College of American Pathologists
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CAP Today




May 2012

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A ‘points to consider’ policy on genomic sequencing

Laboratories and clinics that use whole genome and whole exome sequencing for clinical care should have policies in place related to the disclosure of secondary findings, according to a policy statement issued March 28 by the American College of Medical Genetics and Genomics.

The ACMG released its “Points to Consider in the Clinical Application of Genomic Sequencing” as an educational resource for clinical and laboratory geneticists, saying in the statement that “there are already instances in which genomic sequencing approaches can and should contribute to clinical care.”

Patients should be informed of the laboratory and clinic policies related to secondary (incidental) findings and the types of such findings that will be reported to them and under what circumstances, the ACMG says. “Patients should be given the option of not receiving certain or secondary findings,” the ACMG stresses. And it says that while such policies should be in place, “exceptional circumstances will undoubtedly arise” that need to be handled case by case through consultation between the ordering physician and the laboratory director.

The statement distinguishes between diagnostic results, which explain a patient’s phenotype by identifying a mutation in a gene known to be associated with the patient’s clinical condition or in a gene highly likely to be causative given current knowledge, and the secondary results, which it calls “highly likely, if not inevitable,” whenever whole genome or whole exome sequencing is performed.

According to the policy, WGS/WES should be considered in the clinical diagnostic assessment of a phenotypically affected person when:

  • The phenotype or family history data strongly implicate a genetic etiology but the phenotype does not correspond with a disorder for which a genetic test targeting a specific gene is available clinically.
  • A patient presents with a defined genetic disorder that demonstrates a high degree of genetic heterogeneity.
  • A patient presents with a likely genetic disorder (or a fetus is likely to have a genetic disorder), but the genetic tests available for that phenotype have failed to arrive at a diagnosis.

ACMG president and CAP member Wayne Grody, MD, PhD, professor of pathology and laboratory medicine, pediatrics, and human genetics at the UCLA School of Medicine, said in a statement: “The transition from traditional targeted gene testing to genomewide analysis constitutes a genuine sea change in medicine, offering vastly enhanced diagnostic power along with unprecedented challenges in test interpretation and reporting. This policy represents the first professional guidance for appropriate integration of this new technology into clinical practice.”

The full statement is at

New Quest CEO

Stephen H. Rusckowski on May 1 became president and chief executive officer of Quest Diagnostics. He succeeds Surya N. Mohapatra, PhD. Rusc-kowski had been CEO of Philips Healthcare since 2006.

GE Healthcare acquires SeqWright

GE Healthcare has acquired SeqWright, a provider of nucleic acid sequencing and other genomic services. The acquisition provides Clarient, a unit of GE Healthcare, with complementary genomics capabilities and a platform with which to include next-generation sequencing in its clinical diagnostic offerings. Financial terms of the deal were not disclosed.

“Sequencing, including next-generation DNA sequencing, is an important technology for GE’s medical diagnostics business,” Clarient CEO Carrie Eglinton-Manner said in a statement. “The acquisition of a specialized laboratory with long-standing expertise in the sequencing field as well as an established customer base allows us immediate entry into this high-growth space, and is an ideal complement to Clarient’s existing protein and gene-expression profiling in support of pharmaceutical and in vitro diagnostic studies.”

ACOs and antitrust risk

Two major questions about the ACO “experiment” remain unanswered, write Richard Scheffler, PhD, Stephen Shortell, PhD, MBA, MPH, and Gail Wilensky, PhD, in their April 11 JAMA editorial, “Accountable care organizations and antitrust” (2012. 307:1493–1494). “How can clinical integration be encouraged while preventing excessive antitrust risk; and how can cost shifting from federal to private payers be mitigated?”

In creating ACOs, physician leaders and policymakers will have to consider five major issues, say Dr. Scheffler of the Goldman School of Public Policy and Dr. Shortell of the School of Public Health, University of California, Berkeley, and Dr. Wilensky, of Project HOPE, Lane Millwood, Va.

  • Market definition and power. The Federal Trade Commission and Department of Justice guidelines on antitrust issues related to ACOs create a safety zone in which ACOs that have less than a 30 percent market share in each independent service within a geographic market are unlikely to raise antitrust concerns (and include a rural exception). Differences in markets, they say, “mean that a 30% share in one market could have vastly different implications in terms of concentration and power than a 30% share in another.”
  • Efficiency and quality metrics. The Medicare Shared Savings Program requires ACOs to serve a minimum of 5,000 patients. “The CMS is encouraging larger ACOs by using a graduated savings schedule,” the authors write, and they add that antitrust efforts “are intended not only to prioritize lower prices but also to encourage other components of consumer welfare such as quality-enhancing product innovation.”
  • Physician and hospital exclusivity. “Although recommending that all ACOs avoid exclusive contracting with hospitals, the guidelines suggest that ACOs considered to have high market share avoid exclusive contracting with physicians as well,” the authors say. But they point to the potential efficiency benefits to exclusivity, one of which is that “Increased internal referrals and communication among dedicated physicians is expected to facilitate coordinated, clinically integrated, and high-quality care.”
  • Public-private cost shifting. The authors say there is concern that the Medicare Shared Savings Program may exacerbate cost shifting, “with private payers facing higher rates to recoup reductions in reimbursement from Medicare and Medicaid.”
  • Monitoring. “The CMS plans to risk-adjust beneficiaries in ACOs to ensure that ACOs are not simply selecting the healthiest patients,” they write.

Of the need to reach the right balance between market power and efficiencies, the authors say: “A significant challenge will be in those instances for which there is evidence of increased prices due to market power of large ACOs but also evidence of increased efficiencies in care coordination and patient experience with their care.”

Hiring, hours worked, and more

Forty-five percent of pathologists who responded to the CAP’s 2011 Practice Characteristics Survey said their practice hired one or more pathologists in 2010, and of that 45 percent, 74 percent reported needing specific subspecialties. Hematopathology, GI pathology, nongynecologic cytology, and dermatopathology were the most sought after subspecialties.

That’s just some of the insight into pathology practice to come out of the eighth such survey the CAP has conducted since 1994. The interval for the latest survey was Jan 1, 2010 through Dec. 31, 2010, and 9,374 CAP members were asked to participate. Fifteen percent responded.

The pathologists who responded worked an average 50.4 hours per week in 2010, which is slightly more than the average hours reported in the 2007 survey (49.7 hours). Nearly 80 percent of respondents said they regularly practice in more than one subspecialty and that they provide professional services, on average, in seven subspecialties.

Other findings:

  • Forty-nine percent of respondents said they have some type of patient contact in the course of their work. Of that group, fine-needle aspiration was the service they provide most often. The No. 2 service: providing advice on the implications of test results.
  • Eighty percent said they are involved in managing laboratory utilization, both at their own initiation and at the request of the ordering physician.
  • When asked whether their practices were participating in an accountable care organization, 7.5 percent said their practice was participating or actively negotiating to participate. Another 12.7 percent said they were exploring the feasibility of forming or joining an ACO. Thirty-three percent did not know, and 35.6 percent said they do not participate.

Just over half of all who responded answered the survey questions about electronic medical records, with nearly 75 percent saying they have the same level of access to patient clinical records as treating physicians. Fifteen percent said they are limited to “view only.”