Case-control Genetic Study Research Articles

Abstract TP137: Ethnic/racial Variations Of Intracerebral Hemorrhage Genetics (erich-gene) Study Protocol

Introduction: Epidemiologic studies of intracerebral hemorrhage (ICH) have consistently demonstrated variation in incidence, location, comorbidity burden, age-of-onset, and outcome by race and ethnicity, and genetic studies have identified differences in risk mediated by genetic risk factors such as Apolipoprotein E (APOE). We report the design and methods of the largest multi-ethnic genome-wide association study (GWAS) of ICH risk and outcome conducted to date. Methods: The Ethnic/Racial Variations of ICH Genetics (ERICH-GENE) study is an international, multi-center, genetic case-control study of ICH. Cases are individuals with confirmed primary ICH with biosample availability and consent compatible with shareable genome-wide genotyping or previous genotyping. Central neuroimaging phenotype harmonization of case status, hemorrhage location, and imaging characteristics of cerebral small vessel disease including leukoaraiosis, atrophy, microbleeds, intraventricular hemorrhage severity and volume of ICH measurements will be performed. Controls are ICH-free individuals of compatible age and race/ethnicity from existing studies and biorepositories. Results: As of August 2021, 2,002 ICH cases have been collected and genotyped, in addition to 2,558 already-genotyped ICH cases from the multi-ethnic ERICH study. 5,600 total new ICH cases will be genotyped under ERICH-GENE, with planned meta-analyses across existing ICH GWAS datasets and international biobanks totaling >20,000 cases. We are on schedule to meet our genotyping goal within the study period. Non-European ancestry cases are being prioritized for genotyping and ~66% of the previously genotyped ERICH cases are black or Hispanic. From available cases, a total of 10,621 neuroimaging studies have been uploaded for central adjudication to date with 6,278 having undergone harmonization. Conclusions: ERICH-GENE is a large, multi-ethnic, international, centrally harmonized GWAS of ICH risk and outcome that will identify genetic risk factors across diverse populations for biological discovery and population-specific risk stratification.

A Case-Control Study of the Luteinizing Hormone Level in Luteinizing Hormone Receptor Gene (rs2293275) Polymorphism in Polycystic Ovarian Syndrome Females

Background: Polycystic ovary syndrome (PCOS) is a common heterogeneous disorder characterized by chronic anovulation, infertility, polycystic ovaries, and hyperandrogenic signs. Objective: The aim of this study was to determine the association of luteinizing hormone/chorionic gonadotropin hormone receptor LHCGR polymorphism (rs2293275) with oligomenorrhea, amenorrhea, hirsutism, acne, infertility, LH, LH/FSH ratio, and body mass index (BMI) among PCOS females. Methods: This genetic case-control study recruited 55 PCOS and 55 control females, diagnosed based on the Rotterdam criteria. LH and FSH were measured by the Roche cobas c 502 automated analyzer. Genotypic analysis was carried out using the polymerase chain reaction-restriction fragment length polymorphism and restriction endonuclease digestion. Results: BMI was higher for PCOS patients (28.5 ± 6.59) compared to controls (25.1 ± 5.77), and ovulatory dysfunction was seen among 90% of PCOS females. Oligomenorrhea was common in PCOS (73%), and hirsutism and acne were detected in PCOS (80% and 40%; respectively). LH ≥10 were recoded among 51%, while LH/FSH ≥1.5 was recorded among 33% PCOS females. There is a statistical difference between rs2293275 polymorphism in the AG genotype between PCOS patients and controls. PCOS patients have a significantly higher mean LH level compared to controls (8.36 ± 4.86 and 5.67 ± 2.51, respectively) and showed higher LH/FSH value (1.46 ± 0.81) compared to (0.87 ± 0.30) controls. GG and AG genotypes of LHCGR showed statistically significant higher LH (8.22 ± 4.11; 9.02 ± 3.87) and LH/FSH values (1.57 ± 0.56; 1.64 ± 0.89) compared to controls. Conclusion: LHCGR (rs2293275) GA and GG genetic variants could modulate the hormonal levels of PCOS LH levels and the LH/FSH ratio and associated with hirsutism, oligomenorrhea, BMI, and LH/FSH ratio as risk factors.

Female-Specific Susceptibility Locus in BOC and SEC16B are Associated with Adolescent Idiopathic Scoliosis.

