Pilot Clinical Application Of High Depth Whole Genome Sequencing Based On Maternal Plasma Cell-free DNA In Detecting Fetal Monogenic Diseases With Structural Malformations

OBJECTIVESNIPT has been widely used in the detection of fetal chromosomal and genomic diseases.It improves the efficiency of prenatal screening and reduces the risk of fetal abortion caused by invasive prenatal diagnosis.It has difficulties in the detection of non-specific genomic diseases and monogenic diseases.Due to the limited of probe range,it is unable to detect mutations outside.More than 60% of fetal structural malformations caused by monogenic diseases are De novo mutations.Although there are reports NIPT for monogenic diseases based on WGS,there is a problem of poor detection efficiency.In addition,invasive prenatal diagnosis has limitations such as the need to be carried out in medical institutions qualified for prenatal diagnosis and so on.Therefore,this pilot aims to explore monogenic disorders in fetuses with structural malformations by using high-depth WGS based on maternal plasma cfDNA.At the same time,this study adopted a new method for fetal De novo mutation independent of parental haplotypes.METHODS1)This study included 34 families with fetal structural malformations and fetal genomic diseases or monogenic disorders suggested by invasive prenatal diagnosis.QF-PCR was used to identify the maternal blood contamination of fetal samples.CMA was used for CNVs.Trio-WES was used to perform monogenic diseases(inherited or de novo variants).2)Fetal genotype estimation based on high-depth WGS of maternal plasma cfDNA: WGS on maternal plasma cfDNA at a sequencing depth of 100×,parental peripheral blood cells were sequenced at a depth of 30× by st LFR WGS.Based on the Bayesian model and haplotype,combined with the sequencing information of parental g DNA,to construct the whole fetal genome.De novo mutations were directly screened based on maternal plasma cfDNA high-depth WGS data.3)Calculate the coincidence rate of positive sites.RESULTSIn this study,the fetal whole genome data was constructed by combining cfDNA sequencing data with parental genomic st LFR sequencing data,and the accuracy of all SNP loci was up to 91.92%.The coincidence rate of suspected fetal genomic diseases was 83.33%(10/12).The coincidence rate was 82.35%(14/17),and the coincidence rate was 100%(6/6)in 6 indel families.For 2 De novo mutations,the coincidence rate of positive sites was 100%.CONCLUSIONThis study explore NIPT for monogenic disorders in structural malformations fetuses based on high-depth WGS of maternal plasma cfDNA,which has the advantage of simultaneous detection of genomic diseases and monogenic disorders.Compared with the previous NIPT for monogenic disorders based on targeted capture sequencing technology,this method is not limited to probe coverage and the presence or absence of probands.Compared with the previous NIPT for monogenic disorders based on WGS,the accuracy of fetal genotype and De novo mutations estimation are high.NIPT for structure malformation fetus with genomic diseases or monogenic disorders has a good foundation,showing a good application prospect.