Guidance for reporting SARS-CoV-2 sequencing results

Updated Apr. 9, 2021\u2022 CDC requests laboratories that are sequencing SARS-CoV-2 positive specimens to report those data to state, local, tribal, or territorial public health departments.\u2022 The technical guidance provides detailed instructions and examples for how to report SARS-CoV-2 sequencing results to state, local, tribal, or territorial public health departments.It is critically important for the nation\u2019s COVID-19 pandemic response to understand the genetic diversity, spread, and evolution of SARS-CoV-2, including variant viruses.Regulatory Position on Reporting Sequencing Results to Public Health Departments -- How to Report SARS-CoV-2 Sequencing Results to Public Health Departments -- Technical Guidance for Reporting Sequencing Results to Public Health Departments -- Reporting Scenarios.2021943

Guidance for reporting SARS-CoV-2 sequencing results

Regulatory Position on Reporting Sequencing Results to Public Health Departments -- How to Report SARS-CoV-2 Sequencing Results to Public Health Departments -- Technical Guidance for Reporting Sequencing Results to Public Health Departments -- Reporting Scenarios.20221110

Cancer Patient Experience of Uncertainty While Waiting for Genome Sequencing Results.

There is limited knowledge about cancer patients' experiences of uncertainty while waiting for genome sequencing results, and whether prolonged uncertainty contributes to psychological factors in this context. To investigate uncertainty in patients with a cancer of likely hereditary origin while waiting for genome sequencing results, we collected questionnaire and interview data at baseline, and at three and 12 months follow up (prior to receiving results). Participants (N = 353) had negative attitudes towards uncertainty (M = 4.03, SD 0.68) at baseline, and low levels of uncertainty at three (M = 8.23, SD 7.37) and 12 months (M = 7.95, SD 7.64). Uncertainty about genome sequencing did not change significantly over time [t(210) = 0.660, p = 0.510]. Greater perceived susceptibility for cancer [r(348) = 0.14, p < 0.01], fear of cancer recurrence [r(348) = 0.19, p < 0.01], perceived importance of genome sequencing [r(350) = 0.24, p < 0.01], intention to change behavior if a gene variant indicating risk is found [r(349) = 0.29, p < 0.01], perceived ability to cope with results [r(349) = 0.36, p < 0.01], and satisfaction with decision to have genome sequencing [r(350) = 0.52, p < 0.01] were significantly correlated with negative attitudes towards uncertainty at baseline. Multiple primary cancer diagnoses [B = -2.364 [-4.238, -0.491], p = 0.014], lower perceived ability to cope with results [B = -0.1.881 [-3.403, -0.359], p = 0.016] at baseline, greater anxiety about genome sequencing (avoidance) [B = 0.347 [0.148, 0.546], p = 0.0012] at 3 months, and greater perceived uncertainty about genome sequencing [B = 0.494 [0.267, 0.721] p = 0.000] at 3 months significantly predicted greater perceived uncertainty about genome sequencing at 12 months. Greater perceived uncertainty about genome sequencing at 3 months significantly predicted greater anxiety (avoidance) about genome sequencing at 12 months [B = 0.291 [0.072, 0.509], p = 0.009]. Semi-structured interviews revealed that while participants were motivated to pursue genome sequencing as a strategy to reduce their illness and risk uncertainty, genome sequencing generated additional practical, scientific and personal uncertainties. Some uncertainties were consistently discussed over the 12 months, while others emerged over time. Similarly, some uncertainty coping strategies were consistent over time, while others emerged while patients waited for their genome sequencing results. This study demonstrates the complexity of uncertainty generated by genome sequencing for cancer patients and provides further support for the inter-relationship between uncertainty and anxiety. Helping patients manage their uncertainty may ameliorate psychological morbidity

Primary care physicians’ understanding and utilization of pediatric exome sequencing results