A genetic case-control study. To investigate whether the variants in BOC, SEC16B, and SH2D1B are sex-specifically and functionally associated with the susceptibility of adolescent idiopathic scoliosis (AIS) in Chinese Han population. A recent genome-wide association study identified three female-specific susceptibility loci of AIS in Japanese population. However, the association of these genes with AIS in other populations remains unclear. Further investigation of the functional role of the three genes was warranted. SNPs rs73235136, rs545608, and rs142502288 were genotyped in 1599 AIS patients and 2985 controls. Paraspinal muscle collected from 40 AIS and 30 lumber disc herniation patients during surgical interventions was used for gene expression analysis. The difference regarding genotype and allele frequency between patients and controls was analyzed by chi-square analysis. Expression of BOC and SEC16B was compared between AIS and lumber disc herniation patients by the Student t test. Pearson correlation analysis was performed to evaluate the relationship between gene expression level and clinical phenotypes. SNPs rs73235136 of BOC and rs545608 of SEC16B were found to be remarkably associated with AIS only in females. Allele C of rs73235136 and allele G of rs545608 could significantly add to the risk of female AIS patients, with an odds ratio of 1.087 and 1.033, respectively. However, there was no significant difference between the male patients and controls regarding genotype or allele frequency of rs73235136 and rs545608. No polymorphism at rs142502288 was detected in either patients or controls, and all the subjects had genotype of AA. Moreover, tissue expression of BOC and SEC16B was significantly lower in AIS patients compared with controls. BOC expression was positively associated with bone mineral contents, and expression of SEC16B was negatively correlated with curve severity in AIS patients. Female-specific variants in BOC and SEC16B were associated with AIS. Expression of BOC and SEC16B was significantly lower in AIS patients. The role of BOC and SEC16B in the development of AIS is worthy of further investigation.Level of Evidence: 3.

Concordance rate in cattle and sheep between genotypes differing in Illumina GenCall quality score.

Proper quality control of data prior to downstream analyses is fundamental to ensure integrity of results; quality control of genomic data is no exception. While many metrics of quality control of genomic data exist, the objective of the present study was to quantify the genotype and allele concordance rate between called single nucleotide polymorphism (SNP) genotypes differing in GenCall (GC) score; the GC score is a confidence measure assigned to each Illumina genotype call. This objective was achieved using Illumina beadchip genotype data from 771 cattle (12428767 genotypes in total post-editing) and 80 sheep (1557360 SNPs genotypes in total post-editing) each genotyped in duplicate. The called genotype with the lowest associated GC score was compared to the genotype called for the same SNP in the same duplicated animal sample but with a GC score of >0.90 (assumed to represent the true genotype). The mean genotype concordance rate for a GC score of <0.300, 0.300-0.549, and ≥0.550 in the cattle (sheep in parenthesis) was 0.9467 (0.9864), 0.9707 (0.9953), and 0.9994 (0.99997) respectively; the respective allele concordance rate was 0.9730 (0.9930), 0.9849 (0.9976), and 0.9997 (0.99998). Hence, concordance eroded as the GC score of the called genotype reduced, albeit the impact was not dramatic and was not very noticeable until a GC score of <0.55. Moreover, the impact was greater and more consistent in the cattle population than in the sheep population. Furthermore, an impact of GC score on genotype concordance rate existed even for the same SNP GenTrain value; the GenTrain value is a statistical score that depicts the shape of the genotype clusters and the relative distance between the called genotype clusters.

Association between peroxisome proliferator-activated receptor-alpha, -delta and -gamma gene (PPARA, PPARD, PPARG) polymorphisms and overweight parameters in physically active men.

