Dominant Inheritance Model Research Articles

Replication of genome‐wide association study identified seven susceptibility genes, affirming the effect of rs2856717 on renal function and poor outcome of IgA nephropathy

Meta-analysis of data from a genome-wide association study (GWAS) identified seven single nucleotide polymorphisms (SNPs) as strong predictors of IgA nephropathy (IgAN). To replicate the association of these seven SNPs and understand whether they influence the clinical characteristics of IgAN, a case-control study including 521 IgAN patients and 535 controls was conducted in a Western Han cohort. Data were analyzed using logistic regression and multifactor dimensionality reduction (MDR). Clinical data collected from 459 IgAN patients were investigated to estimate the relationship between the genotype and phenotype of IgAN. A retrospective cohort study of 315 IgAN patients was conducted to investigate the relationship between genotype and progression of renal disease over a mean period of 44.49 ± 19.94 months. Upon Bonferroni correction, none of the seven SNPs were associated with IgAN (corrected P-value [Pc], >0.05). A combination of the rs2856717T/C, rs9275596C/T, and rs2412971A/G had effects on the susceptibility of IgAN (P = 0.001). Marginally significant association of rs2856717 T/C recessive model for the T allele was significantly associated with estimated glomerular filtration rate (eGFR) (<60 mL/min per 1.73 m2 ) in IgAN patients (P = 0.008, Pc = 0.056, odds ratio [OR] = 1.527). The T allele at rs9275596 was significantly associated with macroscopic haematuria of IgAN patients under the dominant and additive models of inheritance, (P < 0.001, Pc = 0.007, OR = 2.983) and (P < 0.001, Pc = 0.007, OR = 2.17), respectively. Kaplan-Meier survival analysis showed that patients carrying the TT + TC genotype for rs2856717 had reduced renal survival rate than those carrying the CC genotype (85.1% vs. 92.7%, P = 0.046). rs2856717 may influence the clinical characteristics and poor outcome of IgAN. Further studies are warranted to explore the mechanisms for such genotype-disease phenotype association.

Haptoglobin levels, but not Hp1-Hp2 polymorphism, are associated with polycystic ovary syndrome.

Proteomic studies suggest an association between haptoglobin (Hp) and polycystic ovary syndrome (PCOS). Hp is a classic inflammatory marker and binds to the intravascular hemoglobin, avoiding the oxidative damages that can be caused by free hemoglobin. Inflammation and oxidative stress are important in the pathogenesis of the PCOS, one of the most frequent metabolic diseases in women. To validate these proteomic studies, we developed a controlled cross-sectional study that aimed to evaluate the Hp levels and allelic and genotypic frequencies of Hp1-Hp2 polymorphism in Brazilian women with PCOS. We also investigated the correlation between Hp levels and several important parameters in PCOS as follows: body mass index (BMI), waist circumference (WC), fasting glucose, post-prandial glucose, homeostatic model assessment (HOMA), lipid accumulation product (LAP), C-reactive protein (CRP), and metabolization test of tetrazolium salts (MTTs-serum antioxidant capacity). Plasma Hp levels were higher in the PCOS group than in controls [8.20 (4.04)g/L; 7.98 (3.31)g/L; p=0.018]. No significant difference was observed in the frequency of Hp1-Hp2 genotypes under additive, recessive, or dominant model of inheritance between the PCOS and the control groups. Plasma Hp levels did not differ according to the genotype. However, plasma Hp showed a negative correlation with MTT (r=-0.383; p=0.028), as well as a positive correlation with CRP (r=0.361; p=0.014) in the PCOS group. Hp1-Hp2 polymorphism is not associated with PCOS but plasma Hp could be a potential biomarker for PCOS and its complications.

