The contribution of de novo coding mutations to autism spectrum disorder.

Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.

Partial bisulfite conversion for unique template sequencing.

We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone.

Physicians Should Play a Role in Ensuring Safe Firearm Ownership.

The USA is unique among industrialized nations in its dramatic rate of firearm violence. Unfortunately, firearm-related issues in America are politically divisive and fraught with controversy, thus impeding the study and implementation of safety strategies. Despite the lack of consensus, there is agreement that firearms should be kept away from individuals with criminal intent and those who are dangerous due to medical impairment. While predicting criminal intent remains challenging, assessment of medical impairment remains a viable target. One approach in which physicians could contribute their expertise includes training a subset of doctors to perform specialized medical evaluations as a prerequisite for gun ownership. Such a process is not unprecedented, as physicians currently have a role in protecting the public's safety through assessments for commercial drivers, pilots, and train operators. Certified physician examiners could conduct these evaluations with a focus on evaluating objective, skill-based metrics to limit potential evaluator bias. The results of the medical evaluation would then be considered by an existing regulatory body to determine if disqualifying criteria are present. This proposal provides a mechanism for trained physicians to meaningfully participate in addressing an alarming public health issue, while still working within existing legal frameworks.

A Systematic Review of Advocacy Curricula in Graduate Medical Education.

BACKGROUND: Professionalism standards encourage physicians to participate in public advocacy on behalf of societal health and well-being. While the number of publications of advocacy curricula for GME-level trainees has increased, there has been no formal effort to catalog them. OBJECTIVE: To systematically review the existing literature on curricula for teaching advocacy to GME-level trainees and synthesize the results to provide a resource for programs interested in developing advocacy curricula. METHODS: A systematic literature review was conducted to identify articles published in English that describe advocacy curricula for graduate medical education trainees in the USA and Canada current to September 2017. Two reviewers independently screened titles, abstracts, and full texts to identify articles meeting our inclusion and exclusion criteria, with disagreements resolved by a third reviewer. We abstracted information and themes on curriculum development, implementation, and sustainability. Learning objectives, educational content, teaching methods, and evaluations for each curriculum were also extracted. RESULTS: After reviewing 884 articles, we identified 38 articles meeting our inclusion and exclusion criteria. Curricula were offered across a variety of specialties, with 84% offered in primary care specialties. There was considerable heterogeneity in the educational content of included advocacy curriculum, ranging from community partnership to legislative advocacy. Common facilitators of curriculum implementation included the American Council for Graduate Medical Education requirements, institutional support, and preexisting faculty experience. Common barriers were competing curricular demands, time constraints, and turnover in volunteer faculty and community partners. Formal evaluation revealed that advocacy curricula were acceptable to trainees and improved knowledge, attitudes, and reported self-efficacy around advocacy. DISCUSSION: Our systematic review of the medical education literature identified several advocacy curricula for graduate medical education trainees. These curricula provide templates for integrating advocacy education into GME-level training programs across specialties, but more work needs to be done to define standards and expectations around GME training for this professional activity.

Pincher, a pinocytic chaperone for nerve growth factor/TrkA signaling endosomes.

A central tenet of nerve growth factor (NGF) action that is poorly understood is its ability to mediate cytoplasmic signaling, through its receptor TrkA, that is initiated at the nerve terminal and conveyed to the soma. We identified an NGF-induced protein that we termed Pincher (pinocytic chaperone) that mediates endocytosis and trafficking of NGF and its receptor TrkA. In PC12 cells, overexpression of Pincher dramatically stimulated NGF-induced endocytosis of TrkA, unexpectedly at sites of clathrin-independent macropinocytosis within cell surface ruffles. Subsequently, a system of Pincher-containing tubules mediated the delivery of NGF/TrkA-containing vesicles to cytoplasmic accumulations. These vesicles selectively and persistently mediated TrkA-erk5 mitogen-activated protein kinase signaling. A dominant inhibitory mutant form of Pincher inhibited the NGF-induced endocytosis of TrkA, and selectively blocked TrkA-mediated cytoplasmic signaling of erk5, but not erk1/2, kinases. Our results indicate that Pincher mediates pinocytic endocytosis of functionally specialized NGF/TrkA endosomes with persistent signaling potential.

