What’s New in Genetic Testing for Cancer Susceptibility?

September 15, 2016

The dilemma for clinicians is how best to understand and manage this rapidly growing body of information to improve patient care. With millions of genetic variants of potential clinical significance and thousands of genes associated with rare but well-established genetic conditions, the complexities of genetic data management clearly will require improved computerized clinical decision support tools, as opposed to continued reliance on traditional rote, memory-based medicine.

The advent of next-generation sequencing, and its transition further into the clinic with the US Food and Drug Administration approval of a cystic fibrosis assay in 2013, have increased the speed and reduced the cost of DNA sequencing. Coupled with a historic ruling by the Supreme Court of the United States that human genes are not patentable, these events have caused a seismic shift in genetic testing in clinical medicine. More labs are offering genetic testing services; more multigene panels are available for gene testing; more genes and gene mutations are being identified; and more variants of uncertain significance, which may or may not be clinically actionable, have been found. All these factors, taken together, are increasing the complexity of clinical management. While these developments have led to a greater interest in genetic testing, risk assessment, and large-scale population screening, they also present unique challenges. The dilemma for clinicians is how best to understand and manage this rapidly growing body of information to improve patient care. With millions of genetic variants of potential clinical significance and thousands of genes associated with rare but well-established genetic conditions, the complexities of genetic data management clearly will require improved computerized clinical decision support tools, as opposed to continued reliance on traditional rote, memory-based medicine.


In 2013, the US Food and Drug Administration (FDA) approved the use of next-generation DNA sequencing in clinical practice-specifically, a cystic fibrosis assay run on Illumina’s MiSeq instrument.[1] Next-generation sequencing (NGS) refers to massively parallel, high-throughput DNA sequencing, and it has deployed a suite of technologies that have drastically increased the speed and decreased the cost of sequencing compared with the traditional Sanger method. The Supreme Court of the United States, also in 2013, invalidated the BRCA patent held by Myriad Genetics,[2] ruling that human genes are not patentable. These two seminal events have created a seismic shift in the genetic testing world, accentuating forces already at work to markedly increase the use of genetic testing for cancer susceptibility in clinical medicine, and companies are vying to make less expensive, more efficient genetic tests.

These profound changes in genetic testing have altered the practice of medicine (Figure 1). It took 13 years and cost $2.7 billion to sequence the first human reference genome.[3] Today, using NGS, a genome can be sequenced for $1,245 in under a week,[4] or in 26 hours for approximately $6,500.[5] As of this writing, the upcoming launch of a $999 genome with clinical grade sequencing coverage and interpretation, and with short turnaround time, has been announced.[1]

In this rapidly evolving field, rather than asking, “What’s new in genetic testing?” perhaps the better question is, “What isn’t new?” New realities include but are not limited to:

• More laboratories doing cancer genetic testing.

• More panels containing varying combinations of genes.

• More genes to understand and manage, with more incidental findings.

• More variants of uncertain significance (VUSs).

• More interest in gene testing.

• More to cover in counseling.

• More interest in population screening.

• More need for clinical decision support (CDS).

More Laboratories Doing Cancer Genetic Testing

Almost immediately after the Supreme Court’s 2013 decision, multiple laboratories began to market BRCA testing, as well as testing for other cancer genes (Table 1). The challenge for physicians, nurse practitioners, and genetic counselors was and remains how to select the appropriate laboratory for a given situation. In choosing between labs, one must consider test accuracy, types of panels offered, accuracy and thoroughness of the interpretation, support in determining management of mutation carriers, coverage by insurance companies, and cost both to the healthcare system and to the patient (in potential out-of-pocket costs). Each clinician and/or health system must weigh these costs and benefits to choose the best laboratory for the situation.

More Panels Containing Varying Combinations of Genes

In the past, a patient at risk for hereditary breast and ovarian cancer (HBOC) syndrome was initially tested solely for BRCA1 and BRCA2. If the results of these tests were negative, the patient’s risk of having other mutations, such as PTEN or TP53, would be assessed and additional tests ordered. This “diagnostic odyssey” (as it is known in pediatric genetics) was expensive, time consuming, and frustrating for both the patient and the clinician; in addition, it was often stopped prematurely, missing the actual gene that was involved.

The marked decrease in the cost of DNA sequencing, and the large number of genes now identified as increasing a person’s cancer susceptibility (Table 2), have led to the development of panel testing, in which large numbers of genes are tested simultaneously at a cost similar to or even less than the cost of sequencing just one or two genes. Various laboratories now offer a variety of panels (see Table 1), from disease-specific panels, such as a breast panel, to “pan-cancer” panels, which test multiple genes that may increase cancer susceptibility for a variety of cancers and inherited cancer syndromes. However, not all these gene mutations have corresponding clinical management guidelines, and this may pose a significant dilemma for physicians.

