A cross-disorder dosage sensitivity map of the human genome.

Rare copy-number variants (rCNVs) include deletions and duplications that occur infrequently in the global human population and can confer substantial risk for disease. In this study, we aimed to quantify the properties of haploinsufficiency (i.e., deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout the human genome. We harmonized and meta-analyzed rCNVs from nearly one million individuals to construct a genome-wide catalog of dosage sensitivity across 54 disorders, which defined 163 dosage sensitive segments associated with at least one disorder. These segments were typically gene dense and often harbored dominant dosage sensitive driver genes, which we were able to prioritize using statistical fine-mapping. Finally, we designed an ensemble machine-learning model to predict probabilities of dosage sensitivity (pHaplo & pTriplo) for all autosomal genes, which identified 2,987 haploinsufficient and 1,559 triplosensitive genes, including 648 that were uniquely triplosensitive. This dosage sensitivity resource will provide broad utility for human disease research and clinical genetics.

Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease.

Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and, with new innovative methods, can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.

Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies.

Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.

Follow the trail: Using insights from the growth of palliative care to propose a roadmap for cancer rehabilitation.

Despite research explicating the benefits of cancer rehabilitation interventions to optimize physical, social, emotional, and vocational functioning, many reports document low rates of referral to and uptake of rehabilitation in oncology. Cancer rehabilitation clinicians, researchers, and policy makers could learn from the multidisciplinary specialty of palliative care, which has benefited from a growth strategy and has garnered national recognition as an important and necessary aspect of oncology care. The purpose of this article is to explore the actions that have increased the uptake and integration of palliative care to yield insights and multimodal strategies for the development and growth of cancer rehabilitation. After examining the history of palliative care and its growth, the authors highlight 5 key strategies that may benefit the field of cancer rehabilitation: 1) stimulating the science in specific gap areas; 2) creating clinical practice guidelines; 3) building clinical capacity; 4) ascertaining and responding to public opinion; and 5) advocating for public policy change. Coordinated and simultaneous advances on these 5 strategies may catalyze the growth, utilization, and effectiveness of patient screening, timely referrals, and delivery of appropriate cancer rehabilitation care that reduces disability and improves quality of life for cancer survivors who need these services.

A structural variation reference for medical and population genetics.

Structural variants (SVs) rearrange large segments of DNA1 and can have profound consequences in evolution and human disease2,3. As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD)4 have become integral in the interpretation of single-nucleotide variants (SNVs)5. However, there are no reference maps of SVs from high-coverage genome sequencing comparable to those for SNVs. Here we present a reference of sequence-resolved SVs constructed from 14,891 genomes across diverse global populations (54% non-European) in gnomAD. We discovered a rich and complex landscape of 433,371 SVs, from which we estimate that SVs are responsible for 25-29% of all rare protein-truncating events per genome. We found strong correlations between natural selection against damaging SNVs and rare SVs that disrupt or duplicate protein-coding sequence, which suggests that genes that are highly intolerant to loss-of-function are also sensitive to increased dosage6. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than all noncoding effects. Finally, we identified very large (over one megabase), rare SVs in 3.9% of samples, and estimate that 0.13% of individuals may carry an SV that meets the existing criteria for clinically important incidental findings7. This SV resource is freely distributed via the gnomAD browser8 and will have broad utility in population genetics, disease-association studies, and diagnostic screening.

Activity-Dependent Degradation of the Nascentome by the Neuronal Membrane Proteasome.

Activity-dependent changes in neuronal function require coordinated regulation of the protein synthesis and protein degradation machinery to maintain protein homeostasis, critical for proper neuronal function. However, the biochemical evidence for this balance and coordination is largely lacking. Leveraging our recent discovery of a neuronal-specific 20S membrane proteasome complex (NMP), we began exploring how neuronal activity regulates its function. Here, we found that the NMP degrades exclusively a large fraction of ribosome-associated nascent polypeptides that are being newly synthesized during neuronal stimulation. Using deep-coverage and global mass spectrometry, we identified the nascent protein substrates of the NMP, which included products encoding immediate-early genes, such as c-Fos and Npas4. Intriguingly, we found that turnover of nascent polypeptides and not full-length proteins through the NMP occurred independent of canonical ubiquitylation pathways. We propose that these findings generally define a neuronal activity-induced protein homeostasis program of coordinated protein synthesis and degradation through the NMP.

