PheWAS and Beyond: The Landscape of Associations with Medical Diagnoses and Clinical Measures across 38,662 Individuals from Geisinger.

Most phenome-wide association studies (PheWASs) to date have used a small to moderate number of SNPs for association with phenotypic data. We performed a large-scale single-cohort PheWAS, using electronic health record (EHR)-derived case-control status for 541 diagnoses using International Classification of Disease version 9 (ICD-9) codes and 25 median clinical laboratory measures. We calculated associations between these diagnoses and traits with ∼630,000 common frequency SNPs with minor allele frequency > 0.01 for 38,662 individuals. In this landscape PheWAS, we explored results within diseases and traits, comparing results to those previously reported in genome-wide association studies (GWASs), as well as previously published PheWASs. We further leveraged the context of functional impact from protein-coding to regulatory regions, providing a deeper interpretation of these associations. The comprehensive nature of this PheWAS allows for novel hypothesis generation, the identification of phenotypes for further study for future phenotypic algorithm development, and identification of cross-phenotype associations.

Puberty and menarche in young females with cerebral palsy and intellectual disability: a qualitative study of caregivers' experiences.

AIM: To explore experiences of parents of young females with cerebral palsy (CP) and intellectual disability at the onset of puberty. METHOD: This was a phenomenological qualitative study. We conducted phone interviews of parents of young females with CP and intellectual disability who had been seen in the CP center at a freestanding children's hospital within the prior 2 years. Inclusion criteria were English-speaking parents of young females who had combined diagnoses of CP and intellectual disability. Interviews were coded and analyzed by the research team facilitated by Dedoose software. RESULTS: Nine interviews were conducted with parents of daughters aged 14 to 24 years. All daughters used wheelchairs for mobility and augmentative technology for communication. Despite homogeneity in functional ability, there was marked variation in parental perception of the significance of puberty for their daughters. Families often learned about reproductive health from informal social networks. Although families acknowledged the need for sexual abuse screening, there was little consensus about how to do it, and most denied that their own daughter could ever be abused. INTERPRETATION: Parents of young females with CP and intellectual disability have diverse reproductive health beliefs that health care providers must explore in order to provide appropriate recommendations for management of puberty. WHAT THIS PAPER ADDS: Parents of young females with cerebral palsy (CP) and intellectual disability have diverse reproductive health beliefs. Approaches to menstrual management in this population must be individualized. Families discounted the likelihood of abuse, despite acknowledging their daughters' risk.

"It'd Be Great to Have the Options There": A Mixed-Methods Study of Gender Identity Questions on Clinic Forms in a Primary Care Setting.

PURPOSE: Transgender youth experience significant barriers to health care. Asking patients about gender identity on clinic intake forms is recommended to improve care in adult populations. Little is known about how to implement these recommendations in adolescent populations. This study aimed to evaluate the addition of gender-related questions in an adolescent primary care setting and to determine if adding these questions to clinic forms could improve documentation of gender identity in the electronic health record (EHR). METHODS: We conducted cognitive interviews with 21 adolescents (n = 11 transgender, n = 10 cisgender) to examine gender-related questions (name, pronoun, gender identity, assigned sex at birth). These questions were added to a clinic intake form. We conducted a retrospective chart review of patients who came to the clinic for a physical examination visit three months before (n = 615) and after (n = 827) the form change and used chi-square tests to examine the differences in EHR documentation of gender identity. RESULTS: In interviews, the new questions were acceptable and interpretable to adolescents of diverse gender identities. Participants described the questions as beneficial to all patients and perceived them as an indicator of a welcoming clinic environment. The retrospective chart review found that provider documentation of gender identity in the EHR significantly increased after the form change from 51.3% to 66.3% (p < .0001). CONCLUSIONS: This intervention was acceptable to adolescents and associated with a significant increase in EHR documentation. Future studies should investigate how the form change may have facilitated discussion about gender and health and implications for provider training and support.