Rutgers Professors Discuss Progress of Genomics in Medicine and Statistics
The field of medicine is continuing to grow with the help of many mathematical and scientific branches, especially through the merging of these professions.
According to the Memorial Sloan Kettering Cancer Center, combining computer algorithms and databases with findings in biology greatly enhances biological research in a field known as computational biology. Some of these computational methods include using genomic data and genomics, which is what principal investigators Tara Matise, Steve Buyske and co-investigator Jinchuan Xing are focused on.
According to the Department of Genetics, all three were awarded a $3.8 million four-year grant to head the coordinating center at the Genome Sequencing Program (GSP) and are involved, on a larger scale, in the merging of the world of biology with the world of computer science and mathematics.
GSP is one of the research efforts funded by the National Human Genome Research (NHGRI), said Professor Tara Matise, professor in the Department of Genetics, head of the Laboratory of Computational Genetics, and a member of the Human Genetics Institute of New Jersey.
NHGRI is part of the National Institutes of Health (NIH), which provides research funding to thousands of scientists, Matise said.
“NHGRI supports the development of resources and technology that will accelerate genome research and its application to human health and funds a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease,” Matise said.
According to National Human Genome Research Institute website, the NHGRI had various accomplishments in recent years, some of which include identifying genes responsible for multiple human genetic diseases as well developing new ways to map, sequence and interpret some vertebrate genomes.
Biological as well as genetic concepts appear to play an important role in medicine.
“I think they play an important role in medicine because those who are looking to pursue a career in this field should be able to understand the ins and outs of the human body,” said Monica Pustylnik, a first-year student in the School of Arts and Sciences. “In so many cases, issues are caused by small, unseeable malfunctions, such as those that can exist within DNA, for example.”
Genomic research’s role in advancing medicine involves the study of genomes. A genome is the collection of all the DNA in one cell of a human, said Steve Buyske, an associate research professor in the Department of Statistics and Biostatistics.
Fifteen to 30 years ago, there would only be a few places in the genome where scientists could determine what the variation was. Most of it was inferred just by what was physically observable, also known as the phenotype. Now with modern machines, scientists can determine almost every single base pair, Buyske said.
The GSP, which is funded by the NHGRI, plays a crucial role in understanding and improving genomic research.
"We run the coordinating center at the GSP, which has several different branches. The NHGRI staff are very involved in this project. One branch focuses on Mendelian disorders, which are diseases that are caused by a single gene change," Buyske said.
Another big branch is the Centers for Common Disease Genomics (CCDG) and this program helps to understand the role genomics plays in conditions such as heart disease, autism, asthma, Type 1 diabetes and more. These conditions have a strong genetic component to them but it is not as simple as it sounds, he said.
Buyske also notes the various types of disease that stem from different genetic backgrounds and causes.
“Whereas in Mendelian Genetics, in which the individual disease is quite rare and there are typically a small number of families, for these common diseases you need to have a bigger sample size in order to detect for the disorder,” Buyske said.
Researchers must not only take biology into consideration, but statistical data as well when doing genomic research.
Generating data and implementing statistical analysis are key steps in most scientific studies, including genomics and other areas of biological research, Matise said.
“In genomics, advancing technologies facilitate the generation of increasingly larger data sets. Specific training is needed to be able to manage and understand these large datasets, and to develop methods and computer programs that can efficiently analyze very large data sets,” she said.
In addition to having a solid foundation in both mathematics and the sciences, researchers must also use certain techniques in genomic research.
Genomic sequencing is the process of determining the DNA sequence of a genome — which is the complete genetic sequence of a human or another organism. In humans (and other mammals), DNA is typically extracted from blood. There are many different methods in use for DNA sequencing, Matise said.
Methods, techniques and the materials genomic researchers work with have advanced.
"I would consider genetic experiments done 40 years ago to be relatively simple," Buyske said. "Today there is a cheap technology called a genome-wide association study (GWAS), which consists of microarrays that can help delineate the genotype not at every place on the genome but, say, 5,000,000 places on a genome."
There is also the potential for unwanted causes that could skew the research.
There is a lot of “noise” for all sorts of reasons such as environmental factors like diet, Buyske said. Another might be that one spot on the genome could get affected by other spots. Statisticians spend a lot of effort in working out techniques that can decrease the “noise.”
Buyske noted he and his colleagues also deal with non-Mendelian disorders, in which it is not a matter of just one gene or one spot on a chromosome being affected.
"There are some conditions that vary from person to person where there are chunks of genes missing or extra chunks inserted. Then the question remains, how does that turn into the architecture of a trait? This is asking what is the extent to which something is genetically determined as opposed to caused mainly by environmental factors. It turns out to be a very complex question," Buyske said.
Despite these complex questions researchers are still trying to answer, there have been breakthroughs and advancements in the fields of genomics and biostatistics.
"My colleague, Professor Buyske, mentioned drastically reduced costs over time for DNA sequencing. Another exciting development (is) tools designed to help patients with rare genetic disorders to share information about their disorder so that affected individuals, their families and the scientists who study these rare disorders can become aware of others with whom they might connect and collaborate," Matise said.
The more patients with the same underlying genetic cause that are included in a study, the greater the power of the study to successfully find the mutation, she said.
As the understanding of human genetics and genomics continues to advance, so will the medical knowledge of certain diseases.
“Being able to grasp these concepts can aid in finding cures to genetic disease, as the preliminary knowledge will help further research and understanding,” Pustylnik said.