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Pediatr Ann ; 51(1): e15-e21, 2022 Jan.
Article En | MEDLINE | ID: mdl-35020509

Cancer predisposition syndromes (CPS), or genetic syndromes leading to increased cancer risk, are responsible for at least 10% of all childhood cancers. With advances in both tumor and germline sequencing, these syndromes have been uncovered both in patients with and without syndromic features and family history of cancer. Recognition of CPS in children and use of associated screening guidelines can improve morbidity and mortality from childhood cancer. Given the multidisciplinary approach needed for management of CPS, knowledge of clinical features and surveillance guidelines are essential for the general pediatrician. Pediatricians also play a vital role in anticipatory guidance regarding cancer prevention strategies and management of psychosocial stressors associated with ongoing screening. This article discusses 10 of the more common pediatric CPS, reasons to refer patients for CPS genetic testing and evaluation, and general cancer prevention strategies. [Pediatr Ann. 2022;51(1):e15-e21.].

Genetic Testing , Neoplasms , Child , Genetic Predisposition to Disease , Humans , Medical History Taking , Neoplasms/diagnosis , Neoplasms/genetics , Pediatricians
J Int Med Res ; 50(1): 3000605211070757, 2022 Jan.
Article En | MEDLINE | ID: mdl-35000471

OBJECTIVE: Breast cancer (BC) is the most common form of cancer among Asian females. Mutations in the BRCA1/BRCA2 genes are often observed in BC cases and largely increase the lifetime risk of having BC. Because of the paucity of high-quality data on the molecular spectrum of BRCA mutations in South Asian populations, we aimed to explore these mutations among South Asian countries. METHODS: A systematic literature search was performed for the BRCA1 and BRCA2 gene mutation spectrum using electronic databases such as PubMed, EMBASE, and Google Scholar. Twenty studies were selected based on specific inclusion and exclusion criteria. RESULTS: The 185delAG (c.68_69del) mutation in exon 2 of BRCA1 was the most common recurrent mutation and founder mutation found. Various intronic variants, variants of unknown significance, large genomic rearrangements, and polymorphisms were also described in some studies. CONCLUSIONS: The South Asian population has a wide variety of genetic mutations of BRCA1 and BRCA2 that differ according to countries and ethnicities. A stronger knowledge of various population-specific mutations in these cancer susceptibility genes can help provide efficient strategies for genetic testing.

Breast Neoplasms , Ovarian Neoplasms , Asia/epidemiology , BRCA1 Protein/genetics , BRCA2 Protein/genetics , Breast Neoplasms/genetics , Female , Genes, BRCA2 , Genetic Predisposition to Disease , Humans , Mutation , Neoplasm Recurrence, Local , Ovarian Neoplasms/genetics , Spectrum Analysis
Clin Lab ; 68(1)2022 Jan 01.
Article En | MEDLINE | ID: mdl-35023674

BACKGROUND: Mutations of the BRCA1/2 genes are associated with increased breast and ovarian cancer. The aim of this study was to investigate the founder mutations of the BRCA1 and BRCA2 genes in the Turkish population in the Aegean region as well as their genotype-phenotype correlations. METHODS: All the patients were provided with BRCA1/2 testing criteria according to the National Comprehensive Cancer Network. QIAseq Targeted DNA Panels were used for the BRCA1/2 coding regions. RESULTS: Of the 181 studied patients, 38 (21%) were found to carry pathogenic or likely pathogenic mutations, while 20 (11%) patients were found to carry variants of unknown significance. The most common pathogenic mutations were NM_000059.4:c.2765dup in the BRCA2 gene and NM_007300.4:c.981_982del and NM_007294.3:c. 5266dup in the BRCA1 gene. p.Lys3326* was the most frequently detected variant of unknown significance (6/ 181). Regarding genotype-phenotype correlations, the NM_007300.4:c.981_982del mutation in BRCA1 gene was found to be milder in terms of breast cancer. The most frequent cancers other than those related to BRCA genes, observed in the relatives of the patients who had pathogenic variants and variants of unknown significance, were endometrium cancer and leukemia, respectively. CONCLUSIONS: NM_007294.3:c.5266dup was found to be a candidate founder mutation in the Turkish population. NM_007300.4:c.981_982del mutation seems to have a milder course in terms of breast cancer. A significantly increased frequency of p.Lys3326* variant in breast cancer and ovarian cancer patients compared with that in the 1,000 Genomes Project suggesting that this variant has a slight effect on BRCA2 function.