Retinoic acid-related orphan receptor alpha (RORA) variants are associated with autism spectrum disorder.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with various epidemiologic, genetic, epigenetic, and environmental factors being associated with it. The observed sex bias in ASD towards male has prompted investigators to propose sex-dependent mechanisms for ASD. Retinoic acid-related orphan receptor-alpha (RORA) is a new autism candidate gene that has been shown to be differentially regulated by male and female hormones. Previous studies have shown deregulation of its expression in the prefrontal cortex and the cerebellum of ASD patients. In the present study we aimed at identification of the possible associations between two functional polymorphisms in the RORA gene (rs11639084 and rs4774388) and the risk of ASD in 518 Iranian ASD patients and 472 age, gender, and ethnic-matched healthy controls by means of tetra primer-amplification refractory mutation system-PCR. The allele and genotype frequencies of rs11639084 were not significantly different between patients and controls. However, the allele frequencies of rs4774388 showed significant overrepresentation of T allele in patients compared with controls (P=0.04, OR (95% CI) =1.21 (1.01-1.46)). The rs4774388-TT genotype was significantly higher in patients compared with controls and was associated with ASD risk in dominant inheritance model (P=0.04, OR (95% CI) =0.77 (0.59-0.99)). Haplotype analysis showed significant association of two estimated blocks of rs11639084/ rs4774388 with ASD risk. Consequently, the present data provide further evidence for RORA participation in the pathogenesis of ASD.

Relationship of phosphodiesterase 4D (PDE4D) gene polymorphisms with risk of ischemic stroke: a hospital based case-control study

Background: Stroke remains a leading cause of death and disability worldwide. Ischemic stroke (IS) accounts for around 80–85% of total stroke and is a complex polygenic multi-factorial disorder which is affected by a complex combination of vascular, environmental, and genetic factors.Objective: The study was conducted with an aim to examine the relationship of single nucleotide polymorphisms (SNPs) of PDE4D (T83C, C87T, and C45T) gene with increasing risk of IS in patients in North Indian population.Methods: In this hospital-based case-control study, 250 IS subjects and 250 age-and sex-matched control subjects were enrolled from the Neurosciences Centre, A.I.I.M.S., New Delhi, India. Deoxyribonucleic acids (DNAs) were extracted using the conventional Phenol–Chloroform isolation method. Different genotypes were determined by Polymerase chain reaction– Restriction fragment length polymorphism method. Odds ratio (OR) and 95% Confidence Interval (CI) of relationship of polymorphisms with risk of IS were calculated by conditional multivariable regression analysis.Results: High blood pressure, low socioeconomic status, dyslipidemia, diabetes, and family history of stroke were observed to be statistically significant risk factors for IS. Multivariable adjusted analysis demonstrated a statistically significant relationship between SNP 83 of PDE4D gene polymorphism and increasing odds of IS under the dominant model of inheritance (OR, 1.59; 95% CI, 1.02 to 2.50; p value = 0.04) after adjustment of potential confounding variables. Stratified analysis on the basis of TOAST classification demonstrated a statistically significant association for increasing 2.73 times odds for developing large vessel disease stroke as compared to controls (OR, 2.73; 95% CI, 1.16 to 0.02; p value = 0.02). We did not find any significant association of SNPs (C87T and C45T) of the PDE4D gene with the risk of IS.Conclusion: SNP 83 of PDE4D gene may increase the risk for developing IS whereas SNP 87 and SNP45 of PDE4D may not be associated with the risk of IS in the North Indian population. Prospective cohort studies are required to corroborate these findings.

Obesity risk prediction among women of Upper Egypt: The impact of serum vaspin and vaspin rs2236242 gene polymorphism

BackgroundVaspin is an adipokine that is potentially linking obesity, insulin resistance, metabolic syndrome and type-2 diabetes. AimThe present study aimed to investigate the impact of vaspin rs2236242 gene polymorphism on the risk of obesity, diabetes, their metabolic traits, and serum vaspin levels in a sample of Upper Egyptian women. Subjects and methodsA total of 224 subjects, 112 obese (62 non diabetics, 50 diabetics) and 112 controls were included in this case control study. Vaspin gene rs2236242 polymorphism was performed using tetra-amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) and serum vaspin levels were estimated by ELISA. ResultsThe minor (A) allele of vaspin rs2236242 gene polymorphism was significantly lower in obese (30.8%) than controls (43.7%) (P=0.005). The protective effect was evident in dominant and recessive inheritance models (TT vs TA+AA, P=0.004 and TT+TA vs AA, P=0.036). After adjusting genotypes for diabetes there were no significant association between vaspin rs2236242 gene polymorphism and obesity but significant association was maintained in the obese diabetics. Vaspin serum levels were found to be lower in minor protective (AA) genotype carriers than the other two genotypes (P<0.001). In the mean-time serum vaspin levels were significantly higher in obese diabetics and non-diabetics than controls (P<0.001 each).There were significant positive correlations between vaspin levels and hs-CRP, cholesterol, LDL-C, fasting glucose, HOMA-IR, insulin, and ALT values (P<0.05 each) and a negative correlation with HDL-C (P<0.01). ConclusionThe minor A allele of vaspin rs2236242 polymorphism plays a protective role against obesity and diabetes but this relation is largely ascribed to its effect on insulin resistance. The serum vaspin concentration was lower in minor protective allele carriers. To the best of our knowledge, this is the first study of vaspin SNP in Upper Egyptian women. The entire understanding of vaspin intimate mechanistic action might enable the development of novel etiology-based treatment strategies for obesity, the complex genetic trait.

