| dc.date.accessioned |
2010-11-25T12:19:58Z |
und |
| dc.date.accessioned |
2017-11-06T11:16:50Z |
|
| dc.date.available |
2010-11-25T12:19:58Z |
und |
| dc.date.available |
2017-11-06T11:16:50Z |
|
| dc.date.issued |
2007-01-29 |
|
| dc.identifier.uri |
http://hdl.handle.net/10138/21427 |
|
| dc.publisher |
Helsingin yliopisto |
fi |
| dc.publisher |
Helsingfors universitet |
sv |
| dc.publisher |
University of Helsinki |
en |
| dc.title |
Computational Identification of Recessive Mutations in Cancers using High Throughput SNP-arrays |
en |
| ethesis.department.URI |
http://data.hulib.helsinki.fi/id/225405e8-3362-4197-a7fd-6e7b79e52d14 |
|
| ethesis.department |
Institutionen för datavetenskap |
sv |
| ethesis.department |
Department of Computer Science |
en |
| ethesis.department |
Tietojenkäsittelytieteen laitos |
fi |
| ethesis.faculty |
Matematisk-naturvetenskapliga fakulteten |
sv |
| ethesis.faculty |
Matemaattis-luonnontieteellinen tiedekunta |
fi |
| ethesis.faculty |
Faculty of Science |
en |
| ethesis.faculty.URI |
http://data.hulib.helsinki.fi/id/8d59209f-6614-4edd-9744-1ebdaf1d13ca |
|
| ethesis.university.URI |
http://data.hulib.helsinki.fi/id/50ae46d8-7ba9-4821-877c-c994c78b0d97 |
|
| ethesis.university |
Helsingfors universitet |
sv |
| ethesis.university |
University of Helsinki |
en |
| ethesis.university |
Helsingin yliopisto |
fi |
| dct.creator |
Laakso, Marko |
|
| dct.issued |
2007 |
|
| dct.language.ISO639-2 |
eng |
|
| dct.abstract |
This thesis presents a highly sensitive genome wide search method for recessive mutations. The method is suitable for distantly related samples that are divided into phenotype positives and negatives. High throughput genotype arrays are used to identify and compare homozygous regions between the cohorts. The method is demonstrated by comparing colorectal cancer patients against unaffected references. The objective is to find homozygous regions and alleles that are more common in cancer patients.
We have designed and implemented software tools to automate the data analysis from genotypes to lists of candidate genes and to their properties. The programs have been designed in respect to a pipeline architecture that allows their integration to other programs such as biological databases and copy number analysis tools. The integration of the tools is crucial as the genome wide analysis of the cohort differences produces many candidate regions not related to the studied phenotype.
CohortComparator is a genotype comparison tool that detects homozygous regions and compares their loci and allele constitutions between two sets of samples. The data is visualised in chromosome specific graphs illustrating the homozygous regions and alleles of each sample. The genomic regions that may harbour recessive mutations are emphasised with different colours and a scoring scheme is given for these regions.
The detection of homozygous regions, cohort comparisons and result annotations are all subjected to presumptions many of which have been parameterized in our programs. The effect of these parameters and the suitable scope of the methods have been evaluated. Samples with different resolutions can be balanced with the genotype estimates of their haplotypes and they can be used within the same study. |
en |
| dct.language |
en |
|
| ethesis.language.URI |
http://data.hulib.helsinki.fi/id/languages/eng |
|
| ethesis.language |
English |
en |
| ethesis.language |
englanti |
fi |
| ethesis.language |
engelska |
sv |
| ethesis.supervisor |
Rousu, Juho |
|
| ethesis.supervisor |
Hautaniemi, Sampsa |
|
| ethesis.thesistype |
pro gradu-avhandlingar |
sv |
| ethesis.thesistype |
pro gradu -tutkielmat |
fi |
| ethesis.thesistype |
master's thesis |
en |
| ethesis.thesistype.URI |
http://data.hulib.helsinki.fi/id/thesistypes/mastersthesis |
|
| dct.identifier.urn |
URN:NBN:fi-fe20071065 |
|
| dc.type.dcmitype |
Text |
|
| dct.rights |
This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited. |
en |
| dct.rights |
Publikationen är skyddad av upphovsrätten. Den får läsas och skrivas ut för personligt bruk. Användning i kommersiellt syfte är förbjuden. |
sv |
| dct.rights |
Julkaisu on tekijänoikeussäännösten alainen. Teosta voi lukea ja tulostaa henkilökohtaista käyttöä varten. Käyttö kaupallisiin tarkoituksiin on kielletty. |
fi |