Breast Neoplasms , Ovarian Neoplasms , BRCA1 Protein/genetics , BRCA2 Protein , Breast Neoplasms/genetics , Female , Genes, BRCA1 , Genetic Association Studies , Genetic Predisposition to Disease , Humans , Mutation , Ovarian Neoplasms/genetics , Turkey
PLoS One ; 17(1): e0260897, 2022.
Article En | MEDLINE | ID: mdl-34995294

BACKGROUND: Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can manifest with varying disease severity and mortality. Genetic predisposition influences the clinical course of infectious diseases. We investigated whether genetic polymorphisms in candidate genes ACE2, TIRAP, and factor X are associated with clinical outcomes in COVID-19. METHODS: We conducted a single-centre retrospective cohort study. All patients who visited the emergency department with SARS-CoV-2 infection proven by polymerase chain reaction were included. Single nucleotide polymorphisms in ACE2 (rs2285666), TIRAP (rs8177374) and factor X (rs3211783) were assessed. The outcomes were mortality, respiratory failure and venous thromboembolism. Respiratory failure was defined as the necessity of >5 litres/minute oxygen, high flow nasal oxygen suppletion or mechanical ventilation. RESULTS: Between March and April 2020, 116 patients (35% female, median age 65 [inter quartile range 55-75] years) were included and treated according to the then applicable guidelines. Sixteen patients (14%) died, 44 patients (38%) had respiratory failure of whom 23 required endotracheal intubation for mechanical ventilation, and 20 patients (17%) developed venous thromboembolism. The percentage of TIRAP polymorphism carriers in the survivor group was 28% as compared to 0% in the non-survivor group (p = 0.01, Bonferroni corrected p = 0.02). Genotype distribution of ACE2 and factor X did not differ between survivors and non-survivors. CONCLUSION: This study shows that carriage of TIRAP polymorphism rs8177374 could be associated with a significantly lower mortality in COVID-19. This TIRAP polymorphism may be an important predictor in the outcome of COVID-19.

COVID-19/genetics , COVID-19/mortality , Membrane Glycoproteins/genetics , Receptors, Interleukin-1/genetics , Aged , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , COVID-19/epidemiology , Cohort Studies , Factor X/genetics , Factor X/metabolism , Female , Genetic Predisposition to Disease/genetics , Genotype , Humans , Male , Membrane Glycoproteins/metabolism , Middle Aged , Netherlands/epidemiology , Polymorphism, Single Nucleotide/genetics , Receptors, Interleukin-1/metabolism , Retrospective Studies , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Severity of Illness Index , Treatment Outcome
BMC Bioinformatics ; 23(1): 28, 2022 Jan 10.
Article En | MEDLINE | ID: mdl-35012447

BACKGROUND/AIM: The polygenic risk score (PRS) shows promise as a potentially effective approach to summarize genetic risk for complex diseases such as alcohol use disorder that is influenced by a combination of multiple variants, each of which has a very small effect. Yet, conventional PRS methods tend to over-adjust confounding factors in the discovery sample and thus have low power to predict the phenotype in the target sample. This study aims to address this important methodological issue. METHODS: This study proposed a new method to construct PRS by (1) approximating the polygenic model using a few principal components selected based on eigen-correlation in the discovery data; and (2) conducting principal component projection on the target data. Secondary data analysis was conducted on two large scale databases: the Study of Addiction: Genetics and Environment (SAGE; discovery data) and the National Longitudinal Study of Adolescent to Adult Health (Add Health; target data) to compare performance of the conventional and proposed methods. RESULT AND CONCLUSION: The results show that the proposed method has higher prediction power and can handle participants from different ancestry backgrounds. We also provide practical recommendations for setting the linkage disequilibrium (LD) and p value thresholds.

Alcoholism , Genetic Predisposition to Disease , Alcoholism/genetics , Genome-Wide Association Study , Humans , Linkage Disequilibrium , Longitudinal Studies , Multifactorial Inheritance , Risk Factors
Nat Commun ; 13(1): 27, 2022 01 14.
Article En | MEDLINE | ID: mdl-35031607

Coordinated programs of gene expression drive brain development. It is unclear which transcriptional programs, in which cell-types, are affected in neuropsychiatric disorders such as schizophrenia. Here we integrate human genetics with transcriptomic data from differentiation of human embryonic stem cells into cortical excitatory neurons. We identify transcriptional programs expressed during early neurogenesis in vitro and in human foetal cortex that are down-regulated in DLG2-/- lines. Down-regulation impacted neuronal differentiation and maturation, impairing migration, morphology and action potential generation. Genetic variation in these programs is associated with neuropsychiatric disorders and cognitive function, with associated variants predominantly concentrated in loss-of-function intolerant genes. Neurogenic programs also overlap schizophrenia GWAS enrichment previously identified in mature excitatory neurons, suggesting that pathways active during prenatal cortical development may also be associated with mature neuronal dysfunction. Our data from human embryonic stem cells, when combined with analysis of available foetal cortical gene expression data, de novo rare variants and GWAS statistics for neuropsychiatric disorders and cognition, reveal a convergence on transcriptional programs regulating excitatory cortical neurogenesis.

