Impact of genome build on RNA-seq interpretation and diagnostics.

Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.

Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder.

PURPOSE: The function of FAM177A1 and its relationship to human disease is largely unknown. Recent studies have demonstrated FAM177A1 to be a critical immune-associated gene. One previous case study has linked FAM177A1 to a neurodevelopmental disorder in four siblings. METHODS: We identified five individuals from three unrelated families with biallelic variants in FAM177A1. The physiological function of FAM177A1 was studied in a zebrafish model organism and human cell lines with loss-of-function variants similar to the affected cohort. RESULTS: These individuals share a characteristic phenotype defined by macrocephaly, global developmental delay, intellectual disability, seizures, behavioral abnormalities, hypotonia, and gait disturbance. We show that FAM177A1 localizes to the Golgi complex in mammalian and zebrafish cells. Intersection of the RNA-seq and metabolomic datasets from FAM177A1-deficient human fibroblasts and whole zebrafish larvae demonstrated dysregulation of pathways associated with apoptosis, inflammation, and negative regulation of cell proliferation. CONCLUSION: Our data sheds light on the emerging function of FAM177A1 and defines FAM177A1-related neurodevelopmental disorder as a new clinical entity.

Increasing equity in science requires better ethics training: A course by trainees, for trainees.

Despite the profound impacts of scientific research, few scientists have received the necessary training to productively discuss the ethical and societal implications of their work. To address this critical gap, we-a group of predominantly human genetics trainees-developed a course on genetics, ethics, and society. We intend for this course to serve as a template for other institutions and scientific disciplines. Our curriculum positions human genetics within its historical and societal context and encourages students to evaluate how societal norms and structures impact the conduct of scientific research. We demonstrate the utility of this course via surveys of enrolled students and provide resources and strategies for others hoping to teach a similar course. We conclude by arguing that if we are to work toward rectifying the inequities and injustices produced by our field, we must first learn to view our own research as impacting and being impacted by society.

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.

Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.

Impact of genome build on RNA-seq interpretation and diagnostics.

Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network (UDN) and Genomics Research to Elucidate the Genetics of Rare Disease (GREGoR) Consortium. We identified 2,800 genes with build-dependent quantification across six routinely-collected biospecimens, including 1,391 protein-coding genes and 341 known rare disease genes. We further observed multiple genes that only have detectable expression in a subset of genome builds. Finally, we characterized how genome build impacts the detection of outlier transcriptomic events. Combined, we provide a database of genes impacted by build choice, and recommend that transcriptomics-guided analyses and diagnoses are cross-referenced with these data for robustness.

Transcriptomics and chromatin accessibility in multiple African population samples.

Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell lines (LCLs) from 599 individuals from six African populations to identify novel transcripts including those not represented in the hg38 reference genome. We used whole genomes from the 1000 Genomes Project and 164 Maasai individuals to identify 8,881 expression and 6,949 splicing quantitative trait loci (eQTLs/sQTLs), and 2,611 structural variants associated with gene expression (SV-eQTLs). We further profiled chromatin accessibility using ATAC-Seq in a subset of 100 representative individuals, to identity chromatin accessibility quantitative trait loci (caQTLs) and allele-specific chromatin accessibility, and provide predictions for the functional effect of 78.9 million variants on chromatin accessibility. Using this map of eQTLs and caQTLs we fine-mapped GWAS signals for a range of complex diseases. Combined, this work expands global functional genomic data to identify novel transcripts, functional elements and variants, understand population genetic history of molecular quantitative trait loci, and further resolve the genetic basis of multiple human traits and disease.

Older Adults' Experiences in a Web-Based Intervention for Loneliness.

Background: Older adults may be vulnerable to loneliness due to natural and age-related transitions. Lonely older adults are at an increased risk of adverse health outcomes due to their loneliness, including cognitive decline, cardiovascular disease, and mortality. Objective: The purpose of this study was to explore the experiences of vulnerable older adults in a web-based loneliness intervention. Methods: Older adult participants in a web-based loneliness intervention (n = 24) participated in semi-structured interviews eliciting feedback about their experience in the program and perceived outcomes. Participants' responses were analyzed using qualitative content analysis. Results: Participants reported fewer negative perceptions of their social skills and future social interactions, gaining new social skills, improved relationships, and increased confidence to initiate and maintain social contact. Conclusions: Findings suggest the efficacy of combining a web-based loneliness intervention with cognitive behavioral therapy, and provide implications for future web-based interventions for older adult populations.

The impact of COVID-19 on older adults: Results from an annual survey.

OBJECTIVES: Assess well-being among older adults through secondary analysis measured during an annual survey in 2018, 2019, and 2020, to determine trends from before and during the COVID-19 pandemic. METHODS: Mailed surveys sent annually included measures related to various psychosocial factors. MAIN FINDINGS: Response rates were 29% in 2018, 25% in 2019, and 24% in 2020. Most respondents reported average or high resilience (89% 2018-2020), high purpose (64% in 2018 and 2019, 63% in 2020), moderate optimism (46% in 2019, 44% in 2020) and low stress (88% in 2019 and 2020). Reported loneliness increased 13% from 2018 to 2020. In 2020, only 45% reported high comfort with technology, decreasing with age (>75). PRINCIPAL CONCLUSION: Psychosocial well-being of respondents were doing well despite changes related to COVID-19. However, increased loneliness may negatively impact long-term health outcomes; thus, a focus on technology options to stay socially connected and access healthcare are needed.

Reducing loneliness and improving well-being among older adults with animatronic pets.