Peroxisome proliferator-activated receptors (PPARs) have unique functions in energy metabolism regulation but are also involved in regulation of the inflammatory process and obesity. The aim of this study was to analyse potential associations between polymorphisms of PPARA (rs1800206), PPARD (rs1053049; rs2267668) and PPARG (rs1801282) and overweight parameters. One hundred and sixty-six males, unrelated Caucasian military professionals, were recruited in the genetic case-control study conducted in the period 2016–2019. All the participants were aged 21–41 and had similar levels of physical activity. Body mass, height and body composition were measured. The participants were divided into two groups depending on their BMI (body mass index) and FMI (fat mass index). The control group consisted of people with BMI between 20.0 and 25.0 or FMI values ≤ 6, while the overweight group consisted of people with BMI of ≥ 25.0 or FMI values > 6. Genomic DNA was isolated from extracted buccal cells. All samples were genotyped using real-time polymerase chain reaction (real-time PCR). It was found that two polymorphisms rs2267668 and rs1053049 of the PPARD gene were significantly associated with BMI: SNP rs2267668 for the dominant (OR = 2.04, 95%CI 1.01–4.11, p-value = 0.04) model (A/G-G/G vs A/A). The likelihood of being overweight was over 2 times smaller for allele A. A relationship between the polymorphism of PPARG (rs1801282) and BMI was found for the overdominant (OR = 2.03, 95%CI 1.03–4.00, p-value = 0.04) model (C/G vs C/C-G/G). Significant associations were found in different models for PPARD, PPARG and PPARA genes with BMI. In SNP rs2267668 for the codominant genetic model (G/G vs A/A) (p-value = 0.04) and in SNP rs1053049 for the codominant (C/C vs T/T) (p-value = 0.01) and the recessive genetic model (C/C vs T/T–C/T) (p-value = 0.004) all polymorphisms were associated with BMI. In conclusion, it was found that three of the four polymorphisms (rs1053049, rs2267668, rs1801282) selected are associated with the risk of being overweight. Having said that, one has to bear in mind that DNA variants do not fully explain the reasons for being overweight. Therefore more research is needed to make a thorough assessment using the latest genomic methods in sequencing and genotyping, combined with epigenomics, proteomics, transcriptomics, and metabolomics.

Novel associations of SNPs MYLIP rs3757354 and ABCA1 2230806 gene with early-onset-preeclampsia: A case-control candidate genetic study.

To investigate the association between MYLIP rs3757354 and ABCA1 2230806 single nucleotide polymorphisms in women with preeclampsia in China. The case-control study involved 205 patients with preeclampsia and 145 controls. All women with preeclampsia were divided into two groups: 78 patients with early-onset preeclampsia and 127 with late-onset preeclampsia. MYLIP rs3757354 and ABCA1 rs2230806 SNPs were analyzed through multiplex PCR for targeted next-generation sequencing technology. A secondary outcome was lipid profile changes and liver function in women with PE. Maternal age (OR: 1.073, 95% CI=1.006-1.145), BMI (OR: 1.118, 95% CI=1.040-1.201), TG/HDL-C (OR: 1.536, 95% CI=1.080-2.183), and TT genotype of SNP rs3757354 (OR: 3.238, 95% CI=1.313-7.990) were associated with EOPE risk. Our study found that patients with TT genotype of ABCA1 rs2230806 had more severe hepatic dysfunction and higher HDL levels in the EOPE group compared with CC/CT genotype. There was no association between rs2230806 and the risk of PE. The polymorphisms of rs3757354 are associated with the risk of EOPE in Chinese pregnant women. The TT genotype in ABCA1 rs2230806 is a strong predictive risk for elevated aminotransferase levels in pregnant women with EOPE.

Novel association between FOXO3 rs2232365 polymorphism and late-onset preeclampsia: a case-control candidate genetic study

BackgroundBoth genetic susceptibility and dysregulated lipid metabolism are important susceptibilities to preeclampsia. In the study, we devote to investigate the associations of FOXO3 and TLR7 genetic polymorphisms with preeclampsia in a Chinese population.MethodsThis case-control study involved 335 Han Chinese pregnant women, including 177 pregnant women with preeclampsia and 158 healthy controls. The preeclampsia group was further sub-grouped into early-onset preeclampsia (EOPE, n = 70)and late-onset preeclampsia (LOPE, n = 107. Three single nucleotide polymorphisms (SNPs), including FOXO3 (rs2232365, rs3761548), and TLR7 rs3853839 were genotyped by multiplex PCR for targeted next-generation sequencing. The χ2 test and multiple interaction effect analyses were performed to determine the association of three SNPs with serum lipid levels and thyroid function in women with preeclampsia.ResultsThe genotype (CC vs. TT + CT) distribution of rs2232365 revealed a significant association with LOPE (P = 0.004, odds ratio = 3.525 (0.95 CI: 1.498–8.164)). No significant difference was found in the genotype and allele frequencies of rs3761548 and rs3853839 between controls and cases (P > 0.05). Moreover, the genotype CT/TT of rs2232365 was significantly correlated with increased TG/HDL levels in the LOPE group (p = 0.014).ConclusionsThe polymorphisms of rs2232365 are associated with the risk of LOPE and may modulate TG/HDL levels in pregnant women with LOPE.

Variation analysis of anti-Müllerian hormone gene in Chinese women with polycystic ovary syndrome.

