of SARS-CoV-2, was implicated in global cognitive decline. Cognitive domain abilities had both unique and shared molecular pathways across the domains.


COVID-19 , Cognitive Dysfunction , Humans , COVID-19/genetics , SARS-CoV-2 , Cognition/physiology , Cognitive Dysfunction/genetics , Attention , Apolipoprotein E4/genetics , Neuropsychological Tests
5.
medRxiv ; 2023 Mar 22.
Article En | MEDLINE | ID: mdl-36993271

Determining the genetic architecture of Alzheimer's disease (AD) pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we performed a genome-wide association study of cortical tau quantified by positron emission tomography in 3,136 participants from 12 independent studies. The CYP1B1-RMDN2 locus was associated with tau deposition. The most significant signal was at rs2113389, which explained 4.3% of the variation in cortical tau, while APOE4 rs429358 accounted for 3.6%. rs2113389 was associated with higher tau and faster cognitive decline. Additive effects, but no interactions, were observed between rs2113389 and diagnosis, APOE4 , and Aß positivity. CYP1B1 expression was upregulated in AD. rs2113389 was associated with higher CYP1B1 expression and methylation levels. Mouse model studies provided additional functional evidence for a relationship between CYP1B1 and tau deposition but not Aß. These results may provide insight into the genetic basis of cerebral tau and novel pathways for therapeutic development in AD.

6.
Genes (Basel) ; 13(12)2022 11 29.
Article En | MEDLINE | ID: mdl-36553504

Structural variations such as copy number variants (CNVs) have been associated with multiple autoimmune diseases. In this study, we explored the association of the Fc gamma receptor 3B gene (FCGR3B) copy number variation (CNV) with rheumatoid arthritis (RA) susceptibility and related serological traits in the Pakistani population. We also performed a meta-analysis of four published FCGR3B CNV studies along with the current study. A total of 927 subjects (597 RA cases, 330 healthy controls) were recruited from three rheumatology centers in Pakistan. Anti-cyclic citrullinated peptide (anti-CCP) antibodies and rheumatoid factor (RF) were measured in RA patients. FCGR3B copy number was assayed using the TaqMan® CN assay (Hs04211858_cn, Applied Biosystems, Foster City, CA, USA) and the copy number was estimated by using CopyCaller® software (version 2.1; Applied Biosystems, USA). Logistic regression was applied to calculate the odds ratio (OR) of RA risk associated with FCGR3B CNV using sex and age as covariates in R. Meta-analysis on four previously published studies and the current study was performed using the random-effect model. We observed a significant association between FCGR3B copy number < 2 and RA susceptibility (OR = 1.53; 95% CI: 1.05 to 2.22; p = 0.0259) and anti-CCP seropositivity (OR 2.56; 95% CI: 1.34 to 4.89; p = 0.0045). A non-significant association of FCGR3B copy number < 2 was also observed between increased rheumatoid factor (RF) seropositivity (OR = 1.74; 95% CI:0.93 to 3.26; p = 0.0816). Meta-analysis on 13,915 subjects (7005 RA cases and 6907 controls) also showed significant association of copy number < 2 with the increased risk of RA (OR = 1.30; 95% CI: 1.07 to 1.56; p = 0.00671). FCGR3B copy number < 2 is associated with increased RA risk and anti-CCP seropositivity.


Arthritis, Rheumatoid , DNA Copy Number Variations , Receptors, IgG , Humans , Anti-Citrullinated Protein Antibodies , Arthritis, Rheumatoid/genetics , Autoantibodies , DNA Copy Number Variations/genetics , Gene Dosage , Genetic Predisposition to Disease , Receptors, IgG/genetics , Rheumatoid Factor/genetics
7.
J Alzheimers Dis ; 88(2): 787-798, 2022.
Article En | MEDLINE | ID: mdl-35694926