Cerebral Cortex/embryology , Gene Expression Regulation, Developmental , Guanylate Kinases/genetics , Neurogenesis , Tumor Suppressor Proteins/genetics , Animals , Cell Differentiation , Cerebral Cortex/cytology , Cerebral Cortex/metabolism , Female , Gene Knockdown Techniques , Genetic Predisposition to Disease , Guanylate Kinases/metabolism , Human Embryonic Stem Cells/metabolism , Humans , Mental Disorders/genetics , Neurogenesis/genetics , Neurogenesis/physiology , Neurons , Pregnancy , Schizophrenia/genetics , Transcriptome , Tumor Suppressor Proteins/metabolism
Gene ; 809: 146019, 2022 Jan 30.
Article En | MEDLINE | ID: mdl-34656741

INTRODUCTION: GST non-functional genotypes can lead to the accumulation of toxic intermediates, resulting in liver damage and increasing susceptibility to ATDH. AIM: To investigate the impact of GST Mu (GSTM1), GST Theta (GSTT1) null genotypes, and GST Pi (GSTP1; adenosine (A) > guanine (G), rs1695) variant allele on the development of ATDH in Tunisian patients treated with anti-tuberculosis therapy. METHODS: This was a case-control study including patients receiving anti-tuberculosis regimen. Cases (n = 23) were tuberculosis patients presenting ATDH during two months of anti-tuberculosis drug therapy. Controls (n = 30) were patients treated for tuberculosis, but presenting no ATDH. Genotyping was performed using a polymerase chain reaction-restriction fragment length polymorphism. RESULTS: No statistically significant association was observed between GSTM1 and GSTT1 homozygous null genotypes, and the risk of ATDH. A statistically significant association between GSTM1 and GSTT1 double null genotypes, and the risk of ATDH was found (p = 0.033) between cases and controls. For GSTP1, the distribution of GG homozygous mutant genotype was significantly associated with ATDH compared with the wild and the transition A to G (AA + AG) genotypes. CONCLUSION: Double deletion of GSTM1 and GSTT1 may predispose to ATDH in a Tunisian population. Moreover, GSTP1 rs1695 (A > G) genotyping can predict susceptibility to developing ATDH.

Antitubercular Agents/adverse effects , Chemical and Drug Induced Liver Injury/genetics , Glutathione S-Transferase pi/genetics , Glutathione Transferase/genetics , Adult , Case-Control Studies , Genetic Predisposition to Disease , Humans , Male , Middle Aged , Pharmacogenomic Variants , Polymorphism, Single Nucleotide , Prospective Studies , Tunisia
Gene ; 809: 146008, 2022 Jan 30.
Article En | MEDLINE | ID: mdl-34656742

BACKGROUND: Genome-wide association studies identified numerous susceptibility loci for multiple sclerosis in populations of European ancestry, but the associations are not always reproducible in other populations due to admixture and different linkage disequilibrium patterns obscuring true association signals. OBJECTIVE: Our aim was to identify genetic predictors of multiple sclerosis in three ethnically homogenous populations from the Volga-Ural region of Russian Federation. METHODS: In the largest to date study of multiple sclerosis in Russian population, involving 2048 participants from the Republic of Bashkortostan, Russian Federation (641 patients with multiple sclerosis and 1407 unaffected individuals), we performed replication analysis of previously identified genome-wide signals for multiple sclerosis. Associations were tested using logistic regression analysis under additive genetic model adjusted for sex. Meta-analysis of the study results in three populations was performed under fixed effects and random effects models. RESULTS: We demonstrate the association with multiple sclerosis of the five variants (INAVA rs7522462, EOMES rs11129295, C6orf10 rs3129934, CD86 rs9282641, and GPR65 rs2119704). The strongest association (OR = 2.16, CI:1.85-2.74, P = 2.53x10-13) was detected for rs3129934 polymorphism in the major histocompatibility region. Multilocus analysis has revealed 322 and 27 allelic patterns associated with multiple sclerosis in women and men, respectively. In women, the highest risk of MS was conferred by C6orf10 rs3129934*T/T + STAT3 rs744166*T combination (OR = 11.87), in men - by C6orf10 rs3129934*T + EOMES rs11129295*C + RPS6KB1 rs180515*C combination (OR = 3.25). CONCLUSION: We confirm five associations with multiple sclerosis previously reported in genome-wide scans in Europeans in three ethnic groups from the Volga-Ural region of Russia.

