Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays

MOTIVATION: Single nucleic polymorphisms (SNPs) are one of the most abundant genetic variations in the human genome. Recently, several platforms for high-throughput SNP analysis have become available, capable of measuring thousands of SNPs across the genome. Tools for analysing and visualizing these large genetic data sets in biologically relevant manner are rare. This hinders effective use of the SNP-array data in research on complex diseases, such as cancer. RESULTS: We describe a computational framework to analyse and visualize SNP-array data, and link the results in relevant databases. Our major objective is to develop methods for identifying DNA regions that likely harbour recessive mutations. Thus, the algorithms are designed to have high sensitivity and the identified regions are ranked using a scoring algorithm. We have also developed annotation tools that automatically query gene IDs, exon counts, microarray probe IDs, etc. In our case study, we apply the methods for identifying candidate regions for recessively inherited colorectal cancer predisposition and suggest directions for wet-lab experiments. AVAILABILITY: R-package implementation is available at http://www.ltdk.helsinki.fi/sysbio/csb/downloads/CohortComparator/     

Cyclin A and Ki-67 with DNA content in benign and malignant prostatic epithelial lesions.

OBJECTIVE: To evaluate the usefulness of immunohistochemical staining of cyclin A and Ki-67 together with DNA content in the classification of benign prostatic hyperplasia, prostatic intraepithelial neoplasm (PIN) and prostatic carcinoma foci and to compare these parameters with each other and with parameters obtained from conventional histopathology. STUDY DESIGN: We selected 37 carcinoma, 18 PIN and 8 hyperplastic foci from prostatectomies done during 1996 and 1997 at Turku University Central Hospital. Cyclin A and Ki-67 staining was assessed by immunohistochemistry and DNA content by image cytometry. RESULTS: The hyperplastic, PIN and carcinoma foci differed clearly in their 2.5c exceeding rates, image cytometric proliferation indices and staining indices for cyclin A and Ki-67. No significant differences were found between these histologic entities in their modal DNA ploidy values. In carcinomas, cyclin A and Ki-67 indices differed between low, intermediate and high Gleason and World Health Organization grading groups. Diploid and tetraploid carcinomas had similar cyclin A and Ki-67 indices, which differed from those of aneuploid carcinomas. CONCLUSION: The 2.5c exceeding rate and image cytometric proliferation index as well as the cyclin A and Ki-67 indices differed significantly between different types of prostatic lesions. Cyclin A and Ki-67 had good correlations with the histologic grade of carcinoma.     

Is Cupressus sempervirens native in Italy? An answer from genetic and palaeobotanical data

This study represents the first large-scale analysis using nuclear molecular markers to assess genetic diversity and structure of Cupressus sempervirens L.. Genetic and fossil data were combined to infer the possible role of human activity and evolutionary history in shaping the diversity of cypress populations. We analysed 30 populations with six polymorphic nuclear microsatellite markers. Dramatic reductions in heterozygosity and allelic richness were observed from east to west across the species range. Structure analysis assigned individuals to two main groups separating central Mediterranean and eastern populations. The two main groups could be further divided into five subgroups which showed the following geographical distributions: Turkey with the Greek islands Rhodes and Samos, Greece (Crete), Southern Italy, Northern Italy, Tunisia with Central Italy. This pattern of genetic structure is also supported by samova and Barrier analyses. Palaeobotanical data indicated that Cupressus was present in Italy in the Pliocene, Pleistocene and Holocene. Furthermore, our molecular survey showed that Italian cypress populations experienced bottlenecks that resulted in reduced genetic diversity and allelic richness and greater genetic differentiation. Recent colonization or introduction may also have influenced levels of diversity detected in the Italian populations, as most individuals found in this range today have multilocus genotypes that are also present in the eastern range of the species. The data reveal a new interpretation of the history of cypress distribution characterized by ancient eastern populations (Turkey and Greek islands) and a mosaic of recently introduced trees and remnants of ancient, depauperate populations in the central Mediterranean range.