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies.

Virtually all genome sequencing efforts in national biobanks, complex and Mendelian disease programs, and medical genetic initiatives are reliant upon short-read whole-genome sequencing (srWGS), which presents challenges for the detection of structural variants (SVs) relative to emerging long-read WGS (lrWGS) technologies. Given this ubiquity of srWGS in large-scale genomics initiatives, we sought to establish expectations for routine SV detection from this data type by comparison with lrWGS assembly, as well as to quantify the genomic properties and added value of SVs uniquely accessible to each technology. Analyses from the Human Genome Structural Variation Consortium (HGSVC) of three families captured ~11,000 SVs per genome from srWGS and ~25,000 SVs per genome from lrWGS assembly. Detection power and precision for SV discovery varied dramatically by genomic context and variant class: 9.7% of the current GRCh38 reference is defined by segmental duplication (SD) and simple repeat (SR), yet 91.4% of deletions that were specifically discovered by lrWGS localized to these regions. Across the remaining 90.3% of reference sequence, we observed extremely high (93.8%) concordance between technologies for deletions in these datasets. In contrast, lrWGS was superior for detection of insertions across all genomic contexts. Given that non-SD/SR sequences encompass 95.9% of currently annotated disease-associated exons, improved sensitivity from lrWGS to discover novel pathogenic deletions in these currently interpretable genomic regions is likely to be incremental. However, these analyses highlight the considerable added value of assembly-based lrWGS to create new catalogs of insertions and transposable elements, as well as disease-associated repeat expansions in genomic sequences that were previously recalcitrant to routine assessment.

Frequency and reasons for unplanned transfer to the primary acute care service of inpatient rehabilitation glioblastoma multiforme patients.

PURPOSE: To determine the percentage of and factors associated with unplanned transfer to the acute care service of glioblastoma multiforme acute rehabilitation inpatients. METHODS: Retrospective review of glioblastoma multiforme acute rehabilitation inpatients admitted 4/1/2016-3/31/2020 at a National Cancer Institute Comprehensive Cancer Center. RESULTS: One hundred thirty-nine consecutive admissions of unique glioblastoma multiforme acute rehabilitation inpatients were analyzed. Fifteen patients (10.7%, 95% confidence interval 6.5-17.1%) were transferred to the acute care service for unplanned reasons. The most common reasons for transfer back were neurosurgical complication 6/15(40%), neurologic decline due to mass effect 4/15(26.7%), and pulmonary embolism 2/15(13.3%). Older age (p = 0.010), infection prior to acute inpatient rehabilitation transfer (p = 0.020), and lower activity measure of post-acute care 6-click basic mobility scores (p = 0.048) were significantly associated with transfer to the acute care service. Patients who transferred to the acute care service had significantly lower overall survival than patients who did not transfer off (log-rank test p = 0.001). CONCLUSION: Acute inpatient physiatrists should closely monitor patients for neurosurgical and neurologic complications. The variables significantly associated with transfer to the acute care service may help identify patients at increased risk for medical complications who may require closer observation.

The critical need to implement and utilize patient-reported measures of function in cancer care delivery.

The study by Smith et al. on the Patient-Reported Outcomes Measurement Information System (PROMIS) Cancer Function Brief 3D Profile shows that it can be used to measure how an individual functions and how his or her function changes during cancer treatments. This is important because most patients will experience a decline in function during cancer treatment and will struggle to fully participate in their life roles. Strong evidence demonstrates that rehabilitation improves function for individuals with cancer; rehabilitation is relatively underutilized. We suggest that using the PROMIS tool as a repeated measure throughout cancer treatment will help to identify those with functional decline who will benefit most from rehabilitation.

Review of needle electromyography complications in thrombocytopenic cancer patients.