Multiple Sclerosis/genetics , Polymorphism, Single Nucleotide/genetics , Adult , B7-2 Antigen/genetics , Bashkiria/ethnology , Carrier Proteins/genetics , Case-Control Studies , Female , Genetic Predisposition to Disease , Humans , Male , Middle Aged , Multiple Sclerosis/etiology , Receptors, G-Protein-Coupled/genetics , T-Box Domain Proteins/genetics
Gut ; 71(1): 89-99, 2022 01.
Article En | MEDLINE | ID: mdl-33563644

OBJECTIVES: Alterations in the intestinal microbiota are linked with a wide range of autoimmune and inflammatory conditions, including inflammatory bowel diseases (IBD), where pathobionts penetrate the intestinal barrier and promote inflammatory reactions. In patients with IBD, the ability of intestinal macrophages to efficiently clear invading pathogens is compromised resulting in increased bacterial translocation and excessive immune reactions. Here, we investigated how an IBD-associated loss-of-function variant in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene, or loss of PTPN2 expression affected the ability of macrophages to respond to invading bacteria. DESIGN: IBD patient-derived macrophages with wild-type (WT) PTPN2 or carrying the IBD-associated PTPN2 SNP, peritoneal macrophages from WT and constitutive PTPN2-knockout mice, as well as mice specifically lacking PTPN2 in macrophages were infected with non-invasive K12 Escherichia coli, the human adherent-invasive E. coli (AIEC) LF82, or a novel mouse AIEC (mAIEC) strain. RESULTS: Loss of PTPN2 severely compromises the ability of macrophages to clear invading bacteria. Specifically, loss of functional PTPN2 promoted pathobiont invasion/uptake into macrophages and intracellular survival/proliferation by three distinct mechanisms: Increased bacterial uptake was mediated by enhanced expression of carcinoembryonic antigen cellular adhesion molecule (CEACAM)1 and CEACAM6 in PTPN2-deficient cells, while reduced bacterial clearance resulted from defects in autophagy coupled with compromised lysosomal acidification. In vivo, mice lacking PTPN2 in macrophages were more susceptible to mAIEC infection and mAIEC-induced disease. CONCLUSIONS: Our findings reveal a tripartite regulatory mechanism by which PTPN2 preserves macrophage antibacterial function, thus crucially contributing to host defence against invading bacteria.

Bacterial Adhesion , Escherichia coli Infections/immunology , Macrophages/immunology , Protein Tyrosine Phosphatase, Non-Receptor Type 2/immunology , Animals , Antigens, CD/metabolism , Carcinoembryonic Antigen/metabolism , Cell Adhesion Molecules/metabolism , Disease Models, Animal , Escherichia coli/genetics , Escherichia coli/physiology , GPI-Linked Proteins/metabolism , Gastrointestinal Microbiome , Genetic Predisposition to Disease , Inflammatory Bowel Diseases/genetics , Inflammatory Bowel Diseases/immunology , Inflammatory Bowel Diseases/microbiology , Mice, Knockout , Protein Tyrosine Phosphatase, Non-Receptor Type 2/genetics
Anticancer Res ; 42(1): 385-395, 2022 Jan.
Article En | MEDLINE | ID: mdl-34969749

BACKGROUND: It has been reported that expression of OCT3 enhanced the sensitivity to melphalan in cells, indicative of potential roles of OCT3 in melphalan transport. Herein we investigated the association of select single nucleotide polymorphisms in SLC22A3 (gene encoding OCT3) with clinical outcomes in multiple myeloma (MM) patients with hematopoietic autologous stem cell transplants followed by high-dose melphalan therapy. MATERIALS AND METHODS: Melphlan concentrations in blood samples from 108 MM patients were measured using liquid chromatography-tandem mass spectrometry (LC-MS/ΜS); genotypes of rs2048327, rs1810126, and rs3088442 in these patients were determined using quatitive RT-PCR assays. RESULTS: Rs3088442 A variant-carriers had a significantly increased risk of severe oral mucositis in comparison with homozygous rs3088442 G-carriers with adjusted odds ratio of 4.00 (95% CI=1.25-14.7; p=0.027). Rs3088442 A carriers tended to have lower creatinine clearance (p=0.10) and higher maximum plasma concentration of melphalan (p=0.07). CONCLUSION: OCT3 might be involved in melphalan transport in MM patients.

Genetic Predisposition to Disease , Multiple Myeloma/therapy , Organic Cation Transport Proteins/genetics , Stomatitis/genetics , Adult , Aged , Genetic Association Studies , Genotype , Humans , Male , Melphalan/adverse effects , Melphalan/therapeutic use , Middle Aged , Multiple Myeloma/complications , Multiple Myeloma/genetics , Multiple Myeloma/pathology , Polymorphism, Single Nucleotide/genetics , Stem Cell Transplantation/adverse effects , Stomatitis/epidemiology , Stomatitis/pathology , Transplantation, Autologous/adverse effects
Gene ; 812: 146099, 2022 Feb 20.
Article En | MEDLINE | ID: mdl-34906645

Nasopharyngeal Carcinoma (NPC) found to be dependent on geographical and racial variation and is more prevalent in Northeast (NE) India. WES-based study was conducted in three states (tribes); Nagaland (Naga), Mizoram (Mizo) and Manipur (Manipuri), which provided an overview of germline variants involved inthemajor signaling pathways. Validation and recurrence assessment of WES data confirmed the risk effect of STEAP3_rs138941861 and JAG1_rs2273059, and the protective role of PARP4_rs17080653 and TGFBR1_rs11568778 variants, where STEAP3_rs138941861conferring Arg290His substitution was the only exonic non-synonymous variant and to be located in proximity to the linking region between the transmembrane and oxidoreductasedomainsof STEAP3 protein, andaffectedits structural and functional dynamics by altering the Electrostatic Potential around this connecting region. Moreover, these significantly associated variants having deleterious effect were observed to have interactions in p53 signaling pathway which emphasizes the importance of this pathway in the causation of NPC.

