Strategies in Biomedical Data Science

Chapter 2 Genome Sequencing

Know Thyself, One Base Pair at a Time Content contributed by Sheetal Shetty and Jacob Brill

Dr. Joel Dudley, the coauthor of the groundbreaking 2013 textbook Exploring Personal Genomics, has stated that you can now “know thyself, one base pair at a time” [1]. Dudley is a leader in biomedical informatics and the director of Biomedical Informatics at the Icahn School of Medicine at Mount Sinai. Exploring Personal Genomics appeared at a time of extremely rapid advances in sequencing technologies and techniques for analyzing all that newly available information.

We’ve seen genomic sequencing costs drop astronomically. The Human Genome Project took 13 years and cost US$3 billion. Now author Peter White of Nationwide Children’s Hospital notes that “even the smallest research groups can complete genomic sequencing in a matter of days” and at a cost of around $1,000 [2, 3]. During a speaking trip to Phoenix in October 2014, Google Cloud Genomics evangelist Dr. Allen Day went so far as to say that “DNA sequencing is well on its way to being free.” [4] This sentiment is shared throughout the omics community, and now the magic and the challenge lie in what the end product has to tell us, what secrets remain tightly locked in the code.

Increasingly the chokepoints lie in the steps following sequencing, which involve calibrating and analyzing the billions of generated data points for genetic variants that could lead to diseases. These steps require time, expense, ...