239 research outputs found
Computational Estimation of Fetal DNA Fraction in Low Coverage Whole Genome Sequencing Data
No full textKäesoleva töö eesmärk oli leida ja kalibreerida arvutuslik metoodika loote rakuvaba DNA fraktsiooni määramiseks raseda naise vereproovis. Tegemist on rakendusliku teadusuuringuga, mis on eeltingimuseks NIPT testi usaldusväärseks rakendamiseks tervishoiusüsteemis. NIPT on kõige täpsem ja kaasaegsem mitteinvasiivne loote sünnieelne kromosoomihaiguste sõeluuring, mis põhineb madala katvusega täisgenoomi sekveneerimisandmete analüüsil. Metoodika võimaldab määrata loote rakuvaba DNA hulka raseda naise vereproovis nii poiss- kui ka tüdruklootele, mis on vajalik, et iga raseduse rakuvaba DNA analüüsi tulemus oleks usaldusväärne ja arstile ning patsiendile edastatud tulemus tõene. Käesolevas töös kasutati madala katvusega üle-genoomsetest Illumina platvormiga läbiviidud sekveneerimise katsetest saadud 416 Eesti päritolu naise NIPT proove, et välja töötada Y-kromosoomi põhine loote rakuvaba DNA hulga määramine poiss-loodetele. Välja töötatud Y-kromosoomi põhist meetodit kasutati SeqFF arvutusliku metoodika valideerimiseks Eesti NIPT proovidel. SeqFF rakendamine Eesti NIPT proovidel võimaldab määrata loote rakuvaba DNA hulka nii poiss- kui ka tüdrukloodetel. Väljatöötatud algoritm on integreeritud Eestis pakutavasse NIPT täppismeditsiini teenusesse NIPTIFY.The aim of this thesis was to find and 'calibrate' computational methodology for estimating the proportion of cell-free fetal DNA (cffDNA) in pregnant women’s blood sample. This work was done as part of an applied research project aimed to develop a whole genome sequencing (WGS) based non-invasive prenatal testing (NIPT) medical screening test. NIPT is the most up-to-date, accurate and easily applied (non-invasive) prenatal screening method to detect fetal aneuploidies (for example trisomy 21, that causes Down syndrome) with high confidence and already during the first trimester of pregnancy. Commonly, NIPT is based on the low coverage WGS data, generated by the means of Illumina or some another platform technology. Computational tools used for aneuploidy detection can also estimate the proportion of cffDNA in maternal blood for both male and female fetus pregnancies. Fetal fraction calculation is a prerequisite to assure the technical credibility of NIPT screening test. In the current study, low coverage cell-free whole genome sequencing data from 416 pregnant women were used to develop a chromosome Y based estimator for the proportion of cffDNA in male-fetus pregnancy cases. Next, the chromosome Y based estimator was used to validate the credibility of SeqFF computational method with Estonian NIPT samples. This developed approach using SeqFF method on Estonian NIPT samples enables to estimate the proportion of cffDNA in both male and female fetus pregnancies. The SeqFF method is now integrated into the NIPT computation workflow service, validated and in daily practical use as part of the NIPTIFY® screening test
Arvutuslikud metoodikad loote trisoomiate ja mikrodeletsioonide riski tuvastamiseks mitteinvasiivses sõeluuringus
No full textVäitekirja elektrooniline versioon ei sisalda publikatsiooneMitteinvasiivne sünnieelne geneetiline testimine (NIPT) on sõeluuringu meetod loote kromosoomhaiguste riski hindamiseks raseda vereproovist. NIPT põhineb platsenta päritolu rakuvaba DNA sekveneerimisel ja andmeanalüüsil. Lisaks loote kromosoomi koopiaarvu muutustele võimaldab NIPT tuvastada ka patogeensete mikrodeletsioonide riski. Mikrodeletsiooni sündroom on lühikese kromosoomiosa kaost põhjustatud kromosoomihaigus, mille kliiniline raskusaste sõltub deleteerunud regioonist. Näiteks 22q11 piirkonnas esinev mikrodeletsioon põhjustab DiGeorge’i sündroomi, mis on seotud südamerikete, huule-suulaelõhe ja vaimupuudega. Loote kromosoomhaiguse riski määramine on bioinformaatiline väljakutse, sest miljonite DNA järjestuste korrektne analüüs eeldab nutikaid arvutuslikke lahendusi.