Cell Cycle Proteins/genetics , Jagged-1 Protein/genetics , Nasopharyngeal Carcinoma/genetics , Nasopharyngeal Neoplasms/genetics , Nuclear Proteins/genetics , Oxidoreductases/genetics , Receptor, Transforming Growth Factor-beta Type I/genetics , Whole Exome Sequencing/methods , Adult , Amino Acid Substitution , Case-Control Studies , Cell Cycle Proteins/chemistry , Female , Genetic Predisposition to Disease , High-Throughput Nucleotide Sequencing , Humans , India , Male , Middle Aged , Models, Molecular , Oxidoreductases/chemistry , Polymorphism, Single Nucleotide , Protein Conformation , Protein Domains
Hypertension ; 79(1): 36-46, 2022 01.
Article En | MEDLINE | ID: mdl-34689596

The pathophysiological link between adiposity and blood pressure is not completely understood, and evidence suggests an influence of sex and genetic determinants. We aimed to identify the relationship between adiposity and blood pressure, independent of a robust set of lifestyle and metabolic factors, and to examine the modulating role of sex and Angiotensin-Converting Enzyme (ACE) insertion/deletion (I/D) polymorphisms. In the Relationship Between Insulin Sensitivity and Cardiovascular Disease (RISC) study cohort, 1211 normotensive individuals, aged 30 to 60 years and followed-up after 3.3 years, were characterized for lifestyle and metabolic factors, body composition, and ACE genotype. Body mass index (BMI) and waist circumference (WC) were independently associated with mean arterial pressure, with a stronger relationship in women than men (BMI: r=0.40 versus 0.30; WC: r=0.40 versus 0.30, both P<0.01) and in individuals with the ID and II ACE genotypes in both sexes (P<0.01). The associations of BMI and WC with mean arterial pressure were independent of age, sex, lifestyle, and metabolic variables (standardized regression coefficient=0.17 and 0.18 for BMI and WC, respectively) and showed a significant interaction with the ACE genotype only in women (P=0.03). A 5 cm larger WC at baseline increased the risk of developing hypertension at follow-up only in women (odds ratio, 1.56 [95% CI, 1.15-2.10], P=0.004) and in II genotype carriers (odds ratio, 1.87 [95% CI, 1.09-3.20], P=0.023). The hypertensive effect of adiposity is more pronounced in women and in people carrying the II variant of the ACE genotype, a marker of salt sensitivity.

Adiposity/genetics , Blood Pressure/genetics , Hypertension/genetics , INDEL Mutation , Peptidyl-Dipeptidase A/genetics , Polymorphism, Single Nucleotide , Adult , Body Mass Index , Female , Genetic Predisposition to Disease , Genotype , Humans , Male , Middle Aged , Sex Factors , Waist Circumference
Biol Psychiatry ; 91(1): 102-117, 2022 01 01.
Article En | MEDLINE | ID: mdl-34099189

BACKGROUND: Sex differences in incidence and/or presentation of schizophrenia (SCZ), major depressive disorder (MDD), and bipolar disorder (BIP) are pervasive. Previous evidence for shared genetic risk and sex differences in brain abnormalities across disorders suggest possible shared sex-dependent genetic risk. METHODS: We conducted the largest to date genome-wide genotype-by-sex (G×S) interaction of risk for these disorders using 85,735 cases (33,403 SCZ, 19,924 BIP, and 32,408 MDD) and 109,946 controls from the PGC (Psychiatric Genomics Consortium) and iPSYCH. RESULTS: Across disorders, genome-wide significant single nucleotide polymorphism-by-sex interaction was detected for a locus encompassing NKAIN2 (rs117780815, p = 3.2 × 10-8), which interacts with sodium/potassium-transporting ATPase (adenosine triphosphatase) enzymes, implicating neuronal excitability. Three additional loci showed evidence (p < 1 × 10-6) for cross-disorder G×S interaction (rs7302529, p = 1.6 × 10-7; rs73033497, p = 8.8 × 10-7; rs7914279, p = 6.4 × 10-7), implicating various functions. Gene-based analyses identified G×S interaction across disorders (p = 8.97 × 10-7) with transcriptional inhibitor SLTM. Most significant in SCZ was a MOCOS gene locus (rs11665282, p = 1.5 × 10-7), implicating vascular endothelial cells. Secondary analysis of the PGC-SCZ dataset detected an interaction (rs13265509, p = 1.1 × 10-7) in a locus containing IDO2, a kynurenine pathway enzyme with immunoregulatory functions implicated in SCZ, BIP, and MDD. Pathway enrichment analysis detected significant G×S interaction of genes regulating vascular endothelial growth factor receptor signaling in MDD (false discovery rate-corrected p < .05). CONCLUSIONS: In the largest genome-wide G×S analysis of mood and psychotic disorders to date, there was substantial genetic overlap between the sexes. However, significant sex-dependent effects were enriched for genes related to neuronal development and immune and vascular functions across and within SCZ, BIP, and MDD at the variant, gene, and pathway levels.

