Participation in genetic screening: testing different outreach methods across a diverse hospital system based patient population.

Introduction: Genomics has the potential to transform medicine by identifying genetic risk factors that predispose people to certain illnesses. Use of genetic screening is rapidly expanding and shifting towards screening all patients regardless of known risk factors, but research is limited on the success of broad population-level outreach for genetic testing and the effectiveness of different outreach methods across diverse populations. In this study, we tested the effectiveness of Digital Only (emailing and texting) and Brochure Plus Digital (mailed brochure, emailing, and texting) outreach to encourage a diverse patient population to participate in a large hospital system's whole genome sequencing program. Methods: Disproportionate stratified sampling was used to create a study population more demographically diverse than the eligible population and response rates were analyzed overall and by demographics to understand the effectiveness of different outreach strategies. Results: 7.5% of all eligible patients enrolled in the program. While approximately 70% of patients invited to complete genetic testing identified in their EHR as being Hispanic, Black or African America, Asian, or another non-White race, these patients generally enrolled at lower rates than the overall population. Other underrepresented groups had higher enrollment rates including people with Medicaid coverage (8.7%) and those residing in rural areas (10.6%). We found no significant difference in enrollment rates between our Digital-Only and our Brochure Plus Digital outreach approaches in the overall population, but enrollment rates were significantly higher for Asian patients and patients who resided in rural areas in the Brochure Plus Digital group. Across both outreach approaches, links provided in emails were most commonly used for enrollment. Discussion: Our study reveals expected enrollment rates for proactive outreach by a hospital system for genetic testing in a diverse population. As more hospital systems are adopting population-scale genetic testing, these findings can inform future outreach efforts to recruit patients for genetic testing including those patients traditionally underrepresented in genomics.

Development and Validation of a Breast Cancer Polygenic Risk Score on the Basis of Genetic Ancestry Composition.

PURPOSE: Polygenic risk scores (PRSs) for breast cancer (BC) risk stratification have been developed primarily in women of European ancestry. Their application to women of non-European ancestry has lagged because of the lack of a formal approach to incorporate genetic ancestry and ancestry-dependent variant frequencies and effect sizes. Here, we propose a multiple-ancestry PRS (MA-PRS) that addresses these issues and may be useful in the development of equitable PRSs across other cancers and common diseases. MATERIALS AND METHODS: Women referred for hereditary cancer testing were divided into consecutive cohorts for development (n = 189,230) and for independent validation (n = 89,126). Individual genetic composition as fractions of three reference ancestries (African, East Asian, and European) was determined from ancestry-informative single-nucleotide polymorphisms. The MA-PRS is a combination of three ancestry-specific PRSs on the basis of genetic ancestral composition. Stratification of risk was evaluated by multivariable logistic regression models controlling for family cancer history. Goodness-of-fit analysis compared expected with observed relative risks by quantiles of the MA-PRS distribution. RESULTS: In independent validation, the MA-PRS was significantly associated with BC risk in the full cohort (odds ratio, 1.43; 95% CI, 1.40 to 1.46; P = 8.6 × 10-308) and within each major ancestry. The top decile of the MA-PRS consistently identified patients with two-fold increased risk of developing BC. Goodness-of-fit tests showed that the MA-PRS was well calibrated and predicted BC risk accurately in the tails of the distribution for both European and non-European women. CONCLUSION: The MA-PRS uses genetic ancestral composition to expand the utility of polygenic risk prediction to non-European women. Inclusion of genetic ancestry in polygenic risk prediction presents an opportunity for more personalized treatment decisions for women of varying and mixed ancestries.

Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study.