BACKGROUND: Alzheimer's disease (AD) is a complex disease influenced by the environment and genetics; however, much of the genetic component remains unaccounted for. OBJECTIVE: The purpose of this work was to use genome-wide association analyses to detect genetic associations with incident AD in a sample of older adults aged 75 and above. METHODS: We performed a genome-wide association study (GWAS) on genome-wide genotyped and imputed data (14,072,053 variants) on the Gingko Evaluation of Memory (GEM) study sample consisting of 424 incident dementia (mean age = 84.46±3.91) and 2,206 non-demented (mean age = 84.55±3.23) subjects. RESULTS: The established association of APOE*4 carriers with AD was confirmed in this community-based sample of older subjects (odds ratio (OR) = 2.22; p = 9.36E-14) and was stronger in females (OR = 2.72; p = 1.74E-10) than in males (OR = 1.88; p = 2.43E-05). We observed a novel genome-wide significant (GWS) locus on chromosome 12 near ncRNA LOC105369711/rs148377161 (OR = 3.31; p = 1.66E-08). In addition, sex-stratified analyses identified two novel associations in males: one near ncRNA LOC729987/rs140076909 on chromosome 1 (OR = 4.51; p = 3.72E-08) and the other approaching GWS near ncRNA LOC105375138/rs117803234 on chromosome 7 (OR = 3.76; p = 6.93E-08). CONCLUSION: The use of community-based samples of older individuals and incident dementia as a phenotype may be a helpful approach for the identification of novel genes for AD, which may not be detected in standard case-control studies. Replication of these signals and further studies of these regions and genes will help to provide a clearer picture for their role in AD.


Alzheimer Disease , Genome-Wide Association Study , Alzheimer Disease/diagnosis , Alzheimer Disease/epidemiology , Alzheimer Disease/genetics , Case-Control Studies , Female , Genetic Predisposition to Disease/genetics , Humans , Male , Polymorphism, Single Nucleotide/genetics
8.
Gene ; 783: 145563, 2021 May 30.
Article En | MEDLINE | ID: mdl-33705809

Genome-wide association studies (GWAS) have identified multiple type 2 diabetes (T2D) loci, mostly among populations of European descent. There is a high prevalence of T2D among Pakistanis. Both genetic and environmental factors may be responsible for this high prevalence. In order to understand the shared genetic basis of T2D among Pakistanis and Europeans, we examined 77 genome-wide significant variants previously implicated among European populations. We genotyped 77 single-nucleotide polymorphisms (SNPs) by iPLEX® Gold or TaqMan® assays in a case-control sample of 1,683 individuals. Association analysis was performed using logistic regression. A total of 16 SNPs (TCF7L2/rs7903146, GLIS3/rs7041847, CHCHD9/rs13292136, PLEKHA1/rs2292626, FTO/rs9936385, CDKAL1/rs7756992, KCNJ11/rs5215, LOC105372155/rs12970134, KCNQ1/rs163182, CTRB1/rs7202877, ST6GAL1/rs16861329, ADAMTS9-AS2/rs6795735, LOC105370275/rs1359790, C5orf67/rs459193, ZBED3-AS1/rs6878122 and UBE2E2/rs7612463) showed statistically significant associations after controlling for the false discovery rate. While KCNQ1/rs163182 and ZBED3-AS1/rs6878122 showed opposite allelic effects, the remaining significant SNPs had the same allelic effects as reported previously. Our data indicate that a selected number of T2D loci previously identified among populations of European descent also affect the risk of T2D in the Pakistani population.


Diabetes Mellitus, Type 2/genetics , Genome-Wide Association Study , Female , Genetic Predisposition to Disease , Genotyping Techniques , Humans , Male , Middle Aged , Pakistan , Polymorphism, Single Nucleotide , Risk Assessment
9.
Mol Psychiatry ; 26(1): 309-321, 2021 01.
Article En | MEDLINE | ID: mdl-30361487

Deposition of amyloid plaques in the brain is one of the two main pathological hallmarks of Alzheimer's disease (AD). Amyloid positron emission tomography (PET) is a neuroimaging tool that selectively detects in vivo amyloid deposition in the brain and is a reliable endophenotype for AD that complements cerebrospinal fluid biomarkers with regional information. We measured in vivo amyloid deposition in the brains of ~1000 subjects from three collaborative AD centers and ADNI using 11C-labeled Pittsburgh Compound-B (PiB)-PET imaging followed by meta-analysis of genome-wide association studies, first to our knowledge for PiB-PET, to identify novel genetic loci for this endophenotype. The APOE region showed the most significant association where several SNPs surpassed the genome-wide significant threshold, with APOE*4 being most significant (P-meta = 9.09E-30; ß = 0.18). Interestingly, after conditioning on APOE*4, 14 SNPs remained significant at P < 0.05 in the APOE region that were not in linkage disequilibrium with APOE*4. Outside the APOE region, the meta-analysis revealed 15 non-APOE loci with P < 1E-05 on nine chromosomes, with two most significant SNPs on chromosomes 8 (P-meta = 4.87E-07) and 3 (P-meta = 9.69E-07). Functional analyses of these SNPs indicate their potential relevance with AD pathogenesis. Top 15 non-APOE SNPs along with APOE*4 explained 25-35% of the amyloid variance in different datasets, of which 14-17% was explained by APOE*4 alone. In conclusion, we have identified novel signals in APOE and non-APOE regions that affect amyloid deposition in the brain. Our data also highlights the presence of yet to be discovered variants that may be responsible for the unexplained genetic variance of amyloid deposition.


