NCOR2 is a novel candidate gene for migraine-epilepsy phenotype.

HYPOTHESIS: To identify genetic factors predisposing to migraine-epilepsy phenotype utilizing a multi-generational family with known linkage to chr12q24.2-q24.3. METHODS: We used single nucleotide polymorphism (SNP) genotyping and next-generation sequencing technologies to perform linkage, haplotype, and variant analyses in an extended Finnish migraine-epilepsy family (n = 120). In addition, we used a large genome-wide association study (GWAS) dataset of migraine and two biobank studies, UK Biobank and FinnGen, to test whether variants within the susceptibility region associate with migraine or epilepsy related phenotypes in a population setting. RESULTS: The family showed the highest evidence of linkage (LOD 3.42) between rs7966411 and epilepsy. The haplotype shared among 12 out of 13 epilepsy patients in the family covers almost the entire NCOR2 and co-localizes with one of the risk loci of the recent GWAS on migraine. The haplotype harbors nine low-frequency variants with potential regulatory functions. Three of them, in addition to two common variants, show nominal associations with neurological disorders in either UK Biobank or FinnGen. CONCLUSION: We provide several independent lines of evidence supporting association between migraine-epilepsy phenotype and NCOR2. Our study suggests that NCOR2 may have a role in both migraine and epilepsy and thus would provide evidence for shared pathophysiology underlying these two diseases.

Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines.

BACKGROUND: Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform's impact. RESULTS: The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (indels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in indel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups. CONCLUSION: We provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies.

Radiogenomic Analysis of Oncological Data: A Technical Survey.

In the last few years, biomedical research has been boosted by the technological development of analytical instrumentation generating a large volume of data. Such information has increased in complexity from basic (i.e., blood samples) to extensive sets encompassing many aspects of a subject phenotype, and now rapidly extending into genetic and, more recently, radiomic information. Radiogenomics integrates both aspects, investigating the relationship between imaging features and gene expression. From a methodological point of view, radiogenomics takes advantage of non-conventional data analysis techniques that reveal meaningful information for decision-support in cancer diagnosis and treatment. This survey is aimed to review the state-of-the-art techniques employed in radiomics and genomics with special focus on analysis methods based on molecular and multimodal probes. The impact of single and combined techniques will be discussed in light of their suitability in correlation and predictive studies of specific oncologic diseases.

New Insights into the Microbiota of Moth Pests.

In recent years, next generation sequencing (NGS) technologies have helped to improve our understanding of the bacterial communities associated with insects, shedding light on their wide taxonomic and functional diversity. To date, little is known about the microbiota of lepidopterans, which includes some of the most damaging agricultural and forest pests worldwide. Studying their microbiota could help us better understand their ecology and offer insights into developing new pest control strategies. In this paper, we review the literature pertaining to the microbiota of lepidopterans with a focus on pests, and highlight potential recurrent patterns regarding microbiota structure and composition.

SeqCompress: an algorithm for biological sequence compression.

The growth of Next Generation Sequencing technologies presents significant research challenges, specifically to design bioinformatics tools that handle massive amount of data efficiently. Biological sequence data storage cost has become a noticeable proportion of total cost in the generation and analysis. Particularly increase in DNA sequencing rate is significantly outstripping the rate of increase in disk storage capacity, which may go beyond the limit of storage capacity. It is essential to develop algorithms that handle large data sets via better memory management. This article presents a DNA sequence compression algorithm SeqCompress that copes with the space complexity of biological sequences. The algorithm is based on lossless data compression and uses statistical model as well as arithmetic coding to compress DNA sequences. The proposed algorithm is compared with recent specialized compression tools for biological sequences. Experimental results show that proposed algorithm has better compression gain as compared to other existing algorithms.

Remediation of soil polluted with petroleum hydrocarbons and its reuse for agriculture: Recent progress, challenges, and perspectives.

