Patient preferences regarding incidental genomic findings discovered during tumor profiling

Development of a novel measure of advanced cancer patients' perceived utility of secondary germline findings from tumor genomic profiling

Objective

Tumor genomic profiling (TGP) can inform advanced cancer patients' treatment decisions, and also reveal secondary germline findings-information about inherited risks for cancer and other disorders. We sought to develop a measure of patient perceptions of the clinical and personal utility of secondary germline findings.

Methods

We developed a draft survey based on literature and patient interview data (n=40). We evaluated and refined the survey through cognitive interviews with advanced cancer patients who received secondary germline findings from TGP (n=10). The survey was psychometrically validated with data from two independent samples of advanced cancer patients undergoing TGP (total n=349).

Results

Cognitive interviews offered opportunities for survey refinement and confirmation of its comprehensible nature. Exploratory and confirmatory factor analysis of the survey identified 16 items across three subscales with strong internal consistency (Cronbach's alpha ≥0.79): perceived utility for others, perceived utility for self and health, and confidence in secondary findings.

Conclusion

We developed a novel valid scale with promise for measuring advanced cancer patients' perceptions of the utility of secondary germline findings.

Innovation

We offer a new patient-derived measure of perceived utility of and confidence in secondary germline findings with potential applications for precision oncology research and clinical communication.

Germline Variants Incidentally Detected via Tumor-Only Genomic Profiling of Patients With Mesothelioma

IMPORTANCE

Patients with mesothelioma often have next-generation sequencing (NGS) of their tumor performed; tumor-only NGS may incidentally identify germline pathogenic or likely pathogenic (P/LP) variants despite not being designed for this purpose. It is unknown how frequently patients with mesothelioma have germline P/LP variants incidentally detected via tumor-only NGS.

OBJECTIVE

To determine the prevalence of incidental germline P/LP variants detected via tumor-only NGS of mesothelioma.

DESIGN, SETTING, AND PARTICIPANTS

A series of 161 unrelated patients with mesothelioma from a high-volume mesothelioma program had tumor-only and germline NGS performed during April 2016 to October 2021. Follow-up ranged from 18 months to 7 years. Tumor and germline assays were compared to determine which P/LP variants identified via tumor-only NGS were of germline origin. Data were analyzed from January to March 2023.

MAIN OUTCOMES AND MEASURES

The proportion of patients with mesothelioma who had P/LP germline variants incidentally detected via tumor-only NGS.

RESULTS

Of 161 patients with mesothelioma, 105 were male (65%), the mean (SD) age was 64.7 (11.2) years, and 156 patients (97%) self-identified as non-Hispanic White. Most (126 patients [78%]) had at least 1 potentially incidental P/LP germline variant. The positive predictive value of a potentially incidental germline P/LP variant on tumor-only NGS was 20%. Overall, 26 patients (16%) carried a P/LP germline variant. Germline P/LP variants were identified in ATM, ATR, BAP1, CHEK2, DDX41, FANCM, HAX1, MRE11A, MSH6, MUTYH, NF1, SAMD9L, and TMEM127.

CONCLUSIONS AND RELEVANCE

In this case series of 161 patients with mesothelioma, 16% had confirmed germline P/LP variants. Given the implications of a hereditary cancer syndrome diagnosis for preventive care and familial counseling, clinical approaches for addressing incidental P/LP germline variants in tumor-only NGS are needed. Tumor-only sequencing should not replace dedicated germline testing. Universal germline testing is likely needed for patients with mesothelioma.

Germline predisposition to haematological malignancies: Best practice consensus guidelines from the UK Cancer Genetics Group (UKCGG), CanGene-CanVar and the NHS England Haematological Oncology Working Group

The implementation of whole genome sequencing and large somatic gene panels in haematological malignancies is identifying an increasing number of individuals with either potential or confirmed germline predisposition to haematological malignancy. There are currently no national or international best practice guidelines with respect to management of carriers of such variants or of their at-risk relatives. To address this gap, the UK Cancer Genetics Group (UKCGG), CanGene-CanVar and the NHS England Haematological Oncology Working Group held a workshop over two days on 28-29th April 2022, with the aim of establishing consensus guidelines on relevant clinical and laboratory pathways. The workshop focussed on the management of disease-causing germline variation in the following genes: DDX41, CEBPA, RUNX1, ANKRD26, ETV6, GATA2. Using a pre-workshop survey followed by structured discussion and in-meeting polling, we achieved consensus for UK best practice in several areas. In particular, high consensus was achieved on issues regarding standardised reporting, variant classification, multidisciplinary team working and patient support. The best practice recommendations from this meeting may be applicable to an expanding number of other genes in this setting.

The Role of Medical Mistrust in Concerns about Tumor Genomic Profiling among Black and African American Cancer Patients

Tumor genomic profiling (TGP) is used in oncology practice to optimize cancer treatment and improve survival rates. However, TGP is underutilized among Black and African American (AA) patients, creating potential disparities in cancer treatment outcomes. Cost, accuracy, and privacy are barriers to genetic testing, but medical mistrust (MM) may also influence how Black and AA cancer patients perceive TGP. From December 2019 to February 2020, 112 Black and AA adults from two outpatient oncology sites in Philadelphia, PA without a known history of having TGP testing conducted completed a cross-sectional survey. Items queried included sociodemographic characteristics, clinical factors, patient-oncologist relationship quality, medical mistrust, and concerns about TGP. A k-means cluster analysis revealed two distinct psychographic clusters: high (MM-H) versus low (MM-L) medical mistrust. Clusters were not associated with any sociodemographic or clinical factors, except for age (MM-H patients older than MM-L patients, p = 0.006). Eleven TGP concerns were assessed; MM-H patients expressed greater concerns than MM-L patients, including distrust of the government, insurance carriers, and pharmaceutical companies. TGP concerns varied significantly based on level of medical mistrust, irrespective of sociodemographic characteristics. Targeted communications addressing TGP concerns may mitigate disparities in TGP uptake among those with medical mistrust.

