1

Introduction1

The initial sequencing of the human genome, carried out by an international group of experts, took 13 years and $2.7 billion to complete. In the decade since that achievement, sequencing technology has evolved at such a rapid pace that today a consumer can have his or her entire genome sequenced by a single company in a matter of days for less than $10,000, though the addition of interpretation may extend this timeframe. With the next-generation sequencing technology currently being developed, the cost is projected to continue to decline significantly over the next few years, to the point that large-scale genome sequencing is expected to become comparable in cost to a single gene test or to a diagnostic imaging test such as a computed tomography (CT) scan (Mardis, 2006).

Given the rapid technological advances, the potential effect on the lives of patients, and the increasing use of genomic information in clinical care, it is important to address how genomics data can be integrated into the clinical setting. Genetic tests are already used to assess the risk of breast and ovarian cancers, to diagnose recessive diseases such as cystic fibrosis, to determine drug dosages based on individual patient metabolism, and to identify therapeutic options for treating lung and breast tumors, melanoma, and leukemia.

Recent studies have also demonstrated the usefulness of genomics for diagnosing disease and guiding treatment in the clinic. For example, genetic

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1 The planning committee’s role was limited to planning the workshop, and the workshop summary has been prepared by the workshop rapporteurs as a factual summary of what occurred at the workshop.



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1 Introduction 1 The initial sequencing of the human genome, carried out by an inter- national group of experts, took 13 years and $2.7 billion to complete. In the decade since that achievement, sequencing technology has evolved at such a rapid pace that today a consumer can have his or her entire genome sequenced by a single company in a matter of days for less than $10,000, though the addition of interpretation may extend this timeframe. With the next-generation sequencing technology currently being developed, the cost is projected to continue to decline significantly over the next few years, to the point that large-scale genome sequencing is expected to become com- parable in cost to a single gene test or to a diagnostic imaging test such as a computed tomography (CT) scan (Mardis, 2006). Given the rapid technological advances, the potential effect on the lives of patients, and the increasing use of genomic information in clinical care, it is important to address how genomics data can be integrated into the clinical setting. Genetic tests are already used to assess the risk of breast and ovarian cancers, to diagnose recessive diseases such as cystic fibrosis, to determine drug dosages based on individual patient metabolism, and to identify therapeutic options for treating lung and breast tumors, melanoma, and leukemia. Recent studies have also demonstrated the usefulness of genomics for diagnosing disease and guiding treatment in the clinic. For example, genetic 1 The planning committee’s role was limited to planning the workshop, and the workshop summary has been prepared by the workshop rapporteurs as a factual summary of what occurred at the workshop. 1

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2 INTEGRATING LARGE-SCALE GENOMIC INFORMATION testing of the relatives of patients newly diagnosed with colon cancer has suggested a prevention strategy for identifying individuals with Lynch syndrome (Coates et al., 2011). Genomics data have been used to pro- vide definitive diagnoses for patients with neuropathy, inflammatory bowel disease, and Proteus syndrome as well as to guide therapeutic care for patients with arterial calcifications, movement disorders, and Miller syn- drome (Bainbridge et al., 2011; Lindhurst et al., 2011; Lupski et al., 2010; Ng et al., 2010; St. Hilaire et al., 2011; Worthey et al., 2011). Although applications of genomics technologies are currently limited in number, their number will only continue to increase. Thus, it is important to determine how genomic data can best be integrated with clinical practice so as to maximize patient benefit. As Bruce Blumberg from Kaiser Permanente observed in the workshop, “During the year in which we plan[ned] the workshop, the future became the present.” It became increasingly clear, he said, that large-scale genomic information would be integrated more fully into clinical practice, which meant that issues related to implementing this change needed to be addressed. Using DNA sequencing data on a large scale in a clinical setting will pose many difficult challenges. The storage, access, and portability of genetic data all raise significant issues. Questions exist about the need for confirmatory testing of results within a Clinical Laboratory Improvement Amendments (CLIA)–certified laboratory. Relevant information will need to be extracted and deposited into the appropriate medical records in a clinically comprehensible manner. The analysis of this information—and re- analysis as new findings emerge—will put further constraints and burdens on health care practitioners and laboratories, particularly as the current health care system lacks a mechanism to reimburse these activities. Ethical issues related to such things as informed consent and stewardship over this information will also need to be considered as integration moves forward. Complicating all of this is the fact that most patients and health care pro- viders have not yet realized just how broad an effect genomic discoveries are likely to have on treatment course and health. With these issues in mind and considering the potential impact that genomic information can have on the prevention, diagnosis, and treatment of disease, the Roundtable on Translating Genomic-Based Research for Health hosted a workshop on July 19, 2011, to highlight and identify the challenges and opportunities in integrating large-scale genomic informa- tion into clinical practice. The workshop was premised on the assumptions that sequencing technology will advance to the point that it can produce clinically meaningful results and that whole-genome sequencing will be cost-effective and comparable in cost to other diagnostic tests. There is little point in deliberating about these assumptions, Blumberg said, because “no

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3 INTRODUCTION matter what the outcome of our debate . . . this is going to happen. This is already happening.” The planning committee for the workshop decided early in its discus- sions that a single workshop would be insufficient to adequately address every issue, challenge, or opportunity related to clinical genomic medicine. Therefore, to begin a discussion about the use of genomic data in the clinic, the workshop committee decided to focus on several key topics, including the analysis, interpretation, and delivery of genomic informa- tion to health care providers plus workforce, ethical, and legal issues. This workshop report summarizes the speakers’ presentations and the discus- sions that followed them. It begins by providing an overview of the current state of the field of genomic medicine, of how approaches to basic and clinical research are changing, and of areas in which steps can be taken immediately to build the necessary infrastructure (Chapter 2). The next two chapters describe the discussions that took place concerning the analysis and interpretation of genomic data (Chapters 3 and 4), while the following three chapters examine practical issues: the delivery of genomic informa- tion (Chapter 5), ethical and legal issues (Chapter 6), and developing the necessary workforce skills and knowledge (Chapter 7). The last chapter describes panel discussions on how to maintain curated databases, the role of the field in public health, and how each stakeholder could be involved in helping address the current challenges (Chapter 8). The main objective of this workshop was to start a discussion of what needs to be done to prepare the necessary infrastructure and to address the various challenges so that patients will be able to benefit from genomics- based research. As Catherine Wicklund from Northwestern University said, the realization that genomics data can be useful in the clinic “is here and we really need to deal with this issue.”

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