Genetic Variation In Candidate Genes Research Articles

Vincristine polyneuropathy in children with acute lymphoblastic leukemia: the association with the hereditary rs924607 polymorphism in the <i>CEP72</i> gene

Background: Vincristine polyneuropathy is a major neurotoxic complication of treatment for acute lymphoblastic leukemia in children. A close relationship between genetic variants in candidate genes associated with the vincristine neurotoxicity in various ethnic groups has been proposed. Therefore, identification of the genetic risk factors underlying the predisposition to vincristine polyneuropathy could allow the development of effective tools for preventive diagnostics aimed at identifying a high-risk group among patients treated with vincristine for a personalized approach to their chemotherapy.
 Aim: To study an association between the rs924607 polymorphism of the CEP72 gene and vincristine polyneuropathy in children with acute lymphoblastic leukemia.
 Materials and methods: This single center cohort study enrolled 199 children aged 3 to 17 years with newly diagnosed acute lymphoblastic leukemia, who received ALL-MB 2015 chemotherapy regimen. All patients were genotyped for the single nucleotide variant rs924607 in the CEP72 gene by real-time polymerase chain reaction and subsequent allelic discrimination. A comparative analysis of the incidence and clinical signs of vincristine polyneuropathy depending on the carrier of the genetic polymorphism was performed.
 Results: The incidence of vincristine polyneuropathy in the study pediatric group was 81.0% (n = 161); mostly these were patients with NCI-STCAE grade 2 severity. The rs924607 single nucleotide variant in the CEP72 gene was significantly associated with the neurotoxic complication, with 19.1% (n = 38) of the patients were homozygous for the minor allele (rs924607 genotype TT) and 46.2% (n = 92) had the ST genotype. Among the carriers of at least one rs924607 risk allele (T), the odds ratio for vincristine polyneuropathy was 2.91 (95% confidence interval 1.415.99, p = 0.004). No significant association between the genetic variant assessed and clinical signs of vincristine-induced polyneuropathy was found.
 Conclusion: The single nucleotide rs924607 polymorphism of the CEP72 gen can be a putative pharmacogenetic marker for vincristine polyneuropathy.

Genetic biomarkers for risk prediction of chronic obstructive pulmonary disease (COPD) in smokers and non-smokers

Chronic Obstructive Pulmonary Disease (COPD) is a progressive disease and not fully reversible. It is the 3rd major cause of death worldwide and ranks 2nd in India. Although the primary etiopathogenic factor is chronic exposure to tobacco smoke, it has been observed that all smokers do not develop COPD and many non-smokers suffer from the disease. This difference in susceptibility can be attributed to individual genetic variations. Therefore, the present study was conducted to analyze the association of genetic variants in candidate genes with COPD susceptibility among smokers and non-smokers. A total of 500 subjects were enrolled in the study (250 each of controls and cases) after ethical approval and informed consent. Fifteen single nucleotide polymorphisms (SNPs) in eight genes viz.IL-1RN, IL-1B, IL-6, TNF-A, SOD2, CAT, ADAM33 and AQP5 were genotyped by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR–RFLP). Data was analyzed using SPSS (ver 21.0) and association with smoking status was determined. Among 250 healthy controls enrolled, 119 were non-smokers and 131 were smokers. Out of 250 COPD cases, only 34 were non-smokers and rest 216 were smokers. The genotypic frequencies of IL-1RN intron2 86 bp VNTR (I,II), IL-1β -511 T/C, IL-6 -597A/G, TNF-α -308G/A, SOD2 + 47C/T, CAT − 21A/T and AQP5 promoter G/A were significantly associated with smoking. Among 07 ADAM33 SNPs, the genotype frequencies of V4exon22C/G and F + 1intron6C/T were significantly associated in smokers, while V1exon22G/T, S2exon19G/C, S1exon19A/G and Q1intron16A/G were associated with non-smokers. The genetic variants (SNPs) in smokers and non-smokers showing differential association with the risk of COPD can be identified as predictive biomarkers.

Genetic variation in TBC1 domain family member 1 gene associates with the risk of lean NAFLD via high-density lipoprotein.