Brain-Derived Neurotrophic Factor Val66Met Gene Polymorphism Impacts on Migraine Susceptibility: A Meta-analysis of Case-Control Studies.

Inconclusive results have been reported in studies investigating the association between the brain-derived neurotrophic factor (BDNF) rs6265 polymorphism and migraine. In the present study, we conducted a systematic review and meta-analysis on the published data in order to quantitatively estimate the relationship between rs6265 and migraine susceptibility. A comprehensive search was performed through PubMed, Web of Knowledge, and Cochrane databases up to October 2016. The pooled odds ratio (OR) with the corresponding 95% confidence interval (CI) was calculated to estimate the strength of the association with rs6265 under an additive, dominant, or recessive model of inheritance. A total of five studies including 1,442 cases and 1,880 controls were identified for the meta-analysis. The pooled data showed an increased risk of migraine for the allelic (OR: 1.17, 95% CI: 1.03–1.34, p = 0.014) or the dominant model of rs6265 (OR: 1.22, 95% CI: 1.05–1.41, p = 0.011). Statistical significance of rs6265 was lost when one single study was excluded from the analysis (dominant OR: 1.17, 95% CI: 1.00–1.38, p = 0.054; allelic OR: 1.14, 95% CI: 0.99–1.31, p = 0.067), suggesting lack of robustness of pooled estimates. When stratified by migraine type, a similar trend of association was detected with both MA and MO, but a statistically significant association of rs6265 was reached only with the MA subtype in the dominant model (OR: 1.22, 95% CI: 1.00–1.47, p = 0.047). The present meta-analysis supports that BDNF rs6265 may act as a genetic susceptibility factor for migraine. Nevertheless, large-scale studies are required to confirm our findings and to assess potential modifiers of the relationship between rs6265 and migraine.

АЛЕЛЬНИЙ ПОЛІМОРФІЗМ ГЕНІВ GSTS У МАТЕРІВ ІЗ ПЛАЦЕНТАРНОЮ ДИСФУНКЦІЄЮ ТА ЇХ НОВОНАРОДЖЕНИХ: АКУШЕРСЬКІ ТА ПЕРИНАТАЛЬНІ НАСЛІДКИ

Роль плаценти зумовлена реалізацією ряду функціональних механізмів забезпечення росту і внутрішньоутробного розвитку плода. Глутатіон-S-трансферази беруть активну участь у знешкодженні продуктів пероксидного окиснення ліпідів та пероксидів ДНК, відновлюючи органічні гідроперекиси в спирти та сприяючи ізомеризації деяких стероїдів та простагландинів. При наявності певних поліморфних варіантів GSTT1, GSTM1, GSTP1 генів сімейства глутатіон-S-трансфераз проходить виснаження глутатіонзалежного АОЗ та пригнічення детоксикаційної функції плаценти.Мета дослідження – визначити алельний поліморфізм генів глутатіон-S-трансфераз GSTT1 та GSTM1 у жінок із плацентарною дисфункцією, в здорових новонароджених та новонароджених із затримкою внутрішньоутробного розвитку на основе проведеного молекулярно-генетичного дослідження пуповинної крові.Матеріли і методи. У дослідження було залучено 105 жінок: основну групу склали 33 жінки з плацетарною дисфункцією (ПД) без затримки внутрішньоутробного розвитку (ЗВУР) у дітей, яких вони народили (перша група), та 17 жінок із ПД та ЗВУР (друга група). Контрольну групу склали 55 жінок (третя група), які народили здорових доношених дітей.Результати досліджень та їх обговорення. Встановлено, що ризик розвитку ПД та ПД зі ЗВУР за домінантної моделі успадкування (313AG + 313GG порівняно з 313AA) достовірно зростав. Перспективними прогностичними моделями міжгенної взаємодії для оцінки розвитку ПД передбачається аналіз варіантів генів GSTM1, GSTP1, а ПД зі ЗВУР – GSTT1, GSTM1, GSTP1. У результаті аналізу проб сироватки пуповинної крові та отриманих даних встановлено, що частота поліморфного варіанта GSTМ1“+” у всіх новонароджених області склала 42,69 %, а GSTМ1 “–” – 57,30 %. Частота поліморфного варіанта GSTT1“+” у всіх новонароджених області становила 79,77 %, а GSTT1 “–” – 20,22 %.Висновки. Результати досліджень розподілу різних алельних варіантів генів GSTM1 і GSTT1 показали їх відмінності у різних групах новонароджених. Виявлено вірогідну різницю між частотами делеційного варіанта гена GSTM1 у здорових новонароджених та новонароджених із ЗВУР. Сукупний аналіз комбінованого впливу декількох чинників виявив, що перебіг вагітності у жінок із ПД, гестозом та генотипом GSTМ1deletion асоціюється із значним зростанням ризику ЗВУР у плодів.