While the experts have urged caution in using these tests,[6] clinicians have moved ahead in large numbers. Many practices now routinely order cancer panels as first-line genetic testing, and recent publications in the breast cancer literature are reporting identification of actionable mutations by sequencing more broadly across a larger number of genes.[7-9] Actionable mutations in cancer genetics have been defined as those that “have significant diagnostic, prognostic, or therapeutic implications in subsets of cancer patients and for specific therapies.”[10] In breast cancer, patients with actionable mutations may consider additional breast imaging and/or elective risk-reducing surgery (Figure 2). However, it should be noted that in this new era, almost no randomized clinical trials have been performed, and “actionable” is determined by expert opinion. In addition to actionable genes, most panels include genes that are less well characterized or that lack management guidelines. This is undoubtedly confusing for both the patient and the physician. As the scale of testing increases, and as more clinical outcomes data accumulate and are published (or at least shared via a growing number of online variant databases), it is hoped that either the discovery of mutations in these genes will be found to have utility or that these genes will be removed from the panels. In addition, it is important to recognize that finding mutations does not always lead to changes in management recommendations, and caution should be exercised when attributing causality to genes with low or moderate penetrance.[11]

Data are accumulating rapidly, as demonstrated by the cumulative results of panel testing as it relates to HBOC syndromes. Tung (two series), Walsh, and Couch have reported the results of panel tests in patients who were at risk for HBOC syndromes and had not yet undergone BRCA testing.[7,8,12,13] Desmond and Maxwell reported on patients at risk for HBOC syndromes who had previously undergone BRCA testing.[9,14] With a small amount of mathematical manipulation (the number of patients who were BRCA-positive in the Desmond and Maxwell series was extrapolated by multiplying the number tested by 1.1155 [based on the percentage of patients who were BRCA-positive on de novo testing, 10.37%-see below]), we have combined these series into a summary of the results from this type of panel testing (Table 3, Figure 3). In those patients who underwent de novo testing, 10.3% were BRCA-positive and 5.41% were positive for other genes. This highlights the fact that about one-third of mutation carriers will be missed if only BRCA1/2 is tested (or that 50% more carriers will be found if panel testing is performed). When BRCA results are excluded, the series can be combined as second-tier testing to show that 6% of patients who are BRCA-negative will test positive for other genes (Table 3). These results raise an important question with regard to the hundreds of thousands of patients who tested as BRCA-negative in the pre-panel era. Should all of these patients be retested now with panels? Or should we only retest the highest-risk patients? Will insurers pay for this additional testing? Obviously many questions remain.

These studies highlight the potential benefit of multigene panels in identifying patients and families with clinically significant mutations that may alter their management recommendations. It almost goes without saying that the current support systems must be extended to help patients who carry such mutations cope with their new diagnosis and the potential associated psychological, financial, and family strains.


Desmond et al took their analysis a step further by looking at the potential actionability of panel results.[9] They re-evaluated the 1,046 HBOC candidates who had tested negative for BRCA1/2 mutations using multigene panel testing, and found that 40 of the subjects (3.8%) had deleterious mutations in non-BRCA genes. In terms of the importance of identifying mutations in non-BRCA genes and potential actionability, the study was expanded to include 23 more patients outside the original cohort in whom mutations were found using gene panels. When all these mutation carriers were taken together, 92% of the patients had mutations correlating with cancers found either in themselves or in their families (strengthening the suggested relationship between these genes and diseases); 33 patients (52%) required a change in management (28 increases in cancer screening, 1 prophylactic colectomy, and 4 prophylactic gastrectomies); and testing of relatives was indicated for 72%, owing to potential changes in management for those relatives. Compared with BRCA1/2 testing, multigene panel testing finds a larger number of patients who may require a change in their clinical management and that of their relatives. For some, however, this may lead to more questions than answers, and it may be unclear what the long-term risks and benefits of these findings will be for any given individual.

More Genes to Understand and Manage, With More Incidental Findings

Increasing numbers of genes related to a variety of cancers have been identified (see Table 2). Mutations in these genes have different incidence rates in the population, cause different spectrums of cancers in a family, and have different levels of penetrance. The same gene mutation can cause different cancers, and the same cancer can be caused by different gene mutations. The permutations are astronomical. The observation has been made that there is an inverse relationship between incidences of mutations in the population and cancer penetrance.[15] When evaluating a patient with a strong family history of HBOC, we can no longer consider just BRCA1 and BRCA2. We must consider other genes as well (see Table 2).

