High-risk Variants Research Articles

Flicker-induced retinal vasodilatation is not dependent on complement factor H polymorphism in healthy young subjects.

PurposeThe complement factor H (CFH) tyrosine 402 histidine (Y402H, rs1061170) variant is known to be significantly associated with age-related macular degeneration (AMD). Whether this genetic variant may impact retinal blood flow regulation is largely unknown. This study investigated whether flicker-induced vasodilation, an indicator for the coupling between neural activity and blood flow, is altered in subjects carrying the rs1061170 risk allele.MethodsOne hundred healthy subjects (aged between 18 and 45 years) were included in this study. Retinal blood flow regulation was tested by assessing retinal vessel calibres in response to stimulation with diffuse flicker light. Retinal vascular flicker responses were determined with a Dynamic Vessel Analyzer (DVA). In addition, genotyping for rs1061170 was performed.ResultsEighteen subjects were homozygous for the risk allele C, 50 were homozygous for the ancestral allele T, and 31 subjects were heterozygous (CT). One subject had to be excluded from data evaluation, as no genetic analysis could be performed due to technical difficulties. Baseline diameters of retinal arteries (p = 0.39) and veins (p = 0.64) were comparable between the three groups. Flicker-induced vasodilation in both retinal arteries (p = 0.38) and retinal veins (p = 0.62) was also comparable between the three studied groups.ConclusionsOur data indicate that homozygous healthy young carriers of the C risk allele at rs1061170 do not show abnormal flicker-induced vasodilation in the retina. This suggests that the high-risk genetic variant of CFH polymorphism does not impact neuro-vascular coupling in healthy subjects.

Explaining the racial difference in AKI incidence.

African Americans face higher risk of AKI than Caucasians. The extent to which this increased risk is because of differences in clinical, socioeconomic, or genetic risk factors is unknown. We evaluated 10,588 African-American and Caucasian participants in the Atherosclerosis Risk in Communities study, a community-based prospective cohort of middle-aged individuals. Participants were followed from baseline study visit (1996-1999) to first hospitalization for AKI (defined by billing code), ESRD, death, or December 31, 2010. African-American participants were slightly younger (61.7 versus 63.1 years, P<0.001), were more often women (64.5% versus 53.2%, P<0.001), and had higher baseline eGFR compared with Caucasians. Annual family income, education level, and prevalence of health insurance were lower among African Americans than Caucasians. The unadjusted incidence of hospitalized AKI was 7.4 cases per 1000 person-years among African Americans and 5.8 cases per 1000 person-years among Caucasians (P=0.002). The elevated risk of AKI among African Americans persisted after adjustment for demographics, cardiovascular risk factors, kidney markers, and time-varying number of hospitalizations (adjusted hazard ratio, 1.20; 95% confidence interval [95% CI], 1.01 to 1.43; P=0.04); however, accounting for differences in income and/or insurance by race attenuated the association (P>0.05). High-risk APOL1 variants did not associate with AKI among African Americans (demographic-adjusted hazard ratio, 1.07; 95% CI, 0.69 to 1.65; P=0.77). In summary, the higher risk of AKI among African Americans may be related to disparities in socioeconomic status.

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Clin. Pract. (2014) 11(2), 139–143 ISSN 2044-9038 part of Parsa A, Kao WH, Xie D et al.; AASK Study Investigators; CRIC Study Investigators. APOL1 risk variants, race and progression of chronic kidney disease. N. Engl. J. Med. 369(23), 2183–2196 (2013). For decades, it has been observed that African–Americans experience a more rapid progression of chronic kidney disease (CKD) in virtually every etiology of kidney disease. This has been ascribed to more severe hypertension, poor risk factor control and noncompliance. Heretofore, a search for genetic determinants among African–Americans has been unrevealing. High-density lipoprotein cholesterol particles contain major apolipoproteins A-I and A-II, and minor apolipoproteins, including A-IV, A-V, C-I, C-II, C-III, D, E, F, H, J, L, M, O and P. Polymorphisms of these apolipoproteins have been associated with changes in reverse cholesterol transport function, oxidation and now, most recently, altered catabolism. High-density lipoprotein is filtered in the glomerulus and then catabolized by the proximal tubular cells. A mutant form of apo-L has been described in African–Americans that may have a protective effect against trypanosomes. APOL1 polymorphisms have a prevalence of approximately 30 and 2% among African–Americans and Caucasians, respectively. In this paper, data from two clinical studies, one exclusively in nondiabetic African–Americans with hypertension (AASK) and the other in patients screened for CKD (CRIC), variants in the gene for APOL1 were assessed according to whether they had two high-risk APOL1 variants (APOL1 high-risk group) or 0 or 1 copy (APOL1 low-risk group) [1]. In both studies, among those with and without diabetes, there was a more rapid progression of CKD, including the need for dialysis, in African–Americans with two alleles containing mutant variants of the APOL1 gene. This and other studies suggest that APOL1 variants are associated with a 50–100% increased risk of rapid progression of CKD and may be related to a toxic or adverse process invoked by proximal tubular cell catabolism of this apoprotein. So, in summary, APOL1 genetic abnormalities appear to be a major genetic basis for the difference between rates of progression of CKD between African–Americans and Caucasians.