Objective: Non-alcoholic fatty liver disease (NAFLD) affects almost a quarter of the world's population. Although NAFLD often co-exists with obesity, a substantial proportion of NAFLD patients are lean which is relatively unexplored. This study aimed to examine the association between genetic variation in candidate genes, e.g., TBC1D1 and the risk of lean NAFLD in the elderly Chinese Han population. Methods: This is an extension of the research on physical examination in the Zhanjiang community center including 5387 residents, Shanghai, China, in 2017. According to the classification in adult Asian populations, participants were categorized into four groups: lean NAFLD (BMI <23, n = 106), non-lean NAFLD (BMI ≥23, n = 644), lean non-NAFLD (BMI <23, n = 216) and non-lean non-NAFLD (BMI ≥23, n = 253).116 NAFLD-related candidate genes, which cover 179 single nucleotide polymorphisms (SNPs) were included in the KEGG enrichment analysis. Independent samples t-test was adopted for the group comparison. The associations between genetic variations with the specific phenotype in five genetic models were analyzed with the "SNPassoc" R package and rechecked with logistic regression analysis. Mediation models were conducted to explore whether the certain phenotype can mediate the association between SNPs and the risk of lean NAFLD. Results: Compared with lean non-NAFLD individuals, lean NAFLD patients had higher BMI, low-density lipoprotein and triglyceride, and lower HDL. The AMPK signaling pathway, which includes TBC1D1 and ADIPOQ genes, was the most significant (p < .001). The A allele frequency of rs2279028 in TBC1D1 (p = .006) and G allele frequency of rs17366568 in ADIPOQ (p = .038) were significantly lower in lean NAFLD. The association between rs2279028 and the risk of lean NAFLD was mediated by HDL (p = .014). No significant mediation effect was found between rs17366568 and the risk of lean NAFLD. Conclusion: This study, for the first time, indicated that rs2279028 of TBC1D1 may contribute to the progression of lean NAFLD through HDL. This finding provides more evidence for exploring the mechanism of lean NAFLD and suggests practical solutions for the treatment of lean NAFLD.

The COVID-19 Pandemic and Explaining Outcomes in Africa: Could Genomic Variation Add to the Debate?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, emanated from the Wuhan Province in China and rapidly spread across the globe causing extensive morbidity and mortality rate, and affecting the global economy and livelihoods. Contrary to early predictions of "body bags" across Africa, the African COVID-19 pandemic was marked by apparent low case numbers and an overall mortality rate when compared with the other geographical regions. Factors used to describe this unexpected pattern included a younger population, a swifter and more effective national health policy, limited testing capacities, and the possibility of inadequate reporting of the cases, among others. However, despite genomics contributing to interindividual variations in many diseases across the world, there are inadequate genomic and multiomics data on COVID-19 in Africa that prevent richer transdisciplinary discussions on the contribution of genomics to the spread of COVID-19 pandemic. To invite future debates on comparative studies of COVID-19 genomics and the pandemic spread around the world regions, this expert review evaluates the reported frequency distribution of genetic variants in candidate genes that are likely to affect COVID-19 infection dynamics/disease outcomes. We propose here that genomic variation should be considered among the many factors determining the COVID-19 infection and its outcomes in African populations and across the world.

Genetic screening of Chinese patients with hydatidiform mole by whole-exome sequencing and comprehensive analysis.

We aim to explore if there are any other candidate genetic variants in patients with a history of at least one hydatidiform mole (HM) besides the well-known variants in NLRP7 and KHDC3L. The diagnosis of HM type was based on histopathology, and available HM tissues were collected for short tandem repeat (STR) genotyping to verify the diagnosis. DNA extracted from blood samples or decidual tissues of the 78 patients was subjected to whole-exome sequencing (WES). We identified five novel variants in NLRP7, two novel variants in KHDC3L, and a chromosome abnormality covering the KHDC3L locus among patients with HM. We found that patients with HM who carried heterozygous variants in KHDC3L had a chance of normal pregnancy. We also detected four novel genetic variants in candidate genes that may be associated with HM. Our study enriched the spectrum of variants in NLRP7 and KHDC3L in Chinese HM patients and provided a new outlook on the effects of heterozygous variants in KHDC3L. The novel candidate genetic variants associated with HMs reported in this study will also contribute to further research on HMs.

