Here we report whole exome sequencing (WES) on a cohort of 71 patients with persistently unresolved white matter abnormalities with a suspected diagnosis of leukodystrophy or genetic leukoencephalopathy. WES analyses were performed on trio, or greater, family groups. Diagnostic pathogenic variants were identified in 35% (25/71) of patients. Potentially pathogenic variants were identified in clinically relevant genes in a further 7% (5/71) of cases, giving a total yield of clinical diagnoses in 42% of individuals. These findings provide evidence that WES can substantially decrease the number of unresolved white matter cases.
Background Increasing numbers of healthy individuals are undergoing predispositional personal genome sequencing. Here we describe the design and early outcomes of the PeopleSeq Consortium, a multi-cohort collaboration of predispositional genome sequencing projects, which is examining the medical, behavioral, and economic outcomes of returning genomic sequencing information to healthy individuals. Methods Apparently healthy adults who participated in four of the sequencing projects in the Consortium were included. Web-based surveys were administered before and after genomic results disclosure, or in some cases only after results disclosure. Surveys inquired about sociodemographic characteristics, motivations and concerns, behavioral and medical responses to sequencing results, and perceived utility. Results Among 1395 eligible individuals, 658 enrolled in the Consortium when contacted and 543 have completed a survey after receiving their genomic results thus far (mean age 53.0 years, 61.4% male, 91.7% white, 95.5% college graduates). Most participants (98.1%) were motivated to undergo sequencing because of curiosity about their genetic make-up. The most commonly reported concerns prior to pursuing sequencing included how well the results would predict future risk (59.2%) and the complexity of genetic variant interpretation (56.8%), while 47.8% of participants were concerned about the privacy of their genetic information. Half of participants reported discussing their genomic results with a healthcare provider during a median of 8.0 months after receiving the results; 13.5% reported making an additional appointment with a healthcare provider specifically because of their results. Few participants (< 10%) reported making changes to their diet, exercise habits, or insurance coverage because of their results. Many participants (39.5%) reported learning something new to improve their health that they did not know before. Reporting regret or harm from the decision to undergo sequencing was rare (< 3.0%). Conclusions Healthy individuals who underwent predispositional sequencing expressed some concern around privacy prior to pursuing sequencing, but were enthusiastic about their experience and not distressed by their results. While reporting value in their health-related results, few participants reported making medical or lifestyle changes. Electronic supplementary material The online version of this article (10.1186/s13073-019-0619-9) contains supplementary material, which is available to authorized users.
As the public's interest in genetics and genomics has increased, there has been corresponding and unprecedented growth in direct-to-consumer genetic testing (DTC-GT). Although regulatory concerns have limited true DTC-GT available without a physician order, the paradigm has shifted to a model of consumer-directed genetic testing (CD-GT) in which patients are researching testing options and requesting specific genetic testing from their health-care providers. However, many nongenetics health-care providers do not have the background, education, interest, or time to order and/or interpret typical clinical genetic testing, let alone DTC-GT. The lines between CD-GT, DTC-GT, and traditional clinical genetic testing are also blurring with the same types of tests available in different settings (e.g., carrier screening) and tests merging medical and nonmedical results, increasing the complexity for consumer decision-making and clinician management. The genetics community has the training to work with CD-GT, but there has been a hesitancy to commit to working with these results and questions about what to do when consumers have more complicated asks, like interpretation of raw data. Additionally, at the rate with which CD-GT is growing, there are questions about having sufficient genetics professionals to meet the potential genetic counseling demand. While there are many complex questions and challenges, this market represents a chance for the genetics community to address and unmet need. We will review the history of the CD-GT/DTC-GT market and outline the issues and opportunities our profession is facing.
Fibrous hamartoma of infancy (FHI) is a benign mesenchymal tumor histologically characterized by a mixture of intersecting fascicles of fibroblasts/myofibroblasts in collagenous stroma, nests of primitive oval or stellate cells in basophilic mucoid stroma, and mature adipose tissue. We hypothesized that FHI, because of histologic overlap with mesenchymal overgrowth tumors seen in CLOVES (Congenital Lipomatous Overgrowth with Vascular, Epidermal, Skeletal anomalies) and Proteus syndromes, may harbor mutations in signaling pathways associated with cellular proliferation. Formalin-fixed paraffin-embedded material from a discovery set of 4 cases of FHI was investigated by targeted next-generation sequencing of a panel of cancer-associated genes. The results were confirmed by targeted Sanger sequencing of EGFR exon 20. A validation set of 8 cases of FHI and 10 cases of other pediatric fatty tumors were investigated by targeted Sanger sequencing of EGFR exon 20. All 12 cases of FHI, and none of the 10 control tumors, showed EGFR exon 20 insertion/duplication mutations. This is the first report of molecular aberrations in FHI. The consistent occurrence of EGFR exon 20 insertion/duplication mutations in 100% of cases of FHI studied suggests that they must play a principal role in the pathogenesis of FHI, likely by conferring a potential for growth and local infiltration. Although surgical treatment will remain the mainstay of FHI treatment, tyrosine kinase inhibitors may have an adjunctive role in cases that are difficult to resect.
Next generation sequencing (NGS) is dramatically increasing the number of clinically available genetic tests and thus the number of patients in which such testing may be indicated. The complex nature and volume of the reported results requires professional interpretation of the testing in order to translate and synthesize the meaning and potential benefit to patients, and genetic counselors are uniquely suited to provide this service. The increased need for genetic counselors in this role, coupled with the time required and a limited number of trained and available counselors presents a challenge to current models for making genetic testing available to patients and their healthcare providers effectively and efficiently. The employment of genetic counselors at genetic/genomic laboratories is one model to expand the resources for providing this service. In this article, we briefly review the advent of NGS and its clinical applications, examine the core skills of genetic counselors and delineate the expanding roles and responsibilities of laboratory-based genetic counselors. We also propose changes to the genetic counseling training program curriculum to account for the increasing opportunities for genetic counselors to contribute and thrive within genetic testing laboratories.
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