waviCGH: a web application for the analysis and visualization of genomic copy number alterations

waviCGH is a versatile web server for the analysis and comparison of genomic copy number alterations in multiple samples from any species. waviCGH processes data generated by high density SNP-arrays, array-CGH or copy-number calls generated by any technique. waviCGH includes methods for pre-processing of the data, segmentation, calling of gains and losses, and minimal common regions determination over a set of experiments. The server is a user-friendly interface to the analytical methods, with emphasis on results visualization in a genomic context. Analysis tools are introduced to the user as the different steps to follow in an experimental protocol. All the analysis steps generate high quality images and tables ready to be imported into spreadsheet programs. Additionally, for human, mouse and rat, altered regions are represented in a biological context by mapping them into chromosomes in an integrated cytogenetic browser. waviCGH is available at http://wavi.bioinfo.cnio.es

Arvutuslikud meetodid DNA koopiaarvu määramiseks

Väitekirja elektrooniline versioon ei sisalda publikatsioone.DNA koopiaarvu variantideks või muutusteks nimetatakse selliseid erinevusi inimeste geneetilises materjalis, mille puhul mingi DNA lõigu koopiaarv on erinev oodatavast koopiaarvust kaks (üks koopia mingit kindlat DNA järjestust emalt päritud kromosoomil ja üks koopia isalt päritud kromosoomil). DNA koopiate vähenemist nimetatakse deletsiooniks ning vastavaid DNA variante nimetatakse deletsioonideks. DNA koopiate juurdetulemist nimetatakse duplitseerumiseks ning selliseid kahest suurema koopiaarvuga variante vastavalt duplikatsioonideks. Antud doktoritöös uuriti inimese DNA koopiaarvu variante, nende seotust erinevate haigustega ja nende tekkimise ja pärandumise eripärasid. Kasutades DNA mikrokiipe ehk geenikiipe uuriti esmalt kas ja millised DNA koopiaarvu muutused võivad olla seotud vaimse arengu mahajäämusega (VAM-ga). Uurides perekondasid, kus ühel või mitmel liikmel oli diagnoositud VAM, leiti mitmeid juba varem VAM-ga seostatud DNA koopiaarvu muutusi ning lisaks leiti ka mitmeid uusi DNA koopiaarvu variante, mille esinemine võib olla seotud VAM-e väljakujunemisega. Sarnane uuring viidi läbi ka korduva spontaanse raseduse katkemise probleemiga paaride ja naiste puhul. Võrreldes nende patsientide gruppi kuuluvate naiste DNA koopiaarvu muutusi ning nende sagedusi terveid emasid sisaldavate kontroll-grupi indiviidide omadega, leiti statistiliselt ja bioloogiliselt oluline erinevus muutunud koopiaarvuga DNA lõigus, mis sisaldab PDZD2 ja GOLPH3 geene ja kus esinevate duplikatsioonide „omamine“ suurendas naistel märkimisväärselt spontaanse raseduse katkemise ohtu. Doktoritöö viimases osas uuriti Tartu Ülikooli Eesti Geenivaramu ja rahvusvahelise HapMap projekti poolt kogutud tõsiste haigusteta inimestel esinevaid DNA koopiaarvu muutusi ja nende pärandumist perekondades. Selle uuringu üheks huvitavamaks tulemuseks oli deletsioonide alapärandumine vanematelt lastele ehk deletsioone kandvaid DNA regioone esines laste genoomides oluliselt vähem, kui normaalse Mendeliaalse (juhusliku) pärandumise korral oleks oodata võinud. Uurides duplikatsioonide regioone perekondades leiti aga, et kaks kolmandikku duplikatsioonides esinevatest DNA koopiatest ei olnud identsed (üksteise täpsed koopiad), vaid mõnevõrra erinevad, demonstreerides seniajani teadmata olnud alleelse varieeruvuse määra DNA duplikatsioonide regioonides.DNA copy number variation is a type of genetic variation in which case the number of copies of a particular region of a chromosome is altered from its normal state. In the non-repetitive portion of the human genome, the normal haploid copy number is one – one copy of each sequence per chromosome. Accordingly, the normal diploid copy number in humans is two – one copy inherited from both parents. A copy number variant (CNV) can result from either a loss of copies (most often called a deletion) or gain of copies (called a duplication or amplification). In this thesis we studied DNA copy number variation in human – how CNVs emerge and how they are inherited from parents to offspring. We also analysed CNVs in the context of few different diseases. By using DNA microarrays we first aimed to determine if CNVs are associated with mental retardation (MR). For this we studied not only index cases with MR but larger nuclear families, where we discovered several already MR-associated CNVs and also a few novel CNV regions that are possibly associated with predisposition to MR. Similar study was conducted in couples and females suffering from recurrent miscarriage. By comparing CNVs and their frequencies in the latter group to these of healthy mothers, we discovered a multi-copy duplication at 5p13.3 that disrupts PDZD2 and GOLPH3 genes and significantly increases maternal risk for pregnancy complications. In the last part of this thesis we studied how CNVs are inherited in Estonian nuclear families (22 trios and 12 families with multiple siblings) and in HapMap Yoruban trios. We determined that deletion-carrying chromosomal regions were observed in the offspring slightly less frequently than expected by random Mendelian inheritance. By analysing duplication-carrying chromosomal regions in these families, we discovered that in two-thirds of such regions the duplicated copies of the underlying DNA sequence were not exactly identical but somewhat different, allowing us to define alternative allelic copies within these copy number gain-carrying chromosomal regions and demonstrating extensive and to-date unmeasured allelic variability in multi-copy CNV regions of the human genome

Visualization-based discovery and analysis of genomic aberrations in microarray data

Abstract Background Chromosomal copy number changes (aneuploidies) play a key role in cancer progression and molecular evolution. These copy number changes can be studied using microarray-based comparative genomic hybridization (array CGH) or gene expression microarrays. However, accurate identification of amplified or deleted regions requires a combination of visual and computational analysis of these microarray data. Results We have developed ChARMView, a visualization and analysis system for guided discovery of chromosomal abnormalities from microarray data. Our system facilitates manual or automated discovery of aneuploidies through dynamic visualization and integrated statistical analysis. ChARMView can be used with array CGH and gene expression microarray data, and multiple experiments can be viewed and analyzed simultaneously. Conclusion ChARMView is an effective and accurate visualization and analysis system for recognizing even small aneuploidies or subtle expression biases, identifying recurring aberrations in sets of experiments, and pinpointing functionally relevant copy number changes. ChARMView is freely available under the GNU GPL at http://function.princeton.edu/ChARMView.</p