Association between Polymorphism of Genes Encoding for 5‐HT1A and 5‐HT2A Receptors and Response to Selective Serotonin Reuptake Inhibitors in Malaysian Patients with Major Depressive Disorder

Inter‐racial variations in genotype frequency have been implicated as a probable cause of the inconsistencies in pharmacogenetic studies of major depressive disorder (MDD). The aim of this study was to determine whether the polymorphisms of the serotonin 1A (5HT1A) 1019C&gt;G and serotonin 2A (5HT2A) 1438A&gt;G are associated with response to SSRI treatment among Malaysian MDD patients. These polymorphic changes are shown to modulate the transcription of these genes and are associated with attenuation of the density of the encoded receptors. Modulation of these receptors is central to the activity of antidepressant medication. The study involved six weeks follow up of incidence and prevalence (diagnosed within 2 years to recruitment) MDD patients from a case‐control hospital based study in Malaysia. Only Malaysians aged 18–65 years and diagnosed with MDD (other Axis 1 psychiatric diagnosis were excluded) on treatment with SSRIs were recruited. One hundred and ninety two patients (females ‐ 71.4% and males – 28.6%) were recruited. A total of 77.7% of the patient showed response to treatment and the rest did not. The response rate was also highest among the females (81%) compared to males (67%). The frequencies of the genotypes 5HT1A1019C&gt;G were GC (34.2%), CC (55.2%), GG (10%) and those of the 5HT2A 1438A&gt;G were GA (45.3%), AA (33%), GG (21.9%). Association testing for response to SSRIs with the 5HT1A 1019C&gt;G polymorphism and not the 5HT2A1438A&gt;G polymorphism revealed a chi‐square score of 3.911 with P≤0.05 (P=0.048) in a dominant model of inheritance. This study revealed that the dominant effect of the G‐allele in both the GG and GC genotypes of the 5HT1A receptor gene was associated with treatment response in Malaysian MDD patients.

Association study of the FTO gene polymorphisms with the risk of pulmonary tuberculosis in a sample of Iranian population.

The aim of the present study was to find out the impact of fat mass and obesity-associated (FTO) gene on risk of pulmonary tuberculosis (PTB) in a sample of Iranian population. This case-control study was carried out on a total of 354 subjects including 185 PTB patients and 169 healthy subjects. Genotyping of FTO rs9939609 and rs8050136 variants was done using polymerase chain reaction-restriction fragment length polymorphism method. FTO rs9939609 variant showed no statistically significant difference in allele and genotype frequencies between PTB patients and controls. The rs8050136 polymorphism marginally increased the risk of PTB in dominant (OR = 1.53, 95% CI = 1.00-2.33, p = 0.055, CA+AA vs. CC) inheritance model tested, where rs8050136 A allele significantly increased the risk of PTB (OR = 1.42, 95% CI = 1.02-1.97, p = 0.045) compared with C allele. The finding of the present study showed an association between FTO rs9939609 variant and risk of PTB. Further studies with larger sample sizes and different ethnicities are necessary to confirm the findings.

Macrophage migration inhibitory factor -173 G > C polymorphism and risk of tuberculosis: A meta-analysis.