Bipolar Disorder/genetics , Depressive Disorder, Major , Psychotic Disorders , Schizophrenia/genetics , Sex Characteristics , Depressive Disorder, Major/genetics , Endothelial Cells , Female , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Male , Polymorphism, Single Nucleotide , Psychotic Disorders/genetics , Receptors, Vascular Endothelial Growth Factor , Sulfurtransferases
Pain ; 163(1): e40-e48, 2022 Jan 01.
Article En | MEDLINE | ID: mdl-34924553

ABSTRACT: To understand a putative causal link for depression and pain, we retrieved summary statistics from genome-wide association studies conducted for pain at 7 different body sites (N = 151,922-226,683) and major depression disorder (MDD, Ncase/control = 246,363/561,190). We conducted a bidirectional Mendelian randomization analysis using distinct genome-wide association studies-identified single nucleotide polymorphisms for each trait as instrumental variables and performed several sensitivity analyses to verify Mendelian randomization assumptions. We also conducted functional annotation analysis using 396 tissue-specific annotations from the roadmap project. Across 7 different body sites, genetic predisposition to depression was associated with pain at the neck/shoulder (odds ratio [OR] = 1.08 per one log-unit increase in depression risk, 95% confidence interval [CI]: 1.06-1.10), back (OR = 1.05, 95% CI: 1.04-1.07), abdominal/stomach (OR = 1.03, 95% CI: 1.02-1.04), as well as headache (OR = 1.10, 95% CI: 1.07-1.12), but not with pain on the face, hip, and knee. In the reverse direction, genetically instrumented multisite chronic pain (OR = 1.78 per one increment in the number of pain site, 95% CI: 1.51-2.11) and headache (OR = 1.55 per one log-unit increase in headache risk, 95% CI = 1.13-2.10) were associated with MDD. Functional annotation analysis showed differential clustering patterns where depression clustered closely with headache and neck/shoulder pain, exhibiting substantial brain tissue enrichment. Our study indicates that depression is a causal risk factor for headache and pain localized at neck/shoulder, back, and abdominal/stomach, rather than pain at face, hip, and knee, and suggests common neurological pathologies underlying the development of depression, headache, and neck/shoulder pain.

Depression , Genome-Wide Association Study , Mendelian Randomization Analysis , Pain , Depression/genetics , Genetic Predisposition to Disease , Humans , Pain/genetics , Polymorphism, Single Nucleotide
Int J Cancer ; 150(1): 73-79, 2022 01 01.
Article En | MEDLINE | ID: mdl-34460111

Polygenic risk scores (PRS) for disease risk stratification show great promise for application in general populations, but most are based on data from individuals of White European origin. We assessed two well validated PRS (SNP18, SNP143) in the Predicting-Risk-of-Cancer-At-Screening (PROCAS) study in North-West England for breast cancer prediction based on ethnicity. Overall, 9475 women without breast cancer at study entry, including 645 who subsequently developed invasive breast cancer or ductal carcinoma in situ provided DNA. All were genotyped for SNP18 and a subset of 1868 controls were genotyped for SNP143. For White Europeans both PRS discriminated well between individuals with and without cancer. For n = 395 Black (n = 112), Asian (n = 119), mixed (n = 44) or Jewish (n = 120) women without cancer both PRS overestimated breast cancer risk, being most marked for women of Black and Jewish origin (P < .001). SNP143 resulted in a potential mean 40% breast cancer risk overestimation in the combined group of non-White/non-European origin. SNP-PRS that has been normalized based on White European ethnicity for breast cancer should not be used to predict risk in women of other ethnicities. There is an urgent need to develop PRS specific for other ethnicities, in order to widen access of this technology.