Anomalous aortic origin of coronary arteries: 'anatomical' surgical repair

Anomalous aortic origin of coronary arteries (left coronary from right sinus or right coronary from left sinus) is a rare congenital defect, which carries a high risk of sudden cardiac death. The risk is particularly high when the interarterial course between the great arteries has an intramural segment, or is hypoplastic/stenotic, or has an abnormal orifice. Various surgical techniques have been used, including coronary artery bypass grafting, pulmonary artery translocation, partial or complete unroofing of the intramural course and patch enlargement of the interarterial course. We favour 'anatomical' repair that creates an enlarged neo-ostium into the appropriate sinus, eliminates completely the intramural segment and restores a normal angle of take-off. Reimplantation of the anomalous coronary artery may be indicated in variants without an intramural course. Surgical correction is mandatory for symptomatic and asymptomatic patients with evidence of myocardial ischaemia under stress; it is recommended in asymptomatic patients with high-risk variants (anomalous left coronary artery with the intramural course), particularly in young patients with strenuous activities.

Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome

Brugada syndrome (BrS) is an inheritable sudden cardiac death disease mainly caused by SCN5A mutations. Traditional approaches can be costly and time-consuming if all candidate variants need to be validated through in vitro studies. Therefore, we developed a new approach by combining multiple in silico analyses to predict functional and structural changes of candidate SCN5A variants in BrS before conducting in vitro studies. Five SCN5A non-synonymous variants (1651G>A, 1776C>G, 1673A>G, 3269C>T and 3578G>A) were identified in 14 BrS patients using direct DNA sequencing. Several bioinformatics algorithms were applied and predicted that 1651G>A (A551T) and 1776C>G (N592K) were high-risk SCN5A variants (odds ratio 59.59 and 23.93). The results were validated by Mass spectrometry and in vitro electrophysiological assays. We concluded that integrating sequence-based information and secondary protein structures elements may help select highly potential variants in BrS before conducting time-consuming electrophysiological studies and two novel SCN5A mutations were validated.

Pathways to Alzheimer's disease.

Recent trials of anti-amyloid agents have not produced convincing improvements in clinical outcome in Alzheimer's disease; however, the reason for these poor or inconclusive results remains unclear. Recent genetic data continue to support the amyloid hypothesis of Alzheimer's disease with protective variants being found in the amyloid gene and both common low-risk and rare high-risk variants for disease being discovered in genes that are part of the amyloid response pathways. These data support the view that genetic variability in how the brain responds to amyloid deposition is a potential therapeutic target for the disease, and are consistent with the notion that anti-amyloid therapies should be initiated early in the disease process.