The aim of the present meta-analysis was to find out the impact of MIF -173 G > C polymorphism on risk of tuberculosis (TB). We conducted a search of case-control studies on the associations of -173 G > C variant of MIF with susceptibility to tuberculosis in PubMed, ISI Web of Science, and Scopus. We extracted the data from eligible studies and achieved a meta-analysis to examine the relationship between MIF -173 G > C polymorphism and the risk of TB. Odds ratios (ORs) with the corresponding 95 % confidence intervals (CIs) were pooled to find out the impact of MIF -173G > C promoter polymorphism on TB risk. The pooled ORs were calculated for the codominant, dominant, recessive, and allelic model comparison. The findings revealed that MIF -173 G > C variant increased the risk of TB in codominant (OR = 1.54, 95 %CI = 1.26-1.88, p < 0.0001; CG vs GG), and dominant (OR = 1.62, 95 %CI = 1.33-1.96, p < 0.00001; GC+CC vs GG) inheritance models tested. The results suggested that the MIF -173 C allele significantly increased the risk of PTB (OR = 1.49, 95 %CI = 1.28-1.74, p < 0.00001). The findings of this meta-analysis propose that MIF -173 G > C variant is associated with the risk of TB. More case-control studies with well-designed in different ethnic groups and larger sample size are needed to confirm the findings.

HOTAIR genetic variants are associated with prostate cancer and benign prostate hyperplasia in an Iranian population

Prostate cancer and benign prostate hyperplasia (BPH) are heterogeneous disorders with a wide array of clinical presentations and high prevalence among men. Several protein coding genes as well as non-coding genes have been shown to contribute in prostate cancer and BPH risk. Among non-coding genes whose contribution in tumorigenesis has been identified is HOX transcript antisense RNA (HOTAIR). In the present study we aimed at identification of the associations between three HOTAIR polymorphisms (rs12826786, rs1899663 and rs4759314) and risk of prostate cancer and BPH by the means of tetra-primer ARMS-PCR in a population of 128 Iranian prostate cancer patients, 143 BPH patients and 250 normal male controls. The study showed that rs1899663 T allele was associated with BPH risk. Comparison between prostate cancer and BPH groups showed that rs1899663 is associated with cancer risk in co-dominant, dominant and recessive inheritance models. The rs12826786 T allele was significantly more presented in both BPH and prostate cancer groups compared with healthy subjects. This SNP was associated with both BPH and prostate cancer risk in co-dominant and recessive models. However, rs4759314 showed no significant difference in allele or genotype frequencies between three mentioned groups. In addition, some haplotypes within this gene were associated with increased prostate cancer and BPH risk. Consequently, HOTAIR can be suggested as a risk locus for prostate cancer and BPH in Iranian population.

Pri-miR-34b/c rs4938723 polymorphism increased the risk of prostate cancer.

The association studies between miR-34b/c rs4938723 polymorphism and cancer risk showed conflicting results. This study aimed to assess the impact of rs4938723 polymorphism on prostate cancer risk. This case-control study was done on 151 prostate cancer (PCa) patients and 152 benign prostate hyperplasia to examine whether rs4938723 polymorphism in the promoter of pri-miR-34b/c was linked to the carcinogenesis of PCa in a sample of Iranian population. Genotyping of Pri-miR-34 b/c rs4938723 polymorphism was performed by using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method. The results showed that rs4938723 variant significantly increased the risk of PCa in codominant (OR = 1.92, 95% CI = 1.15 - 3.18, p= 0.012, TC vs TT), dominant (OR = 1.99, 95% CI = 1.23 - 3.24, p= 0.005, TC + CC vs TT), and allelic (OR = 1.79, 95% CI = 1.20 - 2.68, p= 0.005, C vs T) inheritance model. Our findings propose that Pri-miR-34 b/c rs4938723 variant may be a risk factor for the development of PCa in a sample of Iranian population. Larger sample sizes with different ethnicities are required to validate our findings.

GWAR: robust analysis and meta-analysis of genome-wide association studies.

