Lymphoma Driver Mutations in the Pathogenic Evolution of an Iconic Human Autoantibody.

Pathogenic autoantibodies arise in many autoimmune diseases, but it is not understood how the cells making them evade immune checkpoints. Here, single-cell multi-omics analysis demonstrates a shared mechanism with lymphoid malignancy in the formation of public rheumatoid factor autoantibodies responsible for mixed cryoglobulinemic vasculitis. By combining single-cell DNA and RNA sequencing with serum antibody peptide sequencing and antibody synthesis, rare circulating B lymphocytes making pathogenic autoantibodies were found to comprise clonal trees accumulating mutations. Lymphoma driver mutations in genes regulating B cell proliferation and V(D)J mutation (CARD11, TNFAIP3, CCND3, ID3, BTG2, and KLHL6) were present in rogue B cells producing the pathogenic autoantibody. Antibody V(D)J mutations conferred pathogenicity by causing the antigen-bound autoantibodies to undergo phase transition to insoluble aggregates at lower temperatures. These results reveal a pre-neoplastic stage in human lymphomagenesis and a cascade of somatic mutations leading to an iconic pathogenic autoantibody.

Testing at scale during the COVID-19 pandemic.

Assembly and publication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in January 2020 enabled the immediate development of tests to detect the new virus. This began the largest global testing programme in history, in which hundreds of millions of individuals have been tested to date. The unprecedented scale of testing has driven innovation in the strategies, technologies and concepts that govern testing in public health. This Review describes the changing role of testing during the COVID-19 pandemic, including the use of genomic surveillance to track SARS-CoV-2 transmission around the world, the use of contact tracing to contain disease outbreaks and testing for the presence of the virus circulating in the environment. Despite these efforts, widespread community transmission has become entrenched in many countries and has required the testing of populations to identify and isolate infected individuals, many of whom are asymptomatic. The diagnostic and epidemiological principles that underpin such population-scale testing are also considered, as are the high-throughput and point-of-care technologies that make testing feasible on a massive scale.

The human mitochondrial transcriptome.

The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs, and rRNAs. Here, we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance and precisely resolve transcript processing and maturation events. We identify previously undescribed transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single-nucleotide resolution, revealing regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. This integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA and provides a resource for future studies of mitochondrial function (accessed at http://mitochondria.matticklab.com).

Bringing Generalists to Global Health: a Missed Opportunity and Call to Action.

The credo of the generalist physician has always been the promotion of health for all, in every aspect: not just multiple vulnerable organ systems, but multiple social, cultural, and political factors that contribute to poor health and exacerbate health inequity. In recent years, the field of global health has also adopted this same mission: working across both national and clinical specialty borders to improve health for all and end health disparities worldwide. Yet within the Society for General Internal Medicine, and among American generalists, engagement in global health, both within and outside the USA, remains uncommon. We see this gap as an opportunity, because in fact generalists in America already have the skills and experience that global health badly needs. SGIM could promote generalists to global health's vanguard, with three core steps. First, we generalists must continue to integrate health for the vulnerable into our domestic work, generating care models applicable in low-resource settings around the globe. Conversely, we must also engage with and implement international ideas and solutions for universal access to primary care for vulnerable patients in the USA. And lastly, we must build platforms to connect ourselves with colleagues worldwide to exchange these learnings.

Structural Factors Contributing to Compassion Fatigue, Burnout, and Secondary Traumatic Stress Among Hospital-Based Healthcare Professionals During the COVID-19 Pandemic.

High levels of burnout among healthcare providers (HCPs) have been a widely documented phenomenon, which have been exacerbated during the COVID-19 pandemic. In the United States, qualitative studies that are inclusive of HCPs in diverse professional roles have been limited. Therefore, we utilized a qualitative-quantitative design to examine professional quality of life in terms of compassion fatigue, burnout, and secondary traumatic stress among hospital-based HCPs, including social workers, hospitalists, residents, and palliative care team members during COVID-19. HCPs (n = 26) participated in virtual semi-structured focus groups or individual interviews and online surveys (n = 30) including the Professional Quality of Life (ProQOL) Scale. While ProQOL scores indicated low levels of compassion fatigue, burnout, and secondary traumatic stress, thematic analysis of our qualitative data included rich descriptions of compassion fatigue, burnout, and secondary traumatic stress. Safety concerns and value misalignment characterized structural stressors perceived to contribute to HCP compassion fatigue, burnout, and secondary traumatic stress. The discrepancy between our qualitative and quantitative findings may be indication that modifications to current screenings are warranted. These findings also suggest a need to identify and implement structural and policy changes that increase HCPs' physical and emotional safety and promote better alignment of institutional interests with HCP values.