A systematic review of curricula on relationships between residents and the pharmaceutical industry.

CONTEXT: Research has demonstrated the potential adverse impact of pharmaceutical company marketing techniques on doctor knowledge and prescribing practices. Lack of experience may make resident doctors particularly vulnerable to pharmaceutical industry influence. Curricula addressing resident-pharmaceutical industry relations have been reported, but there is no consensus regarding the best approach to take. OBJECTIVE: This study aimed to review published curricula that address resident-pharmaceutical industry relations and to assess them for content, validity and outcomes measures. METHODS: Curricula were identified via searches of electronic databases and bibliographies of collected articles. Inclusion criteria required articles to describe an educational curriculum, applied in graduate medical education, on relations between doctors and the pharmaceutical industry. RESULTS: The search identified 9 curricula. Most addressed detailing of residents by pharmaceutical representatives. Two articles described curriculum development. Eight articles included an evaluation component; only 1 included a control group for comparison. Modest improvements were noted in resident confidence, knowledge of guidelines, belief in the potential influence of marketing on behaviour, and self-reported acceptance of gifts. Only 2 evaluations used a validated outcome instrument, and no studies included longterm follow-up. CONCLUSIONS: A limited number of curricula have addressed resident-pharmaceutical industry interactions. Inconsistency in content, application and evaluation methodology prevents any meaningful synthesis of data. Resident attitudes and behaviours may be affected, but the outcome measures used lacked sufficient validity to assess improvements in knowledge and analytic skills. A clearer delineation of the curriculum development process and the use of standardised outcome measures would facilitate the reproduction of positive results at other institutions.

Racial and ethnic differences in personal cervical cancer screening amongst post-graduate physicians: results from a cross-sectional survey.

BACKGROUND: Racial and ethnic disparities in cervical cancer screening have been attributed to socioeconomic, insurance, and cultural differences. Our objective was to explore racial and ethnic differences in adherence to cervical cancer screening recommendations among female post-graduate physicians. METHODS: We conducted a cross-sectional survey at one university hospital among a convenience sample of 204 female post-graduate physicians (52% of all potential participants), examining adherence to United States Preventive Services Task Force cervical cancer screening recommendations, perception of adherence to recommendations, and barriers to obtaining care. RESULTS: Overall, 83% of women were adherent to screening recommendations and 84% accurately perceived adherence or non-adherence. Women who self-identified as Asian were significantly less adherent when compared with women who self-identified as white (69% vs. 87%; Relative Risk [RR]=0.79, 95% Confidence Interval [CI], 0.64-0.97; P<0.01). Women who self-identified as East Indian were significantly less likely to accurately perceive adherence or non-adherence when compared to women who self-identified as white (64% vs. 88%; RR=0.73, 95% CI, 0.49-1.09, P=0.04). Women who self-identified as Asian were significantly more likely to report any barrier to obtaining care when compared with women who self-identified as white (60% vs. 35%; RR=1.75, 95% CI, 1.24-2.47; P=0.001) and there was a non-significant tendency toward women who self-identified as East Indian being more likely to report any barrier to obtaining care when compared with women who self-identified as white (60% vs. 34%; RR=1.74, 95% CI, 1.06-2.83; P=0.06). CONCLUSION: Among a small group of insured, highly-educated physicians who have access to health care, we found racial and ethnic differences in adherence to cervical cancer screening recommendations, suggesting that culture may play a role in cervical cancer screening.

Development and implementation of an innovative ward-based program to help medical students acquire end-of-life care experience.