Association of PCSK9 Variants With the Risk of Atherosclerotic Cardiovascular Disease and Variable Responses to PCSK9 Inhibitor Therapy

Genetic polymorphisms or variations, randomly distributed in a population, may cause drug-gene response variations. Investigation into these polymorphisms may identify novel mechanisms contributing to a specific disease process. Such investigation necessitates the use of Mendelian randomization, an analytical method that uses genetic variants as instrumental variables for modifiable risk factors that affect population health.1 In the past decade, advances in our understanding of genetic polymorphisms have enabled the identification of genetic variants in candidate genes that impact low-density lipoprotein cholesterol (LDL-C) regulating pathways and cardiovascular disease (CVD) outcomes. A specific candidate gene of interest is that of the LDL receptor degrading protein, PCSK9. In fact, loss-of-function genetic variants for the PCSK9 gene are what first highlighted this pathway as a candidate for pharmacologic inhibition. PCSK9 inhibitors (PCSK9i) are a class of cholesterol-lowering medications that provide significant reductions in LDL by inhibiting the degradation of LDL receptors (LDLR). These inhibitors have also been found to reduce production and enhance clearance of lipoprotein A (Lp[a]), an LDL-like particle currently under study as a separate risk factor for atherosclerotic CVD. Here, we discuss the promise of personalized medicine in developing a more efficacious and individualized pharmacogenomics-based approach for the use of PCSK9i that considers genetic variation and targets different patient populations. This review explores the pharmacogenomics of PCSK9i in the context of PCSK9 allele variants related to drug-metabolizing enzymes and responses since more studies are demonstrating that some patients are hyporesponsive or non-responsive to PCSK9i.2 In summary, the pharmacogenomics of PCSK9 are a promising therapeutic target and genetic information from prospective randomized clinical trials is warranted to gain a full understanding of the efficacy and cost-effectiveness of such allele and/or gene-guided PCSK9i therapy.

Ischemic Stroke and Genetic Variants: In Search of Association with Severity and Recurrence in a Brazilian Population

ObjectiveThe aim of this study was to investigate the relationship between genetic variants in candidate genes and clinical severity and prognosis (recurrence) of ischemic stroke (IS) in a Brazilian population. MethodsThis was a retrospective study based on clinical and demographic data retrieved from the JOINVASC cohort—Epidemiological Study on Cerebrovascular Diseases in Joinville and on respective DNA samples available at the Joinville Stroke Biobank, over the period 2010-2015. Four hundred and thirty-five subjects were included. Patients were divided into large artery atherosclerosis (195 cases) and cardioembolic IS (240 cases) subgroups according to Trial of Org 10172 in the Acute Stroke Treatment standards. The severity of the event was established from the score obtained using the National Institutes of Health Stroke Scale. The genotypic and allelic frequencies of each variant were acquired by Real-Time Polymerase Chain Reaction. The codominance model was considered for the analysis of the genotypes’ influence. ResultsThere was no association between clinical severity and recurrence with variants rs2383207 (CDKN2B-AS1) for atherothrombotic IS and variants rs879324 (ZFHX3), rs966221 (PDE4D), and rs152312 (PDE4D) for cardioembolic IS. The variants rs1396476, rs2910829, rs6843082, and rs2107595 were not in Hardy-Weinberg equilibrium in the evaluated population. ConclusionsAlthough this study failed to identify an association between genetic variants and clinical response variability, the need to carry out related studies with larger number of cases covering other populations and genetic variants remains, which would allow the uncovering of hypothetical genetic factors governing stroke outcomes and recurrence.

Common Variants in 22 Genes Regulate Response to Metformin Intervention in Children with Obesity: A Pharmacogenetic Study of a Randomized Controlled Trial.

Metformin is a first-line oral antidiabetic agent that has shown additional effects in treating obesity and metabolic syndrome. Inter-individual variability in metformin response could be partially explained by the genetic component. Here, we aimed to test whether common genetic variants can predict the response to metformin intervention in obese children. The study was a multicenter and double-blind randomized controlled trial that was stratified according to sex and pubertal status in 160 children with obesity. Children were randomly assigned to receive either metformin (1g/d) or placebo for six months after meeting the defined inclusion criteria. We conducted a post hoc genotyping study in 124 individuals (59 placebo, 65 treated) comprising finally 231 genetic variants in candidate genes. We provide evidence for 28 common variants as promising pharmacogenetics regulators of metformin response in terms of a wide range of anthropometric and biochemical outcomes, including body mass index (BMI) Z-score, and glucose, lipid, and inflammatory traits. Although no association remained statistically significant after multiple-test correction, our findings support previously reported variants in metformin transporters or targets as well as identify novel and promising loci, such as the ADYC3 and the BDNF genes, with plausible biological relation to the metformin’s action mechanism. Trial Registration: Registered on the European Clinical Trials Database (EudraCT, ID: 2010-023061-21) on 14 November 2011 (URL: https://www.clinicaltrialsregister.eu/ctr-search/trial/2010-023061-21/ES).