Reference standards for next-generation sequencing.

Next-generation sequencing (NGS) provides a broad investigation of the genome, and it is being readily applied for the diagnosis of disease-associated genetic features. However, the interpretation of NGS data remains challenging owing to the size and complexity of the genome and the technical errors that are introduced during sample preparation, sequencing and analysis. These errors can be understood and mitigated through the use of reference standards - well-characterized genetic materials or synthetic spike-in controls that help to calibrate NGS measurements and to evaluate diagnostic performance. The informed use of reference standards, and associated statistical principles, ensures rigorous analysis of NGS data and is essential for its future clinical use.

Community engagement to inform development of strategies to improve referral for hypertension: perspectives of patients, providers and local community members in western Kenya.

BACKGROUND: Hypertension is the leading cause of death and disability. Clinical care for patients with hypertension in Kenya leverages referral networks to provide basic and specialized healthcare services. However, referrals are characterized by non-adherence and delays in completion. An integrated health information technology (HIT) and peer-based support strategy to improve adherence to referrals and blood pressure control was proposed. A formative assessment gathered perspectives on barriers to referral completion and garnered thoughts on the proposed intervention. METHODS: We conducted a qualitative study in Kitale, Webuye, Kocholya, Turbo, Mosoriot and Burnt Forest areas of Western Kenya. We utilized the PRECEDE-PROCEED framework to understand the behavioral, environmental and ecological factors that would influence uptake and success of our intervention. We conducted four mabaraza (customary heterogenous community assemblies), eighteen key informant interviews, and twelve focus group discussions among clinicians, patients and community members. The data obtained was audio recorded alongside field note taking. Audio recordings were transcribed and translated for onward coding and thematic analysis using NVivo 12. RESULTS: Specific supply-side and demand-side barriers influenced completion of referral for hypertension. Key demand-side barriers included lack of money for care and inadequate referral knowledge. On the supply-side, long distance to health facilities, low availability of services, unaffordable services, and poor referral management were reported. All participants felt that the proposed strategies could improve delivery of care and expressed much enthusiasm for them. Participants appreciated benefits of the peer component, saying it would motivate positive patient behavior, and provide health education, psychosocial support, and assistance in navigating care. The HIT component was seen as reducing paper work, easing communication between providers, and facilitating tracking of patient information. Participants also shared concerns that could influence implementation of the two strategies including consent, confidentiality, and reduction in patient-provider interaction. CONCLUSIONS: Appreciation of local realities and patients' experiences is critical to development and implementation of sustainable strategies to improve effectiveness of hypertension referral networks. Incorporating concerns from patients, health care workers, and local leaders facilitates adaptation of interventions to respond to real needs. This approach is ethical and also allows research teams to harness benefits of participatory community-involved research. TRIAL REGISTRATION: Clinicaltrials.gov, NCT03543787, Registered June 1, 2018. https://clinicaltrials.gov/ct2/show/NCT03543787.

The splicing effect of variants at branchpoint elements in cancer genes.

PURPOSE: Branchpoint elements are required for intron removal, and variants at these elements can result in aberrant splicing. We aimed to assess the value of branchpoint annotations generated from recent large-scale studies to select branchpoint-abrogating variants, using hereditary cancer genes as model. METHODS: We identified branchpoint elements in 119 genes associated with hereditary cancer from 3 genome-wide experimentally-inferred and 2 predicted branchpoint data sets. We then identified variants that occur within branchpoint elements from public databases. We compared conservation, unique variant observations, and population frequencies at different nucleotides within branchpoint motifs. Finally, selected minigene assays were performed to assess the splicing effect of variants at branchpoint elements within mismatch repair genes. RESULTS: There was poor overlap between predicted and experimentally-inferred branchpoints. Our analysis of cancer genes suggested that variants at -2 nucleotide, -1 nucleotide, and branchpoint positions in experimentally-inferred canonical motifs are more likely to be clinically relevant. Minigene assay data showed the -2 nucleotide to be more important to branchpoint motif integrity but also showed fluidity in branchpoint usage. CONCLUSION: Data from cancer gene analysis suggest that there are few high-risk alleles that severely impact function via branchpoint abrogation. Results of this study inform a general scheme to prioritize branchpoint motif variants for further study.