The authors developed and implemented a new ward-based end-of-life care experience for third-year medical students at Yale University School of Medicine, which began on a pilot basis in 2005. The primary objectives of the program, which still continues, are to improve students' comfort and skills in communicating with and assessing patients facing the end of life and to reflect on their experiences. Students interview a hospitalized patient, family, and caregivers; assess specified end-of-life domains and management plans; reflect on the experience; and then prepare a report for presentation at a case conference facilitated by dedicated multidisciplinary faculty. Many students interview patients while rotating on psychiatry consults, and the case conference occurs during the psychiatry clerkship. A total of 45 students in the pilot year (2005), 76 students in the following year, and 48 thus far in the current year have completed the program. An assessment of the personal impact of the exercise on the students who completed the program in 2005 and 2006 revealed six themes, including students' recognition of the complexity of patients' reactions to dying, students' appreciation of the value of the clinicians' presence, and students' personal reflections. This experience suggests that a hands-on end-of-life exercise is feasible and will be well received in the acute inpatient setting. Key features for success include separate, dedicated faculty for the case conference (which is integrated into a single clerkship), emphasis on student self-reflection, and a requirement that the written component become part of the student's portfolio.

Discrepancy Between Patient Health Literacy Levels and Readability of Patient Education Materials from an Electronic Health Record.

Limited health literacy is associated with worse health outcomes. It is standard practice in many primary care clinics to provide patients with written patient education materials (PEM), which often come directly from an electronic health record (EHR). We compared the health literacy of patients in a primary care residency clinic with EHR PEM readability by grade level. We assessed health literacy using the Rapid Estimate of Adult Literacy in Medicine-Short Form (REALM-SF), and determined grade level readability for the PEM distributed for the five most common clinical diagnoses using the Simple Measure of Gobbledygook (SMOG) and Flesch-Kincaid metrics. Among 175 participants, health literacy was ≥9th grade for 76 patients (43.4%), 7th to 8th grade for 66 patients (37.7%), and ≤6th grade for 30 patients (17.1%). Average standard PEM readability by SMOG was grade 9.2 and easy-to-read PEM readability was grade 6.8. These findings suggest a discrepancy between the health literacy of most patients who were surveyed and standard PEM readability. Despite national guidelines encouraging clinicians to provide PEM at an appropriate reading level, our results indicate that PEM from EHR may not be readable for many patients. [Health Literacy Research and Practice. 2017;1(4):e203-e207.].

Brief report: Housestaff adherence to cervical cancer screening recommendations.

BACKGROUND: Postgraduate training involves intensive clinical education characterized by long work hours with minimal flexibility. Time demands may be a barrier to obtaining preventive care for housestaff during postgraduate training. OBJECTIVE: Assess adherence to United States Preventive Services Task Force (USPSTF) cervical cancer screening recommendations. DESIGN: Cross-sectional survey. PARTICIPANTS: Convenience sample of female housestaff at 1 university hospital. MEASUREMENTS: Primary outcomes included (1) adherence to USPSTF recommendations, (2) perception of adherence to recommendations, and (3) barriers to obtaining preventive care. RESULTS: Surveys were completed by 204 housestaff. Overall, 81% of housestaff were adherent to USPSTF screening recommendations. Housestaff requiring screening in the past year were less likely to be adherent when compared with housestaff requiring screening in the past 3 years. Overall, 84% accurately perceived their screening behavior as adherent or nonadherent (kappa=0.58). Of the 43% who identified a barrier to obtaining preventive care, not having time to schedule or keep appointments was reported most frequently (n=72). CONCLUSIONS: Housestaff accurately perceived their need for cervical cancer screening and were generally adherent to USPSTF recommendations, even though lack of time during postgraduate training was frequently reported as a barrier to obtaining preventive care. However, we found lower adherence among a small subgroup of housestaff at a slightly greater risk for cervical disease and most likely to benefit from screening.

Indel variant analysis of short-read sequencing data with Scalpel.

As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel (http://scalpel.sourceforge.net) is an open-source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole-genome and whole-exome sequencing data. We provide detailed instructions for an exemplary family-based de novo study, but we also characterize the other two supported modes of operation: single-sample and somatic analysis. Indel normalization, visualization and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be completed in ∼5 h after read mapping.

Altruism as a reason for participation in clinical trials was independently associated with adherence.