Biomarkers, Tumor/genetics , Breast Neoplasms/epidemiology , Carcinoma, Ductal, Breast/epidemiology , Carcinoma, Intraductal, Noninfiltrating/epidemiology , Polymorphism, Single Nucleotide , /genetics , Adult , Aged , Breast Density , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Carcinoma, Ductal, Breast/genetics , Carcinoma, Ductal, Breast/pathology , Carcinoma, Intraductal, Noninfiltrating/genetics , Carcinoma, Intraductal, Noninfiltrating/pathology , Case-Control Studies , England/epidemiology , Female , Follow-Up Studies , Genetic Predisposition to Disease , Humans , Middle Aged , Prognosis , Risk Factors
Int J Cancer ; 150(1): 80-90, 2022 01 01.
Article En | MEDLINE | ID: mdl-34520569

A large proportion of heritability for prostate cancer risk remains unknown. Transcriptome-wide association study combined with validation comparing overall levels will help to identify candidate genes potentially playing a role in prostate cancer development. Using data from the Genotype-Tissue Expression Project, we built genetic models to predict normal prostate tissue gene expression using the statistical framework PrediXcan, a modified version of the unified test for molecular signatures and Joint-Tissue Imputation. We applied these prediction models to the genetic data of 79 194 prostate cancer cases and 61 112 controls to investigate the associations of genetically determined gene expression with prostate cancer risk. Focusing on associated genes, we compared their expression in prostate tumor vs normal prostate tissue, compared methylation of CpG sites located at these loci in prostate tumor vs normal tissue, and assessed the correlations between the differentiated genes' expression and the methylation of corresponding CpG sites, by analyzing The Cancer Genome Atlas (TCGA) data. We identified 573 genes showing an association with prostate cancer risk at a false discovery rate (FDR) ≤ 0.05, including 451 novel genes and 122 previously reported genes. Of the 573 genes, 152 showed differential expression in prostate tumor vs normal tissue samples. At loci of 57 genes, 151 CpG sites showed differential methylation in prostate tumor vs normal tissue samples. Of these, 20 CpG sites were correlated with expression of 11 corresponding genes. In this TWAS, we identified novel candidate susceptibility genes for prostate cancer risk, providing new insights into prostate cancer genetics and biology.

Biomarkers, Tumor/genetics , Epigenesis, Genetic , Gene Expression Regulation, Neoplastic , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Prostatic Neoplasms/pathology , Transcriptome , Case-Control Studies , DNA Methylation , Follow-Up Studies , Genome-Wide Association Study , Humans , Male , Prognosis , Prostatic Neoplasms/epidemiology , Prostatic Neoplasms/genetics , Quantitative Trait Loci , United States/epidemiology
Ann Lab Med ; 42(1): 54-62, 2022 Jan 01.
Article En | MEDLINE | ID: mdl-34374349

Background: Associations between IgA nephropathy (IgAN) and HLA-DRB1 and -DQB1 alleles have been reported in several ethnic groups. We investigated the association of HLA-DRB1 and -DQB1 alleles with the predisposition for IgAN and disease progression to end-stage kidney disease (ESKD) in Korean patients. Methods: We analyzed HLA-DRB1 and -DQB1 genotypes in 399 IgAN patients between January 2000 and January 2019 using a LIFECODES sequence-specific oligonucleotide (SSO) typing kit (Immucor, Stamford, CT, USA) or a LABType SSO Typing Test (One Lambda, Canoga Park, CA, USA). Alleles with a significant difference in two-digit resolution were further analyzed using in-house sequence-based typing and sequence-specific primer PCR. As controls, 613 healthy hematopoietic stem cell donors were included. Kidney survival was analyzed in 281 IgAN patients with available clinical and laboratory data using Cox regression analysis. Where needed, P-values were adjusted using Bonferroni correction. Results: The allele frequencies of HLA-DRB1*04:05 (corrected P [Pc]<0.001), -DQB1 *04:01 (Pc=0.048), and -DQB1*03:02 (Pc=0.021) were significantly higher in IgAN patients than in controls, whereas those of HLA-DRB1*07:01, -DRB1*15:01, -DQB1*02:02, and -DQB1*06:02 (Pc<0.001 for all) were significantly lower in IgAN patients than in controls. The allele frequency of HLA-DQB1*05:03 (Pc=0.016) was significantly lower in the ESKD group than in the non-ESKD group; however, there was no significant difference for ESKD progression between these groups. Conclusions: We report novel associations of HLA-DRB1*15:01, DQB1*02:02, -DQB1*03:02, and -DQB1*04:01 with IgAN. Further studies of HLA alleles associated with IgAN progression in a larger cohort and in various ethnic groups are needed.

