UASIS: Universal Automatic SNP Identification System

Single Nucleotide Polymorphisms in Neonatal Necrotizing Enterocolitis

The etiopathogenesis of necrotizing enterocolitis (NEC) remains unclear, but increasing information suggests that the risk and severity of NEC may be influenced by single nucleotide polymorphisms in many genes. In this article, we have reviewed gene variations that have either been specifically identified in NEC or have been noted in other inflammatory bowel disorders with similar histopathological abnormalities. We present evidence from our own peer-reviewed laboratory studies and data from an extensive literature search in the databases PubMed, EMBASE, and Scopus. To avoid bias in the identification of existing studies, search keywords were short-listed both from our own studies and from PubMed's Medical Subject Heading (MeSH) thesaurus.

Incorporation of personal single nucleotide polymorphism (SNP) data into a national level electronic health record for disease risk assessment, part 1: an overview of requirements

BACKGROUND

Personalized medicine approaches provide opportunities for predictive and preventive medicine. Using genomic, clinical, environmental, and behavioral data, tracking and management of individual wellness is possible. A prolific way to carry this personalized approach into routine practices can be accomplished by integrating clinical interpretations of genomic variations into electronic medical records (EMRs)/electronic health records (EHRs). Today, various central EHR infrastructures have been constituted in many countries of the world including Turkey.

OBJECTIVE

The objective of this study was to concentrate on incorporating the personal single nucleotide polymorphism (SNP) data into the National Health Information System of Turkey (NHIS-T) for disease risk assessment, and evaluate the performance of various predictive models for prostate cancer cases. We present our work as a miniseries containing three parts: (1) an overview of requirements, (2) the incorporation of SNP into the NHIS-T, and (3) an evaluation of SNP incorporated NHIS-T for prostate cancer.

METHODS

For the first article of this miniseries, the scientific literature is reviewed and the requirements of SNP data integration into EMRs/EHRs are extracted and presented.

RESULTS

In the literature, basic requirements of genomic-enabled EMRs/EHRs are listed as incorporating genotype data and its clinical interpretation into EMRs/EHRs, developing accurate and accessible clinicogenomic interpretation resources (knowledge bases), interpreting and reinterpreting of variant data, and immersing of clinicogenomic information into the medical decision processes. In this section, we have analyzed these requirements under the subtitles of terminology standards, interoperability standards, clinicogenomic knowledge bases, defining clinical significance, and clinicogenomic decision support.

CONCLUSIONS

In order to integrate structured genotype and phenotype data into any system, there is a need to determine data components, terminology standards, and identifiers of clinicogenomic information. Also, we need to determine interoperability standards to share information between different information systems of stakeholders, and develop decision support capability to interpret genomic variations based on the knowledge bases via different assessment approaches.

InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia

In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia.