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Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. We demonstrate the method using both simulated data (calibrated from experiments on Drosophila melanogaster) and real data from five distinct crosses within the flowering plant genus Mimulus. Application of GOOGA to the Mimulus data corrects numerous errors (misplaced sequences) in the M. guttatus reference genome and confirms or detects eight large inversions polymorphic within the species complex. Finally, we show how this method can be applied in genomic scans to improve the accuracy and resolution of Quantitative Trait Locus (QTL) mapping.
This article was published in the following journal.
Name: PLoS computational biology
There is an established relationship between primary DNA sequence, secondary and tertiary chromatin structure, and transcriptional activity, suggesting that observed differences in one of these proper...
Elucidating the complete network of protein-protein interactions, or interactome, is a fundamental goal of the post-genomic era, yet existing interactome maps are far from complete. To increase the th...
Circulating tumor cells (CTCs) can reliably be identified in cancer patients and are associated with clinical outcome. Next-generation "liquid biopsy" technologies will expand CTC diagnostic investiga...
Bartonella is a genetically diverse group of vector-borne bacteria. Over 40 species have been characterized to date, mainly from mammalian reservoirs and arthropod vectors. Rodent reservoirs harbor on...
Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequenc...
Whether a mapping algorithm "Ripple-mapping" is able to rapidly identify the areas of long-duration multicomponent electrograms which constitute the targets for ablation for an automated s...
This study uses two AcQMap imaging and electroanatomical mapping systems (Acutus Medical) to simultaneously visualise and map patterns of wavefront propagation in both the left and right a...
The purpose of this study is to assess whether the use of genomics can help identify patient specific treatment choices in cancer. In order to test this, the investigators plan to use geno...
Currently, for a patient with intellectual disability without a recognizable syndrome (most cases), the way to diagnosis is often long, tedious and expensive because different approaches a...
Hepatocellular carcinoma (HCC) is a frequent complication of cirrhosis. Occurrence of HCC could be linked with multiple functional region of genome. The determining of a genomic mapping o...
A method for analyzing and mapping differences in the copy number of specific genes or other large sequences between two sets of chromosomal DNA. It is used to look for large sequence changes such as deletions, duplications, or amplifications within the genomic DNA of an individual (with a tumor for example) or family members or population or between species.
Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.
Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.
A beta-2 selective adrenergic antagonist. It is used primarily in animal and tissue experiments to characterize beta-2 receptor involvement and identify beta-2 receptors.
Methods used for studying the interactions of antibodies with specific regions of protein antigens. Important applications of epitope mapping are found within the area of immunochemistry.
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...