Easton et al effectively summarized our current knowledge about the penetrance of major breast cancer genes.[16] The lifetime risk of developing breast cancer ranges from 75% for BRCA1 to 23% for NBN; the lifetime risk of developing breast cancer for an average woman is 12.4%.[17] This difference in penetrance clearly influences the management recommendations for unaffected women: whereas MRI screening might be suggested for both mutations, risk-reducing mastectomies should only be strongly considered for BRCA1/2, and not NBN (see Figure 2). Because we are now identifying genes of moderate-to-low penetrance, and with different spectra of associated disease, our strategies must be flexible. Medical management should be informed by the penetrance of the gene mutation and by the age, family history, gender, and health of the patient; whether he or she has cancer or not; and if so, what type and stage of cancer it is. A woman in her twenties with a BRCA1 mutation who does not have cancer should have breast MRI screening, and in her late thirties, she should strongly consider prophylactic bilateral oophorectomy and might consider prophylactic mastectomies. If she develops breast cancer, regardless of age, she should consider bilateral mastectomies.[18,19] In comparison, a male BRCA1 carrier will likely do little with regard to this mutation other than inform his relatives and increase prostate screening.[18,19] In yet another scenario, a woman with a CHEK2 mutation might consider breast MRI screening, while prophylactic mastectomies would be discouraged per established guidelines[18,19]; oophorectomy or ovarian screening would be unnecessary, as that is not part of the disease spectrum associated with this mutation. It should be noted that the guidelines for CHEK2 are based on expert opinion, as no outcomes data for MRI screening currently exist. In addition, it is important to recognize that this field is continuously evolving, and recommendations may change frequently as more outcomes are reported.

As we test more and more genes, we will encounter more incidental findings. That is, we will identify gene mutations that we did not anticipate based on the family history. Because many panels include genes for multiple cancers, we now routinely see patients who are being tested for a hereditary breast cancer syndrome who turn out to have a hereditary colon cancer syndrome instead, and vice versa.

Frey et al evaluated 127 patients who underwent noninformative primary genetic screening and subsequent multigene panel testing.[20] Four patients were found to have pathogenic mutations that could be characterized as “incidental” in the context of their personal and family histories. Similarly, Yurgelun et al performed multigene panel testing in 1,260 patients with suspected Lynch syndrome.[21] They reported that 71 patients (5.6%) had a clinically unsuspected mutation in a non–Lynch syndrome cancer susceptibility gene, most commonly BRCA1/2. Of note, the long-term implications of these findings have yet to be verified. Regardless, treating these mutation carriers by established guidelines would be prudent.

Although incidental findings can be distressing for the patient and the clinician, it may be in the best interest of the patient to identify these syndromes before a cancer occurs. While controversial, the American College of Medical Genetics and Genomics (ACMG) guidelines[22] suggest that if an incidental finding is potentially actionable, it should be reported to the patient. The ACMG produced a minimum list of 56 genes they considered theoretically actionable, and this list is expected to grow rapidly. More specifically, they sought to include “conditions for which confirmatory approaches for medical diagnosis would be available…disorders for which preventive measures and/or treatments were available, and disorders in which individuals with pathogenic mutations might be asymptomatic for long periods.”[22]

More VUSs

Genes have variations in their DNA sequences. Many of these variants are benign, such as those that result in a person having blue eyes vs brown eyes, while others are pathogenic and markedly increase the risk of disease. Mutations in or variants of cancer susceptibility genes can be classified into five categories: benign, likely benign, VUS, likely pathogenic, and pathogenic.

Classification of variants can sometimes be easy, such as when the mutation in a gene causes truncation of the protein whose pathogenicity is known to be mediated through loss of function; others are harder to classify, such as when the variant is a change in a single amino acid in the protein, and the effect of that change is not obvious.[23] If it is not possible to determine whether a mutation is disease-causing, the variant is classified as a VUS. In this case, the clinician must rely on the family history to determine the appropriate management. VUSs can be challenging for both the clinician and the patient. One would expect, and it has been shown, that for genes that are rarely tested, the VUS rates will be markedly higher, because there is less clinical and family history data to link with the mutation. However, as more mutations are identified within families that have known clinical diseases/outcomes, the phenotypes can be more clearly defined. Eggington et al showed that the VUS rate for BRCA1 and BRCA2 declined by 84% between 2002, when the rate was 12.8%, and 2013, by which time the rate had dropped to 2.1%, mostly due to the markedly increased rate of testing.[24]

Based on the studies mentioned previously, Frey et al found a 42% VUS rate when panel testing was undertaken.[20] In both cohorts studied by Tung et al, around 40% of individuals had at least one VUS.[7] Yurgelun et al detected one or more VUSs in 38% of their cohort.[21] The most common VUSs were found in ATM, APC, NBN, and BRIP1. The PROMPT Registry[25] was initiated to help classify the VUSs being found in the plethora of genes that are now being tested, as well as to improve our understanding of the penetrance of these genes. This registry allows patients who have a variant in one of the less-studied genes to enter their data online into a central registry.