Petroleum hydrocarbons (PHs) are used as raw materials in many industries and primary energy sources. However, excessive PHs act as soil pollutants, posing serious threats to living organisms. Various ex-situ or in-situ chemical and biological methods are applied to restore polluted soil. However, most of the chemical treatment methods are expensive, environmentally unfriendly, and sometimes inefficient. That attracts scientists and researchers to develop and select new strategists to remediate polluted soil through risk-based analysis and eco-friendly manner. This review discusses the sources of PHs, properties, distribution, transport, and fate in the environment, internal and external factors affecting the soil remediation and restoration process, and its effective re-utilization for agriculture. Bioremediation is an eco-friendly method for degrading PHs, specifically by using microorganisms. Next-generation sequencing (NGS) technologies are being used to monitor contaminated sites. Currently, these new technologies have caused a paradigm shift by giving new insights into the microbially mediated biodegradation processes by targeting rRNA are discussed concisely. The recent development of risk-based management for soil contamination and its challenges and future perspectives are also discussed. Furthermore, nanotechnology seems very promising for effective soil remediation, but its success depends on its cost-effectiveness. This review paper suggests using bio-electrochemical systems that utilize electro-chemically active microorganisms to remediate and restore polluted soil with PHs that would be eco-friendlier and help tailor-made effective and sustainable remediation technologies.

The complete mitochondrial genome of the breed Ningbo brown-marbled grouper (Epinephelus fuscoguttatus).

We used NGS technologies to resequence the complete mitochondrial genome of (Epinephelus fuscoguttatus). The complete mitochondrial genome of the breed Ningbo brown-marbled grouper is a 16,373 bp circular molecule, which contains 37 typical mitochondrial genes (13 protein-coding genes, two rRNAs, and 22 tRNAs) and a D-loop. Its gene arrangement pattern is the same as the accession no. KP013758. Comparing to accession no. KP013758 sequence, the D-loop region is much shorter. ATG is the most common start codon, and TAA is the most common stop codons; the 12S rRNA and 16S rRNA are located between the tRNAPhe and tRNALeu genes and are separated by the tRNAVal gene. Phylogenetic trees indicated E. fuscoguttatus has close relative with Epinephelus coioides and Epinephelus malabaricus.

On the use of algebraic topology concepts to check the consistency of genome assembly.

This paper presents a preliminary work consisting of two contributions. The first one is the design of a very efficient algorithm based on an "Overlap-Layout-Consensus" (OLC) graph to assemble the long reads provided by 3rd generation technologies. The second concerns the analysis of this graph using algebraic topology concepts to determine, in advance, whether the assembly of the genome will be straightforward, i.e., whether it will lead to a pseudo-Hamiltonian path or cycle, or whether the results will need to be scrutinized. In the latter case, it will be necessary to look for "loops" in the OLC assembly graph caused by unresolved repeated genomic regions, and then try to untie the "knots" created by these regions.

Next-generation resequencing the complete mitochondrial genome of Japanese quail (Coturnix japonica).

As the development of the new generation of sequencing (NGS) technologies, it has been used for standard sequencing applications more and more popular. We used NGS technologies to resequence the complete mitochondrial genome of Japanese quail. The complete mitochondrial genome of Japanese quail is a 16,668 bp circular molecule, which contains 37 typical mitochondrial genes (13 protein-coding genes, 2 rRNAs, and 22 tRNAs) and a 1156 bp D-loop. Its gene arrangement pattern is identical with typical other Galliformes. All protein-coding genes start with an ATG codon except COI, which start with GTG. TAA is the most frequent stop codon, although ND2 end with TAG, and COI and ND6 end with AGG, COIII and ND4 end with TGC. The mtDNA sequence contains 12S rRNA and 16S rRNA of rRNA. Except for tRNASer(AGY) and tRNALeu(CUN) without the dihydrouridine (DHU) arm, all tRNAs could be folded into canonical cloverleaf secondary structures. Coturnix japonica has close relative with C. chinensis.