Anti-Müllerian hormone (AMH) is crucial for folliculogenesis. Prenatal exposure to AMH in mice produces a phenocopy of polycystic ovary syndrome (PCOS) in the adult female offspring. The aim of this study was to determine whether genetic variation in AMH gene contribute to PCOS in women of Chinese ancestry. We conducted a case-control genetic study in 383 PCOS case and 433 control women of Chinese ancestry. The exons and the 5' flanking region of AMH were sanger sequenced. Bioinformatic prediction of variant deleteriousness was performed. Seven novel heterozygous variants along with 15 rare known variants in AMH were identified in women with PCOS but not in controls. The novel variants included one frameshift variant (c.125_129delACTTG), one synonymous variant (c.1095C>T), one variant (c.-14T>C) in the 5'-untranslated region (UTR), four variants(c.-775C>T, c.-682C>T, c.-333A>G, c.-137A>T) in 5' flanking sequence. Of all the AMH variants identified in women with PCOS, eight were predicted to be deleterious by bioinformatic analysis. The PCOS carriers of predicted-to-be-deleterious PCOS-specific AMH variants had increased total follicle numbers compared to PCOS noncarriers (p = 0.021). Our findings suggest the AMH plays a role in the development of PCOS. The exact mechanisms by which the predicted-to-be-deleterious novel and rare AMH variants described in our study affect AMH function requires further study.

Association of the matrix metalloproteinase 3 (MMP3) single nucleotide polymorphisms with tendinopathies: case-control study in high-level athletes.

Matrix metalloproteinases (MMPs) play an important role in matrix remodelling, as well as in tendon integrity. Due to overuse, athletes often develop chronic tendinopathies. If not treated, they lead to severe impairment, even complete tendon ruptures. The main purpose of this study was to investigate whether three functional polymorphisms within the MMP3 gene are associated with increased risk of developing tendinopathies in high-level Croatian athletes. We have recruited one hundred fifty-five (63 high-level athletes with diagnosed tendinopathies and 92 asymptomatic controls) unrelated Caucasians for this case-control genetic study. All participants were genotyped for three single nucleotide polymorphisms (SNP) within the MMP3 gene: rs591058 C/T, rs650108 A/G and rs679620 G/A using the pyrosequencing method. The MMP3 rs650108 GG (P = 0.0074) and rs679620 AA (P= 0.0119) genotypes were significantly over-represented in cases compared with controls, while rs591058 TT (P = 0.0759), as well as haplotype variant T - G - A (P = 0.06), implicated that there is an indication of predisposition for tendinopathies. These results support association between functional variants within the MMP3 gene and the risk of tendinopathies in high-level athletes. Further research is needed to replicate these results in a larger population.

Risk of pneumococcal bacteremia in Kenyan children with glucose-6-phosphate dehydrogenase deficiency

BackgroundGlucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency state in humans. The clinical phenotype is variable and includes asymptomatic individuals, episodic hemolysis induced by oxidative stress, and chronic hemolysis. G6PD deficiency is common in malaria-endemic regions, an observation hypothesized to be due to balancing selection at the G6PD locus driven by malaria. G6PD deficiency increases risk of severe malarial anemia, a key determinant of invasive bacterial disease in malaria-endemic settings. The pneumococcus is a leading cause of invasive bacterial infection and death in African children. The effect of G6PD deficiency on risk of pneumococcal disease is undefined. We hypothesized that G6PD deficiency increases pneumococcal disease risk and that this effect is dependent upon malaria.MethodsWe performed a genetic case-control study of pneumococcal bacteremia in Kenyan children stratified across a period of falling malaria transmission between 1998 and 2010.ResultsFour hundred twenty-nine Kenyan children with pneumococcal bacteremia and 2677 control children were included in the study. Among control children, G6PD deficiency, secondary to the rs1050828 G>A mutation, was common, with 11.2% (n = 301 of 2677) being hemi- or homozygotes and 33.3% (n = 442 of 1329) of girls being heterozygotes. We found that G6PD deficiency increased the risk of pneumococcal bacteremia, but only during a period of high malaria transmission (P = 0.014; OR 2.33, 95% CI 1.19–4.57). We estimate that the population attributable fraction of G6PD deficiency on risk of pneumococcal bacteremia in areas under high malaria transmission is 0.129.ConclusionsOur data demonstrate that G6PD deficiency increases risk of pneumococcal bacteremia in a manner dependent on malaria. At the population level, the impact of G6PD deficiency on invasive pneumococcal disease risk in malaria-endemic regions is substantial. Our study highlights the infection-associated morbidity and mortality conferred by G6PD deficiency in malaria-endemic settings and adds to our understanding of the potential indirect health benefits of improved malaria control.