Alzheimer Disease/diagnostic imaging , Alzheimer Disease/metabolism , Amyloid beta-Peptides/metabolism , Aniline Compounds/analysis , Brain/diagnostic imaging , Brain/metabolism , Genome-Wide Association Study , Positron-Emission Tomography , Thiazoles/analysis , Alzheimer Disease/genetics , Apolipoprotein E4/genetics , Endophenotypes , Female , Humans , Male , Polymorphism, Single Nucleotide/genetics
10.
Dis Markers ; 2020: 7189626, 2020.
Article En | MEDLINE | ID: mdl-33101545

OBJECTIVE: Copy number variation (CNV) is a structural variation in the human genome that has been associated with multiple clinical phenotypes. B cells are important components of rheumatoid arthritis- (RA-) mediated immune response; hence, CNV in the regulators of B cells (such as VPREB1) can influence RA susceptibility. In this study, we aimed to explore the association of CNV in the VPREB1 gene with RA susceptibility in the Pakistani population. METHODS: A total of 1,106 subjects (616 RA cases, 490 healthy controls) were selected from three rheumatology centers in Pakistan. VPREB1 CNV was determined using the TaqMan® CN assay (Hs02879734_cn, Applied Biosystems, Foster City, CA, USA), and CNV was estimated by using CopyCaller® (version 2.1; Applied Biosystems, USA) software. Odds ratio (OR) was calculated by logistic regression with sex and age as covariates in R. RESULTS: A significant association between >2 VPREB1 CNV and RA risk was observed with an OR of 3.92 (95% CI: 1.27 - 12.12; p = 0.01746) in the total sample. Whereas <2 CNV showed a significantly protective effect against RA risk in women with an OR of 0.48 (95% CI: 0.29-0.79; p = 0.00381). CONCLUSION: CNV > 2 of VPREB1 is a risk factor for RA in the total Pakistani population, while CNV < 2 is protective in women.


Arthritis, Rheumatoid/genetics , DNA Copy Number Variations , Immunoglobulin Light Chains, Surrogate/genetics , Adult , Case-Control Studies , Female , Genetic Predisposition to Disease , Humans , Male , Middle Aged , Pakistan
11.
PLoS One ; 15(9): e0239426, 2020.
Article En | MEDLINE | ID: mdl-32946523

Rheumatoid arthritis (RA) is a multifactorial autoimmune disease. The interaction of genetic and environmental factors is likely necessary for RA. Among potential genetic factors, many major histocompatibility complex (MHC) and non-MHC variants may be involved in RA susceptibility. CTLA4 is involved in the regulation of T-cell response during an immune reaction, and multiple CTLA4 single nucleotide polymorphisms (SNPs) have been associated with numerous autoimmune diseases, including RA. To our knowledge, the genetic association of CTLA4 with RA risk has not been examined previously in the Pakistani population. In this study, we sequenced the entire CTLA4 gene and flanking regions in 95 Pakistani RA cases followed the screening of identified variants in Study 1 sample consisting of 350 RA cases and controls. Four common significant variants identified in Study 1 sample were further examined in a larger Study 2 replication sample comprising 1,678 independent RA cases and controls. We report significant associations of three variants from the combined analysis: rs3087243 (OR = 1.26, p = 4.47E-03), rs5742909 (OR = 1.78, p = 4.60E-03), and rs11571319 (OR = 1.48, p = 6.64E-03); the latter is a novel association in the Pakistani sample.