BACKGROUND: To determine whether altruism as reason for participation in research is independently associated with adherence to a medical regimen in a clinical trial. METHODS: Participants were 475 participants in the Women's Estrogen for Stroke Trial. Before randomization to estrogen or placebo, all women were questioned about reason for participation and baseline features that may contribute to adherence. Adherence was defined as completion of at least 80% of expected pill intake during the trial. RESULTS: Women who reported at least one altruistic reason for participation were more likely to be college educated, have a higher level of social support, and a better functional status. They were also more likely to be adherent to their study medication {155 of 212 (73%) vs. 158 of 253 (62.5%), P < .01}. On stratified analysis and multivariable regression, the relationship between altruism as reason for participation and adherence was independent of other sociodemographic, psychosocial, and clinical features (relative risk 1.17, Confidence interval 1.03-1.32). CONCLUSION: Altruism may explain a small portion of the variation in adherence among research participants. This relationship may have implications for recruitment of participants in clinical research. The possible contribution of altruism to the relationship between adherence and outcomes in clinical trials is worthy of further investigation.

Infectious disease experimentation involving human volunteers.

The current care of patients with infectious diseases owes a tremendous debt to healthy volunteers who allowed investigators to induce disease in them for the study of transmission, natural history, and treatment. We reviewed the English-language medical literature about the rarely discussed subject of the use of healthy volunteers in human-subject research in infectious diseases to determine the contributions of these experiments to the current understanding of disease transmission. The literature review focused on hepatitis, upper respiratory infections, and malaria, which represent the array of issues involved in this type of research. Researchers successfully induced infection through injecting, nebulizing, and feeding specimens to thousands of volunteers, who included authentic volunteers as well as soldiers and imprisoned subjects. These volunteers often undertook unforeseen and unpredictable risks during these experiments for the benefit of others. Future research in these areas must strike an adequate balance between the risks to participants and the benefits to society.

Informed consent for thrombolytic therapy for patients with acute ischemic stroke treated in routine clinical practice.

BACKGROUND AND PURPOSE: Little is known about informed consent for tissue plasminogen activator (tPA). Our objectives were to determine how frequently informed consent is obtained when tPA is given to stroke patients in clinical practice and whether the person providing consent (patient or surrogate) was the appropriate decision-maker. METHODS: This retrospective cohort included acute stroke patients given tPA in 10 Connecticut hospitals (1996-1998). Consent was defined as any documentation of discussion about risks and benefits of tPA. Patients had adequate decision-making capacity if they were alert, oriented, and without aphasia or neglect (patient was appropriate decision-maker). Patients with any of these deficits were considered to have diminished capacity (surrogate was appropriate decision-maker). RESULTS: Among 63 patients who received tPA, 53 (84%) had informed consent documented; 16/53 (30%) gave their own consent. Among patients with adequate decision-making capacity, 5/8 (63%) had consent by surrogate. Among patients with diminished capacity, 7/38 (18%) provided their own consent. CONCLUSIONS: A substantial percentage of patients who received tPA for stroke had no consent documented. Surrogates often provided consent when the patients had capacity; conversely, patients with diminished capacity sometimes provided their own consent. Given the urgency and weight of the decision regarding tPA, more explicit informed consent and capacity assessment should be considered for treatment protocols.

Sources of ethical conflict in medical housestaff training: a qualitative study.

PURPOSE: Despite increased emphasis on medical ethics and professionalism in medical education, concern about unethical and unprofessional behavior by physicians is widespread. This study sought to identify and classify the range of work-related ethical conflicts experienced by medical house officers. METHODS: We performed a qualitative study using data from in-depth interviews conducted in 2001 with 31 internal medicine residents in one traditional and one primary care residency. Using the constant comparative method, we explored work-related experiences during housestaff training that involved ethical conflict with patients or colleagues. RESULTS: The interviews revealed five categories of ethical conflict: concern over telling the truth, respecting patients' wishes, preventing harm, managing the limits of one's competence, and addressing performance of others that is perceived to be inappropriate. Conflicts occurred between residents and attending physicians, patients or families, and other residents. Many of the conflicts were exacerbated by the function of the hierarchical structure in residency training. CONCLUSIONS: This study provides a classification of work-related ethical conflicts that houseofficers experience, which may be used to improve the working environment for residents and support their professional development. By attending to the challenges that residents face, particularly previously underemphasized conflicts concerning competence and performance, this framework can be used to enhance education in ethics and professionalism.