Retrospective versus prospective score tests for genetic association with case-control data.

Since the seminal work of Prentice and Pyke, the prospective logistic likelihood has become the standard method of analysis for retrospectively collected case-control data, in particular for testing the association between a single genetic marker and a disease outcome in genetic case-control studies. In the study of multiple genetic markers with relatively small effects, especially those with rare variants, various aggregated approaches based on the same prospective likelihood have been developed to integrate subtle association evidence among all the markers considered. Many of the commonly used tests are derived from the prospective likelihood under a common-random-effect assumption, which assumes a common random effect for all subjects. We develop the locally most powerful aggregation test based on the retrospective likelihood under an independent-random-effect assumption, which allows the genetic effect to vary among subjects. In contrast to the fact that disease prevalence information cannot be used to improve efficiency for the estimation of odds ratio parameters in logistic regression models, we show that it can be utilized to enhance the testing power in genetic association studies. Extensive simulations demonstrate the advantages of the proposed method over the existing ones. A real genome-wide association study is analyzed forillustration.

Correlation of Tumor Necrosis Factor-α -308G>A Polymorphism with Susceptibility, Clinical Manifestations, and Severity in Behçet Syndrome: Evidences from an Italian Genetic Case-Control Study.

To investigate the association between a functional drug-response tumor necrosis factor (TNF)α gene polymorphism (at the positions of -308; rs1800629; NG_007462.1:g.4682G>A) and both disease susceptibility and clinical manifestations in a cohort of 130 Italian patients with Behçet syndrome (BS). A group of 100 ethnically, age, and gender matched healthy controls (HC) was also recruited. Genotyping was performed using molecular (amplification and direct sequencing) and in silico methods. The genotype distribution of BS patients and HC underlined a lower percentage of wild-type GG genotype in BS patients versus HC (106/130 patients, 81.5% vs. 91/100 HC, 91%; p < 0.05), while the heterozygous genotype (GA) was identified in 24/130 patients (18.5%) versus 9/100 HC (9%) (p < 0.05). GA genotype was significantly associated with the disease (odds ratio = 2.29, 95% confidence interval 1.01-5.18). No significant association was recognized between the single nucleotide polymorphism (SNP) and the BS clinical manifestations, as well as with disease severity (Krause's index). We found statistically significant higher frequency of TNFα rs1800629 GA genotype in patients than in controls. No significant association was recognized between the polymorphism and the clinical parameters, as well as between the SNP and the disease severity. Our data need to be confirmed in larger cohort of patients and matched controls.

A Novel Coding Variant in SLC39A8 Is Associated With Adolescent Idiopathic Scoliosis in Chinese Han Population.

A genetic case-control association study. The aim of this study was to investigate the association of SLC39A8 with the susceptibility of adolescent idiopathic scoliosis (AIS) in Chinese Han population. A recent exome-wide association study identified a missense variant rs13107325 in SLC39A8 that was associated with AIS. However, there was a lack of study validating the association of this novel mutation with AIS in other populations. The variant rs13107325 was genotyped in 965 AIS patients and 976 healthy controls by allelic specific multiple ligase detection reactions. Variants located in the coding region of SLC39A8 were identified by exon sequencing for 192 AIS patients and 192 controls. Paraspinal muscles from 36 AIS patients and 36 age-matched congenital scoliosis patients were collected for the gene expression analysis. Comparison between the cases and controls was performed with the χ test for genotyping data or with Student t test for gene expression analysis. For the missense variant rs13107325, there was no case of mutation detected in the patients or the controls. All the subjects had homozygous genotype CC. Exon sequencing revealed that a coding variant rs11097773 of SLC39A8 had a significantly different distribution of minor allele frequency between patients and controls (7.81% vs. 14.8%, P = 0.002). The mRNA expression of SLC39A8 in the patients was remarkably lower than that in the controls (0.0015 ± 0.00026 vs. 0.0021 ± 0.00033, P < 0.001). The association of previously reported novel mutation (rs13107325 in SLC39A8) with AIS was not replicated in the Chinese population. Interestingly, a novel coding variant rs11097773 of SLC39A8 is found significantly associated with AIS. Moreover, the expression of SLC39A8 was obviously decreased in AIS patients. Further study is warranted to clarify the functional role of rs11097773 in the development of AIS. 3.

Variation analysis of SOX8 gene in Chinese men with non-obstructive azoospermia or oligozoospermia.