As more and more testing is performed for more and more genes, we anticipate that many VUSs will be reclassified, and the number of VUSs for each gene tested will eventually drop significantly. In the interim, it is important to emphasize that VUS findings should not be used to determine the management of patients. In these patients, management recommendations must be informed by the family history and other patient factors.

More Interest in Gene Testing

Although commercial genetic testing has been available for over 20 years, uptake has been slow and compliance with guidelines has been marginal. It is estimated that more than 90% of unaffected BRCA carriers remain unaware of their status and are mismanaged.[26] Based on National Comprehensive Cancer Network (NCCN) guidelines for breast cancer,[18] millions of women are eligible for BRCA1/2 testing, and similar numbers of men and women are likely eligible for testing for other syndromes, most of whom are unaware of their eligibility.[27] Furthermore, using existing testing guidelines, it has been estimated that up to 50% of BRCA1/2 carriers may be missed as a result of arbitrary factors, such as small family size, higher male-to-female ratio in the family, and nonpaternity (all of which skew family histories to be interpreted as negative).

Why have we been failing? Providers often do not refer patients who need testing, either because there is insufficient time to take a thorough family history, because they lack the genetics expertise to analyze the histories they do take, or because they are unfamiliar with the genetic testing guidelines. It is well known that primary care physicians often do not have time to take a thorough family history,[28] and even oncologists are not taking thorough family histories from cancer patients.[29] Whether due to lack of expertise, lack of time, or lack of resources, many patients are never referred for testing.

On May 14, 2013, Angelina Jolie wrote an article in the New York Times chronicling her experience with breast cancer, genetic testing, and prophylactic surgery.[30] She revealed that she was diagnosed with a BRCA1 mutation and chose to have bilateral mastectomies to significantly reduce her risk of developing and dying from breast cancer. After sharing her story and decision to have prophylactic surgery, the medical community began to notice an increase in other women choosing to have bilateral mastectomies, although not always for the same reasons. This phenomenon has become known as the “Angelina Jolie effect.” To assess the potential impact of the “Angelina Jolie effect,” Evans et al reviewed breast cancer family history referral data from 2012 to 2013 in the United Kingdom, and reported a significant rise in breast cancer family history referrals, demand for BRCA1/2 testing, and inquiries regarding risk-reducing mastectomies.[31] Although awareness of Ms. Jolie’s story has become prevalent, improved understanding has not followed. In a follow-up report, Evans et al published ongoing breast cancer family history referral data that confirmed a persistent increase in bilateral risk-reducing mastectomies among women with and without genetic mutations, noting that the effect was greater in those without a BRCA1/2 mutation.[32]

However, patients are not the only ones missing key information. A patient-survey study from 2013 by McCarthy et al evaluated the rates and predictors of physician recommendations for BRCA1/2 testing among patients with breast cancer.[33] They reported that physician recommendations for BRCA1/2 testing were strongly associated with one’s risk of carrying a mutation, although only 53% of high-risk women reported a testing recommendation. Brown et al reported similar results with a web-based survey of women with early-onset breast cancer, which revealed that only 53% of women with a family history of cancer had been referred to see a genetic counselor, although 81% of Ashkenazi Jewish women had received a referral.[34] Even in a cohort of young women (≤ 40 years old) with breast cancer, Ruddy et al demonstrated that only 24% had undergone genetic testing.[35] These studies highlight a serious problem-namely, that many women who meet criteria for testing may not receive a recommendation for testing from their physician. On analysis of the results of a survey on family history of breast and ovarian cancer and BRCA testing, Vig et al reported that age at diagnosis, Jewish ancestry, and both maternal and paternal family history were strongly predictive of undergoing BRCA testing, likely due to the “high-risk” nature of these features, although age appeared to be more influential than family history in the older population.[36]

Unfortunately, many testing gaps are likely the result of a lack of education. In a national survey of primary care physicians that analyzed physician knowledge on BRCA testing, physicians were asked to select indications for BRCA testing from multiple clinical scenarios.[37] Overall, only 19% correctly selected all of the increased-risk and none of the low-risk scenarios. In a separate study of primary care providers and breast cancer risk assessment, Guerra et al reported that only 18% of physicians had used a software program to calculate breast cancer risk, even though 48% had ordered or referred a patient for BRCA1/2 testing.[38]

