by Kevin Davies in Bio-IT World

published March 16, 2010

‘The day we got Christiane’s diagnosis was a horrible, obviously very painful day. Disbelief. Despair. Sorrow. Agony. Fear. And unbearable pain. It forever changed our path.” – Charlotte Benson

Christiane Benson started to lose her vision two years ago, at just five years of age. She is legally blind, suffering primarily from a loss of visual acuity. “We’d never heard of Batten disease, but it completely changes your life forever,” says her father Craig Benson, CEO of Rules Based Medicine, a biomarker testing laboratory and diagnostic company in Austin, Texas.

As Benson and his wife Charlotte researched their daughter’s incurable neurodegenerative disease, they found many family foundations dedicated to raising money for similarly rare genetic disorders. “With a disease that affects so few people, it’s hard to get attention when there’s so many other good causes,” says Benson. He wanted to make his own foundation—the Beyond Batten Disease Foundation (BBDF)—relevant for an audience outside Batten disease. “Fortunately, I work with people who are a lot smarter than me,” he says. Among them were his business partner, a serially successful scientific entrepreneur named Mark Chandler, who was founder/chairman of Luminex, and his chief medical officer, Mike Spain.

“We thought, treatment and cures are great, but how do we prevent a disease like this? We were familiar with the Tay Sachs model in the Ashkenazi Jewish population that took pretty aggressive carrier screening and family counseling to virtually eliminate that disease in that population over about 15 years,” recalls Benson. “It appeared the only hindrance to taking that exact same proven strategy to a much broader perspective was technology and cost.”

Chandler happened to serve on the board of directors of the National Center for Genome Resources (NCGR) in Santa Fe, New Mexico. Benson called NCGR director Stephen Kingsmore, who has a background in orphan diseases. Kingsmore supported Benson’s ideas about a universal carrier screening strategy using next-generation sequencing to offer, as Benson says, “not just a handful of diseases like CF or Tay Sachs or Pompe’s or adrenoleukodystrophy, but actually try to take every medically devastating autosomal recessive or X-linked condition and multiplex it and put it on a sequencing platform… It’s perhaps the first and initially the best utilization of the sequencing application. You get meaningful, actionable information out of it.

“They decided to be quite audacious about it,” says NCGR’s Callum Bell, formerly of Genzyme. “Rather than just look at a single disease, study the long tail of diseases that are individually very rare, but if you add them up they become quite common. A few percent of live births have some kind of genetically related problem.”

Time and Money

Benson says his goal is “to put 500 diseases we’ve selected, what we consider the most medically devastating diseases, onto a single panel. Our hope is to offer that test for less than $500.”

The current Beyond Batten list is actually 437 disorders. “In OMIM [Online Mendelian Inheritance in Man], there are about 1000 recessive diseases with a known gene. Our panel is aiming to address about 450 of those,” says Bell, who is leading the Beyond Batten project.

The criteria were recessive disorders that caused childhood fatality or extreme childhood disease. Some disease foundations worked with Benson to have their own gene(s) of interest included in the test. “We didn’t want any controversy that these were traits or not life threatening,” says Kingsmore. “We didn’t want to get into any stigma with doing carrier testing. [It had to be] morally unequivocal.” One issue is that there are still some diseases where patent holders are unwilling to share their exclusive rights, a plight Kingsmore calls “tragic, because these tests are not economically viable unless on a panel.”

The NCGR will use a next-generation sequencing platform to sequence the coding regions of all 437 disease genes (see “Technology Target”). The plan is to set up a new CLIA-compliant entity to perform the test. Kingsmore anticipates a limited launch later this year that won’t yet be a billable carrier screening test.

Benson is searching for a permanent location for the DNA analysis lab, with the choice narrowed down to four (unnamed) sites. In addition to target enrichment, compute facilities and sequencing, the partners need economic development resources to raise money to get the program off the ground.

As for when it would be offered, Benson says: “Ultimately we’d like it to become standard-of-care for a young woman at the ob/gyn.” Another likely market will be in vitro fertilization clinics, where Benson says families are already undergoing an extensive out-of-pocket procedure. He sees the Beyond Batten test as providing more information.