Sox8, encoding a SRY-related HMG box transcription factor, is essential in Sertoli cells for germ cell differentiation via regulation of integrity of the blood-testis barrier (BTB) as well as Sertoli-germ cell adhesion. Inactivation of Sox8 gene in mice causes postnatal progressive spermatogenic failure, resulting in male infertility. This study aims to investigate whether variants of SOX8 contribute to pathogenesis of idiopathic non-obstructive azoospermia (NOA) or oligozoospermia. A case-control genetic study was conducted in which all exons and exon-intron boundaries of SOX8 gene were screened in 190 NOA and 139 oligozoospermia cases by Sanger sequencing. The detected variants were examined in 284 normospermic controls. Nine known single-nucleotide polymorphisms (SNPs) of SOX8 gene were identified, and four of them exist simultaneously in oligo/azoospermia patients. A comparison of allele/genotype frequencies of these variants showed no significant difference between oligo/azoospermia cases and controls. The results indicate that deleterious variants in SOX8 gene may not be a common cause for oligo/azoospermia in Chinese men. Considering ethnic diversity, SOX8 could not be ruled out as a candidate gene for male infertility. The role of SOX8-mediated Sertoli cell function and BTB integrity played in the pathogenesis of male infertility needs to be further explored in other populations.

Genetic Association Studies of Red Blood Cell Transfusion Related Alloimmunization: A Systematic Review and Meta-Analysis

Introduction: Blood transfusions are an important treatment modality for patients with either acute or chronic onset anemia such as trauma, sickle cell disease, and hematological malignancies. Transfusion poses a risk for alloimmunization, which may lead to potentially lethal transfusion reactions. A promising strategy to prevent alloimmunization is extensive matching on blood groups, yet this is a costly procedure and should be reserved for patients at highest risk for alloimmunization. Identification of genetic variants that increase the risk for alloimmunization might help to identify high-risk patients and could be used as a screening tool for patients receiving multiple transfusions. Objectives: To summarize all available evidence on genetic risk factors for alloimmunization after blood transfusion. Design: Systematic review with meta-analysis of observational studies. Studies were only included in the meta-analysis if polymorphisms were tested at least 3 times, and if ethnic background of the population and the control populations were comparable between studies. Data sources: The online databases Embase, MEDLINE and the Cochrane Library were search for relevant articles with search terms: 1) transfusion, 2) alloimmunization 3) genetics. The search was last updated March 2018. Eligibility criteria: 1) Primary study that assessed the association of genetic polymorphisms with transfusion related alloimmunization, 2) a human population, 3) studies with at least 50 patients, 4) full text availability. Data extraction: Two reviewers independently screened articles for eligibility, extracted data using a standardized data extraction form. Extracted data included study setting, study population, participant demographics, baseline characteristics, study methodology, comparisons and outcome, and risk of bias. Primary outcome measure: Alloimmunization after one or more blood transfusions. Risk of bias assessment: The quality of the included studies was assessed by the Q-genie tool for genetic association studies. Results: A total of 2045 cases and 24084 controls were derived from 18 genetic case-control studies that were included in this systematic review. Most commonly studied disease group was sickle cell disease (SCD) (8 studies). Three studies included patients with different diseases and seven studies did not report the underlying disease. Eleven studies identified the association of HLA polymorphisms with alloimmunization and 8 studies focused on non-HLA variants. Overall quality of the included studies was moderate (11 studies), 2 studies were of high quality, and 5 studies were ranked as poor. HLA-DRB1*04 (Odds Ratio 7.16, 95%CI 3.87-13.22, P&lt;0.00001) and HLA-DRB1*15 (OR 3.01, 95%CI 1.84-5.53, P&lt;0.0001) were by meta-analysis significantly associated with anti-Fy(a) formation, although there was considerable heterogeneity (I2=78% and 55% respectively). Moreover, HLA-DRB1*10 (OR 2.64, 95%CI 1.41-4.95, P=0.002), HLA*DRB1*11 (OR 2.11, 95%CI 1.34-3.32, P=0.001), and HLA-DRB1*13 (OR 1.71, 95%CI 1.26-2.33, P=0.0006) were overall associated with anti-Kell formation. Heterogeneity was less prominent with an I2 of 0%, 54% and 19% respectively (Figure 1). No other variants were eligible for meta-analysis. Non-HLA variants were tested less extensively, as most variants were reported by only 1 study. Polymorphisms of genes in the immunomodulatory pathways were assessed most frequently. Of these variants, FC-gamma-receptor 2C.nc-ORF was associated with a decreased risk of alloimmunization in SCD (OR 0.26, 95%CI 0.11-0.64, p=0.003). All other associations that were described as significant by the original articles were summarized in Figure 2. Discussion: There is limited evidence supporting the role of genetic risk factors for alloimmunization. The results of our meta-analysis suggest that several HLA polymorphisms potentially influence antigen presentation of the Duffy(a) and Kell antigen. Once confirmed by experimental studies, these polymorphisms could be used as a screening tool for the prevention of alloimmunization among frequently transfused patients. Overall, the effect of genetic variants on alloimmunization has mostly been assessed by small studies, hampering reliable interpretation of the results. Future studies should include large and well-defined cohorts when performing genetic analysis on this complicated subject. Disclosures No relevant conflicts of interest to declare.