To address some of these disparities, Christianson et al conducted three focus groups including a total of 16 primary care providers to obtain input regarding the incorporation of a family health history risk assessment tool into a community healthcare system.[39] In this study, physicians identified their impediments as including deficiencies in the following areas: standard screening guidelines, effective screening tests, genetic counseling resources, and services for high-risk patients. In addition, the providers were concerned about their level of expertise, the cost of preventive healthcare, and genetic discrimination. These findings highlighted the need for consultation and referral services, evidence-based recommendations, and educational resources. Similar focus groups conducted by Sabatino et al also reported “lacking confidence in knowledge of risk and risk assessment” as one of the most common barriers to risk assessment, even though almost all providers agreed that assessing breast cancer risk was a primary care provider’s responsibility.[40]

Fortunately, things are changing. There is increasing interest in genetic testing among both clinicians and patients. As its cost goes down, as clinicians become more comfortable with its use, and as it is more openly discussed in the lay press, an increasing number of patients are undergoing testing. Rosenberg et al recently reported that the rate of genetic testing of women diagnosed with breast cancer at ages ≤ 40 was increasing annually, with 95.3% of such women tested in 2013.[41]

Unfortunately, this success also highlights a failure. Why were these women not identified and tested before they developed breast cancer? We tend to agree with Mary Claire King, who stated, “To identify a woman as a carrier only after she develops cancer is a failure of cancer prevention.”[42] It is hoped that the increase in the testing of cancer patients will be accompanied by a similar, although likely less dramatic, increase in the testing of unaffected women, and women who are diagnosed with breast cancer after the age of 40.

To do better, family histories must be taken and analyzed at the primary care level, and testing must be performed liberally. In addition, a concerted effort must be made to test every blood relative of any known mutation carrier. We must capitalize on the increasing medical and public interest in genetic testing and use every means possible to identify patients before they develop cancer. Although the primary care providers are one part of the solution, it is also clear that better support systems need to be developed to help physicians perform these assessments with efficiency and accuracy, and they need to be developed now.

More to Cover in Counseling

The American Society of Clinical Oncology (ASCO) has set the standard for counseling patients about genetic testing; their recommendations regarding elements of the genetic testing process requiring informed consent were recently updated to take into account panel testing.[43] Providing for informed consent for the first of these elements (“information on specific genetic mutation(s) or genomic variant(s) being tested”) seems impractical with the availability of panels of 20-plus genes, as it does for the second element (“implications of a positive or negative test”). It would be impossible to describe the 20-plus different genes to be tested in advance of testing, as well as the implications of a positive result for each test. The time commitment seems unnecessarily excessive, and the likelihood of the patient retaining useful information seems minimal. The solution suggested in the ASCO update[43]-“that genes be ‘batched,’ that high penetrance syndromes should be described, and that special attention should be paid to less penetrant genes and less well understood syndromes”-does not seem to fix this problem, since it still recommends that a large amount of information be provided prior to testing.

Genetic counseling today takes a significant amount of time per patient. McPherson et al estimate that it takes a genetics professional around 7 hours, on average, to counsel a new patient.[44] This estimate may be too high or may reflect time spent in research, but given that the average cancer genetic counselor sees 10 patients per week, this translates to 4 hours per patient in a 40-hour week. If counselors are expected to discuss all high-penetrance syndromes, less-penetrant syndromes, and less-understood syndromes associated with all the genes in a panel, this time commitment will only increase. The solution may well lie in changing our model of counseling. Perhaps in the current era it would be better to test patients with minimal pretest counseling, and then follow up with intensive counseling for those who test positive for a deleterious mutation or who have a VUS. Currently, less than half of genetic testing is being ordered by genetics professionals in the United States, with lack of clinician recommendation cited as a reason for not seeing a genetic counselor.[45] The solution is not clear, and there are strong opinions on both sides of this question. However, we must make a decision as to whether we should continue to give extensive counseling to a small number of patients or make genetic testing more broadly available to the millions of individuals who need it by truncating the pretest counseling component.[46]

Renewed Interest in Population Screening

There is renewed interest in population-level screening for cancer-causing mutations, since many patients with mutations do not meet criteria for testing under NCCN guidelines (Table 4).[18] These patients will not be found until after they develop cancer, exemplifying the “failure of prevention” noted by King.[42] She suggests: “…it is time to offer genetic screening of these genes [BRCA1 and BRCA2] to every woman, at about age 30, in the course of routine medical care.”[42] Although many experts may recoil in horror at this suggestion, we should step back and determine objectively why this is or is not a good idea.