Käesoleva doktoritöö eesmärk on tõsta NIPT sünnieelse sõeluuringu täpsust, terviseandmete väärindamist ja meditsiiniteenuse kulutõhusust. Doktoritöö käigus loodi uus arvutuslik raamistik NIPT-i tarbeks ning valideeriti ja analüüsiti kliinilistel andmetel varasemalt publitseeritud NIPT algoritme. Lisaks töötati välja ja valideeriti kliiniliselt uudne tarkvarapakett BinDel, mis võimaldab hinnata loote mikrodeletsioonide riski.
Töö tulemusel kvantifitseeriti arvutuslike tööriistade täpsus erineva sekveneerimiskatvuse ja loote DNA osakaalu tingimustes. Tulemused näitasid, et NIPT täpsust mõjutab nii sekveneerimissügavus kui ka loote DNA osakaalu ning algoritmi valik. Uus BinDel tarkvara parandas mikrodeletsioonide tuvastamise võimekust, pakkudes võimalusi täpsemaks ja laialdasemaks sünnieelseks sõeluuringuks. Lisaks töötati välja masinõppepõhine arvutuslik raamistik loote kromosoomi koopiaarvu muutuste tuvastamiseks.Non-invasive prenatal genetic testing (NIPT) is a screening method for assessing the risk of fetal chromosomal disorders from a maternal blood sample. NIPT is based on sequencing and data analysis of cell-free DNA originating from the placenta. In addition to detecting changes in the fetal chromosome copy number, NIPT can also identify the risk of pathogenic microdeletions. A microdeletion syndrome results from the loss of a small segment of a chromosome, and its clinical severity depends on the deleted region. For example, a microdeletion in the 22q11 region causes DiGeorge syndrome, which is associated with heart defects, cleft palate, and intellectual disabilities. Fetal chromosomal disorder risk assessment is a bioinformatics challenge, as the accurate analysis of millions of DNA sequences requires sophisticated computational solutions.
The aim of this doctoral dissertation is to improve the accuracy, data utilization, and cost-effectiveness of NIPT prenatal screening. A new computational framework for NIPT was developed, and previously published NIPT algorithms were validated and analyzed using clinical data. Additionally, a novel software tool, BinDel, was developed and clinically validated for estimating fetal microdeletion risk.
The results quantified the accuracy of computational tools under varying sequencing coverage and fetal DNA fraction levels. The findings showed that NIPT accuracy is influenced by both sequencing depth and the fetal DNA fraction, as well as the choice of algorithm. The new BinDel software improved the ability to detect microdeletions, providing potential for more accurate and widespread prenatal screening. Additionally, a machine learning-based computational framework was developed for detecting fetal chromosomal copy number changeshttps://www.ester.ee/record=b575094
Arvutuslikud meetodid DNA koopiaarvu määramiseks
No full textVäitekirja 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
Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples
No full textNon-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no prior comprehensive, head-to-head accuracy comparison of the various tools has been published. Here, we compared the outcome accuracies obtained for clinically validated samples with five commonly used computational NIPT aneuploidy analysis tools (WisecondorX, NIPTeR, NIPTmer, RAPIDR, and GIPseq) across various sequencing depths (coverage) and fetal DNA fractions. The sample set included cases of fetal trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). We determined that all of the compared tools were considerably affected by lower sequencing depths, such that increasing proportions of undetected trisomy cases (false negatives) were observed as the sequencing depth decreased. We summarised our benchmarking results and highlighted the advantages and disadvantages of each computational NIPT software. To conclude, trisomy detection for lower coverage NIPT samples (e.g. 2.5M reads per sample) is technically possible but can, with some NIPT tools, produce