In the context of genome-wide association studies (GWAS), there is a variety of statistical techniques in order to conduct the analysis, but, in most cases, the underlying genetic model is usually unknown. Under these circumstances, the classical Cochran-Armitage trend test (CATT) is suboptimal. Robust procedures that maximize the power and preserve the nominal type I error rate are preferable. Moreover, performing a meta-analysis using robust procedures is of great interest and has never been addressed in the past. The primary goal of this work is to implement several robust methods for analysis and meta-analysis in the statistical package Stata and subsequently to make the software available to the scientific community. The CATT under a recessive, additive and dominant model of inheritance as well as robust methods based on the Maximum Efficiency Robust Test statistic, the MAX statistic and the MIN2 were implemented in Stata. Concerning MAX and MIN2, we calculated their asymptotic null distributions relying on numerical integration resulting in a great gain in computational time without losing accuracy. All the aforementioned approaches were employed in a fixed or a random effects meta-analysis setting using summary data with weights equal to the reciprocal of the combined cases and controls. Overall, this is the first complete effort to implement procedures for analysis and meta-analysis in GWAS using Stata. A Stata program and a web-server are freely available for academic users at http://www.compgen.org/tools/GWAR. pbagos@compgen.org. Supplementary data are available at Bioinformatics online.

Protective role of +294 T/C (rs2016520) polymorphism of PPARD in Mexican patients with colorectal cancer.

PPARD encodes for peroxisome proliferator-activated receptor delta, which plays a significant role in controlling lipid metabolism, atherosclerosis, inflammation, cancer growth, progression, and apoptosis. Accumulated evidence suggests that the polymorphism rs2016520 in PPARD is associated with lipid metabolism, obesity, metabolic syndrome, and type 2 diabetes mellitus. The aim of this study was to determine whether the single nucleotide polymorphism +294T/C (rs2016520) in PPARD is associated with colorectal cancer (CRC) in the Mexican population. Genomic DNA from 178 CRC patients and 97 healthy blood donors was analyzed. The polymorphism was identified by the polymerase chain reaction-restriction fragment length polymorphism method. Results demonstrated that patients with the T/C genotype for the +294T/C (rs2016520) polymorphism present a protective role against CRC [odds ratio (OR) = 0.39; 95% confidence interval (CI) = 0.22-0.69; P = 0.0008]. This association was also evident for the T/C genotype in the stratified analysis by tumor-node-metastasis stages I+II (OR = 0.26, P = 0.0332) and III+IV (OR = 0.44, P = 0.0067). However, in the stratified analysis by tumor location, we observed an increased risk of rectal cancer (OR = 7.57, P = 0.0403) vs colon cancer (OR = 4.87, P = 0.234) in patients carrying the C/C genotype and under the dominant and recessive models of inheritance. In conclusion, for the first time, the association between the +294T/C (rs2016520) polymorphism and colorectal cancer has been studied in Mexican patients. Our results reveal that variations in PPARD may play a significant role in genetic susceptibility to colorectal cancer.

DROSHA rs642321 Polymorphism Influence Susceptibility to Childhood Acute Lymphoblastic Leukemia: A Preliminary Report.

Introduction:It has been well known that the microRNA biogenesis is involved in the pathogenesis of various diseases. We investigated the possible association between DROSHA rs642321 variant and risk of acute lymphocytic leukemia (ALL).Materials and Methods:We genotyped 75 children diagnosed with ALL and 115 age- and sex-matched children with no history of cancer of any type (as the control group) by the tetra amplification refractory mutation system-polymerase chain reaction.Results:We found that DROSHA rs642321 C > T variant significantly decreased the risk of ALL in codominant (TT vs. CC: odds ratio [OR] = 0.33, 95% confidence interval [CI] = 0.14–0.80, P = 0.020) and dominant (TT + CT vs. CC: OR = 0.51, 95% CI = 0.27–0.94, P = 0.037) inheritance model tested. The rs642321 T allele was associated with protective against ALL (OR = 0.58, 95% CI = 0.38–0.88, P = 0.011) in comparison with C allele.Conclusion:The study findings revealed that DROSHA rs642321 variant decreased the risk of pediatrics ALL in an Iranian population. Larger sample sizes with different ethnicities are needed to validate our findings.