Benign paroxysmal torticollis of infancy does not lead to neurological sequelae.

To elucidate the natural course of benign paroxysmal torticollis, the relationship of this disorder to migraine and other paroxysmal diseases, and to analyse candidate genes. This was a case series of children with benign paroxysmal torticollis of infancy (BPTI) diagnosed from 1998 to 2005, at Astrid Lindgren Children's Hospital, Stockholm, Sweden. A neurological examination and a formalized motor assessment were performed from 2005 to 2007. At a second follow-up, in 2014 to 2015, the children and their parents were interviewed and candidate genes analysed. The mean age of the eight females and three males included in the second follow-up was 13 years 9 months (SD 2y 2mo). All motor assessments were normal. Five had developed migraine, abdominal migraine, and/or cyclic vomiting. Prophylactic treatment or migraine-specific medication during attacks were not needed. No paroxysmal tonic upgaze, benign paroxysmal vertigo, epilepsy, episodic ataxia, or paroxysmal dyskinesia was reported. Rare genetic variants in CACNA1A and ATP1A2 were found in two children. Five had a family history of migraine. BPTI is transient and does not lead to neurological sequelae. Most children afflicted experience either a mild migraine or no paroxysmal disorder at all in their adolescence. Genetic variants in candidate genes were few, indicating potential genetic heterogeneity. After resolution of their benign paroxysmal torticollis of infancy (BPTI), children display no gross motor delay. Most adolescents who previously had BPTI have not developed migraine. No mutations in candidate genes, known to cause hemiplegic migraine, were found. Associated symptoms are often lacking during episodes of torticollis.

Genetic variation in candidate genes and patellar tendinopathy: Prospective cohort study of 126 elite volleyball players

Genetic variation in candidate genes and patellar tendinopathy: Prospective cohort study of 126 elite volleyball players

Deafness and vestibular dysfunction in a Doberman Pinscher puppy associated with a mutation in the PTPRQ gene.

BackgroundA congenital syndrome of hearing loss and vestibular dysfunction affects Doberman Pinschers. Its inheritance pattern is suspected to be autosomal recessive and it potentially represents a spontaneous animal model of an autosomal recessive syndromic hearing loss.Hypothesis/ObjectivesThe objectives of this study were to use whole genome sequencing (WGS) to identify deleterious genetic variants in candidate genes associated with the syndrome and to study the prevalence of candidate variants among a population of unaffected Doberman Pinschers.AnimalsOne affected Doberman Pinscher and 202 unaffected Doberman Pinschers.MethodsWGS of the affected dog with filtering of variants against a database of 154 unaffected dogs of diverse breeds was performed. Confirmation of candidate variants was achieved by Sanger sequencing followed by genotyping of the control population of unaffected Doberman Pinschers.ResultsWGS and variant filtering identified an alteration in a gene associated with both deafness and vestibular disease in humans: protein tyrosine phosphatase, receptor type Q (PTPRQ). There was a homozygous A insertion at CFA15: 22 989 894, causing a frameshift mutation in exon 39 of the gene. This insertion is predicted to cause a protein truncation with a premature stop codon occurring after position 2054 of the protein sequence that causes 279 C‐terminal amino acids to be eliminated. Prevalence of the variant was 1.5% in a cohort of 202 unaffected Doberman Pinschers; all unaffected Doberman Pinschers were heterozygous or heterozygous for the reference allele.Conclusion and Clinical ImportanceWe report the identification of a genetic alteration on the PTPRQ gene that is associated with congenital hearing and vestibular disorder in a young Doberman Pinscher dog.