Arthritis, Rheumatoid/genetics , CTLA-4 Antigen/genetics , Sequence Analysis , Adult , Case-Control Studies , Female , Genotype , Humans , Male , Pakistan , Polymorphism, Single Nucleotide
12.
Dis Markers ; 2020: 1910215, 2020.
Article En | MEDLINE | ID: mdl-32831971

Rheumatoid arthritis (RA) is a complex and multifactorial autoimmune disorder with the involvement of multiple genetic and environmental factors. Genome-wide association studies (GWAS) have identified more than 50 RA genetic loci in European populations. Given the anticipated overlap of RA-relevant genes and pathways across different ethnic groups, we sought to replicate 58 GWAS-implicated SNPs reported in Europeans in Pakistani subjects. 1,959 unrelated subjects comprising 1,222 RA cases and 737 controls were collected from three rheumatology facilities in Pakistan. Genotyping was performed using iPLEX or TaqMan® methods. A total of 50 SNPs were included in the final association analysis after excluding those that failed assay design/run or postrun QC analysis. Fourteen SNPs (LINC00824/rs1516971, PADI4/rs2240336, CEP57/rs4409785, CTLA4/rs3087243, STAT4/rs13426947, HLA-B/MICA/rs2596565, C5orf30/rs26232, CCL21/rs951005, GATA3/rs2275806, VPS37C/rs595158, HLA-DRB1/rs660895, EOMES/rs3806624, SPRED2/rs934734, and RUNX1/rs9979383) were replicated in our Pakistani sample at false discovery rate (FDR) of <0.20 with nominal p values ranging from 4.73E-06 to 3.48E-02. Our results indicate that several RA susceptibility loci are shared between Pakistani and European populations, supporting the role of common genes/pathways.


Arthritis, Rheumatoid/genetics , Gene Regulatory Networks , Genome-Wide Association Study/methods , Polymorphism, Single Nucleotide , Adult , Case-Control Studies , Europe/ethnology , Female , Genetic Predisposition to Disease/ethnology , Humans , Male , Middle Aged , Pakistan
13.
J Alzheimers Dis ; 76(4): 1553-1565, 2020.
Article En | MEDLINE | ID: mdl-32651314

The genetics of late-onset Alzheimer's disease (AD) is complex due to the heterogeneous nature of the disorder. APOE*4 is the strongest genetic risk factor for AD. Genome-wide association studies have identified more than 30 additional loci, each having relatively small effect size. Known AD loci explain only about 30% of the genetic variance, and thus much of the genetic variance remains unexplained. To identify some of the missing heritability of AD, we analyzed whole-exome sequencing (WES) data focusing on non-APOE*4 carriers from two WES datasets: 720 cases and controls from the University of Pittsburgh and 7,252 cases and controls from the Alzheimer's Disease Sequencing Project. Following separate WES analyses in each dataset, we performed meta-analysis for overlapping markers present in both datasets. Among the four variants reaching the exome-wide significance threshold, three were from known AD loci: APOE/rs7412 (odds ratio (OR) = 0.40; p = 5.46E-24), TOMM40/rs157581 (OR = 1.49; p = 4.04E-07), and TREM2/rs75932628 (OR = 4.00; p = 1.15E-07). The fourth significant variant, rs199533, was from a novel locus on chromosome 17 in the NSF gene (OR = 0.78; p = 2.88E-07). NSF was also significant in the gene-based analysis (p = 1.20E-05). In the GTEx data, NSF/rs199533 is a cis-eQTL for multiple genes in the brain and blood, including NSF that is highly expressed across all brain tissues, including regions that typically show amyloid-ß accumulation. Further characterization of genes that are affected by NSF/rs199533 may help to shed light on the roles of these genes in AD etiology.


Alzheimer Disease/genetics , Amyloid beta-Peptides/genetics , Apolipoproteins E/genetics , Genetic Predisposition to Disease/genetics , Aged , Exome/genetics , Female , Genome-Wide Association Study , Humans , Male , Membrane Transport Proteins/genetics , Polymorphism, Single Nucleotide/genetics
14.
Theor Appl Genet ; 133(8): 2477-2497, 2020 Aug.
Article En | MEDLINE | ID: mdl-32462429