troubling rates of inaccurate trisomy detection, especially in low-FF samples.sponsorship: This work was supported by the Ettevotluse Arendamise Sihtasutus [EU48695 to AS, EU53935 to AS and PPalta] (PP, HT, AS, KK, PPalta); and by the Eesti Teadusagentuur [PRG1076 to AS] (PP, HT, AS, KK, PPalta); and Horizon 2020 Framework Programme [EU952516 to AS] (PP, HT, AS, KK, PPalta). The funders had & nbsp;no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (Ettevotluse Arendamise Sihtasutus|EU48695, Ettevotluse Arendamise Sihtasutus|EU53935, Eesti Teadusagentuur|PRG1076, Horizon 2020 Framework Programme|EU952516)status: Publishe
Nooruse valuuta. „Noorkirjanik“ ja „rühmitus“ nullindatel / The Currency of Youth. The "Young Author" and the "Literary Group" in the 2000s
No full textThe article is focused on literary groups and the emergence of young authors in the 2000s. So far literary researchers have mainly studied the influential literary groups of the first third of the 20th century (Noor-Eesti, Siuru, Tarapita etc.). But literary groups have had a remarkable impact on contemporary Estonian literature as well. Many present-day well-known writers entered the literary scene through groups which were active in the 1990s (e.g. TNT and Erakkond). In the 2000s forming a literary group lost its appeal as young authors found more individual ways to introduce themselves to the public. At the beginning of the 2000s a couple of attempts were made to form new literary groups, but those groups were short-lived and unproductive (e.g. TNT! and !peatus).
Young authors were very active in publishing both on paper and online. The emergence of new publishing channels is one of the reasons why young authors did not have the ambition or need to form groups. For example, in the 2000s literary debuts appeared in the web-based literary club POOGEN and the literary magazine Värske Rõhk (established in 2005). So the 2000s actually saw a new type of convergence: web-based literary clubs and forums. Unfortunately, many of the new channels of the 2000s are already out of reach: the web pages of KLOAAK, noortekas.delfi.ee, People&Poetry, Bahama Press and ThePression have been removed from the internet.
Debuts were welcomed by mainstream media eager to spot the next big thing, new rebels and rule breakers. Being “a young author” became a functioning brand, and youth became a form of currency for beginning writers
Author Correction: FinnGen provides genetic insights from a well-phenotyped isolated population
No full textSuunatud ja ülegenoomsel sekveneerimisel põhinevate mitteinvasiivsete sünnieelsete testide arvutusmeetodite ja töövoogude väljatöötamine
No full textVäitekirja elektrooniline versioon ei sisalda publikatsiooneLoote sõeluuring võimaldab avastada lootel esinevaid arenguhäireid ja sagedasemaid kromosoomhaiguseid, nagu näiteks Down’i, Edwards’i ja Patau sündroom. Varajane teave lootel esineva kromosoomhaiguse kohta võimaldab langetada informeeritud otsust raseduse jätkamise osas ning aitab tulevasi vanemaid paremini ette valmistada.
Tavapärane loote sõeluuring sisaldab loote ultraheli uuringut ja vereseerumi analüüsi, mille abil tuvastatakse enamik kromosoomhaigusega loodetest. Lõpliku diagnoosi saamiseks suunatakse kõrge riski saanud patsient edasi invasiivsele protseduurile. Eelnimetatud sõeluuringute puuduseks on arvestatav valepositiivsete hulk, mistõttu enamik positiivse testitulemuse saanud patsientidest kannab täiesti tervet loodet. Sõeluuringule järgnev invasiivne protseduur on neil juhtudel ebavajalik, põhjustab rasedatele asjatut stressi ning sellega võib kaasneda suurenenud oht raseduse katkemiseks.
Antud doktoritöö keskseks teemaks on mitte-invasiivne sünnieelne testimine (NIPT), mis põhineb ema veres leiduva loote päritolu rakuvaba DNA analüüsil. Võrreldes eelmainitud traditsionaalsete sõeluuringu meetoditega, on NIPT oluliselt sensitiivsem ja spetsiifilisem sagedamini esinevate kromosoomihäirete avastamiseks.