BACKGROUND: The use of proactive genetic screening for disease prevention and early detection is not yet widespread. Professional practice guidelines from the American College of Medical Genetics and Genomics (ACMG) have encouraged reporting pathogenic variants that confer personal risk for actionable monogenic hereditary disorders, but only as secondary findings from exome or genome sequencing. The Centers for Disease Control and Prevention (CDC) recognizes the potential public health impact of three Tier 1 actionable disorders. Here, we report results of a large multi-center cohort study to determine the yield and potential value of screening healthy individuals for variants associated with a broad range of actionable monogenic disorders, outside the context of secondary findings. METHODS: Eligible adults were offered a proactive genetic screening test by health care providers in a variety of clinical settings. The screening panel based on next-generation sequencing contained up to 147 genes associated with monogenic disorders within cancer, cardiovascular, and other important clinical areas. Sequence and intragenic copy number variants classified as pathogenic, likely pathogenic, pathogenic (low penetrance), or increased risk allele were considered clinically significant and reported. Results were analyzed by clinical area and severity/burden of disease using chi-square tests without Yates' correction. RESULTS: Among 10,478 unrelated adults screened, 1619 (15.5%) had results indicating personal risk for an actionable monogenic disorder. In contrast, only 3.1 to 5.2% had clinically reportable variants in genes suggested by the ACMG version 2 secondary findings list to be examined during exome or genome sequencing, and 2% had reportable variants related to CDC Tier 1 conditions. Among patients, 649 (6.2%) were positive for a genotype associated with a disease of high severity/burden, including hereditary cancer syndromes, cardiovascular disorders, or malignant hyperthermia susceptibility. CONCLUSIONS: This is one of the first real-world examples of specialists and primary care providers using genetic screening with a multi-gene panel to identify health risks in their patients. Nearly one in six individuals screened for variants associated with actionable monogenic disorders had clinically significant results. These findings provide a foundation for further studies to assess the role of genetic screening as part of regular medical care.

Painting a portrait: Analysis of national health survey data for cancer genetic counseling.

BACKGROUND: Despite a growing body of literature describing the geographic and sociodemographic distribution of cancer genetic testing, work focused on these domains in cancer genetic counseling is limited. Research describing the epidemiology of cancer genetic counseling has mainly focused on isolated populations, a single gender (women) and a single condition (hereditary breast and ovarian cancer). Study findings to date are contradictory, making it unclear what, if any, disparities in receipt of cancer genetic counseling exist. METHODS: Utilizing the 2015 National Health Interview Survey (NHIS)-a cross-sectional, in person interview survey collecting self-reported health data for the US population-geographic and sociodemographic factors were compared between those receiving genetic counseling and the national sample. Bivariate analysis and subsequent multivariable logistic regression were performed with stratification by cancer status (affected/unaffected). Reason for (eg, doctor recommended) and focus of (eg, breast/ovarian) genetic counseling were also assessed. To generate nationally representative estimates, all analyses were adjusted for survey weights. RESULTS: An estimated 4.8 million individuals in the United States had cancer genetic counseling. On bivariate analysis, there were significant differences in proportions undergoing genetic counseling by sex, race/ethnicity, insurance, citizenship, education, age, and cancer status (P < 0.01). After adjustment, however, only female sex (Odds Ratio [OR]: 1.78 [95% CI: 1.18-2.67]) remained a significant predictor of genetic counseling among the affected. Among the unaffected, female sex (OR: 1.70 [1.30-2.21]), non-Hispanic black race (OR: 1.44 [1.02-2.05], reference: non-Hispanic white), graduate education (OR: 1.76 [1.03-2.98], reference: less than high school), and age (OR: 1.06 [1.01-1.11]) predicted higher rates of genetic counseling. An estimated 2.1 million individuals have undergone genetic counseling focused on breast/ovarian cancer, 1.3 million on colorectal cancer, and 1.4 million on "other" cancers. Of those receiving genetic counseling focused on breast/ovarian cancer, 3% were male and 97% female (breast cancer alone-4% male, 96% female); for colorectal cancer, 49% male and 51% female, and for "other" cancers, 60% male and 40% female. The majority of individuals receiving genetic counseling reported they did so because their doctor recommended it (66%), with smaller proportions describing self (12%), family (10%), or media (5%) influences as the primary reason. CONCLUSION: This is the first study to depict the sociodemographic and geographic distribution of cancer genetic counseling at the national level. Despite perceived disparities in access, cancer genetic counseling in the United States appears to be accessed by individuals of diverse racial/ethnic backgrounds, with various insurance coverage and educational levels, and across a broad range of ages and geographic regions. The only sociodemographic factor that independently predicted receipt of genetic counseling across both the affected and unaffected population was sex. With physician recommendation as the predominant driver for counseling, targeting physician education, and awareness is crucial to utilization.

