Péter Sárközy

Multivariate analysis of dopaminergic gene variants as risk factors of heroin dependence.

Background Heroin dependence is a debilitating psychiatric disorder with complex inheritance. Since the dopaminergic system has a key role in rewarding mechanism of the brain, which is directly or indirectly targeted by most drugs of abuse, we focus on the effects and interactions among dopaminergic gene variants. Objective To study the potential association between allelic variants of dopamine D2 receptor (DRD2), ANKK1 (ankyrin repeat and kinase domain containing 1), dopamine D4 receptor (DRD4), catechol-O-methyl transferase (COMT) and dopamine transporter (SLC6A3) genes and heroin dependence in Hungarian patients. Methods 303 heroin dependent subjects and 555 healthy controls were genotyped for 7 single nucleotide polymorphisms (SNPs) rs4680 of the COMT gene; rs1079597 and rs1800498 of the DRD2 gene; rs1800497 of the ANKK1 gene; rs1800955, rs936462 and rs747302 of the DRD4 gene. Four variable number of tandem repeats (VNTRs) were also genotyped: 120 bp duplication and 48 bp VNTR in exon 3 of DRD4 and 40 bp VNTR and intron 8 VNTR of SLC6A3. We also perform a multivariate analysis of associations using Bayesian networks in Bayesian multilevel analysis (BN-BMLA). Findings and conclusions In single marker analysis the TaqIA (rs1800497) and TaqIB (rs1079597) variants were associated with heroin dependence. Moreover, –521 C/T SNP (rs1800955) of the DRD4 gene showed nominal association with a possible protective effect of the C allele. After applying the Bonferroni correction TaqIB was still significant suggesting that the minor (A) allele of the TaqIB SNP is a risk component in the genetic background of heroin dependence. The findings of the additional multiple marker analysis are consistent with the results of the single marker analysis, but this method was able to reveal an indirect effect of a promoter polymorphism (rs936462) of the DRD4 gene and this effect is mediated through the –521 C/T (rs1800955) polymorphism in the promoter.

Additive effects of serotonergic and dopaminergic polymorphisms on trait impulsivity

Twin studies suggest 45% heritability of trait impulsivity. Results from candidate gene studies to date are contradictory; impulsivity phenotypes were measured by different behavioral and questionnaire methods related either to the dopaminergic or to the serotonergic system. Here we report an association study of both dopaminergic (COMT rs4680, DRD4 48 bp VNTR, DRD2/ANKK1 rs1800497) and serotonergic (HTR1A rs6925, HTR1B rs13212041, SLC6A4 5‐HTTLPR) gene polymorphisms and trait impulsivity assessed with the Barratt Impulsiveness Scale (BIS‐11) in a sample of 687 Caucasian young adults. Results showed lower impulsivity in the presence of the DRD4 7‐repeat (P = 0.006) and the HTR1B rs13212041 alleles (P = 0.003). These findings stayed significant after Bonferroni correction. A multivariate analysis using Bayesian networks confirmed independent effects of these two polymorphisms and provided a coherent characterization of the system of dependencies with respect to the impulsivity construct as well as its subscales. These results clearly suggest an additive effect of dopaminergic and serotonergic polymorphisms on trait impulsivity.

Haplotyping of putative microRNA-binding sites in the SNAP-25 gene.

Synaptosomal‐associated protein 25 (SNAP‐25) plays a crucial role in exocitosis. Single nucleotide polymorphisms (rs3746544 and rs1051312) in the 3′ un‐translated region of the SNAP‐25 gene have been described to be in association with attention‐deficit hyperactivity disorder. As the disease affects millions of children world‐wide, understanding the genetic background of attention‐deficit hyperactivity disorder is of crucial importance. Efficient and reliable PCR‐RFLP protocols were elaborated for the genotyping of the rs3746544 and rs1051312 SNPs employing a high‐throughput capillary electrophoresis method for fragment analysis. A novel real‐time PCR‐based technique was used applying sequence specific TaqMan probes to haplotype the two SNPs, and the G–C haplotype could not be detected in a large Caucasian population (N=1376). These findings have been confirmed by molecular biology tools as well as by the PHASE Bayesian computational approach. In silico analyses have suggested that the two SNPs might alter microRNA binding and thus have an effect on SNAP‐25 production. We have demonstrated that this biological information can be revealed only by direct haplotype analysis emphasizing the importance of our novel molecular haplotye analysis protocol. Results of the study of the two SNPs might shed light on the association of SNAP‐25 variants and pathological phenotypes at the molecular level.

VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering

BackgroundThe low concordance between different variant calling methods still poses a challenge for the wide-spread application of next-generation sequencing in research and clinical practice. A wide range of variant annotations can be used for filtering call sets in order to improve the precision of the variant calls, but the choice of the appropriate filtering thresholds is not straightforward. Variant quality score recalibration provides an alternative solution to hard filtering, but it requires large-scale, genomic data.ResultsWe evaluated germline variant calling pipelines based on BWA and Bowtie 2 aligners in combination with GATK UnifiedGenotyper, GATK HaplotypeCaller, FreeBayes and SAMtools variant callers, using simulated and real benchmark sequencing data (NA12878 with Illumina Platinum Genomes). We argue that these pipelines are not merely discordant, but they extract complementary useful information.We introduce VariantMetaCaller to test the hypothesis that the automated fusion of measurement related information allows better performance than the recommended hard-filtering settings or recalibration and the fusion of the individual call sets without using annotations. VariantMetaCaller uses Support Vector Machines to combine multiple information sources generated by variant calling pipelines and estimates probabilities of variants.This novel method had significantly higher sensitivity and precision than the individual variant callers in all target region sizes, ranging from a few hundred kilobases to whole exomes. We also demonstrated that VariantMetaCaller supports a quantitative, precision based filtering of variants under wider conditions. Specifically, the computed probabilities of the variants can be used to order the variants, and for a given threshold, probabilities can be used to estimate precision. Precision then can be directly translated to the number of true called variants, or equivalently, to the number of false calls, which allows finding problem-specific balance between sensitivity and precision.ConclusionsVariantMetaCaller can be applied to small target regions and whole exomes as well, and it can be used in cases of organisms for which highly accurate variant call sets are not yet available, therefore it can be a viable alternative to hard filtering in cases where variant quality score recalibration cannot be used. VariantMetaCaller is freely available at http://bioinformatics.mit.bme.hu/VariantMetaCaller.

Novel genes in Human Asthma Based on a Mouse Model of Allergic Airway Inflammation and Human Investigations

Purpose Based on a previous gene expression study in a mouse model of asthma, we selected 60 candidate genes and investigated their possible roles in human asthma. Methods In these candidate genes, 90 SNPs were genotyped using MassARRAY technology from 311 asthmatic children and 360 healthy controls of the Hungarian (Caucasian) population. Moreover, gene expression levels were measured by RT PCR in the induced sputum of 13 asthmatics and 10 control individuals. t-tests, chi-square tests, and logistic regression were carried out in order to assess associations of SNP frequency and expression level with asthma. Permutation tests were performed to account for multiple hypothesis testing. Results The frequency of 4 SNPs in 2 genes differed significantly between asthmatic and control subjects: SNPs rs2240572, rs2240571, rs3735222 in gene SCIN, and rs32588 in gene PPARGC1B. Carriers of the minor alleles had reduced risk of asthma with an odds ratio of 0.64 (0.51-0.80; P=7×10-5) in SCIN and 0.56 (0.42-0.76; P=1.2×10-4) in PPARGC1B. The expression levels of SCIN, PPARGC1B and ITLN1 genes were significantly lower in the sputum of asthmatics. Conclusions Three potentially novel asthma-associated genes were identified based on mouse experiments and human studies.

Calling Homopolymer Stretches from Raw Nanopore Reads by Analyzing k-mer Dwell Times

Oxford Nanopore Technologies’ (ONT) MinION device is capable of reading single molecule DNA strands tens of thousands of bases long, by passing a strand through a nanopore and recording the changes in electric current. The error rate of the platform is higher than most mature next-generation sequencing (NGS) platforms, with many of the deletions accumulating in stretches of identical bases (homopolymers). However, the mean time each 5-base long subsequence (k-mer) of the molecule spends inside of the pore (dwell time) can also be used to infer the length of the true sequence. We developed a method called NanoTimer, which estimates the homopolymer length from the dwell times. It relies on the redundancy of having multiple reads covering a reference sequence, and the depth of coverage determines its accuracy.

Bootstrap-Based Quality Scores for NGS Variant Calling

Variant calling, the identification of DNA sites that differ from a reference sequence using Next Generation Sequencing (NGS) methods is still an inherently error prone process. Quality scores of variant calling results in NGS studies is a key utility for identifying and prioritizing variants for validation in clinical practice. We investigated the robustness of a wide range of quality scores using bootstrap resampling of the short reads resulting from an NGS exome sequencing study, and evaluated their use as additional quality scores to characterize the called variants. Besides quality scores from the measurement process itself and the biological and clinical relevance of a variant, the bootstrap derived quality scores provide an additional information source for validation prioritization. Additionally, our results indicate possibilities for decreasing the depth of the NGS measurement and increasing the robustness of bioinformatic post-processing.