Association of the MYH9 Gene Polymorphisms with Chronic Renal Disease Secondary to Hypertensive Nephrosclerosis, in a Caucasian Population

Background: Hypertensive nephrosclerosis (HN) is a chronic kidney disease (CKD) associated to essential hypertension, but their causal relationship is controversial. New evidence suggests that MYH9 gene alterations are associated with HN in African Americans. The aim of this study is to investigate the role of this gene in Spanish Caucasians. Methods: We compare high-risk MYH9 variants of patients with HN recruited according to standard clinical criteria (CKD stages 3-5), with essential hypertensives without renal disease (estimated glomerular filtration rate (eGFR) > 60 ml/min/1,73m2 and albuminuria < 300 mg/g creatinine), and also CKD patients with HN and progressive impairment of renal function with those who were stable. Diabetics were excluded. Results: A blood sample was obtained for genetic study of 238 patients with HN-CKD and 233 hypertensive controls. The rs3752462-T and rs4821480-T (risk alleles for CKD) were more frequent in the CKD group, but without significant difference. We found no differences for these SPNs with blood pressure, creatinine, albuminuria or renal disease progression. Conclusions: The effect of two common MYH9 single nucleotide polymorphisms (SPNs) on the development of CKD secondary to HN in our Spanish Caucasian population is low or zero; in any case less than that found in other, mainly African Americans.

The presence of both serotonin 1A receptor (HTR1A) and dopamine transporter (DAT1) gene variants increase the risk of borderline personality disorder.

Dysfunction in the dopaminergic and serotonergic neurotransmitter systems has been demonstrated to be important in the etiology of borderline personality disorder (BPD). We investigated the relationship of two BPD risk factors, the HTR1A promoter polymorphism -1019C > G (rs6295) and the dopamine transporter (DAT1) repeat allele, with BPD in a major depressive disorder cohort of 367 patients. Out-patients with major depressive disorder were recruited for two treatment trials and assessed for personality disorders, including BPD. DNA samples were collected and the rs6295 polymorphism was detected with a TaqMan® assay. The DAT1 repeat allele was genotyped using a modified PCR method. The impact of polymorphisms on BPD was statistically analyzed using uncontrolled logistic and multiple logistic regression models. BPD patients had higher frequencies of the DAT1 9,9 (OR = 2.67) and 9,10 (OR = 3.67) genotypes and also those homozygous HTR1A G allele (OR = 2.03). No significant interactions between HTR1A and DAT1 genotypes, were observed; however, an increased risk of BPD was observed for those patients who were either 9,10; G,G (OR = 6.64) and 9,9; C,G (OR = 5.42). Furthermore, the odds of BPD in patients exhibiting high-risk variants of these two genes differed from those of patients in low-risk groups by up to a factor of 9. Our study provides evidence implicating the importance of the serotonergic and dopaminergic systems in BPD and that the interaction between genes from different neurotransmitters may play a role in the susceptibility to BPD.

The Science of Tobacco Addiction and Cessation

Over the past decade, researchers have found genetic variations that affect how nicotine, the main addictive component of tobacco, interacts with cells in the brain and how fast the body metabolizes it. Carrying a high-risk variant predicts a person's ability to snuff out their cigarettes for good. Genetic testing could help predict which smokers might benefit from nicotine replacement therapy or other prescription medications, much like sequencing of malignant tumors can point to the most effective cancer treatment.

APOL1 Risk Variants, Race, and Progression of Chronic Kidney Disease

BackgroundAmong patients in the United States with chronic kidney disease, black patients are at increased risk for end-stage renal disease, as compared with white patients.MethodsIn two studies, we examined the effects of variants in the gene encoding apolipoprotein L1 (APOL1) on the progression of chronic kidney disease. In the African American Study of Kidney Disease and Hypertension (AASK), we evaluated 693 black patients with chronic kidney disease attributed to hypertension. In the Chronic Renal Insufficiency Cohort (CRIC) study, we evaluated 2955 white patients and black patients with chronic kidney disease (46% of whom had diabetes) according to whether they had 2 copies of high-risk APOL1 variants (APOL1 high-risk group) or 0 or 1 copy (APOL1 low-risk group). In the AASK study, the primary outcome was a composite of end-stage renal disease or a doubling of the serum creatinine level. In the CRIC study, the primary outcomes were the slope in the estimated glomerular filtration rate (eGFR) and the composite of end-stage renal disease or a reduction of 50% in the eGFR from baseline.ResultsIn the AASK study, the primary outcome occurred in 58.1% of the patients in the APOL1 high-risk group and in 36.6% of those in the APOL1 low-risk group (hazard ratio in the high-risk group, 1.88; P<0.001). There was no interaction between APOL1 status and trial interventions or the presence of baseline proteinuria. In the CRIC study, black patients in the APOL1 high-risk group had a more rapid decline in the eGFR and a higher risk of the composite renal outcome than did white patients, among those with diabetes and those without diabetes (P<0.001 for all comparisons).ConclusionsRenal risk variants in APOL1 were associated with the higher rates of end-stage renal disease and progression of chronic kidney disease that were observed in black patients as compared with white patients, regardless of diabetes status. (Funded by the National Institute of Diabetes and Digestive and Kidney Diseases and others.)