“It’s intended to prevent the disease,” says Bell. “It will be for couples considering pregnancy… We’re hoping it’s adopted in same way as Tay Sachs testing. Or for girls at their first ob/gyn appointment, when they get a vaccination for HPV—that would be an optimal point to have them tested. They could later make informed family planning choices based on the test results.”

Benson and Kingsmore were hoping to launch the test this May, but various issues may push that out a little.

Eradicate and Cure

The launch of a test that could encourage some to seek abortions for affected fetuses could provoke controversy, but Benson doesn’t see it that way. “My personal faith would make me concerned about that anyway,” he says. “We were not oblivious to it. Our intention for this test and the market we plan to sell into is not for someone who is 2-3 months pregnant. We’re planning to offer this testing very early, before anyone’s even thinking about a family. We think it will provide useful information for families to make decisions because there are so many choices. IVF, adoption, there are alternatives families can choose that will not lead them down that path.” Benson quotes a saying: “It’s always good to stay on the side of the angels.” That way, he says, “you can always sleep well at night.”

“Our drive is to get the cost of this down to a level that is going to be affordable without insurance,” says Benson. BBDF will get some proceeds from test sales. “We view this test and its commercialization as the means of sustainability and a permanent funding source for our treatment and cure efforts… This is not really a commercial venture,” he concludes. “This is, for us, a legacy.”

Technology Target

The NCGR will sequence the coding regions of a total of 437 selected disease genes—about 2 megabases in all. While the Illumina platform remains the NCGR benchmark, Kingsmore says the Life Technologies SOLiD system is improving, and NCGR is also one of the early-access partners for Pacific Biosciences.

Kingsmore’s original assumption was that he would screen the disease genes using a custom DNA chip, similar to those in use in clinical labs for copy number variant detection. But issues of allelic heterogeneity and the error-filled cataloguing of variants prompted him to reconsider. Taking a longer view, needing a platform that could adapt to the discovery of new mutations or genes, the choice was either redesigning the chip every six months or taking the sequencing route. “I do believe sequencing will become cheaper than chips eventually,” says Kingsmore.

Bell and colleagues have been evaluating four enrichment technologies, including Agilent, febit, and RainDance. The favorites are currently Agilent and RainDance. “Agilent is very cost effective, but there are concerns that there are some targets we can’t design for. RainDance works very nicely, but cost is an issue,” says Kingsmore.

The NCGR team is also facing unexpected challenges in validating variations and improving software. Some of the interpretation challenges Kingsmore’s group has encountered means his team needs to validate its assays to a much higher degree than he’d envisioned just six months ago. “There isn’t a gold standard database of reference material, which surprised me,” says Kingsmore. He’s finding both deleterious mutations that cause devastating childhood diseases that the literature has mis-annotated, as well as variants called deleterious mutations that are sometimes just common SNPs. “It means we’re going to have to fold into this a whole level of discovery effort I hadn’t anticipated. We want something clinically useful and actionable.”

“Everyone’s going to be a carrier for about five disease mutations,” adds Bell. “Plus, how do you deal with those for which you haven’t got a confirmed phenotype—so called Variants of Unknown Significance (VUS)? If you find a nonsense mutation or a frameshift VUS, you may think there’s an obligation to do some kind of reporting around that. A weak link will be the physician that orders the test. I don’t know that the average doctor is equipped to counsel patients based on that number of genes. If you start introducing probability of disease based on an algorithmic approach to VUSs, it gets even more difficult.”

One priority at NCGR is to upgrade the Grindstone Laboratory Information Management System (LIMS) to handle different security levels, since it will be handling clinical data and needs to be CLIA compatible. It also needs to be able to handle multiplexing. Then there’s the Alpheus variant detection pipeline (see, “Jumping on Next-Gen Sequence Data Analysis,” Bio•IT World, July 2009), which Kingsmore says is “designed to do on-the-fly query of datasets. For a diagnostic or carrier screening, we want to lock that down, giving a standard well annotated report. We’ve got to do a lot of code hardening there as well.”