From The MarthLab
Genetic and epigenetic variations (or polymorphisms) are important, often heritable landmarks of a species' genome and many of them cause phenotypic differences. Such inherited or somatic polymorphisms in the human genome can lead to hereditary diseases.
Genetic polymorphisms occur at different levels within the genome. The simplest and most common are single-nucleotide polymorphisms (SNPs) or single-base changes. Often short sections of DNA can be inserted into or deleted from an individual's genome (short INDELs). Often longer regions are deleted from and individual's chormosomes; other regions may be present in multiple copies (chromosomal amplifications); sometimes long sections of chromosomes are translocated. These large-scale variations are termed structural genetic variations. Finally, epigenetic polymorphisms do not involve actual genetic changes but may also cause important phenotypic effects. Examples for epigenetic varitaions are changes in DNA methylation or in histone positioning.
This laboratory develops computational tools (algorithms and computer programs) for the discovery of the full spectrum of genetic polymorphism types. We have had extensive experience with SNP and short-INDEL discovery, and developed one of the first polymorphism discovery computer programs, PolyBayes.
Recently, a number of next-generation sequencing machines became available that produce orders of magnitudes more bases per run than traditional capillary sequencers e.g. those that were used for sequencing the human genome. Our current focus is to develop computer software to process and analyze the vast amount of sequence data generated by the new technologies. We are developing base calling software, reference sequence guided sequence assembly programs, and sequence viewers. We are also updating our SNP discovery software to enable the analysis of data from every new sequencing platform. We are also developing sofware for the detection of structural polymorphisms e.g. in cancer tissue. We are also building tools for transcriptome sequencing applications, both for expression analysis and novel transcript discovery.