Genetic risk transmission in a family affected by familial breast cancer

Breast Cancer is the most common malignancy among women. Family history is the strongest single predictor of breast cancer risk, and thus great attention has been focused on BRCA1 and BRCA2 genes whose mutations lead to a high risk of developing this disease. Today, only 25% of high- and moderate-risk genes are known, suggesting the importance of the discovery of new risk modifiers. Therefore, the investigation of new polygenic alterations is of great importance, especially if considered high- and moderate-risk variants. In this study, the transmission of BRCA1-2 polymorphisms in association with the transmission of polymorphisms in the genes NUMA1, CCND1, COX11, FGFR2, TNRC9 and SLC4A7 were examined in all members of a family with the BRCA2 c.6447_6448dup mutation. This is the first study about the transmission of high-risk polygenic variants in all members of a family with a strong history of breast cancer. The results about the possible polygenic variant associations that could increase and modify the risk suggested the importance to search new variants to better manage patients and their family members.

Rapid 2-stage Norwood I for high-risk hypoplastic left heart syndrome and variants

Preoperative comorbidities (PCMs) are known risk factors for Norwood stage I (NW1). We tested the hypothesis that short-term bilateral pulmonary arterial banding (bPAB) before NW1 could improve the prognosis of these high-risk patients. From January 2006 to October 2011, 17 high-risk patients with hypoplastic left heart syndrome (defined as having ≥4 of the following PCMs: prolonged mechanical ventilation; older age; sepsis; necrotizing enterocolitis; hepatic, renal, or heart failure; coagulopathy; pulmonary edema; high inotropic requirements; anasarca; weight<2.5 kg; and cardiac arrest) were identified. In addition to conventional treatment of PCMs, they underwent bPAB before NW1. bPAB was undertaken with Silastic slings and secured with ligaclips to a luminal diameter of approximately 3.5 to 4.0 mm. The patency of the ductus arteriosus was maintained with prostaglandin. NW1 was performed using a modified, right Blalock-Taussig shunt at a median interval of 8 days after bPAB. The data from these patients were retrospectively reviewed, and the 30-day mortality and 1-year survival were compared with the hypoplastic left heart syndrome population who underwent primary NW1 with <3 PCMs in the same period. Of the bPAB patients, 5 (29.4%) died before NW1. All had ≥5 PCMs. Twelve patients (70.6%) survived to undergo NW1. One early death occurred after NW1 (8.3%). The 1-year survival rate for high-risk patients who underwent NW1 was 66.7%. The early mortality and 1-year survival for the 130 patients with <3 PCMs was 10% and 80%, respectively. Optimizing the balance between the pulmonary and systemic blood flow with a short period of bPAB and ductal patency can improve the perioperative conditions of high-risk patients before NW1. Those who survived bPAB and underwent NW1 had early mortality and 1-year survival comparable to the standard risk category, despite the severity of their initial condition. A rapid 2-stage NW1 strategy with bPAB and prostaglandin to maintain ductal patency can avoid the risks of suboptimal palliation and vascular injuries associated with hybrid procedures.

Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis

Genome-wide association studies and follow-up meta-analyses in Crohn's disease (CD) and ulcerative colitis (UC) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory bowel diseases (IBD). These discoveries have already had a tremendous impact on our understanding of the genetic architecture of these diseases and have directed functional studies that have revealed some of the biological functions that are important to IBD (e.g. autophagy). Nonetheless, these loci can only explain a small proportion of disease variance (∼14% in CD and 7.5% in UC), suggesting that not only are additional loci to be found but that the known loci may contain high effect rare risk variants that have gone undetected by GWAS. To test this, we have used a targeted sequencing approach in 200 UC cases and 150 healthy controls (HC), all of French Canadian descent, to study 55 genes in regions associated with UC. We performed follow-up genotyping of 42 rare non-synonymous variants in independent case-control cohorts (totaling 14,435 UC cases and 20,204 HC). Our results confirmed significant association to rare non-synonymous coding variants in both IL23R and CARD9, previously identified from sequencing of CD loci, as well as identified a novel association in RNF186. With the exception of CARD9 (OR = 0.39), the rare non-synonymous variants identified were of moderate effect (OR = 1.49 for RNF186 and OR = 0.79 for IL23R). RNF186 encodes a protein with a RING domain having predicted E3 ubiquitin-protein ligase activity and two transmembrane domains. Importantly, the disease-coding variant is located in the ubiquitin ligase domain. Finally, our results suggest that rare variants in genes identified by genome-wide association in UC are unlikely to contribute significantly to the overall variance for the disease. Rather, these are expected to help focus functional studies of the corresponding disease loci.

Genetic analysis of neurodegeneration.. the end game

In my talk I will discuss how genetic analysis now allows us to dissect both causative and predisposing genes for neurodegenerative diseases. Mendelian diseases can be found by positional cloning and sequencing... rare, high risk variants can be found by exome sequencing and burden analysis and common low risk variants can be found by genome wide association analyses. I will show how, when loci for disease are found, they map functionally into specific biochemical pathway. This property is also helpful in identifying new loci for which the statistical evidence is less than convincing. With regard to Alzheimer’s disease, the well known mendelian genes are APP and PSEN1 and PSEN2. In addition to apoe, genome wide association studies have identified now nearly 20 loci which map onto four pathways, cholesterol metabolism, the innate immune system, endosomal vesicle recycling and protein ubiquitination. At the time of writing this abstract, TREM2, which is involved in the innate immune system and control of miscroglial activation is the only declared rare variant of high effect (o.r. ~5), but several other genes have data in the publication process. I will discuss these issues and update on the current state of play for Alzheimer genetics and describe how we can move towards the completion of genetic analysis.

Ethical issues in pediatric pharmacogenomics.

Ethical issues in pediatric pharmacogenomics.

The PSEN1, p.E318G Variant Increases the Risk of Alzheimer's Disease in APOE-ε4 Carriers

The primary constituents of plaques (Aβ42/Aβ40) and neurofibrillary tangles (tau and phosphorylated forms of tau [ptau]) are the current leading diagnostic and prognostic cerebrospinal fluid (CSF) biomarkers for AD. In this study, we performed deep sequencing of APP, PSEN1, PSEN2, GRN, APOE and MAPT genes in individuals with extreme CSF Aβ42, tau, or ptau levels. One known pathogenic mutation (PSEN1 p.A426P), four high-risk variants for AD (APOE p.L46P, MAPT p.A152T, PSEN2 p.R62H and p.R71W) and nine novel variants were identified. Surprisingly, a coding variant in PSEN1, p.E318G (rs17125721-G) exhibited a significant association with high CSF tau (p = 9.2×10−4) and ptau (p = 1.8×10−3) levels. The association of the p.E318G variant with Aβ deposition was observed in APOE-ε4 allele carriers. Furthermore, we found that in a large case-control series (n = 5,161) individuals who are APOE-ε4 carriers and carry the p.E318G variant are at a risk of developing AD (OR = 10.7, 95% CI = 4.7–24.6) that is similar to APOE-ε4 homozygous (OR = 9.9, 95% CI = 7.2.9–13.6), and double the risk for APOE-ε4 carriers that do not carry p.E318G (OR = 3.9, 95% CI = 3.4–4.4). The p.E318G variant is present in 5.3% (n = 30) of the families from a large clinical series of LOAD families (n = 565) and exhibited a higher frequency in familial LOAD (MAF = 2.5%) than in sporadic LOAD (MAF = 1.6%) (p = 0.02). Additionally, we found that in the presence of at least one APOE-ε4 allele, p.E318G is associated with more Aβ plaques and faster cognitive decline. We demonstrate that the effect of PSEN1, p.E318G on AD susceptibility is largely dependent on an interaction with APOE-ε4 and mediated by an increased burden of Aβ deposition.

