Genetic Engineering & Biotechnology News

NOV15 2017

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20 | NOVEMBER 15, 2017 | GENengnews.com | Genetic Engineering & Biotechnology News Dan Heller The cost of DNA sequencing has dropped to a point where researchers and clinicians are eyeing liquid biopsies that analyze circulat- ing tumor DNA (ctDNA) as an attractive way to monitor cancer progression. Liquid biopsies could replace traditional solid biop- sies, which are invasive, costly, painful, and sometimes dangerous. The benefits of measuring ctDNA in pa- tients' blood or urine specimens are clear, but the uptake of ctDNA detection technology has been hampered by the technology's high costs (~$2,500 per test) and long processing times (currently two to four weeks). These limitations affect the number of tests that can be completed and the amount of data that can be collected, prolonging and increasing the costs of clinical trials that must be com- pleted before a given test can be cleared by the FDA. Indeed, only a few liquid biopsy tests have been approved to date. Liquid biopsy systems have the potential to increase testing rates and reduce the costs of clinical trials—as well as the prices of in- dividual tests. This potential will not be real- ized, however, unless liquid biopsy systems offer simplicity, economy, and point-of-use convenience in addition to the ability to de- tect clinically relevant levels of ctDNA from blood and urine samples. Liquid biopsy systems possessing the requisite attributes will not only bring more and better tests to market faster and at lower costs, they will also allow testing to be con- ducted in a doctor's office, or even in a pa- tient's home, expediting clinical decisions and courses of treatment. For example, if a patient's cancer were to return, necessitating a change in therapy, the recurrence could be detected within days or weeks, rather than months, potentially ex- tending the patient's lifespan and quality of life, while savings tens or hundreds of thou- sands of dollars in drug costs for a therapy that's no longer effective. Further, the cost of liquid biopsy testing could drop to tens or hundreds of dollars, rather than thousands. Handheld Liquid Biopsy Testing Kits Two Pore Guys (2PG) has developed a novel point-of-use molecular diagnostics platform that has shown promise for liquid biopsy testing. Unlike biological nanopores used in some DNA sequencing technologies, 2PG's system uses silicon nanopore chips to detect single molecules, one by one, like grains of sand passing through an hourglass. When a negatively charged molecule, such as DNA, enters the pore along its transition, it impedes the current, which is continuously measured. The amount of cur- rent shift represents the level of impedance, which is proportional to the molecule's bulk, or thickness, which could be accentuated by secondary structure. The time the mol- ecule takes to pass through the pore is of- ten governed by the length of the molecule, although other molecular features can cause drag (such as the degree to which the mol- ecule interacts with the pore or binds with positively charged chemical species). As each molecule in the chamber passes through the pore and is measured, this "event" is plotted on a 2D graph (Figure 1). The time and the impedance measure- ments are used to produce event signatures that reflect the nature of the molecule. More interestingly, one can alter the molecules to create desired signatures (Figure 2). The molecular structures depicted in Figure 2 carry single-nucleotide polymer (SNP)-spe- cific probes. One probe binds to the wild-type KRAS gene, and another probe binds to the G12D point mutation. To create distinct popu- lations on the current-impedance plot, one probe was tagged with a PEG linker, and the other probe was tagged with two PEG linkers. PEGs provide bulk, so when they pass through the pores, both the depth and duration of the current impedance are affected. Because molecules reach equilibrium within a fluidic buffer, only a small fraction of the total samples need to be tested to achieve 99.9% confidence that a particular target is Handheld System Detects Single Molecules, Measures ctDNA in Blood and Urine Take Liquid Biopsy and Other Apps in Hand OMICS Insights Genomics & Proteomics Vantari Genetics, a full service clinical diagnostics labora- tory, and Translational Software®, Inc. (TSI), a provider of genomic data solutions for clinical decision support, recently announced a partnership aimed at providing genotype testing, actionable genomic information, and custom reporting in support of the Banner Alzheimer's Institute's (BAI) GeneMatch registry. GeneMatch is a na- tional program that leverages genetic testing information to recruit participants for Alzheimer's prevention studies. "We are grateful to be part of a talented, multidisci- plinary team supporting a clinical study infrastructure to help the Banner Alzheimer's Institute enroll and genotype volunteers to advance Alzheimer's research," noted Shaun Opie, Ph.D., chief scientific officer at Vantari Genetics. In recent years, researchers have identified a variety of genes associated with Alzheimer's disease. The most common form of the disease is called late-onset Alzheimer's, which usually begins after age 65 and is associated with a gene called apolipoprotein E (APOE). Vantari Genetics and TSI are collaborating to sup- port the GeneMatch program through APOE testing and interpreting clinical samples from volunteers inter- ested in participating in community-based Alzheimer's research opportunities. The raw genomic and molecular data from the tests are analyzed to provide scientific intelligence about the genetic variants of volunteers, which is used to identify study participants at varying degrees of genetic risk for developing Alzheimer's to match them to available research studies. The companies will work together to provide BAI with in-depth analysis of the APOE data in multiple, customized formats which will be used to help scien- tists identify early brain changes in participants and compare the effectiveness of treatments for people with different APOE profiles. "Our genomic platform is very flexible, which allows us to offer unique genomic testing solutions and data reporting capabilities that can be customized to sup- port single gene testing, in-depth interpretation and analysis, and the integration of independent clinical research," explained Don Rule, CEO of TSI. "We are pleased to be working with Vantari Genetics to support the important work that BAI is doing to help advance the study of genetic risk for Alzheimer's." n Clinical Diagnostics Fuses with Genomic Software to Aid Alzheimer's Assay Tutorial Figure 1. Nanopore sensors enable the analysis of single-molecule "events." Figure 2. Sequence-specific probe payloads enable multiplexed SNP detection.

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