January 15, 2018 (Vol. 38, No. 2)

Big Data Is Rapidly Transforming Medicine

A revolution is transforming the $10 trillion healthcare landscape, promising greater transparency, improved efficiency, and new ways of delivering care, according to a new book entitled, “MoneyBall Medicine: Thriving in the New Data-Driven Healthcare Market” (Productivity Press), written by Harry Glorikian and Malorye Allison Branca.

The authors map out many of the changes taking place, describe how they are impacting everyone from patients to researchers to insurers, and outline some predictions for the healthcare industry in the years to come.

In an exclusive interview with GEN, Glorikian said the book’s main theme is about “how data and technology will transform the practice of medicine and all the associated industries.”

When asked for examples, Glorikian noted that patients will be able to monitor their heart health with a KardiaBand (AliveCor) that pairs with your Apple watch so you can detect atrial fibrillation without having to go to your doctor. Also, artificial intelligence in drug discovery will allow scientists to identify potential therapeutic molecules that were not obvious under typical drug-discovery paradigms.

In personalized medicine, he continues, there will be “wholesale change in how oncology departments will be physically organized to manage the data that comes in from tumor samples. Doctors will then be able to assess and tie that data to the appropriate therapy based on hard data and prescribe the right drug to the right patient at the right time.”

Climbing Everest to Support Cancer Research

Luke Timmerman is a one-man show. He reports, publishes, and markets his own biotechnology newsletter, the Timmerman Report. Turns out he’s also a mountain man.

Luke plans to climb Mount Everest this spring to raise money—his goal is $175,000—for the Fred Hutchinson Cancer Research Center in Seattle. He plans to leave for Nepal in March to begin the 10 weeks of training required to ascend the summit. His body needs time to acclimate to the altitude and to produce more oxygen-ferrying red blood cells. Although Luke has already scaled the highest peaks in North and South America (Denali and Aconcagua, respectively), he is currently running and bicycling and carrying a heavy training backpack uphill to get in tip-top shape. Sponsors are covering his climbing fees, but he is paying for all his personal expenses, including the flight to Kathmandu.

In addition to being an avid climber who wants to tackle the baddest mountain on the planet, Luke is also driven by his desire to support cancer research, much of which he has written about over the past 15 years.

“I see a cancer revolution happening. Immunotherapies are emerging that use our own immune system to attack cancer cells, fighting off cancer like we fight off a flu,” he writes. “That’s amazing. Advances make it possible to detect cancer earlier than ever before, when it’s most easily treated. A cure for cancer has long been their [researchers’] Everest.”

We at GEN wish him Godspeed and good luck.

Luke Timmerman

DNA Sequencing: Achieved a Milestone

On December 14, 2017, the Garvan Institute in Sydney, Australia, acknowledged the achievement of a milestone by some of its researchers on the DNA sequencing front. The institute’s researchers, led by Martin A. Smith, Ph.D., head of genomic technologies in the Kinghorn Centre for Clinical Genomics, announced on Twitter that they had sequenced a single DNA read of more than one million bases long using the increasingly popular MinION nanopore sequencing device from U.K.-based Oxford Nanopore 
Technology (ONT). We chatted with Dr. Smith to find out what this really means in the scope of sequencing, what the team sequenced, and what the lab plans to do next.
GEN: What was the most challenging part about getting a read of more than 1 million bases long?
Dr. Smith: There are quite a few challenges, but DNA extraction and sample preparation are without a doubt the most challenging steps. Even simple pipetting can shear DNA molecules longer than 100 kilobases (kb), so special sample preparation tricks are required, many of them revisited from the ’70s and ’80s. High-molecular-weight DNA samples form a big clump of stringy gel-like substance, rather than a liquid, so even measuring the concentration of the sample is hard because you cannot pipette small volumes of the highly viscous solution (you almost need scissors). Also, an unexpected challenge from reads this long was data analysis—most software tools have been developed for short (<50 kb) reads, therefore, these ultra-long reads are good at finding bugs in code or problems with memory. 
GEN: What technical tips do you have for researchers who are also trying to perform long-read nanopore sequencing?
Dr. Smith: Cut the tips off your pipettes and follow Nick Loman, Ph.D. (@pathogenomenick) and Joshua Quick (@Scalene) on Twitter!
You can read the full interview with Martin A. Smith, Ph.D., online.


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