Incidental germline findings during molecular profiling of tumor tissues for precision oncology: molecular survey and methodological obstacles

Background

A fraction of patients referred for complex molecular profiling of biopsied tumors may harbor germline variants in genes associated with the development of hereditary cancer syndromes (HCS). Neither the bioinformatic analysis nor the reporting of such incidental germline findings are standardized.

Methods

Data from Next-Generation Sequencing (NGS) of biopsied tumor samples referred for complex molecular profiling were analyzed for germline variants in HCS-associated genes. Analysis of variant origin was performed employing bioinformatic algorithms followed by manual curation. When possible, the origin of the variant was validated by Sanger sequencing of the sample of normal tissue. The variants’ pathogenicity was assessed according to ACMG/AMP.

Results

Tumors were sampled from 183 patients (Males: 75 [41.0%]; Females: 108 [59.0%]; mean [SD] age, 57.7 [13.3] years) and analysed by targeted NGS. The most common tumor types were colorectal (19%), pancreatic (13%), and lung cancer (10%). A total of 56 sequence variants in genes associated with HCS were detected in 40 patients. Of them, 17 variants found in 14 patients were predicted to be of germline origin, with 6 variants interpreted as pathogenic (PV) or likely pathogenic (LPV), and 9 as variants of uncertain significance (VUS). For the 41 out of 42 (97%) missense variants in HCS-associated genes, the results of computational prediction of variant origin were concordant with that of experimental examination. We estimate that Sanger sequencing of a sample of normal tissue would be required for ~ 1–7% of the total assessed cases with PV or LPV, when necessity to follow with genetic counselling referral in ~ 2–15% of total assessed cases (PV, LPV or VUS found in HCS genes).

Conclusion

Incidental findings of pathogenic germline variants are common in data from cancer patients referred for complex molecular profiling. We propose an algorithm for the management of patients with newly detected variants in genes associated with HCS.

Psychological predictors of advanced cancer patients' preferences for return of results from comprehensive tumor genomic profiling

This study assessed the psychological predictors of preferences for return of comprehensive tumor genomic profiling (CTGP) results in patients with advanced cancers, enrolled in the Molecular Screening and Therapeutics Program. Patients completed a questionnaire prior to undergoing CTGP. Of the 1434 who completed a questionnaire, 96% would like to receive results that can guide treatment for their cancer, and preference for receiving this type of result was associated with lower tolerance of uncertainty. Sixty-four percent would like to receive results that cannot guide treatment, and lower tolerance of uncertainty, self-efficacy, and perceived importance were associated with this preference. Fifty-nine percent would like to receive variants of unknown significance, which was associated with lower tolerance of uncertainty, higher self-efficacy, and perceived importance. Eighty-six percent wanted to receive germline results that could inform family risk. This was associated with higher self-efficacy, perceived importance, and perceived susceptibility. Although most patients wanted to receive all types of results, given the differing patient preferences regarding the return of results depending on the utility of the different types of results, it appears critical to safeguard patient understanding of result utility to achieve informed patient choices. This should be accompanied by appropriate consent processes.

Participants' Preferences and Reasons for Wanting Feedback of Individual Genetic Research Results From an HIV-TB Genomic Study: A Case Study From Botswana

The feedback of individual results of genomics research is an ethical issue. However, which genetic results African participants would like to receive and why, remains unclear. A qualitative study was conducted to collect data from 44 adolescents and 49 parents/caregivers of adolescents enrolled in a genomic study in Botswana. Almost all the participants wanted to receive genetic results. Parents and caregivers wanted to receive results across all categories of genetic conditions discussed in the study, while adolescents were reluctant to receive results for severe, non-preventable, and unactionable conditions. Participants expressed different reasons for wanting feedback of results, including for awareness, improving lifestyle, accepting one' situation, and preparing for the future. Our findings also reveal that participants' context, relations, and empowerment are important to consider in interpreting their preferences for feedback of results.

A qualitative study among patients with an inherited retinal disease on the meaning of genomic unsolicited findings

Exome-based testing for genetic diseases can reveal unsolicited findings (UFs), i.e. predispositions for diseases that exceed the diagnostic question. Knowledge of patients’ interpretation of possible UFs and of motives for (not) wanting to know UFs is still limited. This lacking knowledge may impede effective counselling that meets patients’ needs. Therefore, this article examines the meaning of UFs from a patient perspective. A qualitative study was conducted and an interpretative phenomenological analysis was made of 14 interviews with patients with an inherited retinal disease. Patients assign a complex meaning to UFs, including three main components. The first component focuses on result-specific qualities, i.e. the characteristics of an UF (inclusive of actionability, penetrance, severity and age of onset) and the consequences of disclosure; the second component applies to a patient’s lived illness experiences and to the way these contrast with reflections on presymptomatic UFs; the third component addresses a patient’s family embedding and its effect on concerns about disease prognosis and genetic information’s family relevance. The complex meaning structure of UFs suggests the need for counselling procedures that transcend a strictly clinical approach. Counselling should be personalised and consider patients’ lived illness experiences and family context.

