Tools and statistical approaches for integrating DNA sequencing into clinical care

The discovery of DNA fundamentally changed the world, revolutionizing our understanding of life and the practice of medicine. After a century of studying DNA, medicine entered a new frontier with the completion of the nearly 20-year billion-dollar effort to sequence the first human genome. We can now sequence a human genome in a matter of days for hundreds (not billions) of dollars. Technological advances and medical geneticists’ robust efforts to interpret human variation have led to exponential clinical sequencing growth. The medical genetics community currently faces three primary challenges: (1) variant interpretation; (2) overcoming difficult detection problems (e.g., structural variants and low-frequency variants); (3) moving beyond a linear poorly-representative reference genome. The work herein addresses how to overcome two specific detection problems. First, I present a novel approach for detecting exon-level copy number variation using exome sequencing. The vast majority of available sequencing collected lacks the power to detect small copy number variants, leading to a significant blind spot in our understanding of genetic variation. I demonstrate how modifying the exome capture step to capture multiple samples simultaneously significantly reduces the inter-sample variance and improves copy number discrimination. I then demonstrate the utility of a novel statistical algorithm specifically for multiplexed-capture exome sequencing. Second, I outline the shortcomings of noninvasive exome sequencing in prenatal genetics. Utilizing cell-free fetal DNA in maternal circulation, we can diagnose a wide range of genetic conditions noninvasively. Efforts have suggested the possibility of noninvasive fetal genome and exome sequencing. However, to-date, no one has demonstrated accurate fetal genotyping purely from cell-free DNA. I use probability theory to demonstrate why efforts have failed, and suggest a path forward for noninvasive fetal genotyping. Finally, I briefly outline my ongoing work in prenatal genetics and propose a validation study to further interrogate exon-level copy number variation.Doctor of Philosoph