Nav: Home

Compiling big data in a human-centric way

May 11, 2017

HOUSTON - (May 11, 2017) - When a group of researchers in the Undiagnosed Disease Network at Baylor College of Medicine realized they were spending days combing through databases searching for information regarding gene variants, they decided to do something about it. By creating MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) they are now able to help not only their own lab but also researchers everywhere search databases all at once and in a matter of minutes.

This collaborative effort among Baylor, the Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital and Harvard Medical School is described in the latest online edition of the American Journal of Human Genetics.

Big data search engine

"One big problem we have is that tens of thousands of human genome variants and phenotypes are spread throughout a number of databases, each one with their own organization and nomenclature that aren't easily accessible," said Julia Wang, an M.D./Ph.D. candidate in the Medical Scientist Training Program at Baylor and a McNair Student Scholar in the Bellen lab, as well as first author on the publication. "MARRVEL is a way to assess the large volume of data, providing a concise summary of the most relevant information in a rapid user-friendly format."

MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER, all separate databases to which researchers across the globe have contributed, sharing tens of thousands of human genome variants and phenotypes. Since there is not a set standard for recording this type of information, each one has a different approach and searching each database can yield results organized in different ways. Similarly, decades of research in various model organisms, from mouse to yeast, are also stored in their own individual databases with different sets of standards.

Dr. Zhandong Liu, assistant professor in pediatrics - neurology at Baylor, a member of the Jan and Dan Duncan Neurological Research Institute at Texas Children's and co-corresponding author on the publication, explains that MARRVEL acts similar to an internet search engine.

"This program helps to collate the information in a common language, drawing parallels and putting it together on one single page. Our program curates model organism specific databases to concurrently display a concise summary of the data," Liu said.

Supporting researchers

A user can first search for a gene or variant, Wang explains. Results may include what is known about this gene overall, whether or not that gene is associated with a disease, whether it is highly occurring in the general population and how it is affected by certain mutations.

"MARRVEL helps to facilitate analysis of human genes and variants by cross-disciplinary integration of 18 million records so we can speed up the discovery process through computation," Liu said. "All this information is basically inaccessible unless researchers can access it efficiently and apply it to their own work to find causes, treatments and hopefully identify new diseases."

Collaboration

This project started as a necessity for the Model Organism Screening Center for the Undiagnosed Disease Network at Baylor, but as it grew, the group began reaching out to researchers in different disciplines for feedback on how MARRVEL might benefit them.

"This program is just the start. I think our tool is going to be a model for us to help clinicians and basic scientists more efficiently use the information already publicly available," Wang said. "It will help us understand and process all of the different mutations that researchers are discovering."

"The most exciting part is how this project is bringing so many different researchers together," Liu said. "We are working with labs we might not have normally collaborated with, trying to put together a puzzle of all this data."

Both Wang and Liu are thankful to the contributions from the genetics communities allowing them access to the databases as they developed MARRVEL.

Others who contributed to the findings include Drs. Rami Al-Ouran, Seon-Young Kim, Ying-Wooi Wan, Michael Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, and Hugo Bellen (Howard Hughes Medical Institute at Baylor) all with Baylor College of Medicine; Yanhui Hu, Aram Comjean, Stephanie E. Mohr, and Norbert Perrimon (Howard Hughes Medical Institute at Harvard Medical School) all with Harvard Medical School.

For full funding and acknowledgements please see full publication (available after embargo lifts)
-end-
Both Wang and Liu are thankful to the contributions from the genetics communities allowing them access to the databases as they developed MARRVEL. Others who contributed to the findings include Drs. Rami Al-Ouran, Seon-Young Kim, Ying-Wooi Wan, Michael Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, and Hugo Bellen (Howard Hughes Medical Institute at Baylor) all with Baylor College of Medicine; Yanhui Hu, Aram Comjean, Stephanie E. Mohr, and Norbert Perrimon (Howard Hughes Medical Institute at Harvard Medical School) all with Harvard Medical School.

For full funding and acknowledgements please see full publication (available after embargo lifts)

Baylor College of Medicine

Related Disease Articles:

Findings support role of vascular disease in development of Alzheimer's disease
Among adults who entered a study more than 25 years ago, an increasing number of midlife vascular risk factors, such as obesity, high blood pressure, diabetes, high cholesterol and smoking, were associated with elevated levels of brain amyloid (protein fragments linked to Alzheimer's disease) later in life, according to a study published by JAMA.
Dietary factors associated with substantial proportion of deaths from heart disease, stroke, and disease
Nearly half of all deaths due to heart disease, stroke, and type 2 diabetes in the US in 2012 were associated with suboptimal consumption of certain dietary factors, according to a study appearing in the March 7 issue of JAMA.
Study links changes in oral microbiome with metabolic disease/risk for dental disease
A team of scientists from The Forsyth Institute and the Dasman Diabetes Institute in Kuwait have found that metabolic diseases, which are characterized by high blood pressure, high blood sugar, and obesity -- leads to changes in oral bacteria and puts people with the disease at a greater risk for poor oral health.
Fatty liver disease contributes to cardiovascular disease and vice versa
For the first time, researchers have shown that a bi-directional relationship exists between fatty liver disease and cardiovascular disease.
Seroprevalence and disease burden of chagas disease in south Texas
A paper published in PLOS Neglected Diseases led by researchers at the National School of Tropical Medicine at Baylor College of Medicine suggests that the disease burden in southern Texas is much higher than previously thought.
Maternal chronic disease linked to higher rates of congenital heart disease in babies
Pregnant women with congenital heart defects or type 2 diabetes have a higher risk of giving birth to babies with severe congenital heart disease and should be monitored closely in the prenatal period, according to a study published in CMAJ.
Citrus fruits could help prevent obesity-related heart disease, liver disease, diabetes
Oranges and other citrus fruits are good for you -- they contain plenty of vitamins and substances, such as antioxidants, that can help keep you healthy.
Gallstone disease may increase heart disease risk
A history of gallstone disease was linked to a 23 percent increased risk of developing coronary heart disease.
New disease gene will lead to better screening for pediatric heart disease
Cardiomyopathy, or a deterioration of the ability of the heart muscle to contract, generally leads to progressive heart failure.
Early weight loss in Parkinson's disease patients may signify more serious form of disease
A study led by a Massachusetts General Hospital investigator finds evidence of an association between weight loss in patients with early Parkinson's disease and more rapid disease progression.

Related Disease Reading:

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Digital Manipulation
Technology has reshaped our lives in amazing ways. But at what cost? This hour, TED speakers reveal how what we see, read, believe — even how we vote — can be manipulated by the technology we use. Guests include journalist Carole Cadwalladr, consumer advocate Finn Myrstad, writer and marketing professor Scott Galloway, behavioral designer Nir Eyal, and computer graphics researcher Doug Roble.
Now Playing: Science for the People

#530 Why Aren't We Dead Yet?
We only notice our immune systems when they aren't working properly, or when they're under attack. How does our immune system understand what bits of us are us, and what bits are invading germs and viruses? How different are human immune systems from the immune systems of other creatures? And is the immune system so often the target of sketchy medical advice? Those questions and more, this week in our conversation with author Idan Ben-Barak about his book "Why Aren't We Dead Yet?: The Survivor’s Guide to the Immune System".