Preferences to receive unsolicited findings of germline genome sequencing in a large population of patients with cancer

BACKGROUND

In precision medicine, somatic and germline DNA sequencing are essential to make genome-guided treatment decisions in patients with cancer. However, it can also uncover unsolicited findings (UFs) in germline DNA that could have a substantial impact on the lives of patients and their relatives. It is therefore critical to understand the preferences of patients with cancer concerning UFs derived from whole-exome (WES) or whole-genome sequencing (WGS).

METHODS

In a quantitative multicentre study, adult patients with cancer (any stage and origin of disease) were surveyed through a digital questionnaire based on previous semi-structured interviews. Background knowledge was provided by showing two videos, introducing basic concepts of genetics and general information about different categories of UFs (actionable, non-actionable, reproductive significance, unknown significance).

RESULTS

In total 1072 patients were included of whom 701 participants completed the whole questionnaire. Overall, 686 (85.1%) participants wanted to be informed about UFs in general. After introduction of four UFs categories, 113 participants (14.8%) changed their answer: 718 (94.2%) participants opted for actionable variants, 537 (72.4%) for non-actionable variants, 635 (87.0%) participants for UFs of reproductive significance and 521 (71.8%) for UFs of unknown significance. Men were more interested in receiving certain UFs than women: non-actionable: OR 3.32; 95% CI 2.05 to 5.37, reproductive significance: OR 1.97; 95% CI 1.05 to 3.67 and unknown significance: OR 2.00; 95% CI 1.25 to 3.21. In total, 244 (33%) participants conceded family members to have access to their UFs while still alive. 603 (82%) participants agreed to information being shared with relatives, after they would pass away.

CONCLUSION

Our study showed that the vast majority of patients with cancer desires to receive all UFs of genome testing, although a substantial minority does not wish to receive non-actionable findings. Incorporation of categories in informed consent procedures supports patients in making informed decisions on UFs.

Motivations and barriers to pursue cancer genomic testing: A systematic review

OBJECTIVES

Single-gene testing is associated with psycho-social challenges for cancer patients. Genomic testing may amplify these. The aim of this study was to understand patients' motivations and barriers to pursue cancer genomic testing, to enable healthcare providers to support their patients throughout the testing process and interpretation of test results.

METHODS

Five databases were searched for original peer reviewed research articles published between January 2001 and September 2018 addressing motivation for genomic cancer testing. QualSyst was used to assess quality.

RESULTS

182 studies were identified and 17 were included for review. Studies were heterogenous. Both somatic and germline testing were included, and 14 studies used hypothetical scenarios. 3249 participants were analyzed, aged 18 to 94. Most were female and white. The most common diagnoses were breast, ovarian, lung and colorectal cancer. Interest in testing was high. Motivations included ability to predict cancer risk, inform disease management, benefit families, and understand cancer. Barriers included concerns about cost, privacy/confidentiality, clinical utility, and psychological harm.

CONCLUSIONS

Despite concerns, consumers are interested in cancer genomic testing if it can provide actionable results for themselves and their families.

PRACTICE IMPLICATIONS

Providers must manage understanding and expectations of testing and translate genetic information into health-promoting behaviours.

Engagement and return of results preferences among a primarily African American genomic sequencing research cohort

Genomics researchers are increasingly interested in what constitutes effective engagement of individuals from underrepresented groups. This is critical for longitudinal projects needed to inform the implementation of precision medicine. Return of results is one opportunity for engagement. The aims of this study were to determine participant perspectives on optimal engagement strategies and priorities for return of results and the extent to which focus groups were an effective modality for gathering input on these topics. We conducted six professionally moderated focus groups with 49 participants in a genomics research study. Transcripts from audio-recorded sessions were coded by two researchers and themes were discussed with the wider research team. All groups raised the issue of mistrust. Individuals participated nonetheless to contribute their perspectives and benefit their community. Many group members preferred engagement modalities that are offered to all participants and allow them to share the nuances of their perspectives over the use of participant representatives and surveys. All groups created a consensus ranking for result return priorities. Results for life-threatening conditions were the highest priority to return, followed by those related to treatable conditions that affect physical or mental health. We advocate for engagement strategies that reach as many participants as possible and allow them to share their perspectives in detail. Such strategies are valued by participants, can be effective for developing return of results policies, and may help institutions become more trustworthy.

Patients' and Oncologists' Knowledge and Expectations Regarding Tumor Multigene Next-Generation Sequencing: A Narrative Review

BACKGROUND

Tumor multigene next-generation sequencing (NGS) is increasingly being offered to cancer patients to guide clinical management and determine eligibility for clinical trials. We undertook a review of studies examining the knowledge and attitudes of patients and oncologists regarding the primary results and potential secondary findings of such testing.

MATERIALS AND METHODS

A search was conducted through the MEDLINE database using the following keywords: "neoplasms" and "molecular sequencing / genome sequencing / tumor profiling / NGS / whole exome sequencing" and "patient / oncologist" and "knowledge / attitudes / satisfaction / experience / evaluation / perspective / practice / preference." Articles meeting the inclusion criteria and additional relevant articles from their references were selected.

RESULTS

From 1,142 publications identified by the search and 9 from references, 21 publications were included in the final review. Patients generally had positive attitudes toward tumor NGS despite relatively little knowledge of test-related genetics concepts, but their expectations often exceeded the reality of low clinical utility. Patients with higher education and greater genetics knowledge had more realistic expectations and a more altruistic view of the role of NGS. Attitudes toward disclosure of secondary findings were highly variable. Oncologists had poor to moderate genomic literacy; they communicated challenges with tempering patient expectations and deciding what information to disclose.

