rmvPFBAM: Removing Primers from BAM Files Based on Amplicon-Based Next-Generation Sequencing and Cloud Computing When Analyzing Personal Genome Data

Personal genomic data constitute one important part of personal health data. However, due to the large amount of personal genomic data obtained by the next-generation sequencing technology, special tools are needed to analyze these data. In this article, we will explore a tool analyzing cloud-based large-scale genome sequencing data. Analyzing and identifying genomic variations from amplicon-based next-generation sequencing data are necessary for the clinical diagnosis and treatment of cancer patients. When processing the amplicon-based next-generation sequencing data, one essential step is removing primer sequences from the reads to avoid detecting false-positive mutations introduced by nonspecific primer binding and primer extension reactions. At present, the removing primer tools usually discard primer sequences from the FASTQ file instead of BAM file, but this method could cause some downstream analysis problems. Only one tool (BAMClipper) removes primer sequences from BAM files, but it only modified the CIGAR value of the BAM file, and false-positive mutations falling in the primer region could still be detected based on its processed BAM file. So, we developed one cutting primer tool (rmvPFBAM) removing primer sequences from the BAM file, and the mutations detected based on the processed BAM file by rmvPFBAM are highly credible. Besides that, rmvPFBAM runs faster than other tools, such as cutPrimers and BAMClipper.

The Need for Education and Clinical Best Practice Guidelines in the Era of Direct-to-Consumer Genomic Testing

Many people share the results of their direct-to-consumer personal genomic testing (DTC-PGT) within the primary care setting, seeking interpretation of and counsel about the results. However, most primary care physicians (PCPs) are not trained to interpret and communicate about DTC-PGT results. New guidelines must be developed to help PCPs maximize the potential of emerging DTC-PGT technologies.

Using Personal Genomic Data within Primary Care: A Bioinformatics Approach to Pharmacogenomics

One application of personalized medicine is the tailoring of medication to the individual, so that the medication will have the highest chance of success. In order to individualize medication, one must have a complete inventory of all current pharmaceutical compounds (a detailed formulary) combined with pharmacogenetic datasets, the genetic makeup of the patient, their (medical) family history and other health-related data. For healthcare professionals to make the best use of this information, it must be visualized in a way that makes the most medically relevant data accessible for their decision-making. Similarly, to enable bioinformatics analysis of these data, it must be prepared and provided through an interface for controlled computational analysis. Due to the high degree of personal information gathered for such initiatives, privacy-sensitive implementation choices and ethical standards are paramount. The Personal Genetic Locker project provides an approach to enable the use of personal genomic data in primary care. In this paper, we provide a description of the Personal Genetic Locker project and show its utility through a use case based on open standards, which is illustrated by the 4MedBox system.

Self-Regulation of Genomic Studies and Prospects of Personified Medicine

A secular trend of the development of medicine in the 20th century was on the ways of strengthening the foundations of public health, formation of systems of affordable medical care. Human genome deciphering opens wide prospects for using the obtained data in medicine. In recent years commercial medical organizations have been developing genetic research and personal genomic testing services. The paper is devoted to the analysis of the importance of legal self-regulation in the field of genomic counseling in the Russian Federation. The authors investigate the prospects of the introduction of personalized medicine and limitations that arise today in one of the areas of the approach under consideration, namely: forecasting predisposition to diseases of mixed nature, which is related to the peculiarities of development of medical and demographic situation in the world. The question is raised about the need for broad population studies to verify the risk values for diseases with low genetic determinacy. The authors conclude that it is impossible to predict what medicine of the future will be, but the results of genome decryption and increasing availability of personal data represent a unique social phenomenon that should be developed within the legal framework. In the coming years, the debate on the role of legal mechanisms in the self-regulation of genetic research and genetic services will become increasingly important. At the international level, this discussion will be focused on the fundamental issue of respect for individual rights in the interpretation of the data received. As genetic advice evolves, the issue of responsibility for the information provided and the availability of national regulatory mechanisms within the framework of state regulation or self-regulated professional associations will become a key concern.

The Need for Education and Clinical Best Practice Guidelines in the Era of Direct-to-Consumer Genomic Testing (Preprint)

UNSTRUCTURED Many people share the results of their direct-to-consumer personal genomic testing (DTC-PGT) within the primary care setting, seeking interpretation of and counsel about the results. However, most primary care physicians (PCPs) are not trained to interpret and communicate about DTC-PGT results. New guidelines must be developed to help PCPs maximize the potential of emerging DTC-PGT technologies.

Genomics Education in the Era of Personal Genomics: Academic, Professional, and Public Considerations

Since the completion of the Human Genome Project in 2003, genomic sequencing has become a prominent tool used by diverse disciplines in modern science. In the past 20 years, the cost of genomic sequencing has decreased exponentially, making it affordable and accessible. Bioinformatic and biological studies have produced significant scientific breakthroughs using the wealth of genomic information now available. Alongside the scientific benefit of genomics, companies offer direct-to-consumer genetic testing which provide health, trait, and ancestry information to the public. A key area that must be addressed is education about what conclusions can be made from this genomic information and integrating genomic education with foundational genetic principles already taught in academic settings. The promise of personal genomics providing disease treatment is exciting, but many challenges remain to validate genomic predictions and diagnostic correlations. Ethical and societal concerns must also be addressed regarding how personal genomic information is used. This genomics revolution provides a powerful opportunity to educate students, clinicians, and the public on scientific and ethical issues in a personal way to increase learning. In this review, we discuss the influence of personal genomics in society and focus on the importance and benefits of genomics education in the classroom, clinics, and the public and explore the potential consequences of personal genomic education.