Reducing INDEL calling errors in whole genome and exome sequencing data.

BACKGROUND: INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library preparation, sequencing biases, and algorithm artifacts. METHODS: We characterized whole genome sequencing (WGS), whole exome sequencing (WES), and PCR-free sequencing data from the same samples to investigate the sources of INDEL errors. We also developed a classification scheme based on the coverage and composition to rank high and low quality INDEL calls. We performed a large-scale validation experiment on 600 loci, and find high-quality INDELs to have a substantially lower error rate than low-quality INDELs (7% vs. 51%). RESULTS: Simulation and experimental data show that assembly based callers are significantly more sensitive and robust for detecting large INDELs (>5 bp) than alignment based callers, consistent with published data. The concordance of INDEL detection between WGS and WES is low (53%), and WGS data uniquely identifies 10.8-fold more high-quality INDELs. The validation rate for WGS-specific INDELs is also much higher than that for WES-specific INDELs (84% vs. 57%), and WES misses many large INDELs. In addition, the concordance for INDEL detection between standard WGS and PCR-free sequencing is 71%, and standard WGS data uniquely identifies 6.3-fold more low-quality INDELs. Furthermore, accurate detection with Scalpel of heterozygous INDELs requires 1.2-fold higher coverage than that for homozygous INDELs. Lastly, homopolymer A/T INDELs are a major source of low-quality INDEL calls, and they are highly enriched in the WES data. CONCLUSIONS: Overall, we show that accuracy of INDEL detection with WGS is much greater than WES even in the targeted region. We calculated that 60X WGS depth of coverage from the HiSeq platform is needed to recover 95% of INDELs detected by Scalpel. While this is higher than current sequencing practice, the deeper coverage may save total project costs because of the greater accuracy and sensitivity. Finally, we investigate sources of INDEL errors (for example, capture deficiency, PCR amplification, homopolymers) with various data that will serve as a guideline to effectively reduce INDEL errors in genome sequencing.

De novo gene disruptions in children on the autistic spectrum.

Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point substitutions, which come mostly from the paternal line in an age-dependent manner. We do not see significantly greater numbers of de novo missense mutations in affected versus unaffected children, but gene-disrupting mutations (nonsense, splice site, and frame shifts) are twice as frequent, 59 to 28. Based on this differential and the number of recurrent and total targets of gene disruption found in our and similar studies, we estimate between 350 and 400 autism susceptibility genes. Many of the disrupted genes in these studies are associated with the fragile X protein, FMRP, reinforcing links between autism and synaptic plasticity. We find FMRP-associated genes are under greater purifying selection than the remainder of genes and suggest they are especially dosage-sensitive targets of cognitive disorders.

Lost in transition: the experience and impact of frequent changes in the inpatient learning environment.

PURPOSE: The traditional "rotating" model of inpatient training remains the gold standard of residency, moving residents through different systems every two to four weeks. The authors studied the experience and impact of frequent transitions on residents. METHOD: This was a qualitative study. Ninety-seven individuals participated in 12 focus groups at three academic medical centers purposefully chosen to represent a range of geographic locations and structural characteristics. Four groups were held at each site: residents only, faculty only, nurses and ancillary staff only, and a mixed group. Grounded theory was used to analyze data. RESULTS: Perceived benefits of transitions included the ability to adapt to new environments and practice styles, improved organization and triage skills, increased comfort with stressful situations, and flexibility. Residents primarily relied on each other to cope with and prepare for transitions, with little support from the program or faculty level. Several potentially problematic workarounds were described within the context of transitions, including shortened progress notes, avoiding pages, hiding information, and sidestepping critical situations. Nearly all residents acknowledged that frequent transitions contributed to a lack of ownership and other potentially harmful effects for patient care. CONCLUSIONS: These findings challenge the value of the traditional "rotating" model in residency. As residents adapt to frequent transitioning, they implicitly learn to value flexibility and efficiency over relationship building and deep system knowledge. These findings raise significant implications for professional development and patient care and highlight an important element of the hidden curriculum embedded within the current training model.