New Computational Tool For Rapid Identification Of Disease-Causing Variations In The Human Genome & Guides to Genomics Resources

Image via Wikipedia

From the 26 June Medical News Today article

Scientists from the University of Utah and Omicia, Inc., a privately held company developing tools to interpret personal genome sequences, have announced the publication in Genome Research of a new software tool called VAAST, the Variant Annotation, Analysis and Selection Tool, a probabilistic disease-causing mutation finder for individual human genomes.

The dramatic decline in DNA sequencing costs is making personal genome sequencing a reality. Already, significant progress has been made in applying whole genome sequencing to cancerprognosis and early childhood disease. Examples include the 2010 publications on Miller Syndrome in Nature Genetics and Science, and similar studies aimed at identifying the unknown genetic defects responsible for some early childhood diseases…

…However, a data interpretation bottleneck has limited the utility of personal genome information for medical diagnosis and preventive care. VAAST is a new algorithm to assist in overcoming this bottleneck. VAAST is the product of a collaboration between Mark Yandell, Ph.D., Associate Professor of Human Genetics at the University of Utah School of Medicine, and colleagues, and the Omicia scientific team under the leadership of Martin Reese, Ph.D., the company’s CEO and Chief Scientific Officer.

In the Genome Research paper, Yandell and colleagues show that VAAST provides a highly accurate, statistically robust means to rapidly search personal genomes for genes with disease-causing mutations. The authors demonstrate that as few as three genomes from unrelated children, or those of the parents and their two children, are sufficient to identify disease causing mutations.

“The big challenge in genomic medicine today is how to sift through the millions of variants in a personal genome sequence to identify the disease-relevant variations,” said Dr. Reese. “It’s a classic needle in a haystack problem, and VAAST goes a long way toward solving it. We look forward to integrating VAAST into the Omicia Genome Analysis System currently under development for clinical applications.”

Dr. Yandell added: “VAAST solves many of the practical and theoretical problems that currently plague mutation hunts using personal genome sequences. Our results demonstrate that this tool substantially improves upon existing methods with regard to statistical power, flexibility, and scope of use. Further, VAAST is automated, fast, works across all variant population frequencies and is sequencing platform independent.”

Two General Genomics Resources

• Public Health Genomics (US Centers for Disease Control and Prevention) information includes
• Family Health History with collection tools (as how to create a family health portrait), FAQs, fact sheets, and more
• Genetic Testing with information on the limitations for most genetic tests, FAQs, and more
• Links to Genomics Resources, including Disease and Genetic Information, Educational Materials, Genetic Testing, and Support Groups

 

• 

• Genetics Home Reference – Your  Guide to Understanding Genetic Conditions with information on diseases and conditions, information on specific genes, a handbook presenting basic information about genetics in clear language and links to online resources, and more

 

Related articles

• “When People Share their Genome on Facebook” (spittoon.23andme.com)
• Genome editing — a next step in genetic therapy — corrects hemophilia in animals (sciencedaily.com)
• Genome Study Solves Twins’ Mystery Illness (nlm.nih.gov)
• Genomics and social network analysis team up to solve disease outbreaks (eurekalert.org)
• Personal genome map solves Calif. teen’s illness (seattletimes.nwsource.com)
• Further Analysis on Improved Genome Assembly Indicates the Outbreak E. coli has Complex Genetics With Resistance to at Least Eight Antibiotics (prnewswire.com)
• Alzheimer’s may cause global cash crunch: experts (physorg.com)
• iPad App Genome Wowser Lets You Browse the Human Genome (news.dice.com)
• Genome sequence could reveal ‘Achilles’ heels’ of important wheat disease (physorg.com)
• We are all mutants (eurekalert.org)
• Now, browse the human genome with iPad app! (news.bioscholar.com)
• Blog – Human Genome Contaminated With Mycoplasma DNA (technologyreview.com)
• Complete Genomics Makes 29 Genomes Public (xconomy.com)
• Decoding human genes is the goal of a new open-source encyclopedia (eurekalert.org)
• Basques (?) in 1000 Genomes IBS (Iberian Spanish) sample (dienekes.blogspot.com)
• Genomics and social network analysis team up to solve disease outbreaks (medicalxpress.com)

Genetic Testing Web Site

The US National Human Genome Institute (NHGRI) **publishes Genetic Testing, which serves as an introduction to non-scientists from a research perspective.

The Web site Genetic Testing includes the following

• Overview of Genetic Testing , with a link to A Brief Primer on Genetic Testing (a summary of current genetic testing)
• The Growth of Genetic Testing Raises Questions
• Legislation on Genetic Testing
• NHGRI Interest in Genetic Testing, including its concerns (as genetic discrimination) and activities (as providing information for genetic counselors)
• Policy Recommendations
• (Links to) Reports on Genetic Testing from government and nonprofit agencies

 

**[ From About the Insitute ]NHGRI’s  initial mission was to map the human genome.  Its role has been expanded to include applying genome technologies to the study of specific diseases and study the genetic components of complex disorders. Its human genome sequence database is available to scientists worldwide.

The NHGRI Web site includes information about

• NHGRI research
• Information about genetics and genomics, rare diseases, patient care and more (for patients, the public, and health professionals)
• Educational materials about genetics and genomics for students and teachers
• Policy, legal and ethical issues in genetic research
• Latest news, media resources and information from NHGRI
• Education, training, professional development and career opportunities at NHGRI
• (Under the For You tab)
  Specialized information for Students, Educators, Patients, Health Professionals

 

Risks of Presymptomatic Direct-to-Consumer Genetic Testing

At home genetic testing kits have been available online for some time.  However geneticists have long warned about the dangers of consumers self testing without clinical guidance in self testing and self diagnosing.

The Food and Drug Administration has sent warning letters to at least 20 companies planning on selling these kits as over the counter items. The letters state  direct-to-c0nsumer  genetic testing may require FDA approval. At least one company has since postponed selling the kits in their stores.

Excerpts from a recent New England Journal of Medicine perspective on home genetic tests

When population screening for medical conditions is independent of any defined individual risk, the screening program should adhere to established principles in order to avoid undue harm and expense: there must be a suitable and acceptable test addressing an important health problem that has a recognizable latent or early symptomatic state, a well-understood natural history, and an accepted and available treatment or intervention.^4,5 Most genetic screening currently cannot meet such expectations. More important, DTC genetic screening may place a substantial burden on the health care system without providing demonstrable benefit.

….

The potential harms of DTC genetic testing include the loss of protections for patients offered by established health care delivery systems (e.g., doctor–patient confidentiality and beneficence), invalid analytic or clinical results from medical devices, and population screening without consensus on interpretation and follow-up. These risks must be balanced against the potential benefits of innovation. The government’s role in this arena should include both regulation and the funding of collaborative research that enables the optimal use of genetic information.