Population-based screening for other genetic diseases is already being done for every baby born in this country under newborn screening guidelines.[47] Our hesitancy to extend population screening for cancer to adults stems back to a time when genetic testing was too expensive, when genetic tests were limited to single genes or syndromes, when choosing the appropriate test required tremendous expertise, and when adults with a genetic cancer predisposition had few options. Today, genetic testing is inexpensive, panel testing is ubiquitous, and management strategies exist to find cancers at an earlier and more treatable stage. Furthermore, there is increasing recognition of wide phenotypic spectra for any given mutation, which may have some overlap with other hereditary syndromes. Thus, when we do a panel test that includes a colorectal cancer gene in a patient with a suspected hereditary breast cancer, we are in many ways doing population-based screening, which might be defined as screening an individual for a cancer gene that is otherwise not suspected on the basis of their family history.

The near future is being tested at Boston Children’s Hospital under the BabySeq protocol,[48] in which newborns are randomized to standard family history collection and care vs full-genome sequencing at birth, with the option of full disclosure to the parents. This “brave new world” approach will not only identify unsuspected syndromes in children, but will also find unsuspected syndromes in their parents, and will identify predispositions to disease expected much later in life-opening the door to early intervention and lifestyle modification. However, it is important to also recognize that, while some may appreciate the benefits of identifying such mutations, syndromes, and predispositions, other patients may live in constant fear of what has been projected-and that particular outcome may never become a reality. Regardless, inexpensive full-genome sequencing is just around the corner and may rapidly make our arguments and concerns moot.

More Need for CDS

The increase in knowledge is continuous and overwhelming, and the human brain is approaching its limit. In genetics specifically, the amount of information is exploding. A query to AuthorMapper[49] regarding articles in Medline that discuss BRCA1 shows 9 articles in the year 1994, when the gene was cloned; that number has grown exponentially-to more than 1,728 in 2015. The National Center for Biotechnology Information Genetic Testing Registry[50] boasts that it has registered more than 32,000 tests for 5,800 conditions and 3,900 genes. It is obvious that we cannot keep up with all the information on just BRCA1, much less for all of breast cancer genetics or for cancer genetics in general-and yet we continue to practice “memory-based medicine.”[51]

To potentially address this challenge, computerized CDS could be investigated as a solution in genetics.[52] CDS accepts machine-readable data about individual patients and then uses computerized knowledge bases, algorithms, guidelines, and models to determine a diagnosis and/or the best management strategy. It then presents that information to the provider in an intuitive format or visualization that helps the provider proceed down the correct path. CDS may help answer the following, as well as many additional questions:

• Who should have genetic testing?

• Which test or panel should be ordered?

• How should the results be interpreted?

• Is a particular variant deleterious?

• What is the risk of cancer(s) for a given gene?

• How can we best screen for or prevent a given cancer?

• How can we best treat a given cancer?

• How should older genetic interpretations be updated as new information becomes available?

Unfortunately, electronic health records (EHRs) lag behind in the tools they provide for CDS, especially as it relates to genetics. Most EHRs store genetic testing results as images of documents. These images cannot be used for CDS, cannot be searched, and cannot be aggregated for research or patient care. It is essential that EHRs adapt quickly to storing structured data and using CDS for genetics.


Genetic testing has entered a new era and our older paradigms are no longer sufficient. It is critical to find every mutation carrier for every hereditary syndrome before the disease occurs, and to change management of affected individuals in a way that prevents disease or finds it at an earlier, more treatable stage. Whether we achieve this with memory-based medicine, CDS, or population-based testing, we must find a way to accomplish this now.

Acknowledgment: The authors wish to acknowledge Ann S. Adams for her writing and editorial consultation.

Financial Disclosure:Dr. Hughes receives honoraria from Myriad Genetics and Veritas Genetics, and is a founder of and has a financial interest in Hughes Risk Apps, LLC. Dr. Hughes’s interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies. Dr. Thakuria is a cofounder and Chief Medical Officer of Veritas Genetics. Dr. Plichta and Ms. Griffin have no significant financial interest in or other relationship with the manufacturer of any product or provider of any service mentioned in this article.


1. Veritas Genetics. Our latest news. https://www.veritasgenetics.com/#sec-4. Accessed April 2, 2016.

2. Ellinger MS. Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc. June 13, 2013. http://www.fr.com/news/myriad-decision. Accessed February 18, 2016.

3. National Institutes of Health; National Human Genome Research Institute. The Human Genome Project completion: frequently asked questions. https://www.genome.gov/11006943. Accessed February 18, 2016.