KEY MESSAGE: This study uses simulations to explore statistical power and false-positive rates for eQTL mapping in allopolyploid organisms and provides guidelines to apply eQTL mapping in these organisms. In recent years, RNA-seq has become the dominant technology for eQTL studies. However, most work has been in diploid organisms. Many species of economic and environmental importance are polyploid, and approaches for eQTL mapping in polyploids are not well developed. High similarity between duplicated genes in polyploids will cause misassignment of sequence reads and may cause false-positive results and/or lack of power to detect eQTL. In this paper, we first explore the similarity of homoeologous transcripts in polyploid organisms. We find that 5-20% of genes (varying with organism) in important agricultural plants such as wheat, soybean, and switchgrass are not sufficiently diverged between duplicated genomes to allow unambiguous assignment of reads. Second, we examine the impact of misassigned reads on eQTL mapping and show that both false-positive and false-negative rates can be greatly inflated. Third, we compare four strategies for dealing with ambiguous reads: (1) dividing ambiguous reads evenly between homoeologous transcripts, (2) assigning them proportionally, (3) using all reads for all genes, and (4) discarding ambiguous reads. We find that the strategy of discarding ambiguous reads gives the best balance of false-positive and false-negative rates for most genes. However, for genes that are very similar between genomes, using all reads is the only choice. This leads to reduced power, but false-positive rates will be maintained. We also discuss QTL mapping in polyploids using allele-specific expression (ASE) and show how the proportion of ASE-informative reads varies according to the divergence between homoeologous genes.


Chromosome Mapping/methods , Crops, Agricultural/genetics , Polyploidy , Sequence Analysis, RNA/methods , Alleles , Diploidy , Panicum/genetics , Panicum/metabolism , Phylogeny , Polymorphism, Single Nucleotide , Quantitative Trait Loci , Glycine max/genetics , Glycine max/metabolism , Triticum/genetics , Triticum/metabolism
15.
BMC Res Notes ; 12(1): 544, 2019 Aug 27.
Article En | MEDLINE | ID: mdl-31455420

OBJECTIVE: Type 1 diabetes (T1D) and rheumatoid arthritis (RA) are autoimmune diseases. It is known that certain genetic loci and factors that increase the overall autoimmunity risk can be shared among different autoimmune diseases. We sought to replicate seven T1D-related SNPs (single nucleotide polymorphisms) that have been previously reported to be associated with RA susceptibility in a small set of mixed family-based and case-control Pakistani sample in a relatively large and independent RA case-control sample from the same population. Seven T1D-associated SNPs (GLIS3/rs7020673, BACH2/rs11755527, SKAP2/rs7804356, GDSMB/rs2290400, C6orf173/rs9388489, LOC399716/rs947474 and DLK1-MEG2/rs941576) were genotyped in a large Pakistani RA case-control sample (n = 1959) using TaqMan® SNP genotyping assays. RESULTS: None of the tested SNPs showed statistically significant association with RA susceptibility; however, one SNP (GLIS3/rs7020673) showed a trend for association (OR = 0.88, p = 7.99E-02). Our study has failed to replicate the previously reported association of seven T1D-associated SNPs with RA risk in a large sample from the same population. Thus, our results do not support a major role of these T1D SNPs in affecting RA susceptibility in the Pakistani population.


Arthritis, Rheumatoid/genetics , Diabetes Mellitus, Type 1/genetics , Genetic Loci/genetics , Genetic Predisposition to Disease/genetics , Polymorphism, Single Nucleotide , Adult , Case-Control Studies , Female , Gene Frequency , Genotype , Humans , Male , Middle Aged , Pakistan
16.
Neurobiol Aging ; 84: 239.e15-239.e24, 2019 12.
Article En | MEDLINE | ID: mdl-30954325

To identify novel loci that affect cognitive decline in older adults free of dementia, we conducted genome-wide and gene-based meta-analyses on longitudinal slopes of 5 cognitive domains (memory, executive function, language, attention/processing speed, and visuospatial ability) derived from 2 population-based cohorts. For decline over time in each cognitive domain, we normalized intraindividual slopes within each cohort, accounting for baseline age, sex, and years of education. Normalized slope for each domain was used in cohort-specific genome-wide analyses after including top principal components as covariates followed by genome-wide and gene-based meta-analyses. Both analyses revealed a novel WDFY2 locus at genome-wide (p = 3.37E-08) and gene-wide (p = 7.10E-07) significance levels for the attention/processing speed domain. In the GTEx eQTL analysis, genome-wide significant single-nucleotide polymorphism was associated with RNA expression levels of WDFY2 in several brain regions: cerebellar hemisphere (p = 1.07E-04), cerebellum (p = 6.92E-04), hippocampus (p = 2.18E-03) and cortex (p = 2.29E-02), and in whole blood (p = 4.41E-05). Our results suggest that WDFY2 genetic variation may affect individual differences in decline over time on tests of attention/processing speed.


