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Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study.

ABSTRACT: Although targeted sequencing improves outcomes for many cancer patients, it remains uncertain how somatic and germ-line whole-exome sequencing (WES) will integrate into care.We conducted surveys and interviews within a study of WES integration at an academic center to determine oncologists' attitudes about WES and to identify lung and colorectal cancer patients' preferences for learning WES findings.One-hundred sixty-seven patients (85% white, 58% female, mean age 60) and 27 oncologists (22% female) participated. Although oncologists had extensive experience ordering somatic tests (median 100/year), they had little experience ordering germ-line tests. Oncologists intended to disclose most WES results to patients but anticipated numerous challenges in using WES. Patients had moderately low levels of genetic knowledge (mean 4 correct out of 7). Most patients chose to learn results that could help select a clinical trial, pharmacogenetic and positive prognostic results, and results suggesting inherited predisposition to cancer and treatable noncancer conditions (all ?95%). Fewer chose to receive negative prognostic results (84%) and results suggesting predisposition to untreatable noncancer conditions (85%).The majority of patients want most cancer-related and incidental WES results. Patients' low levels of genetic knowledge and oncologists' inexperience with large-scale sequencing present challenges to implementing paired WES in practice.Genet Med 18 10, 1011-1019.

SUBMITTER: Gray SW

PROVIDER: S-EPMC4981555 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study.

Gray Stacy W SW Park Elyse R ER Najita Julie J Martins Yolanda Y Traeger Lara L Bair Elizabeth E Gagne Joshua J Garber Judy J Jänne Pasi A PA Lindeman Neal N Lowenstein Carol C Oliver Nelly N Sholl Lynette L Van Allen Eliezer M EM Wagle Nikhil N Wood Sam S Garraway Levi L Joffe Steven S

Genetics in medicine : official journal of the American College of Medical Genetics 20160211 10

<h4>Purpose</h4>Although targeted sequencing improves outcomes for many cancer patients, it remains uncertain how somatic and germ-line whole-exome sequencing (WES) will integrate into care.<h4>Methods</h4>We conducted surveys and interviews within a study of WES integration at an academic center to determine oncologists' attitudes about WES and to identify lung and colorectal cancer patients' preferences for learning WES findings.<h4>Results</h4>One-hundred sixty-seven patients (85% white, 58% ...[more]

PMID: 26866579

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Project description:ImportanceClinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.ObjectiveTo perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome.Design, setting, and patientsObservational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay.Main outcomes and measuresWhole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings.ResultsA molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics.Conclusions and relevanceWhole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients.

Dataset Information

Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study.

Publications

Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study.

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