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.
Public Health Relevance Statement: NARRATIVE Chromosomal abnormalities are a common cause of infertility and loss of pregnancies and their diagnosis can inform reproductive decision making. Several approaches have been developed to aid the detection of chromosomal abnormalities, however none allow large-scale high-resolution aberration diagnosis. An efficient, comprehensive diagnostic method is therefore needed to provide accurate data on variation observed in the reproductive medicine setting.
Project Terms: Accounting; Address; Affect; Aneuploidy; Animals; Benchmarking; Cell Line; Child; Chromosome abnormality; Chromosomes; Clinical; clinically relevant; cloud based; cohort; Collection; computational platform; Computer software; Conceptions; cost; Couples; Cytogenetic Analysis; Cytogenetics; Data; Data Set; Decision Making; design; Detection; Diagnosis; Diagnostic; Diagnostic Procedure; DNA Ligation; DNA Sequence Rearrangement; DNA sequencing; Event; Fetal Viability; Fluorescent in Situ Hybridization; Funding; Future; Gametogenesis; Genetic; genetic testing; Genome; Genomics; Goals; Grant; improved; Industry Standard; Infertility; Karyotype; Karyotype determination procedure; Laboratories; large datasets; Lead; Length; Lesion; Letters; Ligation; Manuals; meetings; Methodology; Methods; Molecular Biology; Mosaicism; Mutation; next generation; novel strategies; Online Systems; Outcome; Performance; Phase; Plants; precision medicine; Pregnancy loss; Process; Protocols documentation; Reagent; Reporting; Reproducibility; Reproduction; reproductive; Reproductive Medicine; Research; Resolution; Sampling; scaffold; Sensitivity and Specificity; Series; Services; Single Nucleotide Polymorphism; Small Business Innovation Research Grant; Software Tools; structural genomics; Study Section; System; Technology; Testing; Time; tool; United States; Variant