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.

The idea that stem cell therapies work only via cell replacement is challenged by the observation of consistent intercellular molecule exchange between the graft and the host. Here we defined a mechanism of cellular signaling by which neural stem/precursor cells (NPCs) communicate with the microenvironment via extracellular vesicles (EVs), and we elucidated its molecular signature and function. We observed cytokine-regulated pathways that sort proteins and mRNAs into EVs. We described induction of interferon gamma (IFN-γ) pathway in NPCs exposed to proinflammatory cytokines that is mirrored in EVs. We showed that IFN-γ bound to EVs through Ifngr1 activates Stat1 in target cells. Finally, we demonstrated that endogenous Stat1 and Ifngr1 in target cells are indispensable to sustain the activation of Stat1 signaling by EV-associated IFN-γ/Ifngr1 complexes. Our study identifies a mechanism of cellular signaling regulated by EV-associated IFN-γ/Ifngr1 complexes, which grafted stem cells may use to communicate with the host immune system.

Network characteristics of a referral system for patients with hypertension in Western Kenya: results from the Strengthening Referral Networks for Management of Hypertension Across the Health System (STRENGTHS) study.

BACKGROUND: Health system approaches to improve hypertension control require an effective referral network. A national referral strategy exists in Kenya; however, a number of barriers to referral completion persist. This paper is a baseline assessment of a hypertension referral network for a cluster-randomized trial to improve hypertension control and reduce cardiovascular disease risk. METHODS: We used sociometric network analysis to understand the relationships between providers within a network of nine geographic clusters in western Kenya, including primary, secondary, and tertiary care facilities. We conducted a survey which asked providers to nominate individuals and facilities to which they refer patients with controlled and uncontrolled hypertension. Degree centrality measures were used to identify providers in prominent positions, while mixed-effect regression models were used to determine provider characteristics related to the likelihood of receiving referrals. We calculated core-periphery correlation scores (CP) for each cluster (ideal CP score = 1.0). RESULTS: We surveyed 152 providers (physicians, nurses, medical officers, and clinical officers), range 10-36 per cluster. Median number of hypertensive patients seen per month was 40 (range 1-600). While 97% of providers reported referring patients up to a more specialized health facility, only 55% reported referring down to lower level facilities. Individuals were more likely to receive a referral if they had higher level of training, worked at a higher level facility, were male, or had more job experience. CP scores for provider networks range from 0.335 to 0.693, while the CP scores for the facility networks range from 0.707 to 0.949. CONCLUSIONS: This analysis highlights several points of weakness in this referral network including cluster variability, poor provider linkages, and the lack of down referrals. Facility networks were stronger than provider networks. These shortcomings represent opportunities to focus interventions to improve referral networks for hypertension. TRIAL REGISTRATION: Trial Registered on ClinicalTrials.gov NCT03543787 , June 1, 2018.

Term Newborn Care Recommendations Provided in a Kenyan Postnatal Ward: A Rapid, Focused Ethnographic Assessment.

