http://www.digitaljournal.com/tech-and-science/science/new-open-software-allows-diagnosis-of-genetic-diseases/article/497034

New open software allows diagnosis of genetic diseases

Posted Jul 6, 2017 by Tim Sandle
Genetic diseases are difficult to diagnose and the accuracy (or otherwise) of the diagnosis impact upon patient health. To help with this a new open-source software tool called Mendel, MD has been launched.
The structure of the DNA
The structure of the DNA
Zephyris / Wikipedia
The Mendel, MD platform could help medics to analyze patients' genetic data and from this diagnose diseases caused by gene mutations. The reference in the software title to “Mendel” is a reference to Gregor Johann Mendel. Mendel was a scientist, Augustinian friar and abbot of St. Thomas' Abbey in Brno, Margraviate of Moravia. He is best known as the founder of the modern science of genetics.
To assist with the diagnosis of diseases caused by genetic mutations advances have been made with gene sequencing, allowing for the sequencing of a patient's entire genome or exome. Gene sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases — adenine, guanine, cytosine, and thymine — in a strand of DNA. Sequencing relating to the exome is more specialized still; the “exome” consists of all the genome’s exons, which are the coding portions of genes. These are the parts of the genome used to build proteins.
Through these processes medics can pinpoint culprit mutations and make an accurate diagnosis. There’s one downside: more often the software needed to analyze these sequences is too costly or too complex for many healthcare professionals to use. This where the idea for Mendel, MD came in. The core idea was create software both easy for physicians to use and which was free of charge.
To use the software, a medic can upload a patient's whole genome or exome sequence though an Internet accessible interface. Once uploaded the sequence is analyzed and filtered using computational tools and then cross-checked against databases of disease-causing mutations. The output allows a clinically investigation to take place and this aids the medic in arriving at a final diagnosis.
To test out the open source platform, the developers from the Universidade Federal de Minas Gerais, Brazil ran a series of trials in their own institution and at GENE -- Núcleo de Genética Médica, Brazil, and the Children's University Hospital in Dublin, Ireland. The findings indicate that Mendel,MD is efficient and accurate for identifying disease-causing mutations in patients.
The new software and its application have been described in the journal PLOS Computational Biology. The research paper is titled “Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders.”