A sequence polymorphism on 8q24 is associated with survival in hepatocellular carcinoma patients who received radiation therapy

There is a growing consensus that genetic variation in candidate genes can influence cancer progression and treatment effects. In this study, we genotyped the rs9642880 G > T polymorphism using DNA isolated from blood samples of 271 hepatocellular carcinoma (HCC) patients who received radiotherapy treatment. We found that patients who carried the GT or TT genotypes had significantly shorter median survival times (MSTs) compared to patients with the GG genotype (14.6 vs.21.4 months). The multivariate P value was 0.027, the hazard ratio (HR) was 1.38, and the 95% confidence interval was 1.04–1.84. Further analysis revealed that patients with the variant genotypes had an increased risk of poor tumour response to radiotherapy (P = 0.036 and 0.002 for stable disease and progressive disease, respectively) and higher incidence of multiple intrahepatic lesions (P = 0.026) and BCLC C stage (P = 0.027). Moreover, further stratified survival analyses revealed that at least radioresponse and BCLC stage contributed to the association between the rs9642880 G > T polymorphism and survival of HCC patients in this study (P value, 0.017 vs 0.053 for BCLC C stage vs B stage; 0.011 vs 0.531 for radioresponse SD + PD vs CR + PR). These results illustrate the potential association between rs9642880 G > T and survival in HCC patients who received radiotherapy treatment.

Candidate genes for migration do not distinguish migratory and non-migratory birds

Migratory traits in birds have been shown to have a strong heritable component and several candidate genes have been suggested to control these migratory traits. To investigate if the genetic makeup of one or a set of these candidate genes can be used to identify a general pattern between migratory and non-migratory birds, we extracted genomic sequence data for 25 hypothesised candidate genes for migration from 70 available genomes across all orders of Aves and characterised sequence divergence between migratory and non-migratory phenotypes. When examining each gene separately across all species, we did not identify any genetic variants in candidate genes that distinguished migrants from non-migrants; any resulting pattern was driven by the phylogenetic signal. This was true for each gene analysed independently, but also for concatenated sequence alignments of all candidate genes combined. We also attempted to distinguish between migrant and non-migrants using structural features at four candidate genes that have previously been reported to show associated with migratory behaviour but did not pick up a signal for migratory phenotype here either. Finally, a screen for dN/dS ratio across all focal candidate genes to probe for putative features of selection did not uncover a pattern, though this might not be expected given the broad phylogenetic scale used here. Our study demonstrates the potential of public genomic data to test for general patterns of migratory gene candidates in a cross-species comparative context, and raise questions on the applicability of candidate gene approaches in a macro-evolutionary context to understand the genetic architecture of migratory behaviour.

Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance.

In bovines, artificial selection has produced a large number of breeds which differ in production, environmental adaptation, and health characteristics. To investigate the genetic basis of these phenotypical differences, several bovine breeds have been sequenced. Millions of new SNVs were described at every new breed sequenced, suggesting that every breed should be sequenced. Guzerat or Guzerá is an indicine breed resistant to drought and parasites that has been the base for some important breeds such as Brahman. Here, we describe the sequence of the Guzerá genome and the in silico functional analyses of intragenic breed-specific variations. Mate-paired libraries were generated using the ABI SOLiD system. Sequences were mapped to the Bos taurus reference genome (UMD 3.1) and 87% of the reference genome was covered at a 26X. Among the variants identified, 2,676,067 SNVs and 463,158 INDELs were homozygous, not found in any database searched, and may represent true differences between Guzerá and B. taurus. Functional analyses investigated with the NGS-SNP package focused on 1069 new, non-synonymous SNVs, splice-site variants (including acceptor and donor sites, and the conserved regions at both intron borders, referred to here as splice regions) and coding INDELs (NS/SS/I). These NS/SS/I map to 935 genes belonging to cell communication, environmental adaptation, signal transduction, sensory, and immune systems pathways. These pathways have been involved in phenotypes related to health, adaptation to the environment and behavior, and particularly, disease resistance and heat tolerance. Indeed, 105 of these genes are known QTLs for milk, meat and carcass, production, reproduction, and health traits. Therefore, in addition to describing new genetic variants, our approach provided groundwork for unraveling key candidate genes and mutations.

Genetic determinants of warfarin maintenance dose and time in therapeutic treatment range: a RE-LY genomics substudy.

We investigated associations between genetic variation in candidate genes and on a genome-wide scale with warfarin maintenance dose, time in therapeutic range (TTR), and risk of major bleeding. In total, 982 warfarin-treated patients from the RE-LY trial were studied. After adjusting for SNPs in VKORC1 and CYP2C9, SNPs in DDHD1 (rs17126068) and NEDD4 (rs2288344) were associated with dose. Adding these SNPs and CYP4F2 (rs2108622) to a base model increased R(2) by 2.9%. An SNP in ASPH (rs4379440) was associated with TTR (-6.8% per minor allele). VKORC1 was associated with time less than INR 2.0. VKORC1 and CYP2C9 were associated with time more than INR 3.0, but not with major bleeding. We identified two novel genes associated with warfarin maintenance dose and one gene associated with TTR. These genes need to be replicated in an independent cohort.