SNPs and breast cancer risk prediction for African American and Hispanic women.

For African American or Hispanic women, the extent to which clinical breast cancer risk prediction models are improved by including information on susceptibility single nucleotide polymorphisms (SNPs) is unknown, even though these women comprise increasing proportions of the US population and represent a large proportion of the world's population. We studied 7539 African American and 3363 Hispanic women from the Women's Health Initiative. The age-adjusted 5-year risks from the BCRAT and IBIS risk prediction models were measured and combined with a risk score based on >70 independent susceptibility SNPs. Logistic regression, adjusting for age group, was used to estimate risk associations with log-transformed age-adjusted 5-year risks. Discrimination was measured by the odds ratio (OR) per standard deviation (SD) and the area under the receiver operator curve (AUC). When considered alone, the ORs for African American women were 1.28 for BCRAT, and 1.04 for IBIS. When combined with the SNP risk score (OR 1.23), the corresponding ORs were 1.39 and 1.22. For Hispanic women the corresponding ORs were 1.25 for BCRAT, and 1.15 for IBIS. When combined with the SNP risk score (OR 1.39), the corresponding ORs were 1.48 and 1.42. There was no evidence that any of the combined models were not well calibrated. Including information on known breast cancer susceptibility loci provides approximately 10 and 19% improvement in risk prediction using BCRAT for African Americans and Hispanics, respectively. The corresponding figures for IBIS are approximately 18 and 26%, respectively.

BRCA-mutated Invasive Breast Carcinomas: Immunohistochemical Analysis of Insulin-like Growth Factor II mRNA-binding Protein (IMP3), Cytokeratin 8/18, and Cytokeratin 14.

To evaluate the expression of insulin-like growth factor II mRNA-binding protein (IMP3), CK8/18, and CK14 in BRCA mutated and sporadic invasive breast carcinoma. Immunohistochemistry for IMP3, CK8/18, and CK14 was performed on 39 cases of invasive breast carcinomas with BRCA mutation (24 BRCA1, 14 BRCA2, and 1 dual BRCA1/BRCA2) and 54 cases of sporadic invasive breast carcinomas. The relationship between the IMP3, CK8/18, and CK14 and the tumor grade and molecular phenotypes were analyzed. IMP3, CK8/18, and CK14 positivity were present in 20 (51%), 22 (56%), and 14 (36%) of 39 BRCA-mutated breast carcinomas, and 11 (20%), 53 (98%), and 24 (44%) of 54 sporadic breast carcinomas respectively. The rates of IMP3 expression and absence of CK8/18 (44% versus 2%) in BRCA-mutated breast carcinomas was significantly higher than the sporadic breast carcinomas (p = 0.002 and p < 0.001). No significant difference was observed for CK14 among the two groups (p = 0.408). No significant difference was observed among BRCA1-related and BRCA2-related breast carcinomas in the immunoprofile for IMP3, CK8/18, and CK14. No significant correlation was identified between the expression of IMP3 and CK8/18 and the tumor grade in both BRCA-mutated and sporadic breast carcinomas (p > 0.05). In cases with luminal A and B phenotypes, the rates of expression of IMP3 and loss of CK8/18 were significantly higher in BRCA-mutated as compared to sporadic breast carcinoma (p < 0.001). In cases with basal-like phenotype, the absence of CK8/18 expression was significantly higher in BRCA-mutated breast carcinomas (54% versus 0%, p = 0.001), while no difference was observed for IMP3 expression (p = 0.435). Regardless of mutation type, histologic grade, or molecular phenotype, the absence of CK8/18 expression and presence of IMP3 expression are seen at much higher rate in BRCA mutated breast carcinomas.