Cognitive Dysfunction/genetics , Genome-Wide Association Study , Aged , Aged, 80 and over , Attention , Dementia , Humans
17.
J Hand Microsurg ; 8(1): 21-6, 2016 Apr.
Article En | MEDLINE | ID: mdl-27616824

INTRODUCTION: Carpal tunnel steroid injections (CTIs) have the potential risk of damaging underlying critical structures, including the median nerve (MN), radial artery (RA), and ulnar neurovascular bundle (UB). The purpose of this study was to analyze the safety of a volar radial (VR) and volar ulnar (VU) CTI, using standardized anatomical "safe zones." MATERIALS AND METHODS: This study was performed on 87 cadaveric arms using a percentage of the total wrist width as a guide for placement of a VR (30 and 33% of total wrist width) and VU (60 and 66% of total wrist width) injection. RESULTS: Our results demonstrate a wide range of anatomic variations in the location of these critical neurovascular structures near the carpal canal, indicating that using superficial landmarks alone for CTIs may result in an increased risk of iatrogenic injury to these critical structures. DISCUSSION: We propose a technique using a percentage of total wrist width as a guide for CTIs. Both VR (30% of wrist width) and VU (60% of wrist width) CTIs offer relatively safe and reliable CTI locations to the carpal canal. LEVEL OF EVIDENCE: Not applicable/cadaveric study.

18.
Neurotoxicology ; 47: 88-98, 2015 Mar.
Article En | MEDLINE | ID: mdl-25732874

Systemic off-target toxicities, including neurotoxicity, are prevalent side effects in cancer patients treated with a number of otherwise highly efficacious anticancer drugs. In the current study, we have: (1) developed a new analytical metric for the in vivo preclinical assessment of systemic toxicities/neurotoxicity of new drugs and delivery systems; and (2) evaluated, in mice, the in vivo efficacy and toxicity of a versatile and modular NanoDendron (ND) drug delivery and imaging platform that we recently developed. Our paclitaxel-carrying ND prodrug, ND(PXL), is activated following proteolytic cleavage by MMP9, resulting in localized cytotoxic chemotherapy. Using click chemistry, we combined ND(PXL) with a traceable beacon, ND(PB), yielding ND(PXL)-ND(PB) that functions as a theranostic compound. In vivo fluorescence FRET imaging of this theranostic platform was used to confirm localized delivery to tumors and to assess the efficiency of drug delivery to tumors, achieving 25-30% activation in the tumors of an immunocompetent mouse model of breast cancer. In this model, ND-drug exhibited anti-tumor efficacy comparable to nab-paclitaxel, a clinical formulation. In addition, we combined neurobehavioral metrics of nociception and sensorimotor performance of individual mice to develop a novel composite toxicity score that reveals and quantifies peripheral neurotoxicity, a debilitating long-term systemic toxicity of paclitaxel therapy. Importantly, mice treated with nab-paclitaxel developed changes in behavioral metrics with significantly higher toxicity scores indicative of peripheral neuropathy, while mice treated with ND(PXL) showed no significant changes in behavioral responses or toxicity score. Our ND formulation was designed to be readily adaptable to incorporate different drugs, imaging modalities and/or targeting motifs. This formulation has significant potential for preclinical and clinical tools across multiple disease states. The studies presented here report a novel toxicity score for assessing peripheral neuropathy and demonstrate that our targeted, theranostic NDs are safe and effective, providing localized tumor delivery of a chemotherapeutic and with reduced common neurotoxic side-effects.


Antineoplastic Agents, Phytogenic/therapeutic use , Breast Neoplasms/drug therapy , Drug Delivery Systems , Mammary Neoplasms, Experimental/drug therapy , Paclitaxel/therapeutic use , Prodrugs/therapeutic use , Animals , Antineoplastic Agents, Phytogenic/administration & dosage , Antineoplastic Agents, Phytogenic/adverse effects , Heterografts , Matrix Metalloproteinase 9/metabolism , Mice , Motor Activity/drug effects , Nociception/drug effects , Paclitaxel/administration & dosage , Paclitaxel/adverse effects , Prodrugs/administration & dosage , Prodrugs/adverse effects
19.
J Urol ; 193(4): 1226-31, 2015 Apr.
Article En | MEDLINE | ID: mdl-25451829

