Prediction of breast cancer risk based on flow variant analysis of circulating peripheral blood mononuclear cells

Identifying women at high risk for developing breast cancer is potentially lifesaving. Patients with pathogenic genetic variants can embark on a program of surveillance for early detection, chemoprevention, and/or prophylactic surgery. Newly diagnosed cancer patients can also use the results of gene panel sequencing to make decisions about surgery; therefore, rapid turnaround time for results is critical. Cancer Risk B (CR-B), a test that uses flow variant assays to assess the effects of variants in the DNA double-strand break repair, was applied to two groups of subjects who underwent coincidental gene panel testing, thereby allowing an assessment of sensitivity, specificity and accuracy, and utility for annotating variants of uncertain significance (VUS). The test was compared in matched peripheral blood mononuclear cells (PBMCs) and lymphoblastoid cells (LCLs) and tested for rescue in LCLs with gene transfer. The CR-B phenotype demonstrated a bimodal distribution: CR-B+ indicative of DSB repair defects, and CR-B-, indicative of wild-type repair. When comparing matched LCLs and PBMCs and inter-day tests, CR-B yielded highly reproducible results. The CR-B- phenotype was rescued by gene transfer using wild-type cDNA expression plasmids. The CR-B- phenotype predicted VUS as benign or likely benign. CR-B could represent a rapid alternative to panel sequencing for women with cancer and identifying women at high risk for cancer and is a useful adjunct for annotating VUS.

Precision oncology: lessons learned and challenges for the future

The decreasing cost of and increasing capacity of DNA sequencing has led to vastly increased opportunities for population-level genomic studies to discover novel genomic alterations associated with both Mendelian and complex phenotypes. To translate genomic findings clinically, a number of health care institutions have worked collaboratively or individually to initiate precision medicine programs. These precision medicine programs involve designing patient enrollment systems, tracking electronic health records, building biobank repositories, and returning results with actionable matched therapies. As cancer is a paradigm for genetic diseases and new therapies are increasingly tailored to attack genetic susceptibilities in tumors, these precision medicine programs are largely driven by the urgent need to perform genetic profiling on cancer patients in real time. Here, we review the current landscape of precision oncology and highlight challenges to be overcome and examples of benefits to patients. Furthermore, we make suggestions to optimize future precision oncology programs based upon the lessons learned from these "first generation" early adopters.

Video Education on Hereditary Breast and Ovarian Cancer (HBOC) for Physicians: an Interventional Study

The National Comprehensive Cancer Network (NCCN) guidelines are the gold standard in hereditary cancer risk assessment, screening, and treatment. A minority of physicians follow NCCN guidelines for BRCA1 or BRCA2 mutations. This study assesses the impact of an interventional educational program on HBOC in terms of knowledge. Physicians were sent an invite to join either an intervention survey (web-training offered prior to the knowledge survey) or control survey (web-training offered after the knowledge survey). Sixty-nine physicians in the intervention arm and 67 physicians in the control arm completed the survey. The interventional group regularly answered items correctly at a higher frequency than the control group. For example, 64.71% (n = 44) of physicians in the intervention group knew that multi-gene testing does not have to include only highly penetrant genes compared to 32.84% (n = 22) of the control group (p < 0.01). Similar results were seen with other specific survey items. The current study is important in that it shows web-based education to be a feasible and effective modality for training on hereditary breast cancer. This type of education may be incorporated into CME programs and can be used as a foundation for further studies as well.

KBG syndrome involving a single-nucleotide duplication in ANKRD11

KBG syndrome is a rare autosomal dominant genetic condition characterized by neurological involvement and distinct facial, hand, and skeletal features. More than 70 cases have been reported; however, it is likely that KBG syndrome is underdiagnosed because of lack of comprehensive characterization of the heterogeneous phenotypic features. We describe the clinical manifestations in a male currently 13 years of age, who exhibited symptoms including epilepsy, severe developmental delay, distinct facial features, and hand anomalies, without a positive genetic diagnosis. Subsequent exome sequencing identified a novel de novo heterozygous single base pair duplication (c.6015dupA) in ANKRD11, which was validated by Sanger sequencing. This single-nucleotide duplication is predicted to lead to a premature stop codon and loss of function in ANKRD11, thereby implicating it as contributing to the proband's symptoms and yielding a molecular diagnosis of KBG syndrome. Before molecular diagnosis, this syndrome was not recognized in the proband, as several key features of the disorder were mild and were not recognized by clinicians, further supporting the concept of variable expressivity in many disorders. Although a diagnosis of cerebral folate deficiency has also been given, its significance for the proband's condition remains uncertain.

SCN8A mutation in a child presenting with seizures and developmental delays

The SCN8A gene encodes the sodium voltage-gated channel alpha subunit 8. Mutations in this gene have been associated with early infantile epileptic encephalopathy type 13. With the use of whole-exome sequencing, a de novo missense mutation in SCN8A was identified in a 4-yr-old female who initially exhibited symptoms of epilepsy at the age of 5 mo that progressed to a severe condition with very little movement, including being unable to sit or walk on her own.