INTRODUCTION/AIMS: Needle electromyography (EMG) is understood to be a relatively safe procedure based on clinical experience. There are no evidence-based guidelines for EMG procedures in thrombocytopenic patients. The purpose of this study was to determine whether there is an increased risk of bleeding complications associated with needle EMG in patients with thrombocytopenia. METHODS: This retrospective study included patients with a primary cancer and thrombocytopenia who underwent needle EMG between January 1, 2016 and October 30, 2020. Patients' medical records were reviewed for demographics; diagnoses; platelet counts within a 7-day period of EMG examination; concurrent use of anticoagulants or antiplatelet medications; number of sites sampled by needle EMG, including anatomical differentiation of paraspinal and both deep and superficial limb muscles; and associated complications not limited to bleeding within 30 days of EMG examination. RESULTS: The initial data search identified 198 patients with a documented diagnosis of thrombocytopenia; 124 met these criteria and were included in the study. A total of 1001 muscle sample sites were documented, with 111 sites in paraspinal muscles, 876 sites in superficial limb muscles, and 14 sites within deep limb muscles. Five patients were concurrently using therapeutic anticoagulation and 3 were using antiplatelet medications. There were no clinically significant complications, but five minor incidents were documented in the medical records within 30 days post-EMG examination. DISCUSSION: Our findings suggest that bleeding complications from standard needle EMG in oncology patients with documented thrombocytopenia are rare. Testing of high-risk muscles in this patient population appears to be safe.

Usability, acceptability, and implementation strategies for the Exercise in Cancer Evaluation and Decision Support (EXCEEDS) algorithm: a Delphi study.

INTRODUCTION: Oncology guidelines recommend participation in cancer rehabilitation or exercise services (CR/ES) to optimize survivorship. Yet, connecting the right survivor, with the right CR/ES, at the right time remains a challenge. The Exercise in Cancer Evaluation and Decision Support (EXCEEDS) algorithm was developed to enhance CR/ES clinical decision-making and facilitate access to CR/ES. We used Delphi methodology to evaluate usability, acceptability, and determine pragmatic implementation priorities. METHODS: Participants completed three online questionnaires including (1) simulated case vignettes, (2) 4-item acceptability questionnaire (0-5 pts), and (3) series of items to rank algorithm implementation priorities (potential users, platforms, strategies). To evaluate usability, we used Chi-squared test to compare frequency of accurate pre-exercise medical clearance and CR/ES triage recommendations for case vignettes when using EXCEEDS vs. without. We calculated mean acceptability and inter-rater agreement overall and in 4 domains. We used the Eisenhower Prioritization Method to evaluate implementation priorities. RESULTS: Participants (N = 133) mostly represented the fields of rehabilitation (69%), oncology (25%), or exercise science (17%). When using EXCEEDS (vs. without), their recommendations were more likely to be guideline concordant for medical clearance (83.4% vs. 66.5%, X2 = 26.61, p < .0001) and CR/ES triage (60.9% vs. 51.1%, X2 = 73.79, p < .0001). Mean acceptability was M = 3.90 ± 0.47; inter-rater agreement was high for 3 of 4 domains. Implementation priorities include 1 potential user group, 2 platform types, and 9 implementation strategies. CONCLUSION: This study demonstrates the EXCEEDS algorithm can be a pragmatic and acceptable clinical decision support tool for CR/ES recommendations. Future research is needed to evaluate algorithm usability and acceptability in real-world clinical pathways.

Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD.

OBJECTIVE: Both the gut microbiome and host genetics are known to play significant roles in the pathogenesis of IBD. However, the interaction between these two factors and its implications in the aetiology of IBD remain underexplored. Here, we report on the influence of host genetics on the gut microbiome in IBD. DESIGN: To evaluate the impact of host genetics on the gut microbiota of patients with IBD, we combined whole exome sequencing of the host genome and whole genome shotgun sequencing of 1464 faecal samples from 525 patients with IBD and 939 population-based controls. We followed a four-step analysis: (1) exome-wide microbial quantitative trait loci (mbQTL) analyses, (2) a targeted approach focusing on IBD-associated genomic regions and protein truncating variants (PTVs, minor allele frequency (MAF) >5%), (3) gene-based burden tests on PTVs with MAF <5% and exome copy number variations (CNVs) with site frequency <1%, (4) joint analysis of both cohorts to identify the interactions between disease and host genetics. RESULTS: We identified 12 mbQTLs, including variants in the IBD-associated genes IL17REL, MYRF, SEC16A and WDR78. For example, the decrease of the pathway acetyl-coenzyme A biosynthesis, which is involved in short chain fatty acids production, was associated with variants in the gene MYRF (false discovery rate <0.05). Changes in functional pathways involved in the metabolic potential were also observed in participants carrying rare PTVs or CNVs in CYP2D6, GPR151 and CD160 genes. These genes are known for their function in the immune system. Moreover, interaction analyses confirmed previously known IBD disease-specific mbQTLs in TNFSF15. CONCLUSION: This study highlights that both common and rare genetic variants affecting the immune system are key factors in shaping the gut microbiota in the context of IBD and pinpoints towards potential mechanisms for disease treatment.