BACKGROUND: Studies consistently demonstrate that older adults who are lonely have higher rates of depression and increased mortality risk. Pet ownership may be a solution for loneliness; however, challenges related to pet ownership exist for older adults. Therefore, researchers and practitioners are examining the use of animatronic pets to reduce loneliness. OBJECTIVE: To determine the feasibility of an animatronic pet program, and whether ownership of animatronic pets would decrease loneliness and improve well-being among lonely older adults. METHODS: Eligible individuals were identified as lonely through a prior survey. Participants were provided with the choice of an animatronic pet and completed T1/T2/T3 surveys. RESULTS: Attrition was high; 168 (63%) participants completed T1/T2 surveys, and 125 (48%) also completed a T3 survey. Post survey data indicated that loneliness decreased, while mental well-being, resilience, and purpose in life improved. Frequent interactions with the pets were associated with greater improvement in mental well-being and optimism. CONCLUSIONS: Animatronic pets appear to provide benefits for the well-being of lonely older adults. Future studies should employ randomized controlled designs examining the impact of animatronic pets.

Older Adult Caregivers' Experiences in an Online, Interactive Mindfulness Intervention.

BACKGROUND: While today's older adults experience longevity, they often manage several chronic conditions and increasingly serve as informal caregivers for aging parents, children with life-long disabilities, and spouses. Older adult caregivers managing personal chronic illness often experience significant psychosocial hardships. OBJECTIVE: The primary purpose of this study was to explore the experiences of older adult caregivers in an online, interactive mindfulness intervention. METHODS: Self-reported older caregivers who participated in an online-based mindfulness program (n = 20) were recruited for semi-structured interviews. Participants were asked to provide feedback about any previous experience with mindfulness and/or meditation, hopes or goals held prior to the start of the program, desired expectations, motivation for joining, impressions of sessions, most beneficial topics, potential application of content, and any perceived effects. Participants' responses were analyzed using qualitative content analysis. RESULTS: Five themes emerged from the analysis: Managing the Comprehensive Effects of Caregiving, Openness to Meditation and Mindfulness, Course Engagement and Incremental Growth, Building Rapport through Shared Experiences, and Ongoing Application and Opportunities for Refinement. Participants reported both short-term post-exercise benefits such as increased calm, relaxation, and stress relief, as well as long-term positive outcomes. Notably, participants found the program's unique interactive feature to be particularly beneficial as a form of perceived social support. CONCLUSIONS: Caregivers for older adults may derive benefit and potentially experience reduced subjective caregiver burden as a result of participating in a Mindfulness-Based Stress Reduction (MBSR) program, particularly when the program is augmented with a self-compassion approach and perceived social support.

Robotic Pet Use Among Community-Dwelling Older Adults.

OBJECTIVE: The primary purpose of this study was to explore the efficacy of robotic pets in alleviating loneliness for older adults. METHOD: Self-reported lonely individuals with AARP Medicare Supplement plans insured by UnitedHealthcare who participated in a program with a robotic pet (n = 20) were recruited to participate in semi-structured interviews. Participants were asked to provide feedback about their experiences interacting with a robotic pet, their perceptions about the potential impact on loneliness, and recommendations for improving the program. Interviews were audio-recorded and transcribed verbatim. Participants' responses were analyzed using qualitative content analysis. Constant comparison and consensus-gaining processes were used to develop categories that later formed representative themes. RESULTS: Seven themes emerged from analysis: Openness to Adoption of Robotic Pet, Reactions to Pet and its Attributes, Integration of Pet in Daily Life, Strategic Utilization and Forging New Connections, Deriving Comfort and Camaraderie, Advice for Future Users, and Recommendations for Enhancing Ownership Experience. Participants living alone, with fewer social connections and less active lifestyles, derived the most benefit from interacting with their pets. Common responses to pets included cuddling, petting, grooming, and sleeping with them. Some shared or loaned their pets, while others refused to loan their pets to interested peers. Most reported showing their pets to others, which helped some facilitate communication and social connections. CONCLUSION: Robotic pets may be an effective solution for alleviating loneliness in older adults, especially among those who live alone, have fewer social connections, and live less active lifestyles.

Complex phenotype of dyskeratosis congenita and mood dysregulation with novel homozygous RTEL1 and TPH1 variants.

Dyskeratosis congenita (DC) is an inherited bone marrow failure syndrome caused by germline mutations in telomere biology genes. Patients have extremely short telomeres for their age and a complex phenotype including oral leukoplakia, abnormal skin pigmentation, and dysplastic nails in addition to bone marrow failure, pulmonary fibrosis, stenosis of the esophagus, lacrimal ducts and urethra, developmental anomalies, and high risk of cancer. We evaluated a patient with features of DC, mood dysregulation, diabetes, and lack of pubertal development. Family history was not available but genome-wide genotyping was consistent with consanguinity. Whole exome sequencing identified 82 variants of interest in 80 genes based on the following criteria: homozygous, <0.1% minor allele frequency in public and in-house databases, nonsynonymous, and predicted deleterious by multiple in silico prediction programs. Six genes were identified likely contributory to the clinical presentation. The cause of DC is likely due to homozygous splice site variants in regulator of telomere elongation helicase 1, a known DC and telomere biology gene. A homozygous, missense variant in tryptophan hydroxylase 1 may be clinically important as this gene encodes the rate limiting step in serotonin biosynthesis, a biologic pathway connected with mood disorders. Four additional genes (SCN4A, LRP4, GDAP1L1, and SPTBN5) had rare, missense homozygous variants that we speculate may contribute to portions of the clinical phenotype. This case illustrates the value of conducting detailed clinical and genomic evaluations on rare patients in order to identify new areas of research into the functional consequences of rare variants and their contribution to human disease.