Acceptance of technology-based tools in a sample of Parkinson's patients

Objectives Parkinson's disease is the second most common neurodegenerative movement disorder in the United States. Patients' opinions of technology-based tools for education and communication as related to Parkinson's disease are unclear with little documented research addressing the issue. The goal of this research was to investigate patient opinions about technology-based tools with a focus on differences between patients of different age groups. Methods A cross-sectional survey was used to assess views on using multiple different electronic methods for receiving instructions and communicating with healthcare providers in 109 Parkinson's disease patients. Results Approximately 28% (n = 28) of the subjects reported having unmet needs related to Parkinson's disease. Those 65 and over were less likely to believe that using technology to communicate with the healthcare center would result in themselves having a better understanding of their care (odds ratio = 0.36, 95% confidence interval: 0.14, 0.95). Those over 75 had a lower odds of being willing to use electronic methods (odds ratio = 0.33, 95% confidence interval: 0.14, 0.79), a lower odds of believing that technology would result in better self-understanding of medical needs (odds ratio = 0.27, 95% confidence interval: 0.12, 0.63) and a lower odds of believing that technology would result in their healthcare providers better understanding their needs (odds ratio = 0.32, 95% confidence interval: 0.14, 0.73). Discussion The results of this study indicate that older Parkinson's disease patients report a less favorable view regarding the role of technology in communicating with healthcare providers and for understanding their care.

Physician Risk Assessment Knowledge Regarding BRCA Genetics Testing

The study aim was to evaluate the association between genetics referrals, training in medical school, residency, or continuing medical education and physician knowledge of hereditary breast and ovarian cancer (HBOC). A survey of 55 questions was administered to 140 physicians evaluating knowledge and practice patterns regarding HBOC. Physicians with genetics training during residency were more likely to recognize that most instances of ovarian cancer are not hereditary (odds ratio (OR) = 3.16; 95 % confidence interval (CI) 1.32, 7.58). Physicians with continuing medical education (CME) training on genetics were more likely to identify that screening can be improved for those with a hereditary mutation (OR = 4.28; 95 % CI 1.32, 13.90). Primary care physicians who frequently referred for genetics were more likely to recognize that maternal history is not more important than paternal history (OR = 2.51; 95 % CI 1.11, 5.66), that screening can be improved for those with hereditary risk (OR = 4.06; 95 % CI 1.08, 15.22), and that females with a hereditary breast cancer risk would have different recommendations for screening than someone without this risk (OR = 4.91; 95 % CI 1.04, 23.25). Our data suggest that training and frequency of genetics referrals may be associated with knowledge of general risk assessment for HBOC.

Impact of academic affiliation and training on knowledge of hereditary colorectal cancer

BACKGROUND

Knowledge about hereditary colorectal cancer (CRC) can aid cancer screening and prevention in high-risk patients. Genetic testing, once conducted primarily at academic centers, is now routinely performed in a variety of clinics. Nonacademic physicians may not be aware of hereditary CRC standards of care.

METHODS

From August to November 2012, a survey was administered to predominantly primary care physicians evaluating academic center affiliation, past training in genetics and knowledge regarding hereditary CRC.

RESULTS

One hundred forty physicians completed the survey. Knowledge of hereditary CRC was neither associated with academic affiliation nor with training during medical school or residency, but with continuing medical education (CME) training. Those with CME training were more likely to know that screening could be enhanced for patients with a hereditary cancer risk (OR = 4.49, 95% CI = 1.40-14.38) and that an individual with hereditary CRC would have different screening recommendations (OR = 7.49, 95% CI = 1.37-40.81). Residency training and CME training were associated with more frequent hereditary risk assessment.

CONCLUSION

Genetics training may be associated with physicians' knowledge and assessment of hereditary CRC. Training at the CME level in particular may be integral to the delivery of genetic services in clinical practice.

No mutations in the serotonin related TPH1 and HTR1B genes in patients with monogenic sclerosing bone disorders

Since the identification of LRP5 as the causative gene for the osteoporosis pseudoglioma syndrome (OPPG) as well as the high bone mass (HBM) phenotype, LRP5 and the Wnt/β-catenin signaling have been extensively studied for their role in the differentiation and proliferation of osteoblasts, in the apoptosis of osteoblasts and osteocytes and in the response of bone to mechanical loading. However, more recently the direct effect of LRP5 on osteoblasts and bone formation has been questioned. Gene expression studies showed that mice lacking lrp5 have increased expression of tph1, the rate limiting enzyme for the production of serotonin in the gut. Furthermore mice lacking either tph1 or htr1B, the receptor for serotonin on the osteoblasts, were reported to have an increased bone mass due to increased bone formation. This led to the still controversial hypothesis that LRP5 influences bone formation indirectly by regulating the expression of thp1 and as a consequence influencing the production of serotonin in the gut. Based on these data we decided to evaluate the role of TPH1 and HTR1B in the development of craniotubular hyperostoses, a group of monogenic sclerosing bone dysplasias. We screened the coding regions of both genes in 53 patients lacking a mutation in the known causative genes LRP5, LRP4 and SOST. We could not find disease-causing coding variants in neither of the tested genes and therefore, we cannot provide support for an important function of TPH1 and HTR1B in the pathogenesis of sclerosing bone dysplasias in our tested patient cohort.

