College of American Pathologists
Printable Version






February 2010

Raymond D. Aller, MD
Hal Weiner

Supercomputer tackles genetic sequencing for HIV Supercomputer tackles genetic sequencing for HIV

The world’s fastest computer, dubbed the Roadrunner, has been used to map the largest ever family tree of HIV.

The IBM computer, housed at New Mexico’s Los Alamos National Laboratory, or LANL, served as the workhorse for a project that compared the evolutionary history of more than 10,000 genetic sequences from more than 400 HIV-infected people. The long-term goal of the project is to identify vaccine target areas that would make the body immune to HIV before the virus mutates into a form that resists vaccines.

Roadrunner, which was developed through a partnership between IBM, LANL, and the National Nuclear Security Administration, was chosen for the project because it can exceed speeds of one petaflop, or one quadrillion, calculations per second.

The process of building an evolutionary genetic family tree, called a phylogenetic tree, focused on the search for similarities in acute versus chronic sequences, says physicist Tanmoy Bhattacharya, PhD, a principal investigator on the project, an initiative of the Center for HIV/AIDS Vaccine Immunology, a National Institutes of Health consortium. Roadrunner allowed scientists to look for similarities across whole populations of acute patients, he explains. Scientists used the computer to compare evolutionary relationships between chronic and acute infections, using statistics to find inter-connecting branches.

This means the study compared indicators of when HIV is not yet under the control of the immune system, as with acute patients, with those apparent when the immune system continues to fight the virus, as with chronic patients. “It is these interconnections where a specially designed vaccine might be most effective,” Dr. Bhattacharya tells CAP TODAY.

As DNA-sequencing technology advances, scientists find themselves on the cusp of obtaining more than 100,000 viral sequences from a single person. “[The] study begins to move us into this new era,” says HIV researcher Bette Korber, PhD, also a principal investigator on the project.

But Roadrunner isn’t the only sophisticated computer capable of large-scale genetic sequencing. “Any large computing cluster could accomplish this type of work,” says Marcus Daniels, PhD, a LANL computer scientist. “What made Roadrunner advantageous is its speed.”

Lawson Software to buy Healthvision Solutions Lawson Software to buy Healthvision Solutions

Lawson Software has announced plans to acquire Healthvision Solutions by purchasing its parent holding company, Quovadx Holdings.

The acquisition of Healthvision will allow Lawson to connect multiple source systems and offer health care providers timely access to clinical, financial, and operational information, regardless of the source system.

Dallas-based Healthvision markets Cloverleaf integration technology, the MediSuite family of information systems, and other health care solutions and services.

St. Paul, Minn.-based Lawson markets enterprise software, services, and support in a variety of market sectors, including health care.

Halfpenny system transfers lab results to smartphones Halfpenny system transfers lab results to smartphones

Halfpenny Technologies has introduced ITF-Mobile, a handheld results-reporting system that allows physicians to securely access laboratory, pathology, and radiology results reports from their iPhone, BlackBerry, or Android-powered smartphone.

ITF-Mobile provides physicians with visual and audio alerts of incoming clinical messages and abnormal results. The product embodies user-defined rules, so it can be set up to deliver all lab results, test results with abnormal values, or only those results specifically ordered by a clinician or requested by a patient. Physicians can also select specific lab test results for automatic trending.

ITF-Mobile is an extension of Halfpenny’s ITF-Portal, a Web-based connectivity solution that allows physicians to securely order lab procedures and review results reports through a standard, HIPAA-compliant Web browser. ITF-Mobile securely transfers clinical data to mobile devices via Halfpenny’s ITF-SecureConnect architecture, which eliminates the need for ITF-Mobile to make a physical connection to a remote server to view reports.

Mediware offers interface to U.S. Biovigilance Network Mediware offers interface to U.S. Biovigilance Network

Mediware Information Systems has developed an interface that will enable facilities using its LifeTrak blood donor management software to electronically transmit blood donation data to the U.S. Biovigilance Network.

The new interface will link the network’s donor hemovigilance module to LifeTrak software. “Rather than having to re-key this information into the network’s systems, our customers will be able to point and click to participate in this important initiative without any additional labor or impact on their business,” says Noel Strong, Mediware’s vice president of research and development and chief technology officer.

The U.S. Biovigilance Network is a collaboration between the federal government and organizations involved in blood collection, transfusion, and tissue and organ transplantation medicine that promotes the sharing of information and improved safety.

Bio-Key launches SaaS solution for biometric ID Bio-Key launches SaaS solution for biometric ID

Bio-Key International is marketing TruDonor ID, a fully hosted fingerprint-based biometric identification solution tailored to the blood collection industry.

The secure software-as-a-service donor ID product interfaces to blood management platforms or can operate as a standalone offering.

“With TruDonor ID, blood centers have secure 24/7 access to their donor database on a superior computing environment supported by expert technicians,” says Mike DePasquale, CEO of Bio-Key.

Government sets up grants for IT training programs Government sets up grants for IT training programs

The Office of the National Coordinator for Health Information Technology has announced the availability of $38 million in American Recovery and Reinvestment Act grants to develop health care information technology training programs at four-year colleges.

Under the new program, the ONC will award eight to 12 grants, totaling $32 million, to establish university-based certificate and advanced degree health information technology training programs that can be completed in one year or less. The government is also offering a single $6 million grant to develop and administer a set of health information technology competency examinations.

Late last year, the ONC announced the availability of $70 million in grants to create or expand health care information technology training at community colleges.

CAP releases updated XML version of cancer checklists CAP releases updated XML version of cancer checklists

The College of American Pathologists has released an updated XML version of the CAP electronic cancer checklists, CAP eCC, its informatics tool to advance cancer reporting.

The CAP eCC enhances the management and interoperability of health information through its XML format, which can be easily integrated into pathology and cancer registry systems.

“The CAP eCC is a powerful tool in the war on cancer, delivering on the promise of improved patient outcomes through the use of health information technology by leveraging universally accepted standards, such as XML and SNOMED CT,” says Kevin Donnelly, vice president and general manager of CAP SNOMED Terminology Solutions, the CAP division that produces the CAP eCC. “Developed by key stakeholders from pathology, surgery, cancer registries, and public health, it provides the basis for comprehensive cancer reporting across multiple systems.”

The new CAP eCC, released Dec. 30, contains 69 cancer checklists representing new and updated content in the CAP cancer protocols posted on the College’s website,, last October.

“The comprehensiveness and complexity of today’s pathology reports increases the challenge of effectively recording and sharing this information accurately and effectively,” says John Madden, MD, PhD, co-chair of the CAP’s Pathology Electronic Reporting Task Force. “The CAP has confronted the challenge head on with this timely release of a data standard for communicating and storing cancer report data electronically.”

LifePoint supplies clinical data tools for Web platform LifePoint supplies clinical data tools for Web platform

LifePoint Informatics is collaborating with the American Medical Association to offer physicians its LifePoint.Web clinical order-entry and results-reporting solutions through the AMA’s new online health information solutions platform.

LifePoint.Web is a secure online data storage area used by health care providers to quickly access their patients’ clinical results reports.

The new AMA platform was created to provide physicians access to information, products, services, and resources to improve patient care and administrative processes.

Dr. Aller is director of automated disease surveillance and team lead for disaster preparedness Focus B, Los Angeles County Department of Public Health. He can be reached at Hal Weiner is president of Weiner Consulting Services, LLC, Florence, Ore. He can be reached at