Actionable exomic incidental findings in 6503 participants: challenges of variant classification.

Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.

Exome sequencing for the diagnosis of 46,XY disorders of sex development.

CONTEXT: Disorders of sex development (DSD) are clinical conditions where there is a discrepancy between the chromosomal sex and the phenotypic (gonadal or genital) sex of an individual. Such conditions can be stressful for patients and their families and have historically been difficult to diagnose, especially at the genetic level. In particular, for cases of 46,XY gonadal dysgenesis, once variants in SRY and NR5A1 have been ruled out, there are few other single gene tests available. OBJECTIVE: We used exome sequencing followed by analysis with a list of all known human DSD-associated genes to investigate the underlying genetic etiology of 46,XY DSD patients who had not previously received a genetic diagnosis. DESIGN: Samples were either submitted to the research laboratory or submitted as clinical samples to the UCLA Clinical Genomic Center. Sequencing data were filtered using a list of genes known to be involved in DSD. RESULTS: We were able to identify a likely genetic diagnosis in more than a third of cases, including 22.5% with a pathogenic finding, an additional 12.5% with likely pathogenic findings, and 15% with variants of unknown clinical significance. CONCLUSIONS: Early identification of the genetic cause of a DSD will in many cases streamline and direct the clinical management of the patient, with more focused endocrine and imaging studies and better-informed surgical decisions. Exome sequencing proved an efficient method toward such a goal in 46,XY DSD patients.

Impact of family history on choosing risk-reducing surgery among BRCA mutation carriers.

OBJECTIVE: Despite substantial survival benefits of risk-reducing mastectomy (RRM) and risk-reducing bilateral salpingo-oophorectomy (RRBSO) among BRCA mutation carriers, only a minority elect to undergo these procedures. This study investigates factors that might influence decision making regarding prophylactic surgeries among women with BRCA mutations. STUDY DESIGN: Unaffected BRCA mutation carriers who were counseled at our center and either underwent prophylactic surgery or participated in a high-risk surveillance program at our institution from 1998 through 2010 were included in the study. Medical records were reviewed and data collected included age, family history, parity, mutation type, history of breast biopsy or cosmetic surgery, and uptake of prophylactic surgeries. RESULTS: Among 136 unaffected women with BRCA mutations, uptake of RRM was 42% and uptake of RRBSO was 52%. Family history of first- and second-degree relatives being deceased from breast cancer was predictive of uptake of RRM and of RRBSO (odds ratio [OR], 11.0; P = .005; and OR, 15.8; P = .023, respectively), and history of a mother lost to pelvic cancer was predictive of uptake of RRBSO (OR, 7.9; P = .001). Parity also predicted both RRM and RRBSO uptake (OR, 4.2; P = .001; and OR, 5.4; P = .003, respectively). Age at the time of genetic testing and history of breast biopsy or cosmetic surgery were not predictive of RRM uptake. CONCLUSION: Perceptions of cancer risk are heavily influenced by particular features of an individual's family history and may be motivators in preventive surgery more than actual cancer risk estimations themselves. Awareness of subtle factors beyond the statistical risk for cancers is relevant when counseling at-risk women.

Novel LMNA mutations in patients with Emery-Dreifuss muscular dystrophy and functional characterization of four LMNA mutations.

