scholarly journals High-Throughput Sequencing Haplotype Analysis Indicates in LRRK2 Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic

Life ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 121
Author(s):  
Kristyna Kolarikova ◽  
Radek Vodicka ◽  
Radek Vrtel ◽  
Julia Stellmachova ◽  
Martin Prochazka ◽  
...  
Keyword(s):  
Risk Factor ◽  
High Throughput ◽  
Potential Risk ◽  
High Throughput Sequencing ◽  
Genome Project ◽  
Potential Risk Factor ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Lrrk2 Gene ◽  
Project Data

Parkinson’s disease and parkinsonism are relatively common neurodegenerative disorders. This study aimed to assess potential genetic risk factors of haplotypes in genes associated with parkinsonism in a population in which endemic parkinsonism and atypical parkinsonism have recently been found. The genes ADH1C, EIF4G1, FBXO7, GBA, GIGYF2, HTRA2, LRRK2, MAPT, PARK2, PARK7, PINK1 PLA2G6, SNCA, UCHL1, and VPS35 were analyzed in 62 patients (P) and 69 age-matched controls from the researched area (C1). Variants were acquired by high-throughput sequencing using Ion Torrent workflow. As another set of controls, the whole genome sequencing data from 100 healthy non-related individuals from the Czech population were used (C2); the results were also compared with the Genome Project data (C3). We observed shared findings of four intron (rs11564187, rs36220738, rs200829235, and rs3789329) and one exon variant (rs33995883) in the LRRK2 gene in six patients. A comparison of the C1–C3 groups revealed significant differences in haplotype frequencies between ratio of 2.09 for C1, 1.65 for C2, and 6.3 for C3, and odds ratios of 13.15 for C1, 2.58 for C2, and 7.6 for C3 were estimated. The co-occurrence of five variants in the LRRK2 gene (very probably in haplotype) could be an important potential risk factor for the development of parkinsonism, even outside the recently described pedigrees in the researched area where endemic parkinsonism is present.

scholarly journals Discovery of tandem and interspersed segmental duplications using high throughput sequencing

2018 ◽  
Author(s):  
Arda Soylev ◽  
Thong Le ◽  
Hajar Amini ◽  
Can Alkan ◽  
Fereydoun Hormozdiari
Keyword(s):  
False Discovery Rate ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Real Data ◽  
Whole Genome Sequencing Data ◽  
Data Sets ◽  
Segmental Duplications ◽  
Sequencing Data ◽  
Link Type ◽  
False Discovery

AbstractMotivationSeveral algorithms have been developed that use high throughput sequencing technology to characterize structural variations. Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions, and short inversions. In fact, complex SVs are of crucial importance and several have been associated with genomic disorders. To better understand the contribution of complex SVs to human disease, we need new algorithms to accurately discover and genotype such variants. Additionally, due to similar sequencing signatures, inverted duplications or gene conversion events that include inverted segmental duplications are often characterized as simple inversions; and duplications and gene conversions in direct orientation may be called as simple deletions. Therefore, there is still a need for accurate algorithms to fully characterize complex SVs and thus improve calling accuracy of more simple variants.ResultsWe developed novel algorithms to accurately characterize tandem, direct and inverted interspersed segmental duplications using short read whole genome sequencing data sets. We integrated these methods to our TARDIS tool, which is now capable of detecting various types of SVs using multiple sequence signatures such as read pair, read depth and split read. We evaluated the prediction performance of our algorithms through several experiments using both simulated and real data sets. In the simulation experiments, using a 30× coverage TARDIS achieved 96% sensitivity with only 4% false discovery rate. For experiments that involve real data, we used two haploid genomes (CHM1 and CHM13) and one human genome (NA12878) from the Illumina Platinum Genomes set. Comparison of our results with orthogonal PacBio call sets from the same genomes revealed higher accuracy for TARDIS than state of the art methods. Furthermore, we showed a surprisingly low false discovery rate of our approach for discovery of tandem, direct and inverted interspersed segmental duplications prediction on CHM1 (less than 5% for the top 50 predictions).AvailabilityTARDIS source code is available at https://github.com/BilkentCompGen/tardis, and a corresponding Docker image is available at https://hub.docker.com/r/alkanlab/tardis/[email protected] and [email protected]

scholarly journals Biological foundation for periodontitis as a potential risk factor for atherosclerosis

2005 ◽  
Vol 40 (1) ◽  
pp. 87-95 ◽  
Author(s):  
Yong-Hee P. Chun ◽  
Kyoung-Ryul J. Chun ◽  
De'Avlin Olguin ◽  
Hom-Lay Wang
Keyword(s):  
Risk Factor ◽  
Potential Risk ◽  
Potential Risk Factor ◽  
Biological Foundation

scholarly journals Evaluation of blood type as a potential risk factor for early postpartum hemorrhage

PLoS ONE ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. e0214840 ◽  
Author(s):  
Mais Ali-Saleh ◽  
Ofer Lavie ◽  
Yoram Abramov
Keyword(s):  
Risk Factor ◽  
Potential Risk ◽  
Postpartum Hemorrhage ◽  
Potential Risk Factor ◽  
Blood Type ◽  
Early Postpartum

Positive peritoneal washing cytology is a potential risk factor for the recurrence of curatively resected colorectal cancer

Surgery Today ◽  
2013 ◽  
Vol 44 (6) ◽  
pp. 1084-1089 ◽  
Author(s):  
Yoichiro Homma ◽  
Takashi Hamano ◽  
Yasuhiro Akazawa ◽  
Yoshiro Otsuki ◽  
Shinichi Shimizu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Risk Factor ◽  
Potential Risk ◽  
Potential Risk Factor ◽  
Peritoneal Washing ◽  
Peritoneal Washing Cytology

scholarly journals Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 29-40 ◽  
Author(s):  
Sten Anslan ◽  
R. Henrik Nilsson ◽  
Christian Wurzbacher ◽  
Petr Baldrian ◽  
Leho Tedersoo ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Computation Time ◽  
Potential Effect ◽  
Data Sets ◽  
Sequencing Data ◽  
Operational Taxonomic Units ◽  
High Throughput Sequencing Data ◽  
Recent Developments

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

Lifestyle and Occupational Stress: A Potential Risk Factor for Obstructive Sleep Apnea in Nonobese Male Subjects

2017 ◽  
Vol 27 (8) ◽  
pp. 716-721
Author(s):  
Arvind Tripathi ◽  
Soumyojeet Bagchi ◽  
Juhi Singh ◽  
Paritosh Pandey ◽  
Suryakant Tripathi ◽  
...  
Keyword(s):  
Obstructive Sleep Apnea ◽  
Risk Factor ◽  
Sleep Apnea ◽  
Occupational Stress ◽  
Potential Risk ◽  
Potential Risk Factor ◽  
Obstructive Sleep ◽  
Male Subjects

scholarly journals Uncontrolled maternal chronic respiratory diseases in pregnancy: A new potential risk factor suggested to be associated with anorectal malformations in offspring

2018 ◽  
Vol 111 (2) ◽  
pp. 62-69 ◽  
Author(s):  
Romy van de Putte ◽  
Ivo de Blaauw ◽  
Rianne Boenink ◽  
Monique H.E. Reijers ◽  
Paul M.A. Broens ◽  
...  
Keyword(s):  
Risk Factor ◽  
Potential Risk ◽  
Respiratory Diseases ◽  
Anorectal Malformations ◽  
Potential Risk Factor ◽  
Chronic Respiratory Diseases ◽  
In Pregnancy
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