Association between rs2303861 polymorphism in CD82 gene and non-alcoholic fatty liver disease: a preliminary case-control study

AimTo investigate the genetic factors involved in the development of non-alcoholic fatty liver disease (NAFLD) and its sequelae in a Middle Eastern population.MethodsThis genetic case-control association study, conducted in 2018, enrolled 30 patients with NAFLD and 30 control individuals matched for age, sex, and body mass index. After quality control measures, entire exonic regions of 3654 genes associated with human diseases were sequenced. Allelic association test and enrichment analysis of the significant genetic variants were performed.ResultsThe association analysis was conducted on 27 NAFLD patients and 28 controls. When Bonferroni correction was applied, NAFLD was significantly associated with rs2303861, a variant located in the CD82 gene (P = 2.49 × 10−7, adjusted P = 0.0059). When we used Benjamini-Hochberg adjustment for correction, NAFLD was significantly associated with six more variants. Enrichment analysis of the genes corresponding to all the seven variants showed significant enrichment for miR-193b-5p (P = 0.00004, adjusted P = 0.00922).ConclusionA variant on CD82 gene and a miR-193b expression dysregulation may have a role in the development and progression of NAFLD and its sequelae.

Association of Nod‐like receptor protein‐1 (rs2670660) and Toll‐like receptor‐4 (rs4986790) with non‐segmental vitiligo: A case–control study in South Indian population

Non-segmental vitiligo (NSV) is an autoimmune skin disease. Genetics plays a predominant part in disease pathogenesis. Nucleotide-binding and oligomerization domain (NOD)-like receptors and pyrin-containing protein (NLRP) and Toll-like receptors (TLR) are pattern recognition receptors in mediating innate immunity. They participate in presenting pathogens and mediating the immune responses. NLRP and TLRs are involved in mediating immune response in various dermatological diseases. Understanding the influence of genetic polymorphisms of NLRP and TLRs associated with immune homeostasis might help us to understand the complex etiopathogenesis of NSV. Thus, we aimed to study the association of NLRP-1 (rs2670660) and TLR-4 (rs4986790) and the synergistic effects on disease spectrum, disease activity of NSV in South Indian population. This research was designed as a case-control genetic study with 264 patients and 264 controls. Genotyping of NLRP-1 (rs2670660) and TLR-4 (rs4986790) was performed by Taqman 5' allele discrimination assay and ARMS-PCR. Plasma levels of proteins were measured by enzyme-linked immunosorbent assay (ELISA). A statistically significant difference was observed with the frequency of homozygous GG genotype of NLRP-1 (rs2670660) (17.8% in cases vs. 5.3% in controls) (p<0.0001; OR-3.73; 95% CI-1.94-7.14). Allele G was significantly frequent in 38% of the cases than in controls with 30% (p=0.004; OR-1.46; 95% CI-1.13-1.89). Plasma NLRP-1 level was significantly higher in patients compared to controls (p<0.05). Amongst cases, the plasma NLRP-1 levels did not show any difference with respect to their genotypes (p>0.05). In TLR-4 (rs4986790), no significant difference in the frequency of genotypes and allele between cases and controls (p=0.80) was observed; nevertheless, plasma TLR-4 was analogous between cases and controls (p>0.05). Influence of genotype on plasma TLR-4 showed no significant difference in TLR-4 levels between GG and ancestral genotype AA, whilst heterozygous AG genotype showed a significant increase of TLR-4 compared to AA and GG (p=0.02) amongst NSV cases. The obtained results suggest that NLRP-1 (rs2670660), and not TLR-4 ((rs4986790), is associated with increased risk of NSV in South Indian population.