Doktoritöö raames arendati välja TAC-seq põhine analüüsi töövoog, mida rakendati 21. kromosoom trisoomia tuvastamiseks. Lisaks töötati välja NIPT analüüsiraamistik, mis kasutab erinevaid masinõppe metoodikaid loote trisoomia määramiseks rakuvaba DNA-st. Niisamuti viidi Eesti rasedate kohordil läbi NIPT metoodika validatsiooni uuring, milles rakendati ülegenoomsel sekveneerimisel põhinevat töövoogu sagedamate loote kromosoomihäirete määramiseks.
Üldiselt on nii suunatud kui ka ülegenoomsel NIPT meetoditel muutnud rasedate sõeluuring varasemast veel täpsemaks. Kui suunatud sekveneerimise suureks eeliseks on kulutõhusus, siis ülegenoomne lähenemine tuvastab valimatult kõikvõimalikke geneetilisi aberratsioone üle kogu genoomi.Fetal screening allows to detect congenital anomalies and more frequent chromosomal abnormalities, such as Down, Edwards and Patau syndrome. Early information about a fetus’s possible health problem allows to make an informed decision about the continuation of the pregnancy and better prepare the future parents.
Conventional screening includes an ultrasound and blood serum analysis by way of which most of the fetal chromosomal abnormalities are detected. For a final diagnosis, the patients who are deemed to have a high risk for fetal chromosomal aberrations are referred to an invasive procedure. The disadvantage of the aforementioned screening method is a considerable number of false positive results, which is why most of the patients who receive a positive result are actually carrying a fully healthy fetus. The invasive procedure that follows the screening is unnecessary for those patients, causes them undue stress and this may also lead to a higher risk of miscarriage.
The focal point of this doctoral thesis is non-invasive prenatal testing (NIPT), which is based on the analysis of cell-free DNA (cfDNA) of fetal origin that is found in maternal blood. In comparison to the above-mentioned conventional screening methods, NIPT is considerably more sensitive and specific for detecting the most common chromosomal abnormalities.
In the framework of the thesis, TAC-seq based analysis workflow was developed and used to detect chromosome 21 trisomy. In addition, NIPT analysis framework, which uses different machine learning methods, was developed for determining fetal trisomies from cfDNA sample. Also, a validation study of NIPT was carried out on pregnant women in Estonian cohort using a whole-genome sequencing based workflow.
In general, both targeted and whole-genome sequencing based NIPT methods have made prenatal screening of fetal aneuplodies even more accurate than before. While cost-effectiveness is a major advantage of the targeted sequencing based approach, the whole-genome sequencing based NIPT possibly detects all kinds of genetic aberrations across the genome.https://www.ester.ee/record=b549777
Opportunities to Improve the Warehouse Efficiency on the Example of OÜ Pro Beauté
No full textLõputöös keskendus autor ettevõtte lao efektiivsuse tõstmise võimalustele. Töös kasutas autor struktureerimata intervjuud ja kvalitatiiv-kvantitatiivset küsimustikku, mida analüüsides selgitas välja ettevõtte laotoimingutes esinevad kitsaskohad. Autor tegi probleemide lahendamiseks omapoolsed parendusettepanekud, mida käsitletakse töö teoreetilises osas. Töö autori arvates on parendusettepanekute elluviimisel võimalik optimeerida ettevõtte laoprotsesse. Vabanenud ressursse on võimalik kasutada teisteks väärtust lisavateks toiminguteks.The author of the thesis focused on the opportunities to improve the company’s warehouse efficiency. Author conducted an unstructured interview and qualitative-quantitative survey which were analysed to identify the shortcomings in the company's warehousing operations. Author of the thesis made proposals which were discussed in the theoretical part of the paper to optimize the processes in the company. The author believes that company’s warehouse processes can be optimized by putting proposals into the practice. Unallocated resources can be used for other value-adding activities
Construction of solar tracking beeswax melting equipment
No full textKäesoleva töö eesmärk on päikest järgiva vahasulatusseadme ehitamine ja ehitamiseks kuluvate materjalide valiku tegemine. Automaatne vahasulatusseade ehitati kahe energiakasutuse eriala üliõpilase poolt: bakalaureusetöö koostaja ja Marten Lillemäe. Bakalaureusetöö koostaja ülesandeks oli seadme konstruktsiooni valik ja seadme ehitus. M.Lillemäe ülesandeks oli seadmele tarkvaralise ning riistvaralise lahenduse leidmine. Töö autor ehitas vahasulatusseadme, mis sobiks eelkõige väiksemate mesilastarude omanikele. Vahasulatusseade kasutab mesilaskärgede sulatamiseks päikesest tulevat soojust. Vahasulatusseade keerab ennast iga tunni aja jooksul päikese suunaga kaasa, kasutades selleks samm-mootorit. Samm-mootori töötamiseks vajalik toide saadakse päikesepaneelilt.
