Global genetic analysis

Porcine single nucleotide polymorphism (SNP) development and population structure of pigs assessed by validated SNPs

In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3'-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3'-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples.

Protein biomarkers for amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease with largely unknown pathogenesis that typically results in death within a few years from diagnosis. There are currently no effective therapies for ALS. Clinical diagnosis usually takes several months to complete and the long delay between symptom onset and diagnosis limits the possibilities for effective intervention and clinical trials. The establishment of protein biomarkers for ALS may aid an earlier diagnosis, facilitating the search for effective therapeutic interventions and monitoring drug efficacy during clinical trials. Biomarkers could also be used to discriminate between subtypes of ALS, to measure disease progression and to detect susceptibility for developing ALS or monitor adverse effects of drug treatment. The present review will discuss the opportunities and proteomic platforms used for biomarker discovery efforts in ALS, summarizing putative ALS protein biomarkers identified in different biofluids.

Haemophilia A: molecular insights

Haemophilia A is the most common inherited bleeding disorder caused by defects in the

Clin Chem Lab Med 2007;45:450–61.

Rapid genetic mapping in Neurospora crassa

Forward genetic analysis is the most broadly applicable approach to discern gene functions. However, for some organisms like the filamentous ascomycete Neurospora crassa, genetic mapping frequently represents a limiting step in forward genetic approaches. We describe an efficient method for genetic mapping in N. crassa that makes use of a modified bulked segregant analysis and PCR-based molecular markers. This method enables mapping with progeny from a single cross and requires only 90 PCR amplifications. Genetic distances between syntenic markers have been determined to ensure complete coverage of the genome and to allow interpolation of linkage data. As a result, most mutations should be mapped in less than one month to within 1-5 map units, a level of resolution sufficient to initiate map-based cloning efforts. This system also will facilitate analyses of recombination at a genome-wide level and is applicable to other perfect fungi when suitable markers are available.

A modified mutation detection method for large-scale cloning of the possible single nucleotide polymorphism sequences

Although the human genome has been nearly completely sequenced, the functions and the roles of the vast majority of the genes, and the influences of single nucleotide polymorphisms (SNPs) in these genes are not entirely known. A modified mutation detection method was developed for large-scale cloning of the possible SNPs between tumor and normal cells for facilitating the identification of genetic factors that associated with cancer formation and progression. The method involves hybridization of restriction enzyme-cut chromosomal DNA, cleavage and modification of the sites of differences by enzymes, and differential cloning of sequence variations with a designed vector. Experimental validations of the presence and location of sequence variations in the isolated clones by PCR and DNA sequencing support the capability of this method in identifying sequence differences between tumor cells and normal cells.

Translation research: from accurate diagnosis to appropriate treatment

This review article focuses on the various aspects of translational research, where research on human subjects can ultimately enhance the diagnosis and treatment of future patients. While we will use specific examples relating to the asbestos related cancer mesothelioma, it should be stressed that the general approach outlined throughout this review is readily applicable to other diseases with an underlying molecular basis. Through the integration of molecular-based technologies, systematic tissue procurement and medical informatics, we now have the ability to identify clinically applicable "genotype"-"phenotype" associations across cohorts of patients that can rapidly be translated into useful diagnostic and treatment strategies. This review will touch on the various steps in the translational pipeline, and highlight some of the most essential elements as well as possible roadblocks that can impact success of the program. Critical issues with regard to Institutional Review Board (IRB) and Health Insurance Portability and Accountability Act (HIPAA) compliance, data standardization, sample procurement, quality control (QC), quality assurance (QA), data analysis, preclinical models and clinical trials are addressed. The various facets of the translational pipeline have been incorporated into a fully integrated computational system, appropriately named Dx2Tx. This system readily allows for the identification of new diagnostic tests, the discovery of biomarkers and drugable targets, and prediction of optimal treatments based upon the underlying molecular basis of the disease.