Physical function predicts mortality in patients with cancer: a systematic review and meta-analysis of observational studies.

PURPOSE: This systematic review and meta-analysis aimed to determine whether physical function can predict mortality in patients with cancer. METHODS: Literature searches were conducted in Web of Science, CINAHL, the Cochrane Library, ProQuest, PEDro, and PubMed for articles published before September 2020. Four review authors retrieved studies using predetermined eligibility criteria and conducted quality assessment and data extraction. RESULTS: A total of 1356 titles and abstracts were screened; ultimately, 26 studies were determined to be suitable for meta-analysis. Grip strength was significantly associated with mortality risk in patients with cancer (hazard ratio [HR] = 1.15, P = 0.005). Gait speed was also associated with mortality risk (HR = 1.58, P = 0.0004). In grip strength and gait speed, the subgroup comprised of patients with cancer aged ≥ 80 years had a higher effect size than that of patients aged < 80 years. The short physical performance battery measurement was markedly associated with mortality risk, showing the largest effect size (HR = 2.37, P < 0.00001). The 6-min walking test distance was significantly associated with mortality risk (HR = 1.55, P = 0.001). The timed up and go test was significantly associated with mortality risk with a high effect size (HR = 2.66, P < 0.00001). CONCLUSION: This systematic review and meta-analysis demonstrated that physical function predicted mortality in patients with cancer. Furthermore, physical function outcomes in patients aged 80 years and above reflected a higher mortality.

Development of the Exercise in Cancer Evaluation and Decision Support (EXCEEDS) algorithm.

PURPOSE: Participation in exercise or rehabilitation services is recommended to optimize health, functioning, and well-being across the cancer continuum of care. However, limited knowledge of individual needs and complex decision-making are barriers to connect the right survivor to the right exercise/rehabilitation service at the right time. In this article, we define the levels of exercise/rehabilitation services, provide a conceptual model to improve understanding of individual needs, and describe the development of the Exercise in Cancer Evaluation and Decision Support (EXCEEDS) algorithm. METHODS: From literature review, we synthesized defining characteristics of exercise/rehabilitation services and individual characteristics associated with safety and efficacy for each service. We developed a visual model to conceptualize the need for each level of specialized care, then organized individual characteristics into a risk-stratified algorithm. Iterative review with a multidisciplinary expert panel was conducted until consensus was reached on algorithm content and format. RESULTS: We identified eight defining features of the four levels of exercise/rehabilitation services and provide a conceptual model of to guide individualized navigation for each service across the continuum of care. The EXCEEDS algorithm includes a risk-stratified series of eleven dichotomous questions, organized in two sections and ten domains. CONCLUSIONS: The EXCEEDS algorithm is an evidence-based decision support tool that provides a common language to describe exercise/rehabilitation services, a practical model to understand individualized needs, and step-by-step decision support guidance. The EXCEEDS algorithm is designed to be used at point of care or point of need by multidisciplinary users, including survivors. Thus, implementation may improve care coordination for cancer exercise/rehabilitation services.

Detection of rare disease variants in extended pedigrees using RVS.

SUMMARY: Family-based sequencing studies enable researchers to identify highly penetrant genetic variants too rare to be tested in conventional case-control studies, by studying co-segregation of variant and disease phenotypes. When multiple affected subjects in a family are sequenced, the probability that a variant or a set of variants is shared identical-by-descent by some or all affected relatives provides evidence against the null hypothesis of complete absence of linkage and association. The Rare Variant Sharing software package RVS implements a suite of tools to assess association and linkage between rare genetic variants and a dichotomous disease indicator in family pedigrees. AVAILABILITY AND IMPLEMENTATION: RVS is available as open source software from the Bioconductor webpage at https://bioconductor.org/packages/release/bioc/html/RVS.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Detection of de novo copy number deletions from targeted sequencing of trios.