CONCLUSION

Patients considering undergoing tumor NGS should be provided with easily understandable resources explaining the procedure, goals, and probable outcomes, whenever possible based on evidence-based guidelines. Continuing medical education programs on this topic for oncology health care professionals should strive to improve their genomic literacy and instruct them on how to optimally present this information to their patients.

IMPLICATIONS FOR PRACTICE

Oncologists are increasingly offering tumor multigene testing to patients with advanced cancers to guide more "personalized" treatment and/or determine eligibility for clinical trials. However, patients often have inadequate understanding and unrealistic expectations. Oncologists must ensure that they themselves have sufficient knowledge of the benefits and limitations of testing and must provide their patients with appropriate educational resources. Prior to testing, patients should be told the likelihood of finding a mutation in their specific tumor type for which a targeted treatment or clinical trial is available. Patients also need clear information about the possibility and implications of secondary findings.

Do solidarity and reciprocity obligations compel African researchers to feedback individual genetic results in genomics research?

Background

A key ethical question in genomics research relates to whether individual genetic research results should be disclosed to research participants and if so, which results are to be disclosed, by whom and when. Whilst this issue has received only scarce attention in African bioethics discourse, the extension of genomics research to the African continent has brought it into sharp focus.

Methods

In this qualitative study, we examined the views of adolescents, parents and caregivers participating in a paediatric and adolescent HIV-TB genomic study in Botswana on how solidarity and reciprocity obligations could guide decisions about feedback of individual genetic research results. Data were collected using deliberative focus group discussions and in-depth interviews.

Results

Findings from 93 participants (44 adolescents and 49 parents and caregivers) demonstrated the importance of considering solidarity and reciprocity obligations in decisions about the return of individual genetic research results to participants. Participants viewed research participation as a mutual relationship and expressed that return of research results would be one way in which research participation could be reciprocated. They noted that when reciprocity obligations are respected, participants feel valued and not respecting reciprocity expectations could undermine participant trust and participation in future studies.

Conclusions

We conclude that expectations of solidarity and reciprocity could translate into an obligation to feedback selected individual genetic research results in African genomics research.

Implications of Incidental Germline Findings Identified In the Context of Clinical Whole Exome Sequencing for Guiding Cancer Therapy

PURPOSE

Identification of incidental germline mutations in the context of next-generation sequencing is an unintended consequence of advancing technologies. These data are critical for family members to understand disease risks and take action.

PATIENTS AND METHODS

A retrospective cohort analysis was conducted of 1,028 adult patients with metastatic cancer who were sequenced with tumor and germline whole exome sequencing (WES). Germline variant call files were mined for pathogenic/likely pathogenic (P/LP) variants using the ClinVar database and narrowed to high-quality submitters.

RESULTS

Median age was 59 years, with 16% of patients ≤ 45 years old. The most common tumor types were breast cancer (12.5%), colorectal cancer (11.5%), sarcoma (9.3%), prostate cancer (8.4%), and lung cancer (6.6%). We identified 3,427 P/LP variants in 471 genes, and 84% of patients harbored one or more variant. One hundred thirty-two patients (12.8%) carried a P/LP variant in a cancer predisposition gene, with BRCA2 being the most common (1.6%). Patients with breast cancer were most likely to carry a P/LP variant (19.2%). One hundred ten patients (10.7%) carried a P/LP variant in a gene that would be recommended by the American College of Medical Genetics and Genomics to be reported as a result of clinical actionability, with the most common being ATP7B (2.7%), BRCA2 (1.6%), MUTYH (1.4%), and BRCA1 (1%). Of patients who carried a P/LP variant in a cancer predisposition gene, only 53% would have been offered correct testing based on current clinical practice guidelines. Of 471 mutated genes, 231 genes had a P/LP variant identified in one patient, demonstrating significant genetic heterogeneity.

CONCLUSION

The majority of patients undergoing clinical cancer WES harbor a pathogenic germline variation. Identification of clinically actionable germline findings will create additional burden on oncology clinics as broader WES becomes common.

Public interest in whole genome sequencing and information needs: an online survey study

Aim: To survey the general public about whole genome sequencing interest, including pharmacogenomic testing, and to identify information important for sequencing decisions. Patients & methods: An online survey of 901 members of the general public in an eastern Canadian province. Results: Interest in whole genome sequencing, including pharmacogenomic testing, was high with few differences among demographic variables. Issues identified as very important to sequencing decisions included familial implications of testing, whether treatment was available for conditions tested and knowing who could access genomic information. Most respondents would value support when interpreting sequencing results. Conclusion: Findings reveal the kind of information and support users of sequencing services would value and could inform the implementation of sequencing into care in ways that accord with public preferences and needs.

Advanced Cancer Patient Knowledge of and Attitudes towards Tumor Molecular Profiling

Limited research has indicated that despite their overwhelming interest in tumor molecular profiling (MP),1 cancer patients have poor knowledge about MP. The current study aimed to investigate demographic and psychological predictors of knowledge and perceived importance of MP in an advanced cancer patient cohort. Eligible participants had advanced solid cancers of any histological type with sufficient accessible tissue for MP and were enrolled in the Molecular Screening and Therapeutics (MoST) Program. A questionnaire was completed by 1074 participants (91% response rate) after consent, prior to undergoing MP. Overall, participants had poor to moderate knowledge of MP, yet perceived MP to have high importance. Higher education, speaking English at home, and greater satisfaction with the decision to undergo MP were associated with higher knowledge scores. More negative attitudes towards uncertainty, greater self-efficacy to cope with results, and lower perceived likelihood of cancer progression were associated with greater perceived importance of MP. Less educated participants and those who do not speak English at home will need clear explanations, visual aids and ample opportunity to ask questions about MP at the time of their decision-making. Clinicians also need to consider psychological factors relevant to patients' decision to pursue MP. Given the increased awareness of and demand for cancer genomic information and the rapidly changing nature of the actionability of MP, these findings will help inform an important ongoing debate on how to facilitate ethical and informed consent and manage patient expectations about personalized treatments.