Genetic risk factors for restenosis after percutaneous coronary intervention in Kazakh population.

BackgroundAfter coronary stenting, the risk of developing restenosis is from 20 to 35 %. The aim of the present study is to investigate the association of genetic variation in candidate genes in patients diagnosed with restenosis in the Kazakh population.MethodsFour hundred fifty-nine patients were recruited to the study; 91 patients were also diagnosed with diabetes and were excluded from the sampling. DNA was extracted with the salting-out method. The patients were genotyped for 53 single-nucleotide polymorphisms. Genotyping was performed on the QuantStudio 12K Flex (Life Technologies). Differences in distribution of BMI score among different genotype groups were compared by analysis of variance (ANOVA). Also, statistical analysis was performed using R and PLINK v.1.07. Haplotype frequencies and LD measures were estimated by using the software Haploview 4.2.ResultsA logistic regression analysis found a significant difference in restenosis rates for different genotypes. FGB (rs1800790) is significantly associated with restenosis after stenting (OR = 2.924, P = 2.3E−06, additive model) in the Kazakh population. CD14 (rs2569190) showed a significant association in the additive (OR = 0.08033, P = 2.11E−09) and dominant models (OR = 0.05359, P = 4.15E−11). NOS3 (rs1799983) was also highly associated with development of restenosis after stenting in additive (OR = 20.05, P = 2.74 E−12) and recessive models (OR = 22.24, P = 6.811E−10).ConclusionsOur results indicate that FGB (rs1800790), CD14 (rs2569190), and NOS3 (rs1799983) SNPs could be genetic markers for development of restenosis in Kazakh population. Adjustment for potential confounder factor BMI gave almost the same results.

Cardiac dyssynchrony and response to cardiac resynchronisation therapy in heart failure: can genetic predisposition play a role?

Cardiac resynchronisation therapy (CRT) is an accepted treatment for heart failure patients with depressed left ventricular (LV) function and dyssynchrony. However, despite better clinical outcome and improved cardiac function after CRT in the majority of eligible heart failure patients, a large proportion of implanted patients do not seem to benefit clinically from this therapy. In this review we consider whether genetic factors may play a role in modulating response to CRT and summarise the few genetic studies that have investigated the role of genetic variation in candidate genes.

Pharmacogenetic determinants of response to infliximab in pediatric inflammatory bowel disease

Anti-tumor necrosis factor (TNF) agents, in particular infliximab, have become the mainstay of treatment in refractory inflammatory bowel diseases (IBD), also in pediatric patients. Furthermore, they also seem to be promising as first line treatment in the early stages of disease, yet their widespread use may not be affordable by the National Health Service. While the general mechanism of action of anti-TNF agents has been investigated, it is still largely unknown why clinical response differs among patients. Currently, there are no clinical, pharmacological or molecular predictors of response to anti-TNF therapy available for translation in clinical practice. In fact, interindividual differences in response to therapy could be influenced by several interacting factors. Therefore, strategies integrating clinical, pharmacokinetic, pharmacodynamic and pharmacogenomic information could lead to the identification of subsets of patients with a higher probability of response and to personalization of anti-TNF treatment, resulting in more cost-effective therapies. Loss of response in patients treated with infliximab may be in part the result of failure to achieve and maintain adequate drug levels and/or of the formation anti-infliximab antibodies. Recent findings also suggest that membrane TNF expression on the intestinal mucosa may predict therapeutic response (1). Several studies have evaluated the effect of genetic variants in candidate genes involved in infliximab pharmacokinetics and pharmacodynamics on the response to the medication even if no unique marker has been identified; recent studies however indicate that relevant variants to predict infliximab response are those in IL6 and TNF genes (2). The aim of the present study was therefore to evaluate the role of these candidate genetic factors on the response to infliximab in an Italian cohort of children and young adults with IBD. Patients with IBD treated with infliximab were enrolled by the Department of Pediatrics of Burlo Garofolo Children's Hospital in Trieste; clinical data were collected retrospectively. Response to infliximab was evaluated as a decrease in disease activity score after induction therapy and as the need to switch therapy with infliximab within 12 months of follow-up. The most relevant functional SNP for each gene considered were characterized by PCR-RFLP (rs1800795, -174G/C in IL6 and rs1800629, -308A/G in TNF) assays on patients' DNA extracted from peripheral blood. Sixty-four young patients with IBD were enrolled. Of these, 48.4% were female, median age at infliximab start was 13.4 years (interquartile range, IQR 10.9–16.1). IBD diagnosis was Crohn's disease in 65.6% and ulcerative colitis in 34.4%. At the beginning of infliximab therapy, disease had been lasting for a median of 1.1 year (IQR 0.53–2.5); infliximab was administered at a dose of 5 mg/kg according to the standard schedule. Genotyping showed minor allele frequencies of 39.8% for rs1800795, 10.1% for rs1800629, consistent with previous reports in Europeans. Assessment of response to infliximab showed that 21.9% of patients did not respond to induction therapy; moreover, 36.8% needed to switch therapy within 12 months. Genotyping analysis identified an association between the homozygous CC variant of IL6 and diminished response to induction therapy: frequency of non-response in patients with this genotype was almost three times that of patients with a GG/GC genotype (p<0.05). This is the first study evaluating the effect of pharmacogenetic variants on response to infliximab in Italian patients with pediatric IBD, showing relevant associations. This report supports the utility of genotyping candidate genes to predict infliximab response in children with IBD and should be further validated by larger and prospective studies and improved by integrating pharmacokinetic and pharmacodynamic evaluations.