4. National Institutes of Health; National Human Genome Research Institute. The cost of sequencing a human genome. https://www.genome.gov/sequencingcosts. Accessed February 18, 2016.

5. Miller NA, Farrow EG, Gibson M, et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Med. 2015;7:100.

6. Mauer CB, Pirzadeh-Miller SM, Robinson LD, Euhus DM. The integration of next-generation sequencing panels in the clinical cancer genetics practice: an institutional experience. Genet Med. 2014;16:407-12.

7. Tung N, Battelli C, Allen B, et al. Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. Cancer. 2015;121:25-33.

8. Walsh T, Casadei S, Lee MK, et al. Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Proc Natl Acad Sci USA. 2011;108:18032-7.

9. Desmond A, Kurian AW, Gabree M, et al. Clinical actionability of multigene panel testing for hereditary breast and ovarian cancer risk assessment. JAMA Oncol. 2015;1:943-51.

10. Dancey JE, Bedard PL, Onetto N, Hudson TJ. The genetic basis for cancer treatment decisions. Cell. 2012;148:409-20.

11. Axilbund JE. Panel testing is not a panacea. J Clin Oncol. 2016;34:1433-5.

12. Couch FJ, Hart SN, Sharma P, et al. Inherited mutations in 17 breast cancer susceptibility genes among a large triple-negative breast cancer cohort unselected for family history of breast cancer. J Clin Oncol. 2015;33:304-11.

13. Tung N, Lin NU, Kidd J, et al. Frequency of germline mutations in 25 cancer susceptibility genes in a sequential series of patients with breast cancer. J Clin Oncol. 2016;34:1460-8.

14. Maxwell KN, Wubbenhorst B, D’Andrea K, et al. Prevalence of mutations in a panel of breast cancer susceptibility genes in BRCA1/2-negative patients with early-onset breast cancer. Genet Med. 2015;17:630-8.

15. Ambry Genetics. Hereditary cancer panels: clinician guide.

. Accessed February 27, 2016.

16. Easton DF, Pharoah PD, Antoniou AC, et al. Gene-panel sequencing and the prediction of breast-cancer risk. N Engl J Med. 2015;372:2243-57.

17. National Institutes of Health; National Cancer Institute. SEER cancer statistics review, 1975-2013. http://seer.cancer.gov/csr/1975_2013/. Accessed August 4, 2016.

18. Daly M, Pilarski R, Axilbund J, et al. NCCN clinical practice guidelines in oncology: genetic/familial high-risk assessment: breast and ovarian. Version 2.2015. J Natl Compr Canc Netw. 2016;14:153-62.

19. Gradishar WJ, Anderson BO, Balassanian R, et al. NCCN clinical practice guidelines in oncology: breast cancer. Version 1.2016. J Natl Compr Canc Netw. 2016;14:324-54.

20. Frey MK, Kim SH, Bassett RY, et al. Rescreening for genetic mutations using multi-gene panel testing in patients who previously underwent non-informative genetic screening. Gynecol Oncol. 2015;139:211-5.

21. Yurgelun MB, Allen B, Kaldate RR, et al. Identification of a variety of mutations in cancer predisposition genes in patients with suspected Lynch syndrome. Gastroenterology. 2015;149:604-13.

22. Green RC, Berg JS, Grody WW, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013;15:565-74.

23. Emory Genetics Laboratory. Emory Genetics Laboratory classification definitions. http://geneticslab.emory.edu/emvclass/EGLClassificationDefinitions.php. Accessed March 26, 2016.

24. Eggington JM, Bowles KR, Moyes K, et al. A comprehensive laboratory-based program for classification of variants of uncertain significance in hereditary cancer genes. Clin Genet. 2014;86:229-37.

25. Patient Crossroads. Prospective registry of MultiPlex testing (PROMPT). https://connect.patientcrossroads.org/?org=prompt. Accessed February 27, 2016.

26. Drohan B, Roche CA, Cusack JC Jr, Hughes KS. Hereditary breast and ovarian cancer and other hereditary syndromes: using technology to identify carriers. Ann Surg Oncol. 2012;19:1732-7.

27. Polubriaginof FC, Drohan B, Bosinoff P, et al. Implications of following the guidelines for genetic testing and MRI use for breast cancer. J Clin Oncol. 2014;32(suppl 5s):abstr 1549.

28. Acheson LS, Wiesner GL, Zyzanski SJ, et al. Family history-taking in community family practice: implications for genetic screening. Genet Med. 2000;2:180-5.