Patients' views on variants of uncertain significance across indications

As genomic sequencing expands into more areas of patient care, an increasing number of patients learn of the variants of uncertain significance (VUSs) that they carry. Understanding the potential psychosocial consequences of the disclosure of a VUS can help inform pre- and post-test counseling discussions. Medical uncertainty in general elicits a variety of responses from patients, particularly in the growing field of medical genetics and genomics. It is important to consider patients' responses to the ambiguous nature of VUSs across different indications and situational contexts. Genetic counselors and other providers ordering genetic testing should be prepared for the possibility of their patients' misinterpretation of such results. Pre-test counseling should include a discussion of the possibility of VUSs and what it would mean for the patient's care and its potential psychosocial impacts. When a VUS is found, post-test counseling should include additional education and a discussion of the variant's implications and medical management recommendations based on the results. These discussions may help temper subjective interpretations, unrealistic views, and decisional regret.

Patients' willingness to reconsider cancer genetic testing after initially declining: Mention it again

Patients at risk for hereditary cancer syndromes sometimes decline clinically appropriate genetic testing. The purpose of the current study was to understand what preferences, concerns, and desires informed their refusal as well as their current level of interest in being tested. We interviewed patients who had been seen in a hereditary cancer clinic at Vanderbilt University Medical Center and had declined genetic testing. In all, 21 in-depth, semi-structured qualitative interviews were conducted. Although patients provided many reasons for declining testing, they most often cited their psychosocial state at the time of the initial invitation to participate in genetic testing as their reason for refusal. The majority (67%) said that they either would or had changed their mind about testing if/when their clinicians 'mentioned it again'. Patients at risk for hereditary cancer who refuse testing at the time of genetic counseling may later change their mind. In particular, if a patient declines testing around the time of a major medical diagnosis or intervention, clinicians who are providing ongoing care may want to raise the topic afresh after the patient has had time to recover from initial distress related to diagnosis or treatment. Strategies to prompt clinicians to have these conversations are suggested.

Attitudes of French populations towards the disclosure of unsolicited findings in medical genetics

Next-generation sequencing techniques enable unsolicited findings to be detected. This discovery raises ethical questions concerning the return of these findings. Our study aimed to highlight the views of the general public, patients under supervision and health professionals concerning the acceptability of disclosing unsolicited results to patients. In total, 449 participants assessed scenarios, consisted of all combinations of three factors (patient's information and consent, prevention and treatment of the unsolicited disease and doctor's decision). The response profiles were grouped into six clusters. The participants took ethical aspects into account, but health professionals also considered the medical aspects to a greater extent.

Prognostic tumor sequencing panels frequently identify germ line variants associated with hereditary hematopoietic malignancies

Next-generation sequencing (NGS)-based targeted gene capture panels are used to profile hematopoietic malignancies to guide prognostication and treatment decisions. Because these panels include genes associated with hereditary hematopoietic malignancies (HHMs), we hypothesized that these panels could identify pathogenic germ line variants in malignant cells, thereby identifying patients at risk for HHMs. In total, pathogenic or likely pathogenic variants in ANKRD26, CEBPA, DDX41, ETV6, GATA2, RUNX1, or TP53 were identified in 74 (21%) of 360 patients. Germ line tissue was available for 24 patients with 25 pathogenic or likely pathogenic variants with variant allele frequencies >0.4. Six (24%) of these 25 variants were of germ line origin. Three DDX41 variants, 2 GATA2 variants, and a TP53 variant previously implicated in Li-Fraumeni syndrome were of germ line origin. No likely pathogenic/pathogenic germ line variants possessed variant allele frequencies <0.4. This study demonstrates that NGS-based prognostic panels may identify individuals at risk for HHMs despite not being designed for this purpose. Furthermore, variants known to cause Li-Fraumeni syndrome as well as known pathogenic variants in genes such as DDX41 and GATA2 are especially likely to be of germ line origin. Thus, tumor-based panels may augment, but should not replace, comprehensive germ line-based testing and counseling.

Attitudes toward genomic tumor profiling tests in Japan: patients, family members, and the public

Genomic tumor profiling tests (GTPTs) to find molecular targeted drugs for patients with advanced cancer are being introduced into clinical settings, which may result in secondary germline findings. Although small-scale qualitative studies have revealed patients’ attitudes toward GTPTs and preferences on receiving germline findings, no large-scale quantitative research exists that includes family members. We conducted anonymous surveys with 757 cancer patients (CPs), 763 family members (FMs), and 3697 general adults (GAs) in Japan. Awareness of GTPTs was low in all groups, however, both CPs and FMs showed a higher degree of recognition in the benefits of GTPTs. FMs wanted information on germline findings to be shared more than the CPs. Since advanced CPs may have psychological burdens that make it difficult to express their opinions on their therapeutic options and sharing germline findings, GTPTs should be offered with advanced care planning for patients.

Clinical utility of next-generation sequencing in precision oncology

The Precision Medicine Initiative (PMI) aims to change the way diseases are diagnosed and treated by taking into account a patient's genome, lifestyle, and environment. This type of research also uncovers potential biomarkers that can lead to the development of novel targeted therapies. Next-generation sequencing (NGS) is a new technology that facilitates collection of this genetic information by processing large amounts of DNA in an efficient and cost-effective way. NGS is particularly useful in oncology and has already begun to transform cancer management.

High-frequency actionable pathogenic exome variants in an average-risk cohort

Exome sequencing is increasingly utilized in both clinical and nonclinical settings, but little is known about its utility in healthy individuals. Most previous studies on this topic have examined a small subset of genes known to be implicated in human disease and/or have used automated pipelines to assess pathogenicity of known variants. To determine the frequency of both medically actionable and nonactionable but medically relevant exome findings in the general population we assessed the exomes of 70 participants who have been extensively characterized over the past several years as part of a longitudinal integrated multiomics profiling study. We analyzed exomes by identifying rare likely pathogenic and pathogenic variants in genes associated with Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. We then used American College of Medical Genetics (ACMG) guidelines for the classification of rare sequence variants. Additionally, we assessed pharmacogenetic variants. Twelve out of 70 (17%) participants had medically actionable findings in Mendelian disease genes. Five had phenotypes or family histories associated with their genetic variants. The frequency of actionable variants is higher than that reported in most previous studies and suggests added benefit from utilizing expanded gene lists and manual curation to assess actionable findings. A total of 63 participants (90%) had additional nonactionable findings, including 60 who were found to be carriers for recessive diseases and 21 who have increased Alzheimer's disease risk because of heterozygous or homozygous APOE e4 alleles (18 participants had both). Our results suggest that exome sequencing may have considerably more utility for health management in the general population than previously thought.

Preferences for learning different types of genome sequencing results among young breast cancer patients: Role of psychological and clinical factors

The growing importance of genome sequencing means that patients will increasingly face decisions regarding what results they would like to learn. The present study examined psychological and clinical factors that might affect these preferences. 1,080 women diagnosed with breast cancer at age 40 or younger completed an online survey. We assessed their interest in learning various types of genome sequencing results: risk of preventable disease or unpreventable disease, cancer treatment response, uncertain meaning, risk to relatives' health, and ancestry/physical traits. Multivariable logistic regression was used to examine whether being "very" interested in each result type was associated with clinical factors: BRCA1/2 mutation status, prior genetic testing, family history of breast cancer, and psychological factors: cancer recurrence worry, genetic risk worry, future orientation, health information orientation, and genome sequencing knowledge. The proportion of respondents who were very interested in learning each type of result ranged from 16% to 77%. In all multivariable models, those who were very interested in learning a result type had significantly higher knowledge about sequencing benefits, greater genetic risks worry, and stronger health information orientation compared to those with less interest (p-values < .05). Our findings indicate that high interest in return of various types of genome sequencing results was more closely related to psychological factors. Shared decision-making approaches that increase knowledge about genome sequencing and incorporate patient preferences for health information and learning about genetic risks may help support patients' informed choices about learning different types of sequencing results.

Responsibility, identity, and genomic sequencing: A comparison of published recommendations and patient perspectives on accepting or declining incidental findings

BACKGROUND

The use of genomic sequencing techniques is increasingly being incorporated into mainstream health care. However, there is a lack of agreement on how "incidental findings" (IFs) should be managed and a dearth of research on patient perspectives.

METHODS

In-depth qualitative interviews were carried out with 31 patients undergoing genomic sequencing at a regional genetics service in England. Interviews explored decisions around IFs and were comparatively analyzed with published recommendations from the literature.

RESULTS

Thirteen participants opted to receive all IFs from their sequence, 12 accepted some and rejected others, while six participants refused all IFs. The key areas from the literature, (a) genotype/phenotype correlation, (b) seriousness of the condition, and (c) implications for biological relatives, were all significant; however, patients drew on a broader range of social and cultural information to make their decisions.

CONCLUSION

This study highlights the range of costs and benefits for patients of receiving IFs from a genomic sequence. While largely positive views toward the dissemination of genomic data were reported, ambivalence surrounding genetic responsibility and its associated behaviors (e.g., duty to inform relatives) was reported by both IF decliners and accepters, suggesting a need to further explore patient perspectives on this highly complex topic area.

A systematic literature review of individuals' perspectives on privacy and genetic information in the United States

Concerns about genetic privacy affect individuals' willingness to accept genetic testing in clinical care and to participate in genomics research. To learn what is already known about these views, we conducted a systematic review, which ultimately analyzed 53 studies involving the perspectives of 47,974 participants on real or hypothetical privacy issues related to human genetic data. Bibliographic databases included MEDLINE, Web of Knowledge, and Sociological Abstracts. Three investigators independently screened studies against predetermined criteria and assessed risk of bias. The picture of genetic privacy that emerges from this systematic literature review is complex and riddled with gaps. When asked specifically "are you worried about genetic privacy," the general public, patients, and professionals frequently said yes. In many cases, however, that question was posed poorly or only in the most general terms. While many participants expressed concern that genomic and medical information would be revealed to others, respondents frequently seemed to conflate privacy, confidentiality, control, and security. People varied widely in how much control they wanted over the use of data. They were more concerned about use by employers, insurers, and the government than they were about researchers and commercial entities. In addition, people are often willing to give up some privacy to obtain other goods. Importantly, little attention was paid to understanding the factors-sociocultural, relational, and media-that influence people's opinions and decisions. Future investigations should explore in greater depth which concerns about genetic privacy are most salient to people and the social forces and contexts that influence those perceptions. It is also critical to identify the social practices that will make the collection and use of these data more trustworthy for participants as well as to identify the circumstances that lead people to set aside worries and decide to participate in research.