BACKGROUND: Neonatal mortality (death within 0-28 d of life) in Kenya is high despite strong evidence that newborn care recommendations save lives. In public healthcare facilities, nurses counsel caregivers on term newborn care, but knowledge about the content and quality of nurses' recommendations is limited. PURPOSE: To describe the term newborn care recommendations provided at a tertiary-level, public referral hospital in Western Kenya, how they were provided, and related content taught at a university nursing school. METHODS: A rapid, focused ethnographic assessment, guided by the culture care theory, using stratified purposive sampling yielded 240 hours of participant observation, 24 interviews, 34 relevant documents, and 268 pages of field notes. Data were organized using NVivo software and key findings identified using applied thematic analysis. RESULTS: Themes reflect recommendations for exclusive breastfeeding, warmth, cord care, follow-up examinations, and immunizations, which were provided orally in Kiswahili and some on a written English discharge summary. Select danger sign recommendations were also provided orally, if needed. Some recommendations conflicted with other providers' guidance. More recommendations for maternal care were provided than for newborn care. IMPLICATIONS FOR PRACTICE: There is need for improved consistency in content and provision of recommendations before discharge. Findings should be used to inform teaching, clinical, and administrative processes to address practice competency and improve nursing care quality. IMPLICATIONS FOR RESEARCH: Larger studies are needed to determine whether evidence-based recommendations are provided consistently across facilities and other populations, such as community-born and premature newborns, who also experience high rates of neonatal mortality in Kenya.

Green synthesis as a simple and rapid route to protein modified magnetic nanoparticles for use in the development of a fluorometric molecularly imprinted polymer-based assay for detection of myoglobin.

We have developed a low-cost molecularly imprinted polymer (MIP)-based fluorometric assay to directly quantify myoglobin in a biological sample. The assay uses a previously unreported method for the development of microwave-assisted rapid synthesis of aldehyde functionalized magnetic nanoparticles, in just 20 min. The aldehyde functionalized nanoparticles have an average size of 7.5 nm ± 1.8 and saturation magnetizations of 31.8 emu g-1 with near-closed magnetization loops, confirming their superparamagnetic properties. We have subsequently shown that protein tethering was possible to the aldehyde particles, with 0.25 ± 0.013 mg of myoglobin adsorbed to 20 mg of the nanomaterial. Myoglobin-specific fluorescently tagged MIP (F-MIP) particles were synthesized and used within the assay to capture myoglobin from a test sample. Excess F-MIP was removed from the sample using protein functionalized magnetic nanoparticles (Mb-SPION), with the remaining sample analyzed using fluorescence spectroscopy. The obtained calibration plot of myoglobin showed a linear correlation ranging from 60 pg ml-1 to 6 mg ml-1 with the limit of detection of 60 pg ml-1. This method was successfully used to detect myoglobin in spiked fetal calf serum, with a recovery rate of more than 93%.

Human-centered implementation research: a new approach to develop and evaluate implementation strategies for strengthening referral networks for hypertension in western Kenya.

BACKGROUND: Human-centered design (HCD) is an increasingly recognized approach for engaging stakeholders and developing contextually appropriate health interventions. As a component of the ongoing STRENGTHS study (Strengthening Referral Networks for Management of Hypertension Across the Health System), we report on the process and outcomes of utilizing HCD to develop the implementation strategy prior to a cluster-randomized controlled trial. METHODS: We organized a design team of 15 local stakeholders to participate in an HCD process to develop implementation strategies. We tested prototypes for acceptability, appropriateness, and feasibility through focus group discussions (FGDs) with various community stakeholder groups and a pilot study among patients with hypertension. FGD transcripts underwent content analysis, and pilot study data were analyzed for referral completion and reported barriers to referral. Based on this community feedback, the design team iteratively updated the implementation strategy. During each round of updates, the design team reflected on their experience through FGDs and a Likert-scale survey. RESULTS: The design team developed an implementation strategy consisting of a combined peer navigator and a health information technology (HIT) package. Overall, community participants felt that the strategy was acceptable, appropriate, and feasible. During the pilot study, 93% of referrals were completed. FGD participants felt that the implementation strategy facilitated referral completion through active peer engagement; enhanced communication between clinicians, patients, and health administrators; and integrated referral data into clinical records. Challenges included referral barriers that were not directly addressed by the strategy (e.g. transportation costs) and implementation of the HIT package across multiple health record systems. The design team reflected that all members contributed significantly to the design process, but emphasized the need for more transparency in how input from study investigators was incorporated into design team discussions. CONCLUSIONS: The adaptive process of co-creation, prototyping, community feedback, and iterative redesign aligned our implementation strategy with community stakeholder priorities. We propose a new framework of human-centered implementation research that promotes collaboration between community stakeholders, study investigators, and the design team to develop, implement, and evaluate HCD products for implementation research. Our experience provides a feasible and replicable approach for implementation research in other settings. TRIAL REGISTRATION: Clinicaltrials.gov, NCT02501746 , registration date: July 17, 2015.

