Non-invasive determination of complete fetal genomes from cfDNA using HaploSeq

DESCRIPTION provided by applicant Genetic defects including single gene Mendelian disorders and aneuploidies are among the leading causes of miscarriages and congenital birth disorders Non invasive prenatal testing NIPT is currently used to detect aneuploidies but given the falling cost of next generation sequencing NGS growing sophistication in molecular biochemical methods and ever increasing computational power complete determination of the fetal genome i e genotypes and haplotypes at the level of both SNVs and large aneuploidies seems within reach In this regard cell free DNA cfDNA in the maternal plasma has been targeted for non invasive detection and diagnosis of fetal genetic defects as cfDNA contains a mixture of genetic material derived from both the mother and the fetus But because the fraction of cfDNA derived from the fetus is small and consists of DNA that is highly fragmented determination of fetal genotypes to the level of single nucleotide variants SNV remains challenging and presently involves excessively costly deep sequencing of cfDNA up to X In addition to knowledge of genotypes for diagnosing single gene Mendelian disorders non invasive deconvolution of fetal haplotypes is likely necessary for assessing the risk for complex multi genic disorders Efforts have been made to determine fetal genome with parental haplotypes but the current methods to haplotype parents generally suffer from excessive costs methodological and instrumentation complexity and or reliance on genetic material that is difficult or impossible to obtain and they provide only partial haplotype information short haplotype blocks and incomplete phasing of variants hindering their utility in cost effective complete fetal genome determination Our team previously developed an innovative approach HaploSeq that can solve this problem The HaploSeq method preserves haplotype information by preferentially recovering physically linked DNA variants on a homologous chromosome via proximity ligation and NGS as per the established HiC protocol HaploSeq achieves truly chromosome spanning haplotypes resolving the vast majority of alleles andgt at high accuracy in human genomes thus constituting the first scalable cost effective method for assembling complete human haplotypes Here we propose an innovative approach HaploSeq Ft for non invasive determination of complete fetal genotype and haplotype using HaploSeq to generate chromosome spanning parental haplotypes from blood samples In addition HaploSeqandapos s whole genome phasing capabilities also facilitate utilization of very low depth cfDNA sequencing from maternal plasma for complete fetal genotype and haplotype determination Taken together by leveraging our proprietary haplotyping technology to inform novel cfDNA sequencing analysis algorithms one HaploSeq Ft blood test will enable parents to know the complete genotype and haplotype of their fetus in a cost effective manner that does not endanger the pregnancy PUBLIC HEALTH RELEVANCE With the concurrent rise of next generation sequencing NGS technologies and non invasive prenatal testing NIPT the development of a cost effective NGS based assay that enables non invasive determination of a complete fetal genome will be essential for the future of timely diagnosis of fetal genetic disorders We propose a novel method HaploSeq Ft that leverages our proprietary haplotyping technology and new computational approaches to provide precision medicine for prenatal clinical care HaploSeq Ft will be developed as a simple non invasive cost effective blood test that enables parents to know the complete genotype and haplotype of their fetus without endangering the pregnancy