Glomerulonephritis, IGA , Alleles , Genetic Predisposition to Disease , Glomerulonephritis, IGA/diagnosis , Glomerulonephritis, IGA/genetics , HLA-DRB1 Chains/genetics , Histocompatibility Testing , Humans , Republic of Korea
Article En | MEDLINE | ID: mdl-34637926

Through seven decades the inverse association between HDL cholesterol concentrations and risk of atherosclerotic cardiovascular disease (ASCVD) has been observed in case-control and prospective cohort studies. This robust inverse association fuelled the enthusiasm towards development of HDL cholesterol increasing drugs, exemplified by the cholesteryl ester transfer protein (CETP) inhibitor trials and the extended-release niacin HPS2-THRIVE trial. These HDL cholesterol increasing trials were launched without conclusive evidence from human genetics, and despite discrepant species dependent evidence from animal studies. Evidence from human genetics and from randomized clinical trials over the last 13 years now point in the direction that concentrations of HDL cholesterol, do not appear to be a viable future path to target therapeutically for prevention of ASCVD. A likely explanation for the strong observational association between low HDL cholesterol and high ASCVD risk is the concomitant inverse association between HDL cholesterol and atherogenic triglyceride-rich lipoproteins. The purpose of the present review is to bring HDL cholesterol increasing trials into a human genetics context exemplified by candidate gene studies of key players in HDL biogenesis as well as by HDL cholesterol related genome-wide association studies.

Adaptor Protein Complex 3/genetics , Adaptor Protein Complex beta Subunits/genetics , Atherosclerosis/blood , Cholesterol Ester Transfer Proteins/genetics , Cholesterol, HDL/genetics , Atherosclerosis/epidemiology , Atherosclerosis/genetics , Cholesterol, HDL/blood , Genetic Predisposition to Disease , Genome-Wide Association Study , Heart Disease Risk Factors , Humans , Niacin/therapeutic use , Randomized Controlled Trials as Topic
Eur J Radiol ; 146: 110074, 2022 Jan.
Article En | MEDLINE | ID: mdl-34902667

PURPOSE: Breast cancer gene (BRCA) 1 and 2 mutations are frequently studied gene mutations (GM); the incidence of checkpoint kinase 2 (CHEK2) is increasing. We describe the imaging features of breast cancer (BC) in CHEK2 mutations, compared to BRCA 1 and 2 using mammography, ultrasound (US) and magnetic resonance imaging (MRI). METHOD: Inclusion criteria were primary BC in GM carriers, treated in the same hospital. Age at diagnosis, histology, hormone receptor and human epidermal growth factor receptor 2 (HER2) status were retrieved. Mammography descriptors were mass, asymmetry and suspicious microcalcifications. The enhancement pattern (MRI), shape and border, architectural distortion, the presence of a hyperechoic rim and cystic complex structure (US) were documented. Analyses were performed using SAS software (version 9.4). Fishers' exact test was used to test associations between two categorical variables. RESULTS: In 191 women, 233 malignant lesions were diagnosed (78 in BRCA1, 109 in BRCA2, 46 in CHEK2). In CHEK2 carriers, mammographically, suspicious microcalcifications (54%) were more prevalent (BRCA2 (48%) and BRCA1 carriers (33%)) (p-value = 0.057) compared to mass lesions (35%). On US, lesions were most frequently ill-defined (86%) (p = 0.579) and irregular (94.5%) (p = 0.098) compared to BRCA2 (77% and 80% resp.) and BRCA1 carriers (71% and 72% resp.). On MRI, mass lesions showed a type 3 curve in CHEK2 (67%) compared to BRCA1 (36%) and BRCA2 (50%) (p = 0.056). CONCLUSIONS: Malignant radiological characteristics of breast cancer, more specifically suspicious microcalcifications, were more frequently seen in CHEK2 and BRCA2 compared to BRCA1 mutation carriers (without a significant difference) indicating the importance of mammography in follow-up of CHEK2 carriers.

Breast Neoplasms , Genes, BRCA2 , BRCA1 Protein/genetics , BRCA2 Protein/genetics , Breast Neoplasms/diagnostic imaging , Breast Neoplasms/genetics , Checkpoint Kinase 2/genetics , Female , Genetic Predisposition to Disease , Humans , Mammography , Mutation
Handb Exp Pharmacol ; 268: 313-329, 2022.
Article En | MEDLINE | ID: mdl-34085121

Asthma genes have been identified through a range of approaches, from candidate gene association studies and family-based genome-wide linkage analyses to genome-wide association studies (GWAS). The first GWAS of asthma, reported in 2007, identified multiple markers on chromosome 17q21 as associates of the childhood-onset asthma. This remains the best replicated asthma locus to date. However, notwithstanding undeniable successes, genetic studies have produced relatively heterogeneous results with limited replication, and despite considerable promise, genetics of asthma and allergy has, so far, had limited impact on patient care, our understanding of disease mechanisms, and development of novel therapeutic targets. The paucity of precise replication in genetic studies of asthma is partly explained by the existence of numerous gene-environment interactions. Another important issue which is often overlooked is that of time of the assessment of the primary outcome(s) and the relevant environmental exposures. Most large GWASs use the broadest possible definition of asthma to increase the sample size, but the unwanted consequence of this is increased phenotypic heterogeneity, which dilutes effect sizes. One way of addressing this is to precisely define disease subtypes (e.g. by applying novel mathematical approaches to rich phenotypic data) and use these latent subtypes in genetic studies.

Asthma , Hypersensitivity , Asthma/genetics , Child , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Hypersensitivity/genetics