A Case of Two Young Brothers with Natural-Killer/T-Cell Lymphoma

Introduction:Natural-killer/T-cell lymphoma (NKTL) is a rare subset of non-Hodgkin's lymphoma that is more prevalent in Asia than in the West. We report a case of two brothers who were diagnosed with NKTL and died of their disease at 23 and 37 years old respectively, and further investigations performed to determine the underlying genetic basis to their disease.MethodsBoth patients were recruited into the Singapore lymphoma study where retrieval of their clinical data and biospecimens had been approved by the Singhealth instititutional review board. Their clinical courses are described using information from electronic medical records.For the older brother we extracted tumor DNA from a patient-derived xenograft (PDX), and DNA from a buccal swab and peripheral blood (PB) sample. In the younger brother DNA was extracted from normal and tumor tissue from archived formalin fixed paraffin embedded (FFPE) samples. DNA from the unaffected mother, older brother and paternal aunt were obtained from PB and buccal swab samples. We performed whole exome sequencing (WES) on the younger affected brother's tumor, the older affected brother's, mother's and unaffected brother's blood sample. Subsequent analysis of variants took into account autosomal recessive (AR), X-linked recessive (XR) and autosomal dominant (AD) inheritance models. Candidate genes are validated using Sanger sequencing. Microarray on the older affected brother and 12 sporadic NKTL cases were analyzed.ResultsThe older affected brother was 35 years old when he presented with left nasal blockage in March 2013. He was diagnosed with stage IIA NKTL and treated with 4 cycles of bortezomib-GIFOX as part of a clinical trial followed by radiotherapy to the nasal region. He had primary refractory disease and was further treated with 4 cycles of SMILE followed by high dose chemotherapy and autologous stem cell transplantation (HDC/ASCT). He progressed and received off-label ruxolitinib, and everolimus/HDAC inhibitor as part of a clinical trial. He then had radiotherapy to an ulcerating penile lesion before he died of progressive disease 27months after diagnosis. The younger affected brother was 18 years old when he was diagnosed with NKTL in 1998. He received 6 cycles of CHOP with intravenous high-dose methotrexate and intrathecal methotrexate and went into remission. Three years later, he was diagnosed with chronic myeloid leukemia and 6 years later, he had a relapse of NKTL for which he received ESHAP, TBI and allogeneic bone marrow transplant. He died of transplant related complication 6 years after diagnosis. They both have an older unaffected brother. Their father died of non-malignant condition in his fifties and their mother remains well. They have no other relatives with hematologic malignancy.We have identified several candidate variants and genes on WES that are being validated and functional studies are ongoing. GEP shows 234 genes that are significantly upregulated in the affected brother's tumor compared to 12 sporadic NKTL tumors including p53 and 12 genes that were significantly downregulated including CTLA4 and virus entry pathways.Conclusion:We describe a case of two brothers with a rare lymphoma and the ongoing efforts in elucidating the genetic basis of their disease. To the best of our knowledge this is the first study of its kind to be presented. DisclosuresNo relevant conflicts of interest to declare.

Exome Sequencing in Venous Thromboembolic Disease Identifies Excess Mutation Burden in PROS1, PROC, SERPINC1 and STAB2

Deep vein thrombosis and pulmonary embolism, collectively referred to as venous thromboembolism (VTE), are the third leading cause of cardiovascular death in the United States. Genetic factors account for 50-60% of VTE risk and a recent meta-analysis of genome-wide association studies confirmed that common variants in F5, ABO, and seven other loci are associated with VTE. Rare mutations in the anticoagulant genes PROC, PROS1 and SERPINC1 have been linked to VTE in family studies. In order to identify new genetic variants altering the risk for VTE, we performed whole exome sequencing (WES) in 373 unrelated individuals of European ancestry with unprovoked VTE and compared results to a previously sequenced control cohort of 5784 unrelated Europeans. To avoid variant calling bias, only SNVs from exons with >10X coverage and less than 5% difference in coverage between cases and controls were included, removing 11,813 of 188,689 intervals. We used an emerging framework for a "collapsing" analysis on genes, defining qualifying variants on the basis of annotation and minor allele frequency <0.05%, and assumed a dominant model of inheritance. Tests were performed via a Fisher’s exact test for a total of 11,585 CCDS genes. Strikingly, ranked by p-value, the top 4 genes were PROS1 (P= 2.01E-09, OR 11.8), STAB2 (P=2.70E-7, OR 3.37), PROC (P=3.24E-05, OR 11.0) and SERPINC1 (P=1.10E-04, OR 8.5). We detected 29 qualifying variants in 373 cases and 106 qualifying variants in 5784 controls in STAB2. This gene encodes Stabilin-2, which is a transmembrane glycoprotein scavenger receptor. Common variants at ABO are associated with VTE and are also known to regulate von Willebrand Factor (VWF) and coagulation Factor VIII (F8) plasma levels. Common variants in STAB2 are also associated with VWF/F8 levels in a large GWAS and with VTE risk in a smaller candidate gene study, suggesting that haploinsufficiency for Stabilin-2 may increase VTE risk through elevated levels of VWF/F8. Although replication and functional testing of these findings is warranted, this study demonstrates the utility of collapsing analyses using WES data to identify multiple loci harboring an excess of rare variants in individuals with a common complex disease trait. DisclosuresGinsburg:Shire: Equity Ownership, Membership on an entity’s Board of Directors or advisory committees, Patents & Royalties: recombinant VWF and recombinant ADAMTS13; Portola Pharmaceuticals: Membership on an entity’s Board of Directors or advisory committees.

