A next-generation method for cytogenomics using Hi-C proximity ligation sequencing

ABSTRACT Reproductive genetic tests are a disparate collection of methodologies with identify specific classes of mutations known to interfere with gametogenesis, conception and fetal viability. The number and variety of tests addressing this clinical need reflect the scale of genetic lesions that are relevant to reproductive medicine, ranging from whole chromosome aneuploidy to single nucleotide variants. In this proposal, we describe a highly scalable reproductive genetic test that can deliver results that span this scale at high resolution, lower cost, and faster turnaround time than current tests. Our approach uses a proximity ligation DNA sequencing method called Hi-C, which captures ultra-long-range genomic contiguity information using ubiquitious short-read sequencing and benchtop molecular biology. We have demonstrated extensively that Hi-C data can be used to order and orient genome assemblies, reconstructing end-to-end chromosome sequences. This method also identifies structural genomic rearrangements including balanced translocations, inversions, and other aberrations not detectable by typical sequencing approaches. We propose to apply high-throughput proximity ligation as a cytogenomic method to detect the breadth of chromosomal aberrations at high resolution and low cost. This proposal outlines a path to a commercially available product and service, which will establish a highly validated method for use in research and eventually in a diagnostic setting. This will be accomplished by 1) designing an easy to use Hi-C protocol amenable to multiwell plate handling, 2) building a robust computational platform to reproducibly call chromosome aberrations from Hi-C data, and 3) proving the validity and reproducibility of these methods on real world samples. The resulting kit and software product will be a new cytogenomic method called Karyotyping by SequencingTM (KBS) that we will deploy as a Precision Medicine test for the reproductive testing market.