Bakalaureusetöö käigus valmis päikest järgiv vahasulatusseade. Valminud seade on vihmakindel, vastupidav tuulele, väikeste mõõtmetega ja kerge kaaluga. Valminud vahasulatusseadmega hoitakse kokku aeg, mis muidu kuluks vaha mesilas raamidest välja lõikamisele ja kuumal pliidil aeglaselt sulatades.This thesis has been written to construct a solar tracking beeswax melting equipment. Solar tracking beeswax melting equipment was built by two electrical engineering student: Bachelor thesis author and Marten Lillemäe. Bachelor thesis author aim was to construct and to choose right materials for solar tracking beeswax melting equipment. M.Lillemäe aim was to design software and hardware selection of a solar tracking beeswax melting equipment control system. Bachelor thesis author built beeswax melting equipment which fits for smaller beekeepers. Beeswax melting equipment uses solar heat in order to melt bee wax. Beeswax melting equipment turns towards sun once every hour using step-motor. Step-motor gets its energy from solar panel.
In this thesis author built beeswax melting equipment which is rainproof, wind resistant, with small dimensions and light weight. Finished beeswax melting equipment can save time spent on cutting beewax from frames and melting them over stove
The Risk Analysis of Eurostauto OÜ’s Workshop
No full textLõputöö eesmärgiks oli teostada Eurostauto OÜ Tallinna esinduse töökojas töökeskkonna riskianalüüs, et kaardistada töökohas esinevad ohutegurid ning nende riskitase. Uurimuse tulemuste alusel oli sihiks koostada ettevõttele tegevuskava, et töökeskkonnas olevad ohud viia miinimumini või likvideerida. Andmete kogumiseks kasutas töö autor töökeskkonna vaatlust ning töötajate seas läbi viidud küsitlust. Lisaks teostas autor töökeskkonnas mürataseme mõõtmised. Riskianalüüsi tegemisel kasutati Euroopa Töötervishoiu ja Tööohutuse agentuuri eestikeelse riskianalüüsi koostamise juhendi abi. Peale selle võrdles töö koostaja ettevõttes olevaid tingimusi seadustes ettenähtuga. Võtnud kõik saadud tulemused kokku, esitas uurimustöö autor ettevõttele tegevuskava puuduste likvideerimiseks.The following graduation thesis The Risk Analysis of Eurostauto OÜ’s Workshop is written in order of finding out any shortcomings in working environment safety at Eurostauto OÜ Tallinn based workshop. Eurostauto OÜ is an Estonian based company, which has contracts with Nissan Nordic Europe and Inchcape Motors Finland, therefore being an official dealership of Nissan and Mazda brands in Tallinn and Pärnu. This investigation has practical value as the last work environment risk analysis was done back in December of 2010. It was important to understand how has the working environment been evolving over 6 years and what could be done to make the environment safer and healthier. Survey and poll were used to gather information about subject. Author got inspiration for poll and survey topics from European Agency for Safety & Health at Work made instructions. Additionaly noise level were measured by the author of the thesis. Also all information gathered, analysis followed. In the analysis phase all the potential threats were rated as I (low risk), II (medium risk) or III (high risk). No high risk threats were found in the working environment. Suggestions for improvements were given by author for most of the problematic factors. In the final paragraph action plan was presented to the company. It consists of 14 suggestions, including deadlines and approximate costs, to improve safety of working environment
- …
