Loote DNA osahulga arvutamine madala katvusega täisgenoomi sekveneerimisandmetest
Date
2019
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Abstract
Käesoleva 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.
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.