Additional germline findings from a tumor profiling program

Background

Matched tumor-normal sequencing, applied in precision cancer medicine, can identify unidentified germline Medically Actionable Variants (gMAVS) in cancer predisposition genes. We report patient preferences for the return of additional germline results, and describe various gMAV scenarios delivered through a clinical genetics service.

Methods

Tumor profiling was offered to 1960 advanced cancer patients, of which 1556 underwent tumor-normal sequencing with multigene hotspot panels containing 20 cancer predisposition genes. All patients were provided with an IRB-approved consent for return of additional gMAVs.

Results

Of the whole cohort 94% of patients consented to be informed of additional germline results and 5% declined, with no statistically significant differences based on age, sex, race or prior genetic testing. Eight patients were found to have gMAVs in a cancer predisposition gene. Five had previously unidentified gMAVs: three in TP53 (only one fulfilled Chompret’s Revised criteria for Li-Fraumeni Syndrome), one in SMARCB1 in the absence of schwannomatosis features and one a TP53 variant at low allele frequency suggesting an acquired event in blood.

Conclusion

Interest in germline findings is high among patients who undergo tumor profiling. Disclosure of previously unidentified gMAVs present multiple challenges, thus supporting the involvement of a clinical genetics service in all tumor profiling programs.

Electronic supplementary material

The online version of this article (10.1186/s12920-018-0383-5) contains supplementary material, which is available to authorized users.

Impact of Receiving Secondary Results from Genomic Research: A 12-Month Longitudinal Study

The impact of returning secondary results from exome sequencing (ES) on patients/participants is important to understand as ES is increasingly utilized in clinical care and research. Participants were recruited from studies using ES and were separated into two arms: 107 who had ES and were offered the choice to learn secondary results (ES group) and 85 who had not yet had ES (No ES group). Questionnaires were administered at baseline and 1 and 12 months, following results disclosure (ES group) or enrollment (No ES group). While the majority (65%) elected to learn all results following pre-test counseling, it was reduced from the 76% who indicated a desire for all results at baseline. Thirty-seven percent received results associated with an increased personal disease risk. There were no differences in changes in any of the psychological and social measures from baseline to post-results disclosure between the ES and No ES groups. Receiving a wide range of secondary findings appeared to have little measurable impact on most participants. The experience of learning secondary results may be related to participants' previous experiences with genetics, as well as the genetic counseling provided. Future research with a more diverse, genetically naïve group, as well as scalable methods of delivery, is needed.

Universal genetic testing for inherited susceptibility in children and adults with myelodysplastic syndrome and acute myeloid leukemia: are we there yet?

Comprehensive genomic profiling of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) cases have enabled the detection and differentiation of driver and subclonal mutations, informed risk prognostication, and defined targeted therapies. These insights into disease biology, and management have made multigene-acquired mutation testing a critical part of the diagnostic assessment of patients with sporadic MDS and AML. More recently, our understanding of the role of an increasing number of inherited genetic factors on MDS/AML risk and management has rapidly progressed. In recognition of the growing impact of this field, clinical guidelines and disease classification systems for both MDS and AML have recently incorporated familial MDS/AML predisposition syndromes into their diagnostic algorithms. In this perspective piece, we contemplate the advantages, disadvantages, and barriers that would need to be overcome to incorporate inherited MDS/AML genetic testing into the upfront molecular diagnostic work-up of every MDS/AML patient. For centers already performing panel-based tumor-only testing, including genes associated with familial forms of MDS/AML (e.g., RUNX1, CEBPA, GATA2, TP53), we advocate optimizing these tests to detect all types of germline variants in these genes and moving toward upfront paired tumor/germline testing to maximize detection and streamline patient care.

Decision-Making Preferences About Secondary Germline Findings That Arise From Tumor Genomic Profiling Among Patients With Advanced Cancers

Purpose

In patients with advanced cancers, tumor genomic profiling (TGP) can reveal secondary germline findings (SGFs) regarding inherited disease risks. This study examines the process by which patients with advanced cancers would make the decision about whether or not to learn these SGFs, and their preferences regarding specific challenging decision scenarios including whether patients should be required to receive SGFs and whether SGFs should be returned to family after a patient's death.

Patients and Methods

We conducted qualitative semi-structured interviews with 40 patients with advanced breast, bladder, colorectal, or lung cancer who had TGP. Data were collected regarding participants' perspectives about the hypothetical decision to learn their SGFs including their anticipated approach to the decision-making process, as well as their preferences about challenging decision scenarios. Data were evaluated using thematic content analysis.

Results

We identified themes regarding participants' preferred degree of decisional autonomy, perceived vital role of doctors, information needs, and anticipated process of deliberation. Although participants reported that this decision was ultimately their own, many wanted input from family and trusted others. Oncologists were expected to provide decision guidance and key clarifying information. Most participants stated that patients should be able to make a choice about receiving actionable SGFs, and a majority stated that SGFs should be available to family after a patient's death.

Conclusion

These results provide insight into SGFs decision-making processes of patients with advanced cancers, which can allow clinicians to provide patients optimal decision support in this context. Patients with advanced cancers have specific information needs and decision-making preferences that educational and communication interventions should address to ensure that patients make informed choices about learning SGFs.

The who, what, and why of research participants' intentions to request a broad range of secondary findings in a diagnostic genomic sequencing study

PURPOSE

In a diagnostic exome sequencing study (the North Carolina Clinical Genomic Evaluation by Next-Generation Exome Sequencing project, NCGENES), we investigated adult patients' intentions to request six categories of secondary findings (SFs) with low or no medical actionability and correlates of their intentions.