Pathway-based association study of multiple candidate genes and multiple traits using structural equation models.

There is increasing interest in the joint analysis of multiple genetic variants from multiple genes and multiple correlated quantitative traits in association studies. The classical approach involves testing univariate associations between genotypes and phenotypes and correcting for multiple testing that results in loss of power to detect associations. In this paper, we propose modeling complex relationships between genetic variants in candidate genes and measured correlated traits using structural equation models (SEM), taking advantage of prior knowledge on clinical and genetic pathways. We adopt generalized structured component analysis (GSCA) as an approach to SEM and develop a single association test between multiple genetic variants in a gene and a set of correlated traits, taking into account all available data from other genes and other traits. The performance of this test is investigated by simulations. We apply the proposed method to the Quebec Child and Adolescent Health and Social Survey (1999) data to investigate genetic associations with cardiovascular disease-related traits.

Parental smoking during pregnancy and offspring cardio-metabolic risk factors at ages 17 and 32

ObjectiveTo examine the association of maternal and/or paternal smoking during pregnancy with offspring cardio-metabolic risk (CMR) factors at adolescence and early adulthood, taking into account socio-demographic, medical and lifestyle characteristics of parents and offspring, as well as offspring common genetic variation. MethodsWe used a population-based cohort of all 17 003 births in Jerusalem during 1974–76, with available archival data on parental and birth characteristics. Measurements at age 17 were assessed at military induction examinations for 11 530 offspring. 1440 offspring from the original 1974–1976 birth cohort were sampled using a stratified sampling approach, and were interviewed and examined at age 32. Parental smoking during pregnancy (i.e. maternal, paternal and any parent) was primarily defined dichotomously (any number of cigarettes smoked daily by mother or father during pregnancy vs. non-smokers). Additionally, smoking was assessed by quantity of cigarettes smoked daily. Linear regression models were used to evaluate the associations of parental smoking during pregnancy with various offspring CMR factors, after controlling for potential confounders and for genetic variation in candidate genes. ResultsPrevalence of exposure to parental smoking in-utero (i.e. smoking of any parent) was 53.2% and 48.4% among the 17 years old and 32 years old samples, respectively. At age 17, smoking of at least one parent during pregnancy was significantly associated with weight (B = 1.39), height (B = 0.59), BMI (B = 0.32) and pulse rate (B = −0.78) (p-values < 0.001). At age 32, parental smoking, adjusted for covariates, was associated with 2.22 kg higher mean offspring weight, 0.95 cm higher mean offspring height, 0.57 kg/m2 higher BMI, and 1.46 cm higher waist-circumference (p-values ≤ 0.02). Similar results, reflecting a dose response, were observed when maternal and paternal smokings were assessed by number of cigarettes smoked daily. ConclusionsThis prospective study demonstrates a potential long-term adverse effect of parental smoking during pregnancy on offspring health and calls for increasing efforts to promote smoking cessation of both parents before pregnancy.