Clinical and mutational spectrum of neurofibromatosis type 1-like syndrome

CONTEXT

Autosomal dominant inactivating sprouty-related EVH1 domain-containing protein 1 (SPRED1) mutations have recently been described in individuals presenting mainly with café au lait macules (CALMs), axillary freckling, and macrocephaly. The extent of the clinical spectrum of this new disorder needs further delineation.

OBJECTIVE

To determine the frequency, mutational spectrum, and phenotype of neurofibromatosis type 1-like syndrome (NFLS) in a large cohort of patients.

DESIGN, SETTING, AND PARTICIPANTS

In a cross-sectional study, 23 unrelated probands carrying a SPRED1 mutation identified through clinical testing participated with their families in a genotype-phenotype study (2007-2008). In a second cross-sectional study, 1318 unrelated anonymous samples collected in 2003-2007 from patients with a broad range of signs typically found in neurofibromatosis type 1 (NF1) but no detectable NF1 germline mutation underwent SPRED1 mutation analysis.

MAIN OUTCOME MEASURES

Comparison of aggregated clinical features in patients with or without a SPRED1 or NF1 mutation. Functional assays were used to evaluate the pathogenicity of missense mutations.

RESULTS

Among 42 SPRED1-positive individuals from the clinical cohort, 20 (48%; 95% confidence interval [CI], 32%-64%) fulfilled National Institutes of Health (NIH) NF1 diagnostic criteria based on the presence of more than 5 CALMs with or without freckling or an NF1-compatible family history. None of the 42 SPRED1-positive individuals (0%; 95% CI, 0%-7%) had discrete cutaneous or plexiform neurofibromas, typical NF1 osseous lesions, or symptomatic optic pathway gliomas. In the anonymous cohort of 1318 individuals, 34 different SPRED1 mutations in 43 probands were identified: 27 pathogenic mutations in 34 probands and 7 probable nonpathogenic missense mutations in 9 probands. Of 94 probands with familial CALMs with or without freckling and no other NF1 features, 69 (73%; 95% CI, 63%-80%) had an NF1 mutation and 18 (19%; 95% CI, 12%-29%) had a pathogenic SPRED1 mutation. In the anonymous cohort, 1.9% (95% CI, 1.2%-2.9%) of individuals with the clinical diagnosis of NF1 according to the NIH criteria had NFLS.

CONCLUSIONS

A high SPRED1 mutation detection rate was found in NF1 mutation-negative families with an autosomal dominant phenotype of CALMs with or without freckling and no other NF1 features. Among individuals in this study, NFLS was not associated with the peripheral and central nervous system tumors seen in NF1.

Array comparative genomic hybridisation of 52 subjects with a Smith-Magenis-like phenotype: identification of dosage sensitive loci also associated with schizophrenia, autism, and developmental delay

BACKGROUND

Smith-Magenis syndrome (SMS) is caused by del(17)(p11.2), including the retinoic acid induced 1 gene (RAI1), or mutation of RAI1. Haploinsufficiency of RAI1 results in developmental delay, mental retardation, sleep disturbance, self-abusive behaviors, and most features commonly seen in SMS. In this study, 52 subjects were referred for molecular analysis of RAI1 due to the presence of an SMS-like phenotype in each case. For this cohort, deletion and mutation analyses of RAI1 were negative; thus, the clinical diagnosis of SMS could not be confirmed and suggested that at least one other locus was responsible for the phenotype(s) observed.

METHODS

Here, we present whole-genome array comparative genomic hybridization and detailed phenotypic data of these 52 subjects.

RESULTS

This SMS-like cohort exhibited developmental delays, sleep disturbance, self-abusive behaviors, motor dysfunction, and hyperactivity of the same type and prevalence as that of SMS. In this analysis, we identified at least 5 new loci that likely contribute to the SMS-like phenotype, including CNVs that were found in more than one subject. Genes in these regions function in development, neurological integrity, and morphology, all of which are affected in SMS.

CONCLUSIONS

Given the phenotypic overlap between SMS and the SMS-like cases, these data may provide some insight into the function of RAI1, including the pathways in which it may be involved and the genes it may regulate. These data will improve diagnosis, understanding, and potentially treatment of these complex behavior and mental retardation syndromes.

Bronchial anomalies in VACTERL association

VACTERL association is an acronym made of associated defects including vertebral anomalies, anal atresia, cardiac, tracheal-esophageal fistula, and renal/radial limb anomalies. Tracheal bronchus is a condition characterized by ectopic location of the right upper lobe bronchus at the mid to distal trachea. This condition is associated with congenital anomalies and has been reported in one previous case of VACTERL. We report another infant with VACTERL presenting with respiratory complications due to presence of tracheal bronchus. She also had a narrowed segment of her right main stem bronchus.