METHODS

At enrollment, eligible participants (n = 152) completed measures assessing their sociodemographic, clinical, and literacy-related characteristics. Prior to and during an in-person diagnostic result disclosure visit, they received education about categories of SFs they could request. Immediately after receiving education at the visit, participants completed measures of intention to learn SFs, interest in each category, and anticipated regret for learning and not learning each category.

RESULTS

Seventy-eight percent of participants intended to learn at least some SFs. Logistic regressions examined their intention to learn any or all of these findings (versus none) and interest in each of the six individual categories (yes/no). Results revealed little association between intentions and sociodemographic, clinical, or literacy-related factors. Across outcomes, participants who anticipated regret for learning SFs reported weaker intention to learn them (odds ratios (ORs) from 0.47 to 0.71), and participants who anticipated regret for not learning these findings reported stronger intention to learn them (OR 1.61-2.22).

CONCLUSION

Intentions to request SFs with low or no medical actionability may be strongly influenced by participants' desire to avoid regret.

Incidental detection of germline variants of potential clinical significance by massively parallel sequencing in haematological malignancies

Massively parallel sequencing (MPS) technology has become routinely available for diagnosis, prognostication and therapeutic decision-making in haematological malignancies. However, increased throughput and wider coverage of genes can have unintended consequences. Germline variants of potential clinical significance (GVPCSs) detected during cancer testing may have implications for patients and families beyond the biological evaluation of a specific tumour. 721 reports generated from MPS panels used in the routine testing of myeloid and lymphoid malignancies were reviewed and variants within genes of potential germline relevance (TP53, RUNX1, GATA2 and WT1 in all contexts and CBL, KRAS and NRAS in the setting of juvenile myelomonocytic leukaemia) were analysed. A variant allele fraction threshold of ≥33.09% for considering germline origin of variants within cancer samples was established. The detection rate of incidental, pathogenic germline variants was 0.42%. Patient education and confirmatory germline sample testing of GVPCSs in appropriate circumstances are recommended.

Interest and Attitudes of Patients With Advanced Cancer With Regard to Secondary Germline Findings From Tumor Genomic Profiling

PURPOSE

Tumor genomic profiling (TGP) can reveal secondary findings about inherited disease risks in a patient with cancer. Little is known about how patients with advanced cancer, currently the primary users of TGP, perceive the benefits and harms of secondary germline findings.

METHODS

We conducted semistructured interviews with 40 patients with advanced breast, bladder, colorectal, or lung cancer who had TGP. Qualitative interview data were evaluated by using a thematic content analysis approach.

RESULTS

Most participants expressed interest in the prospect of learning their secondary germline findings (57%), although a minority was equivocal (29%) or disinterested (14%). Reasons for these preferences varied but were influenced by participants' perceptions of diverse benefits and harms of this information, which they regarded as relevant to themselves; their families; and other patients with cancer, medical science, and society. These attitudes were uniquely shaped by participants' personal disease experiences and health status.

CONCLUSION

Many patients with advanced cancer are interested in learning secondary germline findings and hold optimistic and perhaps unrealistic beliefs about the potential health benefits. Patients also have important concerns about clinical and emotional implications of this information. These perceptions are necessary to address to ensure that patients make informed decisions about learning secondary germline findings.

The Prevalence and Role of Hemoglobin Variants in Biometric Screening of a Multiethnic Population: One Large Health System's Experience

OBJECTIVES

To characterize and quantitate hemoglobin (Hb) variants discovered during biometric hemoglobin A1c (HbA1c) analyses in a large multiethnic population with a focus on the effect of variants on testing method and results.

METHODS

In total, 13,913 individuals had their HbA1c measured via ion-exchange high-performance liquid chromatography. Samples that had a variant Hb detected or HbF fraction more than 25% underwent variant Hb characterization and confirmation by gel electrophoresis. RBC indices were also evaluated for possible concomitant thalassemia.

RESULTS

Of the 13,913 individuals evaluated, 524 (3.77%) had an Hb variant. The prevalence of each variant was as follows: HbS trait (n = 396, 2.85%), HbSS disease (n = 4, 0.03%), HbC trait (n = 85, 0.61%), HbCC disease (n = 2, 0.01%), HbSC disease (n = 5, 0.04%), HbE trait (n = 18, 0.13%), HbD or G trait (n = 9, 0.06%), HbS β-thalassemia + disease (n = 1, 0.01%), hereditary persistence of HbF (n = 2, 0.01%), and HbMontgomery trait (n = 1, 0.01%). Concomitant α-thalassemia was detected in 20 (3.82%) of the 524 individuals with an Hb variant.

CONCLUSIONS

This study represents one of the largest epidemiologic investigations into the prevalence of Hb variants in a North American metropolitan, multiethnic workforce and their dependents and reinforces the importance of method selection in populations with Hb variants.

Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic

A pilot program was initiated using whole genome sequencing (WGS) to diagnose suspected genetic disorders in the Genetics Clinic at Children's Hospital of Wisconsin. Twenty-two patients underwent WGS between 2010 and 2013. Initially, we obtained a 14% (3/22) diagnosis rate over 2 years; with subsequent reanalysis, this increased to 36% (8/22). Disease causing variants were identified in SKIV2L, CECR1, DGKE, PYCR2, RYR1, PDGFRB, EFTUD2, and BCS1L. In 75% (6/8) of diagnosed cases, the diagnosis affected treatment and/or medical surveillance. Additionally, one case demonstrated a homozygous A18V variant in VLDLR that appears to be associated with a previously undescribed phenotype.