Article

Rare Variants in Ischemic Stroke: An Exome Pilot Study

The University of Hong Kong, Hong Kong
PLoS ONE (Impact Factor: 3.53). 04/2012; 7(4):e35591. DOI: 10.1371/journal.pone.0035591
Source: PubMed

ABSTRACT The genetic architecture of ischemic stroke is complex and is likely to include rare or low frequency variants with high penetrance and large effect sizes. Such variants are likely to provide important insights into disease pathogenesis compared to common variants with small effect sizes. Because a significant portion of human functional variation may derive from the protein-coding portion of genes we undertook a pilot study to identify variation across the human exome (i.e., the coding exons across the entire human genome) in 10 ischemic stroke cases. Our efforts focused on evaluating the feasibility and identifying the difficulties in this type of research as it applies to ischemic stroke. The cases included 8 African-Americans and 2 Caucasians selected on the basis of similar stroke subtypes and by implementing a case selection algorithm that emphasized the genetic contribution of stroke risk. Following construction of paired-end sequencing libraries, all predicted human exons in each sample were captured and sequenced. Sequencing generated an average of 25.5 million read pairs (75 bp×2) and 3.8 Gbp per sample. After passing quality filters, screening the exomes against dbSNP demonstrated an average of 2839 novel SNPs among African-Americans and 1105 among Caucasians. In an aggregate analysis, 48 genes were identified to have at least one rare variant across all stroke cases. One gene, CSN3, identified by screening our prior GWAS results in conjunction with our exome results, was found to contain an interesting coding polymorphism as well as containing excess rare variation as compared with the other genes evaluated. In conclusion, while rare coding variants may predispose to the risk of ischemic stroke, this fact has yet to be definitively proven. Our study demonstrates the complexities of such research and highlights that while exome data can be obtained, the optimal analytical methods have yet to be determined.

1 Bookmark
 · 
173 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Background The advent of massively parallel sequencing technologies (Next Generation Sequencing, NGS) profoundly modified the landscape of human genetics. In particular, Whole Exome Sequencing (WES) is the NGS branch that focuses on the exonic regions of the eukaryotic genomes; exomes are ideal to help us understanding high-penetrance allelic variation and its relationship to phenotype. A complete WES analysis involves several steps which need to be suitably designed and arranged into an efficient pipeline. Managing a NGS analysis pipeline and its huge amount of produced data requires non trivial IT skills and computational power. Results Our web resource WEP (Whole-Exome sequencing Pipeline web tool) performs a complete WES pipeline and provides easy access through interface to intermediate and final results. The WEP pipeline is composed of several steps: 1) verification of input integrity and quality checks, read trimming and filtering; 2) gapped alignment; 3) BAM conversion, sorting and indexing; 4) duplicates removal; 5) alignment optimization around insertion/deletion (indel) positions; 6) recalibration of quality scores; 7) single nucleotide and deletion/insertion polymorphism (SNP and DIP) variant calling; 8) variant annotation; 9) result storage into custom databases to allow cross-linking and intersections, statistics and much more. In order to overcome the challenge of managing large amount of data and maximize the biological information extracted from them, our tool restricts the number of final results filtering data by customizable thresholds, facilitating the identification of functionally significant variants. Default threshold values are also provided at the analysis computation completion, tuned with the most common literature work published in recent years. Conclusions Through our tool a user can perform the whole analysis without knowing the underlying hardware and software architecture, dealing with both paired and single end data. The interface provides an easy and intuitive access for data submission and a user-friendly web interface for annotated variant visualization. Non-IT mastered users can access through WEP to the most updated and tested WES algorithms, tuned to maximize the quality of called variants while minimizing artifacts and false positives. The web tool is available at the following web address: http://www.caspur.it/wep
    BMC Bioinformatics 04/2013; 14(7). DOI:10.1186/1471-2105-14-S7-S11 · 2.67 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Understanding the genetic architecture of cerebrovascular disease holds promise of novel stroke prevention strategies and therapeutics that are both safe and effective. Apart from a few single-gene disorders associated with cerebral ischemia or intracerebral hemorrhage, stroke is a complex genetic phenotype that requires careful ascertainment and robust association testing for discovery and validation analyses. The recently uncovered shared genetic contribution between clinically manifest stroke syndromes and closely related intermediate cerebrovascular phenotypes offers effective and efficient approaches to complex trait analysis.
    Neurologic Clinics 11/2013; 31(4):915-28. DOI:10.1016/j.ncl.2013.05.001 · 1.61 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The development of novel technologies for high-throughput DNA sequencing is having a major impact on our ability to measure and define normal and pathologic variation in humans. This review discusses advances in DNA sequencing that have been applied to benign hematologic disorders, including those affecting the red blood cell, the neutrophil, and other white blood cell lineages. Relevant examples of how these approaches have been used for disease diagnosis, gene discovery, and studying complex traits are provided. High-throughput DNA sequencing technology holds significant promise for impacting clinical care. This includes development of improved disease detection and diagnosis, better understanding of disease progression and stratification of risk of disease-specific complications, and development of improved therapeutic strategies, particularly patient-specific pharmacogenomics-based therapy, with monitoring of therapy by genomic biomarkers.
    Blood 09/2013; DOI:10.1182/blood-2013-07-460337 · 9.78 Impact Factor

Full-text (2 Sources)

Download
82 Downloads
Available from
Jun 1, 2014