Single Nucleotide Polymorphisms as Genomic Markers for High-Throughput Pharmacogenomic Studies

Clinical Validation of a 106-SNV MALDI-ToF MS Pharmacogenomic Panel

BACKGROUND

Laboratorians have the opportunity to help minimize the frequency of adverse drug reactions by implementing pharmacogenomic testing and alerting care providers to possible patient/drug incompatibilities before drug treatment is initiated. Methods combining PCR with MALDI-ToF MS have allowed for sensitive, economical, and multiplexed pharmacogenomic testing results to be delivered in a timely fashion.

METHOD

This study evaluated the analytical performance of the Agena Biosciences iPLEX® PGx 74 panel and a custom iPLEX panel on a MassARRAY MALDI-TOF MS instrument in a clinical laboratory setting. Collectively, these panels evaluate 112 SNVs across 34 genes implicated in drug response. Using commercially available samples (Coriell Biorepository) and in-house extracted DNA, we determined ideal reaction conditions and assessed accuracy, precision, and robustness.

RESULTS

Following protocol optimization, the Agena PGx74 and custom panels demonstrated 100% concordance with the 1000 Genomes Project Database and clinically validated hydrolysis probe genotyping assays. 100% concordance was also observed in all assessments of assay precision when appropriate QC metrics were applied.

CONCLUSIONS

Significant development time was required to optimize sample preparation and instrumental analysis and 3 assays were removed due to inconsistent performance. Following modification of the manufacturer's protocol and instituting manual review of each assay plate, the Agena PGx74 and custom panel constitute a cost-effective, robust, and accurate method for clinical identification of 106 SNVs involved in drug response.

Extensive In Silico Analysis of ATL1 Gene : Discovered Five Mutations That May Cause Hereditary Spastic Paraplegia Type 3A

BACKGROUND

Hereditary spastic paraplegia type 3A (SPG3A) is a neurodegenerative disease inherited type of Hereditary spastic paraplegia (HSP). It is the second most frequent type of HSP which is characterized by progressive bilateral and mostly symmetric spasticity and weakness of the legs. SPG3A gene mutations and the phenotype-genotype correlations have not yet been recognized. The aim of this work was to categorize the most damaging SNPs in ATL1 gene and to predict their impact on the functional and structural levels by several computational analysis tools.

METHODS

The raw data of ATL1 gene were retrieved from dbSNP database and then run into numerous computational analysis tools. Additionally; we submitted the common six deleterious outcomes from the previous functional analysis tools to I-mutant 3.0 and MUPro, respectively, to investigate their effect on the structural level. The 3D structure of ATL1 was predicted by RaptorX and modeled using UCSF Chimera to compare the differences between the native and the mutant amino acids.

RESULTS

Five nsSNPs out of 249 were classified as the most deleterious (rs746927118, rs979765709, rs119476049, rs864622269, and rs1242753115).

CONCLUSIONS

In this study, the impact of nsSNPs in the ATL1 gene was investigated by various in silico tools that revealed five nsSNPs (V67F, T120I, R217Q, R495W, and G504E) are deleterious SNPs, which have a functional impact on ATL1 protein and, therefore, can be used as genomic biomarkers specifically before 4 years of age; also, it may play a key role in pharmacogenomics by evaluating drug response for this disabling disease.

In Silico Genetics Revealing 5 Mutations in CEBPA Gene Associated With Acute Myeloid Leukemia

Background:

Acute myeloid leukemia (AML) is an extremely heterogeneous malignant disorder; AML has been reported as one of the main causes of death in children. The objective of this work was to classify the most deleterious mutation in CCAAT/enhancer-binding protein-alpha (CEBPA) and to predict their influence on the functional, structural, and expression levels by various Bioinformatics analysis tools.

Methods:

The single nucleotide polymorphisms (SNPs) were claimed from the National Center for Biotechnology Information (NCBI) database and then submitted into various functional analysis tools, which were done to predict the influence of each SNP, followed by structural analysis of modeled protein followed by predicting the mutation effect on energy stability; the most damaging mutations were chosen for additional investigation by Mutation3D, Project hope, ConSurf, BioEdit, and UCSF Chimera tools.

Results:

A total of 5 mutations out of 248 were likely to be responsible for the structural and functional variations in CEBPA protein, whereas in the 3′-untranslated region (3′-UTR) the result showed that among 350 SNPs in the 3′-UTR of CEBPA gene, about 11 SNPs were predicted. Among these 11 SNPs, 65 alleles disrupted a conserved miRNA site and 22 derived alleles created a new site of miRNA.

Conclusions:

In this study, the impact of functional mutations in the CEBPA gene was investigated through different bioinformatics analysis techniques, which determined that R339W, R288P, N292S, N292T, and D63N are pathogenic mutations that have a possible functional and structural influence, therefore, could be used as genetic biomarkers and may assist in genetic studies with a special consideration of the large heterogeneity of AML.

POLYMORPHISMS OF DRUG-METABOLIZING ENZYMES CYP1A2, CYP2D6, GST, NAT2 AND TRANSPORTER MDR1 IN POPULATION OF BELARUS: COMPARISON WITH SELECTED EUROPEAN AND ASIAN POPULATIONS

Drug therapeutic efficiency and development of unfavorable pharmacologic responses as well as the disease predisposition are caused first of all by patient’s genetic features. Genetic variations in genes encoding drug-metabolizing enzymes and transporter proteins are essential to understand the ethnic differences in disease occurrence, development, prognosis, therapeutic response and toxicity of drugs. For that reason, it is necessary to establish the normative frequency distribution of genotypes and alleles of these genes in a particular population. Data on frequency of pharmacogenetic polymorphisms in the of Belarus population are limited. The goal of our investigation was to analyze the frequency distribution of genotypes and alleles of genes encoding drug-metabolizing enzymes (CYP1А2, CYP2D6 – I phase; GSTs, NAT2 – II phase) and transporter protein MDR1 in the population of Belarus and comparisons with other ethnic populations. Our results indicate that clinically important genes are genetically highly variable and differ considerably between populations. Differences in allele frequencies across continents should be considered when designing clinical trials of new drugs continents should be considered when designing clinical trials of new drugs.