Association of a rare NOTCH4 coding variant with systemic sclerosis: a family-based whole exome sequencing study.

BackgroundSystemic sclerosis (SSc) is a rheumatologic disease with a multifactorial etiology. Genome-wide association studies imply a polygenic, complex mode of inheritance with contributions from variation at the human leukocyte antigen locus and non-coding variation at a locus on chromosome 6p21, among other modestly impactful loci. Here we describe an 8-year-old female proband presenting with diffuse cutaneous SSc/scleroderma and a family history of SSc in a grandfather and maternal aunt.MethodsWe employed whole exome sequencing (WES) of three members of this family. We examined rare missense, nonsense, splice-altering, and coding indels matching an autosomal dominant inheritance model. We selected one missense variant for Sanger sequencing confirmation based on its predicted impact on gene function and location in a known SSc genetic locus.ResultsBioinformatic analysis found eight candidate variants meeting our criteria. We identified a very rare missense variant in the regulatory NODP domain of NOTCH4 located at the 6p21 locus, c.4245G > A:p.Met1415Ile, segregating with the phenotype. This allele has a frequency of 1.83 × 10−5 by the data of the Exome Aggregation Consortium.ConclusionThis family suggests a novel mechanism of SSc pathogenesis in which a rare and penetrant coding variation can substantially elevate disease risk in contrast to the more modest non-coding variation typically found at this locus. These results suggest that modulation of the NOTCH4 gene might be responsible for the association signal at chromosome 6p21 in SSc.Electronic supplementary materialThe online version of this article (doi:10.1186/s12891-016-1320-4) contains supplementary material, which is available to authorized users.

FOXP3 gene variations and susceptibility to autism: A case–control study

Autism Spectrum Disorders (ASD) are a group of heterogeneous neurodevelopmental disorders associated with immune system dysregulation. There are supporting evidences for the role of Forkhead Box P3 (FOXP3) gene as a lineage specification factor of regulatory T cells in the pathogenesis of ASD. The aim of this study was to explore possible relationship between genetic variants rs2232365 and rs3761548 of FOXP3 and ASD in 523 ASD patients versus 472 control individuals. Allele frequency analyses showed significant overpresentation of rs2232365-G allele in cases versus controls. In addition, rs2232365 GG genotype was associated with ASD in dominant inheritance model. Haplotype analysis revealed no significant association of any estimated block of rs2232365/rs3761548 with ASD. Our study indicated that rs2232365 is associated with ASD.

Analysis of the association between the LUM rs3759223 variant and high myopia in a Japanese population.

PurposeMany studies have investigated the relationship of the lumican gene (LUM) rs3759223 variant with the risk of high myopia, but the results have been inconsistent and inconclusive. In this study, we investigated whether LUM rs3759223 is associated with high myopia in a Japanese population.MethodsWe recruited 1,585 Japanese patients with high myopia (spherical equivalent [SE] <−9.00 diopters [D]) and 1,011 Japanese healthy controls (SE ≥−1.00 D). The rs3759223 variant was genotyped using the TaqMan assay, and the allelic and genotypic diversity among cases and controls was analyzed according to the SE level.ResultsIn the allelic tests, the odds ratio (OR) for the T allele of rs3759223 tended to increase with the progression of SE, and the highest OR (1.56) was found in patients with SE <−15 D in both eyes. The OR of the T allele tended to increase with the progression of SE in the additive, dominant, and recessive inheritance models. However, we found no significant associations for any of the alleles or genotype models.ConclusionThese data support the possibility that the LUM rs3759223 T allele accelerates the progression of SE in the Japanese population, although no significant associations were observed in this study. Additional genetic studies with larger samples that take into account the degree of SE are needed to clarify the contribution of rs3759223 to the risk of high myopia.