Global health on the front lines: an innovative medical student elective combining education and service during the COVID-19 pandemic.

BACKGROUND: An innovative medical student elective combined student-directed, faculty-supported online learning with COVID-19 response field placements. This study evaluated students' experience in the course, the curriculum content and format, and its short-term impact on students' knowledge and attitudes around COVID-19. METHODS: Students responded to discussion board prompts throughout the course and submitted pre-/post-course reflections. Pre-/post-course questionnaires assessed pandemic knowledge and attitudes using 4-point Likert scales. Authors collected aggregate data on enrollment, discussion posts, field placements, and scholarly work resulting from course activities. After the elective, authors conducted a focus group with a convenience sample of 6 participants. Institutional elective evaluation data was included in analysis. Authors analyzed questionnaire data with summary statistics and paired t-tests comparing knowledge and attitudes before and after the elective. Reflection pieces, discussion posts, and focus group data were analyzed using content analysis with a phenomenological approach. RESULTS: Twenty-seven students enrolled. Each student posted an average of 2.4 original discussion posts and 3.1 responses. Mean knowledge score increased from 43.8 to 60.8% (p <  0.001) between pre- and post-course questionnaires. Knowledge self-assessment also increased (2.4 vs. 3.5 on Likert scale, p <  0.0001), and students reported increased engagement in the pandemic response (2.7 vs. 3.6, p <  0.0001). Students reported increased fluency in discussing the pandemic and increased appreciation for the field of public health. There was no difference in students' level of anxiety about the pandemic after course participation (3.0 vs. 3.1, p = 0.53). Twelve students (44.4%) completed the institutional evaluation. All rated the course "very good" or "excellent." Students favorably reviewed the field placements, suggested readings, self-directed research, and learning from peers. They suggested more clearly defined expectations and improved balance between volunteer and educational hours. CONCLUSIONS: The elective was well-received by students, achieved stated objectives, and garnered public attention. Course leadership should monitor students' time commitment closely in service-learning settings to ensure appropriate balance of service and education. Student engagement in a disaster response is insufficient to address anxiety related to the disaster; future course iterations should include a focus on self-care during times of crisis. This educational innovation could serve as a model for medical schools globally.

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome.

The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing. These features are consistent with their role as modular epigenetic regulators. We describe here the key studies and technological advances that have shaped our understanding of the dimensions, dynamics, and biological relevance of the mammalian noncoding transcriptome.

Innovative Implementation Strategies for Hypertension Control in Low- and Middle-Income Countries: a Narrative Review.

PURPOSE OF REVIEW: This review summarizes the most recent and innovative implementation strategies for hypertension control in low- and middle-income countries (LMICs). RECENT FINDINGS: Implementation strategies from Latin America, Africa, and Asia were organized across three levels: community, health system, and policy/population. Multicomponent interventions involving task-shifting strategies, with or without mobile health tools, had the most supporting evidence, with policy or population-level interventions having the least, focused only on salt reduction with mixed results. More research is needed to better understand how context affects intervention implementation. There is an emerging evidence base for implementation strategies for hypertension control and CVD risk reduction in LMICs at the community and health system levels, but further research is needed to determine the most effective policy and population-level strategies. How to best account for local context in adapting and implementing these evidence-based interventions in LMICs still remains largely unknown. Accelerating the translation of this implementation research into policy and practice is imperative to improve health and save lives globally.

Biocompatible superparamagnetic core-shell nanoparticles for potential use in hyperthermia-enabled drug release and as an enhanced contrast agent.