PURPOSE: Observational data suggest that androgen deprivation therapy increases the risk of diabetes and cardiovascular disease. Using data from the population based PCOS we evaluated whether age at diagnosis and comorbidity impact the association of androgen deprivation therapy with incident diabetes and cardiovascular disease. MATERIALS AND METHODS: We identified men with nonmetastatic prostate cancer diagnosed from 1994 to 1995 who were followed through 2009 to 2010. We used multivariable logistic regression models to assess the relationship of androgen deprivation therapy exposure (2 or fewer years, greater than 2 years or none) with incident diabetes and cardiovascular disease, adjusting for age at diagnosis, race, stage and comorbidity. RESULTS: Of 3,526 eligible study participants 2,985 without diabetes and 3,112 without cardiovascular disease comprised the cohorts at risk. Androgen deprivation therapy was not associated with an increased risk of diabetes or cardiovascular disease in men diagnosed with prostate cancer before age 70 years. Prolonged androgen deprivation therapy and increasing age at diagnosis in older men was associated with an increased risk of diabetes (at age 76 years OR 2.1, 95% CI 1.0-4.4) and cardiovascular disease (at age 74 years OR 1.9, 95% CI 1.0-3.5). Men with comorbidities were at greater risk for diabetes (OR 4.3, 95% CI 2.3-7.9) and cardiovascular disease (OR 8.1, 95% CI 4.3-15.5) than men without comorbidities. CONCLUSIONS: Prolonged androgen deprivation therapy exposure increases the risk of cardiovascular disease and diabetes in men diagnosed with prostate cancer who are older than approximately 75 years, especially those with other comorbidities. Older men who receive prolonged androgen deprivation therapy should be closely monitored for diabetes and cardiovascular disease.


Androgen Antagonists/therapeutic use , Cardiovascular Diseases/chemically induced , Cardiovascular Diseases/epidemiology , Diabetes Complications/chemically induced , Diabetes Complications/epidemiology , Diabetes Mellitus/chemically induced , Diabetes Mellitus/epidemiology , Prostatic Neoplasms/complications , Prostatic Neoplasms/drug therapy , Age Factors , Aged , Aged, 80 and over , Cardiovascular Diseases/complications , Cohort Studies , Diabetes Complications/complications , Humans , Incidence , Male , Middle Aged , Prospective Studies , Risk , Survivors
20.
Urology ; 85(1): 92-100, 2015 Jan.
Article En | MEDLINE | ID: mdl-25261048

OBJECTIVE: To provide population-based estimates of other-cause mortality by age and comorbidity in men with prostate cancer for use at the point of care in shared decision making. MATERIALS AND METHODS: We sampled 3183 men with nonmetastatic prostate cancer from the Prostate Cancer Outcomes Study, a US population-based prospective cohort. Survival analysis accounting for competing risks was used to provide predictions of other-cause and cancer-specific mortality by age, comorbidity, and tumor risk through 14 years of follow-up. RESULTS: Older men had a higher absolute risk of other-cause mortality associated with comorbidity. For men with comorbidity counts of 0, 1, 2, and 3+, cumulative incidence of other-cause mortality at 14 years was 9%, 18%, 30%, and 35% for those younger than 60 years; 26%, 26%, and 48%, and 52% for those aged 60-70 years; and 49%, 57%, 66%, and 74% for those older than 70 years. Prostate cancer mortality at 14 years was 5%, 8%, and 23% for men with low-, intermediate-, and high-risk disease. Competing risk pictograms for each age/comorbidity/tumor-risk pair provide visual characterization of these risks over time. CONCLUSION: Our survival tables may be used at the point of care as part of shared decision making. Men aged >60 years with multiple comorbidities have substantial risk of other-cause mortality within 15 years of diagnosis and should consider conservative management for low-risk disease, given its low incidence of cancer-specific mortality. Men with high-risk disease, regardless of age or comorbidity, are at greater risk for cancer mortality and may still be appropriate candidates for aggressive treatment.


Prostatic Neoplasms/mortality , Aged , Cause of Death , Humans , Male , Middle Aged , Neoplasm Staging , Prognosis , Prospective Studies , Prostatic Neoplasms/complications , Prostatic Neoplasms/pathology , Survival Rate , Time Factors
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