29. Wood ME, Kadlubek P, Pham TH, et al. Quality of cancer family history and referral for genetic counseling and testing among oncology practices: a pilot test of quality measures as part of the American Society of Clinical Oncology Quality Oncology Practice Initiative. J Clin Oncol. 2014;32:824-9.

30. Jolie A. My medical choice. New York Times. May 14, 2013 (A25).

31. Evans DG, Barwell J, Eccles DM, et al. The Angelina Jolie effect: how high celebrity profile can have a major impact on provision of cancer related services. Breast Cancer Res. 2014;16:442.

32. Evans DG, Wisely J, Clancy T, et al. Longer term effects of the Angelina Jolie effect: increased risk-reducing mastectomy rates in BRCA carriers and other high-risk women. Breast Cancer Res. 2015;17:143.

33. McCarthy AM, Bristol M, Fredricks T, et al. Are physician recommendations for BRCA1/2 testing in patients with breast cancer appropriate? A population-based study. Cancer. 2013;119:3596-603.

34. Brown KL, Hutchison R, Zinberg RE, McGovern MM. Referral and experience with genetic testing among women with early onset breast cancer. Genet Test. 2005;9:301-5.

35. Ruddy KJ, Gelber S, Shin J, et al. Genetic testing in young women with breast cancer: results from a Web-based survey. Ann Oncol. 2010;21:741-7.

36. Vig HS, McCarthy AM, Liao K, et al. Age at diagnosis may trump family history in driving BRCA testing in a population of breast cancer patients. Cancer Epidemiol Biomarkers Prev. 2013;22:1778-85.

37. Bellcross CA, Kolor K, Goddard KA, et al. Awareness and utilization of BRCA1/2 testing among U.S. primary care physicians. Am J Prev Med. 2011;40:61-6.

38. Guerra CE, Sherman M, Armstrong K. Diffusion of breast cancer risk assessment in primary care. J Am Board Fam Med. 2009;22:272-9.

39. Christianson CA, Powell KP, Hahn SE, et al. The use of a family history risk assessment tool within a community health care system: views of primary care providers. J Genet Couns. 2012;21:652-61.

40. Sabatino SA, McCarthy EP, Phillips RS, Burns RB. Breast cancer risk assessment and management in primary care: provider attitudes, practices, and barriers. Cancer Detect Prev. 2007;31:375-83.

41. Rosenberg SM, Ruddy KJ, Tamimi RM, et al. BRCA1 and BRCA2 mutation testing in young women with breast cancer. JAMA Oncol. 2016;2:730-6.

42. King MC, Levy-Lahad E, Lahad A. Population-based screening for BRCA1 and BRCA2: 2014 Lasker Award. JAMA. 2014;312:1091-2.

43. Robson ME, Bradbury AR, Arun B, et al. American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility. J Clin Oncol. 2015;33:3660-7.

44. McPherson E, Zaleski C, Benishek K, et al. Clinical genetics provider real-time workflow study. Genet Med. 2008;10:699-706.

45. Armstrong J, Toscano M, Kotchjo, N, et al. Utilization and outcomes of BRCA genetic testing and counseling in a national commercially insured population. JAMA Oncol. 2015;1:1251-60.

46. Narod S. Genetic testing for BRCA mutations today and tomorrow-about the ABOUT study. JAMA Oncol. 2015;1:1225-6.

47. US Department of Health and Human Services Advisory Committee on Heritable Disorders in Newborns and Children. Recommended uniform screening panel. http://www.hrsa.gov/advisorycommittees/mchbadvisory/heritabledisorders/recommendedpanel/ Accessed August 18, 2016.

48. G2P: Research in Translational Genomics and Health Outcomes. The BabySeq project: genome sequence–based screening for childhood risk and newborn illness. http://www.genomes2people.org/babyseqproject. Accessed January 27, 2016.

49. AuthorMapper. BRCA testing from 1994. http://www.authormapper.com/search.aspx?q=BRCA1%20testing%20from%201994. Accessed February 28, 2016.

50. National Center for Biotechnology Information Genetic Testing Registry. http://www.ncbi.nlm.nih.gov/gtr. Accessed February 20, 2016.

51. Crane RM, Raymond B. Fulfilling the potential of clinical information systems. Permanente J. 2003;7:62-7.

52. Welch BM, Kawamoto K, Drohan B, Hughes KS. Clinical decision support for personalized medicine. In: Greenes R, editor. Clinical decision support: the road to broad adoption. 2nd ed. Burlington, MA: Elsevier; 2014. p. 383-413.

53. Ambry Genetics-search. http://www.ambrygen.com/search/node. Accessed April 10, 2016.

54. Myriad mySupport360. https://ms360.myriad.com. Accessed April 10, 2016.