Superparamagnetic iron oxide nanoparticles (SPIONs) and core-shell type nanoparticles, consisting of SPIONs coated with mesoporous silica and/or lipid, were synthesised and tested for their potential theranostic applications in drug delivery, magnetic hyperthermia and as a contrast agent. Transmission Electron Microscopy (TEM) confirmed the size of bare and coated SPIONs was in the range of 5-20 nm and 100-200 nm respectively. The superparamagnetic nature of all the prepared nanomaterials as indicated by Vibrating Sample Magnetometry (VSM) and their heating properties under an AC field confirm their potential for hyperthermia applications. Scanning Column Magnetometry (SCM) data showed that extrusion of bare-SPION (b-SPION) dispersions through a 100 nm polycarbonate membrane significantly improved the dispersion stability of the sample. No sedimentation was apparent after 18 h compared to a pre-extrusion estimate of 43% settled at the bottom of the tube over the same time. Lipid coating also enhanced dispersion stability. Transversal relaxation time (T2) measurements for the nanoparticles, using a bench-top relaxometer, displayed a significantly lower value of 46 ms, with a narrow relaxation time distribution, for lipid silica coated SPIONs (Lip-SiSPIONs) as compared to that of 1316 ms for the b-SPIONs. Entrapment efficiency of the anticancer drug, Doxorubicin (DOX) for Lip-SPIONs was observed to be 35% which increased to 58% for Lip-SiSPIONs. Moreover, initial in-vitro cytotoxicity studies against human breast adenocarcinoma, MCF-7 cells showed that % cell viability increased from 57% for bSPIONs to 82% for Lip-SPIONs and to 87% for Lip-SiSPIONs. This suggests that silica and lipid coatings improve the biocompatibility of bSPIONs significantly and enhance the suitability of these particles as drug carriers. Hence, the magnetic nanomaterials prepared in this work have potential theranostic properties as a drug carrier for hyperthermia cancer therapy and also offer enhancement of contrast agent efficacy and a route to a significant increase in dispersion stability.

TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa.

BACKGROUND: The androgen-regulated gene TMPRSS2 to the ETS transcription factor gene ERG fusion is the most common genomic alteration acquired during prostate tumorigenesis and biased toward men of European ancestry. In contrast, African American men present with more advanced disease, yet their tumors are less likely to acquire TMPRSS2-ERG. Data for Africa is scarce. METHODS: RNA was made available for genomic analyses from 181 prostate tissue biopsy cores from Black South African men, 94 with and 87 without pathological evidence for prostate cancer. Reverse transcription polymerase chain reaction was used to screen for the TMPRSS2-ERG fusion, while transcript junction coordinates and isoform frequencies, including novel gene fusions, were determined using targeted RNA sequencing. RESULTS: Here we report a frequency of 13% for TMPRSS2-ERG in tumors from Black South Africans. Present in 12/94 positive versus 1/87 cancer negative prostate tissue cores, this suggests a 92.62% predictivity for a positive cancer diagnosis (P = 0.0031). At a frequency of almost half that reported for African Americans and roughly a quarter of that reported for men of European ancestry, acquisition of TMPRSS2-ERG appears to be inversely associated with aggressive prostate cancer. Further support was provided by linking the presence of TMPRSS2-ERG to low-grade disease in younger patients (P = 0.0466), with higher expressing distal ERG fusion junction coordinates. CONCLUSIONS: Only the second study of its kind for the African continent, we support a link between TMPRSS2-ERG status and prostate cancer racial health disparity beyond the borders of the United States. We call for urgent evaluation of androgen deprivation therapy within Africa.

Improved definition of the mouse transcriptome via targeted RNA sequencing.

Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.

Representing genetic variation with synthetic DNA standards.

The identification of genetic variation with next-generation sequencing is confounded by the complexity of the human genome sequence and by biases that arise during library preparation, sequencing and analysis. We have developed a set of synthetic DNA standards, termed 'sequins', that emulate human genetic features and constitute qualitative and quantitative spike-in controls for genome sequencing. Sequencing reads derived from sequins align exclusively to an artificial in silico reference chromosome, rather than the human reference genome, which allows them them to be partitioned for parallel analysis. Here we use this approach to represent common and clinically relevant genetic variation, ranging from single nucleotide variants to large structural rearrangements and copy-number variation. We validate the design and performance of sequin standards by comparison to examples in the NA12878 reference genome, and we demonstrate their utility during the detection and quantification of variants. We provide sequins as a standardized, quantitative resource against which human genetic variation can be measured and diagnostic performance assessed.