Mutations in LMNA cause a variety of diseases affecting striated muscle including autosomal Emery-Dreifuss muscular dystrophy (EDMD), LMNA-associated congenital muscular dystrophy (L-CMD), and limb-girdle muscular dystrophy type 1B (LGMD1B). Here, we describe novel and recurrent LMNA mutations identified in 50 patients from the United States and Canada, which is the first report of the distribution of LMNA mutations from a large cohort outside Europe. This augments the number of LMNA mutations known to cause EDMD by 16.5%, equating to an increase of 5.9% in the total known LMNA mutations. Eight patients presented with either p.R249W/Q or p.E358K mutations and an early onset EDMD phenotype: two mutations recently associated with L-CMD. Importantly, 15 mutations are novel and include eight missense mutations (p.R189P, p.F206L, p.S268P, p.S295P, p.E361K, p.G449D, p.L454P, and p.W467R), three splice site mutations (c.IVS4 + 1G>A, c.IVS6 - 2A>G, and c.IVS8 + 1G>A), one duplication/in frame insertion (p.R190dup), one deletion (p.Q355del), and two silent mutations (p.R119R and p.K270K). Analysis of 4 of our lamin A mutations showed that some caused nuclear deformations and lamin B redistribution in a mutation specific manner. Together, this study significantly augments the number of EDMD patients on the database and describes 15 novel mutations that underlie EDMD, which will contribute to establishing genotype-phenotype correlations.

Absence of TGFBR2 mutations in patients with spontaneous spinal CSF leaks and intracranial hypotension.

A heritable connective-tissue-disorder often is suspected in patients with spontaneous spinal CSF leaks and intracranial hypotension, but the nature of the disorder remains unknown in most patients. The aim of this study was to assess the gene encoding TGF-beta receptor-2 (TGFBR2) as a candidate gene for spinal CSF leaks. We searched the TGFBR2 gene for mutations in eight patients with spontaneous spinal CSF leaks who also had other features associated with TGFBR2 mutations, i.e., skeletal features of Marfan syndrome, arterial tortuosity, and(or) thoracic aortic aneurysm. The mean age of these 7 women and 1 man was 38 years (range 14-60 years). We detected no TGFBR2 mutations and conclude that TGFBR2 mutations are not a major factor in spontaneous spinal CSF leaks.

Connective tissue disorders with spontaneous spinal cerebrospinal fluid leaks and intracranial hypotension: a prospective study.

OBJECTIVE: Intracranial hypotension attributable to a spontaneous spinal cerebrospinal fluid (CSF) leak is an increasingly recognized cause of postural headaches. The cause of these leaks is poorly understood, but it is likely multifactorial and may involve a primary connective tissue disorder. We undertook a study to estimate the contribution of systemic connective tissue disorders to the development of spontaneous spinal CSF leaks. METHODS: We examined a group of 18 consecutive patients with spontaneous spinal CSF leaks for features of a connective tissue disorder. RESULTS: The mean age of the 15 female patients and 3 male patients was 38 years (range, 22-55 yr). Seven patients (38%) demonstrated stigmata of a systemic connective tissue disorder, and three distinct types of disorders could be identified, as follows. 1) The association of spontaneous spinal CSF leaks and minor skeletal features of Marfan syndrome was noted for three patients. 2) Ehlers-Danlos syndrome Type II was noted for two patients. 3) Joint hypermobility associated with marked attenuation of the dorsal muscular fascia, precluding proper wound closure, was noted for two patients. In addition, isolated small-joint hypermobility was observed for five patients (28%). Slit-lamp ocular examinations, echocardiographic evaluations, histopathological examinations of skin biopsy specimens, and renal scanning did not reveal any other features of a systemic connective tissue disorder. CONCLUSION: Findings suggesting connective tissue disorders are common among patients with spontaneous spinal CSF leaks, and manifestations may be subtle. A variety of disorders can be identified, probably reflecting genetic heterogeneity. Problems with wound healing may occur as a result of the systemic nature of the underlying connective tissue disorder.