Optimizing exome sequencing (ES) utility requires effective communication and collaboration between primary care physicians (PCPs) and genetics healthcare providers (GHP). To explore how PCPs use ES results to coordinate multipart management plans for complex pediatric patients, we assessed result understanding and utilization. Twenty‐seven PCPs of pediatric patients with ES results from a genetics clinic completed a mixed methods 45‐question survey measuring perceived genetics knowledge, confidence performing genetics tasks, understanding of ES technology and results, and expectations of GHP. Quantitative and qualitative data analysis classified by ES result types generated descriptive statistics, Pearson correlation coefficients, and common themes. Forty‐five‐percent of PCPs interpreted variant of uncertain significance results as diagnostic (implementing management changes and recommending familial testing). Most PCPs (85%) identified positive ES results impacts, but only 65% indicated ES was beneficial to care. The majority (74%) expected GHP and patients’ families to assume follow‐up care responsibility and future ES results re‐interpretations. Limited knowledge may be a factor, as 59% desired more patient care information from GHP. Our results suggest optimizing continuity of care and collaboration for pediatric patients with ES results requires additional communication between GHP and PCPs, along with continuing genetics education for PCPs aimed at improving genetic literacy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153256/1/jgc41163-sup-0001-DATAS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153256/2/jgc41163_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153256/3/jgc41163.pd

Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results

PepExplorer aids in the biological interpretation of de novo sequencing results; this is accomplished by assembling a list of homolog proteins obtained by aligning results from widely adopted de novo sequencing tools against a target‐decoy sequence database. Our tool relies on pattern recognition to ensure that the results satisfy a user‐given false‐discovery rate (FDR). For this, it employs a radial basis function neural network that considers the precursor charge states, de novo sequencing scores, the peptide lengths, and alignment scores. PepExplorer is recommended for studies addressing organisms with no genomic sequence available. PepExplorer is integrated into the PatternLab for proteomics environment, which makes available various tools for downstream data analysis, including the resources for quantitative and differential proteomics. © 2015 by John Wiley & Sons, Inc.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152617/1/cpbi1327.pd

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

peer-reviewedBackground Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data differed depending on the primers and sequencing platform that were used. The results demonstrate the risks in comparing data generated using different sequencing approaches and highlight the merits of choosing a standardised approach for sequencing in situations where a comparison across multiple sequencing runs is required.This publication has emanated from research supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Numbers SFI/12/RC/2273 and 11/PI/1137 and by FP7 funded CFMATTERS (Cystic Fibrosis Microbiome-determined Antibiotic Therapy Trial in Exacerbations: Results Stratified, Grant Agreement no. 603038)

Understanding the psychological impact of pediatric whole exome sequencing results on parents

The field of genetics and genomics is continuing to expand as technology becomes more accessible in a clinical setting. The use of whole exome sequencing (WES) has rapidly increased and many individuals now have diagnoses that would not have been made, or made as quickly, through traditional forms of genetic testing. WES has proven to produce a high diagnostic yield, and has led to the discovery of new pathogenic mutations, which can potentially identify novel genetic conditions. Although WES has ended the diagnostic odyssey for many individuals, little research has been conducted examining the psychosocial outcomes for individuals and their families undergoing WES. Much research has focused on the psychological outcomes of predictive genetic testing; however, diagnostic testing differs in many aspects. There are many factors that contribute to the psychological impact of WES, including uncertainty. Parents of children who underwent WES testing at Columbia University Medical Center were contacted for potential enrollment and participants were asked to complete a survey. It is important to understand how individuals and families undergoing WES respond to their test results and the uncertainty that may go along with it. This study aims to examine the degree of uncertainty experienced by parents of children undergoing WES, and thus the psychological impact of the test by examining a MICRA questionnaire. Analysis is pending. By understanding the psychological impact of WES, genetic counselors and other health professionals can adjust (or adapt) their pre-test counseling to help families have a positive experience with testing

Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system.

Precise genetic modifications in model animals are essential for biomedical research. Here, we report a programmable "base editing" system to induce precise base conversion with high efficiency in zebrafish. Using cytidine deaminase fused to Cas9 nickase, up to 28% of site-specific single-base mutations are achieved in multiple gene loci. In addition, an engineered Cas9-VQR variant with 5'-NGA PAM specificities is used to induce base conversion in zebrafish. This shows that Cas9 variants can be used to expand the utility of this technology. Collectively, the targeted base editing system represents a strategy for precise and effective genome editing in zebrafish.The use of base editing enables precise genetic modifications in model animals. Here the authors show high efficient single-base editing in zebrafish using modified Cas9 and its VQR variant with an altered PAM specificity