MOTIVATION: De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. RESULTS: We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability. AVAILABILITY AND IMPLEMENTATION: MDTS is freely available as open source software from the Bioconductor repository. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bayesian copy number detection and association in large-scale studies.

BACKGROUND: Germline copy number variants (CNVs) increase risk for many diseases, yet detection of CNVs and quantifying their contribution to disease risk in large-scale studies is challenging due to biological and technical sources of heterogeneity that vary across the genome within and between samples. METHODS: We developed an approach called CNPBayes to identify latent batch effects in genome-wide association studies involving copy number, to provide probabilistic estimates of integer copy number across the estimated batches, and to fully integrate the copy number uncertainty in the association model for disease. RESULTS: Applying a hidden Markov model (HMM) to identify CNVs in a large multi-site Pancreatic Cancer Case Control study (PanC4) of 7598 participants, we found CNV inference was highly sensitive to technical noise that varied appreciably among participants. Applying CNPBayes to this dataset, we found that the major sources of technical variation were linked to sample processing by the centralized laboratory and not the individual study sites. Modeling the latent batch effects at each CNV region hierarchically, we developed probabilistic estimates of copy number that were directly incorporated in a Bayesian regression model for pancreatic cancer risk. Candidate associations aided by this approach include deletions of 8q24 near regulatory elements of the tumor oncogene MYC and of Tumor Suppressor Candidate 3 (TUSC3). CONCLUSIONS: Laboratory effects may not account for the major sources of technical variation in genome-wide association studies. This study provides a robust Bayesian inferential framework for identifying latent batch effects, estimating copy number, and evaluating the role of copy number in heritable diseases.

A Survey Regarding the Knowledge, Attitudes, and Beliefs of Graduates of Cancer Rehabilitation Fellowship Program.

Currently there are limited options for physiatrists to further subspecialize in cancer rehabilitation. Since 2007, few cancer rehabilitation fellowship programs have been started. There is currently absolutely no information about such training programs and their graduates. This study is the first to survey a small number of graduates from two cancer rehabilitation fellowship programs. The purpose of this study was to report characteristics, attitudes, and beliefs of cancer rehabilitation fellowship graduates. Graduates of cancer rehabilitation fellowship programs from 2008 through 2015 responded to a 26-question survey. Information collected included exposure to cancer rehabilitation prior to fellowship training, usefulness of fellowship training program, information about current practice, and suggested areas of improvement. The setting of the study is online survey. Participants were graduates of two cancer rehabilitation fellowship programs from 2008 through 2015. Participants were contacted via email about completion of an online survey and information was collected anonymously. Primary outcome measure was satisfaction of respondents with their fellowship training program in meeting the rehabilitation needs of their cancer patients. Sixteen responses, with a response rate of 89%, were recorded. Sixty-three percent of the respondents had exposure to cancer rehabilitation prior to post-graduate year 3 (PGY-3). Majority of graduates had practice involving at least 50% of care to cancer patients. Fifty percent indicated that their position was specifically created after their job interview. Career development was one of the major areas of suggested improvement in training. Graduates of cancer rehabilitation fellowship programs strongly value their training. Majority of the graduates were able to continue their career into jobs that were primarily cancer rehabilitation related. Further work needs to be done to define this subspecialty further and incorporate building practice as part of this training.

Whole exome association of rare deletions in multiplex oral cleft families.

By sequencing the exomes of distantly related individuals in multiplex families, rare mutational and structural changes to coding DNA can be characterized and their relationship to disease risk can be assessed. Recently, several rare single nucleotide variants (SNVs) were associated with an increased risk of nonsyndromic oral cleft, highlighting the importance of rare sequence variants in oral clefts and illustrating the strength of family-based study designs. However, the extent to which rare deletions in coding regions of the genome occur and contribute to risk of nonsyndromic clefts is not well understood. To identify putative structural variants underlying risk, we developed a pipeline for rare hemizygous deletions in families from whole exome sequencing and statistical inference based on rare variant sharing. Among 56 multiplex families with 115 individuals, we identified 53 regions with one or more rare hemizygous deletions. We found 45 of the 53 regions contained rare deletions occurring in only one family member. Members of the same family shared a rare deletion in only eight regions. We also devised a scalable global test for enrichment of shared rare deletions.