Prospect Hill Academy Charter School
Cambridge, MA

Katherine Chao
Medical and Population Genetics

Chineze became interested in science “while taking biology, where I especially enjoyed learning about genetics.” Little did Chineze know her interest in genetics would lead her to join BSSP and work in the Translational Genomics Group (TGG). The TGG has a goal to discover the genetic basis of rare diseases. By increasing our understanding of the genetic basis underlying disease, we can shorten diagnostic odysseys and alter clinical outcomes for affected individuals. To this end, the TGG applies genomic technologies as well as novel methods to analyze data on thousands of rare disease families. There are many quality control methods that are put in place to ensure the accuracy of the genomic data being analyzed. One of these methods is accurately inferring the sex of the samples. This summer, Chineze and her partner Jiji worked on polishing sex inference code that can be used to accurately infer the sex of any given exome or genome sequencing sample. At the end of the summer, Chineze was able to optimize the code and then release it in a GitHub repository that can be accessed by anyone in the world. Additionally, as she was testing the code, she noticed there was an unexpected distribution of chromosome Y (chrY) ploidies when trying to infer the sex of the DNA samples. Instead of seeing a bimodal distribution for chrY ploidy (as expected for individuals carrying XX or XY), she saw a trimodal distribution. By plotting the distribution of chrY ploidy using different parameters, she realized a potential reason for this unexpected observation was due to differences in sequencing technologies used to obtain some of the DNA samples. When comparing samples sequenced using the same technology, she observed the expected bimodal Y distribution. Through her work, Chineze will facilitate the work of scientists around the world studying rare genetic diseases. When asked about her favorite part about being a Broadie, Chineze highlights the supportive environment at the Broad. “At first, I was scared to ask for help but I realized how excited everyone was to help me understand difficult concepts in the best way possible.”