Regulation of p14ARF expression by HPV‐18 E6 variants

A common causative agent for uterine cervical cancer is the human papillomavirus type 18 (HPV-18) which has three phylogenic variants: Asian-Amerindian, European, and African. Each variant shows significant molecular differences in the E6 gene. E6 oncoprotein is a negative regulator of tumor suppressor protein p53, hence, this oncoprotein indirectly regulates the expression of tumor-suppressor p14(ARF) . p14(ARF) and p16(INK4A) genes are overexpressed in--and have been proposed as markers for--HPV-related cervical cancer. In order to dissect the role of E6 on the regulation of p14(ARF) expression, separating it from that of other intervening factors, transfection of E6 variants to MCF-7 cells was performed, assessing cDNA transcript levels by RT-PCR, whereas p14(ARF) and p53 expression were evaluated by immunocytochemistry and Western blot. E6 transfected cells differentially expressed transcripts of two molecular forms: E6 and E6*. The ratio of these two forms varied with the transfected E6 variant. With the Asian-Amerindian variant, the ratio was E6 > E6*, whereas with the European and the African the ratio was E6* > E6. As expected with the E6* construct, E6* transcripts were solely observed. In addition, when E6 > E6* and p53 expression was low, p14(ARF) was high and when E6* > E6 and p53 expression was high, p14(ARF) was low. In conclusion, each E6 variant distinctively affects p53 levels and consequently p14(ARF) expression, finding that could be related with the differences in oncogenic effect of infection with the diverse high-risk HPV variants.

High-risk variants of cutaneous squamous cell carcinoma in patients with discoid lupus erythematosus: a case series

Cutaneous squamous cell carcinoma, the second most common form of non-melanotic skin cancer, may develop in long-standing discoid lesions, especially those that are depigmented and located in sun-exposed areas. The clinical course of this complication may be aggressive, with early metastases and a risk of mortality. We report three cases demonstrating this emerging trend of secondary squamous cell carcinoma in discoid lesions as the incidence of this secondary malignancy in other diseased skin lesions is on the decline.

Cutaneous Squamous Cell Carcinoma: Defining the High-Risk Variant

With a lifetime incidence of approximately 10% in the general population, cutaneous squamous cell carcinoma (CSCC) is the second most common type of nonmelanoma skin cancer.Most CSCCs are benign and can be completely eradicated by surgery or other dermatological procedures. There is, however, a subgroup associated with an increased likelihood of lymph node metastases and, therefore, with high morbidity and mortality.This article analyzes the various factors that define aggressive CSCC. We propose a method for defining high-risk SCC on the basis of a series of major and minor criteria. This method will allow better prognostic evaluation and enable personalized management of patients with high-risk SCC, possibly leading to improved overall survival.

Huntington disease in the South African population occurs on diverse and ethnically distinct genetic haplotypes

Huntington disease (HD) is a neurodegenerative disorder resulting from the expansion of a CAG trinucleotide repeat in the huntingtin (HTT) gene. Worldwide prevalence varies geographically with the highest figures reported in populations of European ancestry. HD in South Africa has been reported in Caucasian, black and mixed subpopulations, with similar estimated prevalence in the Caucasian and mixed groups and a lower estimate in the black subpopulation. Recent studies have associated specific HTT haplotypes with HD in distinct populations. Expanded HD alleles in Europe occur predominantly on haplogroup A (specifically high-risk variants A1/A2), whereas in East Asian populations, HD alleles are associated with haplogroup C. Whether specific HTT haplotypes associate with HD in black Africans and how these compare with haplotypes found in European and East Asian populations remains unknown. The current study genotyped the HTT region in unaffected individuals and HD patients from each of the South African subpopulations, and haplotypes were constructed. CAG repeat sizes were determined and phased to haplotype. Results indicate that HD alleles from Caucasian and mixed patients are predominantly associated with haplogroup A, signifying a similar European origin for HD. However, in black patients, HD occurs predominantly on haplogroup B, suggesting several distinct origins of the mutation in South Africa. The absence of high-risk variants (A1/A2) in the black subpopulation may also explain the reported low prevalence of HD. Identification of haplotypes associated with HD-expanded alleles is particularly relevant to the development of population-specific therapeutic targets for selective suppression of the expanded HTT transcript.