Characteristics of severe life events, attachment style, and depression - Using a new online approach.

Severe life events are established as provoking agents for depression in combination with vulnerability factors. Identifying features of severe events improves the prediction of disorder but are rarely utilized, mainly because life event research is increasingly dominated by self-report checklists with no capacity for inferring such characteristics. This paper investigates the association of severe life events' features with depression and insecure attachment styles using a new online measure of life events in a clinical and control sample. A total of 202 participants (75 clinical and 127 matched control participants), taken from an earlier national Depression Case Control genetic study and followed up after 12years, completed the Computerised Life Events Assessment Record to assess characteristics of life events, the Vulnerable Attachment Style Questionnaire to measure attachment insecurity, and the General Health Questionnaire to measure depression. The clinical group had higher self-reported depression, severe life events, and insecure attachment style. They also reported more loss, danger, humiliation, and trauma severe events. Intra-respondent analysis showed individuals experiencing these types of events were more likely to report depression. Insecure attachment style and severe life events were both significantly related to recent depression and history of depressive disorder. Anxious attachment style was significantly related to relationship events and bereavements, as well as severe loss or humiliation events, whereas avoidant style wasnot. Identifying salient features of severe life events improves associations with depression and insecure attachment style. Utilizing a new online approach can aid research and clinical approaches for depression at low cost. Salient features of severe life events (e.g., loss, humiliation) give insight into the potential impact on attachment vulnerability and depression. Clinicians and researchers can use online methods to economically gain detailed life event information needed for clinical formulation and valid data on stressors. The self-reported scale for recent depression is only a proxy measure of clinical disorder, but the clinical group selection is a more robust criterion for depression history.

Novel WEE2 gene variants identified in patients with fertilization failure and female infertility

To determine whether variants in the WEE2 (WEE1 homolog 2, also known as WEE1B) gene, which has been known to function in the formation of pronuclei during fertilization, contribute to fertilization failure. Case-control genetic study. University hospital. Ninety infertile women with repeated cycles of pronucleus formation failure undergoing invitro fertilization and/or intracytoplasmic sperm injection treatment as well as 200 fertile control women. Genomic DNA was extracted from the peripheral blood. The whole exons of WEE2 were amplified by means of polymerase chain reaction and then Sanger sequencing was performed. Variants analysis of WEE2 gene. We identified five subjects that were subjected to homozygous or compound-heterozygous variants of WEE2: case 1 (from a consanguineous family) with homozygous frameshift variant: c.293_294insCTGAGACACCAGCCCAACC (p.Pro98Pro fsX2); case 2 with homozygous missense variant: c.1576T>G (p.Tyr526Asp); and three cases with compound-heterozygous variants: case 3: c.991C>A (p.His331Asn) and c.1304_1307delCCAA (p.Thr435Met fsX31); case 4: c.341_342 del AA (p.Lys114Asn fsX20) and c.864G>C (p.Gln288His); and case 5: c.1A>G (p.0?) and c.1261G>A (p.Gly421Arg). Besides c.1576T>G (from case 2) and c.864G>C (from case 4), which have been previously reported as rare single nucleotide polymorphisms (SNPs), the other six variants were novel and predicted by software to be deleterious. The parental genotypes of case 1 and case 2 indicated that the detected homozygous variants were inherited in an autosomal recessive mode. All of the detected variants were absent from the control cohort. Novel variants found in WEE2, which is autosomal-recessive inherited, may be related to recurrent pronucleus formation failure and female infertility.

Ranking the Importance of Genetic Factors by Variable-Selection Confidence Sets

SummaryThe widespread use of generalized linear models in case–control genetic studies has helped to identify many disease-associated risk factors typically defined as DNA variants, or single-nucleotide polymorphisms (SNPs). Up to now, most literature has focused on selecting a unique best subset of SNPs based on some statistical perspective. When the noise is large compared with the signal, however, multiple biological paths are often found to be supported by a given data set. We address the ambiguity related to SNP selection by constructing a list of models—called a variable-selection confidence set (VSCS)—which contains the collection of all well-supported SNP combinations at a user-specified confidence level. The VSCS extends the familiar notion of confidence intervals in the variable-selection setting and provides the practitioner with new tools aiding the variable-selection activity beyond trusting a single model. On the basis of the VSCS, we consider natural graphical and numerical statistics measuring the inclusion importance of an SNP based on its frequency in the most parsimonious VSCS models. This work is motivated by available case–control genetic data on age-related macular degeneration, which is a widespread disease and leading cause of loss of vision.