Identification of constrained sequence elements across 239 primate genomes.

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.

The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations.

Preventable deaths involving opioids in England and Wales, 2013-2022: a systematic case series of coroners' reports.

BACKGROUND: Opioid deaths have increased in England and Wales. Coroners' Prevention of Future Deaths reports (PFDs) provide important insights that may enable safer use and avert harms, yet reports implicating opioids have not been synthesized. We aimed to identify opioid-related PFDs and explore coroners' concerns to prevent future deaths. METHODS: In this systematic case series, we screened 3897 coronial PFDs dated between 01 July 2013 and 23 February 2022, obtained by web scraping the UK's Courts and Tribunals Judiciary website. PFDs were included when an opioid was implicated in the death. Included PFDs were descriptively analysed, and content analysis was used to assess concerns reported by coroners. RESULTS: Opioids were involved in 219 deaths reported in PFDs (5·6% of PFDs), equating to 4418 years of life lost (median 33 years/person). Morphine (29%), methadone (23%) and diamorphine (16%) were the most common implicated opioids. Coroners most frequently raised concerns regarding systems and protocols (52%) or safety issues (15%). These concerns were most often addressed to National Health Service (NHS) organizations (51%), but response rates were low overall (47%). CONCLUSIONS: Opioids could be used more safely if coroners' concerns in PFDs were addressed by national organizations such as NHS bodies, government agencies and policymakers, as well as individual prescribing clinicians.

Identifying and managing adverse drug reactions: Qualitative analysis of patient reports to the UK yellow card scheme.

INTRODUCTION: Adverse drug reactions (ADRs) can have significant negative impact on peoples' daily lives, with physical, economic, social and/or psychological effects. Patient reporting of ADRs has been facilitated by pharmacovigilance systems across Europe. However, capturing data on patients' experiences of ADRs has proved challenging. Existing patient reports to the UK Yellow Card Scheme contain free-text comments which could be useful sources of information. OBJECTIVES: To investigate patients' experiences of ADRs and their impact on patients as described in free-text data within patient Yellow Card (YC) reports submitted to the Medicines and Healthcare products Regulatory Agency. METHODS: A qualitative review of narrative texts was conducted on free-text data from 2255 patient YC reports from July to December 2015. RESULTS: Three key narrative themes emerged from analysis of the free-text data in 2255 reports: (1) identification of ADRs, (2) severity and impact of ADRs, and (3) management of ADRs. Temporal associations were the most common method of identification followed by differential diagnoses and confirmation with information sources such as healthcare professionals (HCPs). A combination of explicit and implicit impacts were described: physical, psychological, economic and social effects often persisted and caused serious disruption to many patients' lives. A range of strategies were used to manage ADRs, including consultation with HCPs, stopping/reducing the medicine or taking medicines to alleviate symptoms. CONCLUSION: Free-text data from YC reports has been an underutilised resource to date, but this research has confirmed its potential value to pharmacovigilance and medication safety research.

Identification of different side effects between PARP inhibitors and their polypharmacological multi-target rationale.

AIMS: The aim of this study was to determine the differences and potential mechanistic rationale for observed adverse drug reactions (ADRs) between four approved PARP inhibitors (PARPi). METHODS: The Medicines and Healthcare products Regulatory Authority (MHRA) Yellow Card drug analysis profiles and NHS secondary care medicines database enabled the identification of suspected ADRs associated with the PARPi in the UK from launch to 2020. The polypharmacology of the PARPi were data-mined from several public data sources. RESULTS: The overall ADRs per 100 000 Rx identified across the four PARPi are statistically significant (χ2 test, P < .001). Rucaparib has the greatest relative suspected ADRs, which can be explained by its least clean kinome and physicochemical properties. The suspected gastrointestinal ADRs of rucaparib and niraparib can be ascribed to their kinase polypharmacology. Suspected blood and lymphatic system ADRs of PARPi can be linked to their high volume of distribution (Vd ). The thrombocytopenia rate of niraparib > rucaparib > olaparib tracked with the Vd trend. Hypertension is only associated with niraparib and could be explained by the therapeutically achievable inhibition of DYRK1A and/or transporters. Arrhythmia cases are potentially linked to the structural features of hERG ion-channel inhibition found in rucaparib and niraparib. Enhanced psychiatric/nervous disorders associated with niraparib can be interpreted from the diverse neurotransporter off-targets reported. CONCLUSIONS: Despite their similar mode of action, the differential polypharmacology of PARP inhibitors influences their ADR profile.

Risk Analysis: Celebrating the Accomplishments and Embracing Ongoing Challenges.

As part of the celebration of the 40th anniversary of the Society for Risk Analysis and Risk Analysis: An International Journal, this essay reviews the 10 most important accomplishments of risk analysis from 1980 to 2010, outlines major accomplishments in three major categories from 2011 to 2019, discusses how editors circulate authors' accomplishments, and proposes 10 major risk-related challenges for 2020-2030. Authors conclude that the next decade will severely test the field of risk analysis.

Perioperative Cerebral Microbleeds After Adult Cardiac Surgery.

Background and Purpose- Cerebral microbleeds (CMBs) have been observed using magnetic resonance imaging in patients with cardiovascular risk factors, cognitive deterioration, small vessel disease, and dementia. They are a well-known consequence of cerebral amyloid angiopathy, chronic hypertension, and diffuse axonal injury, among other causes. However, the frequency and location of new CMBs postadult cardiac surgery, in association with cognition and perioperative risk factors, have yet to be studied. Methods- Pre- and postsurgery magnetic resonance susceptibility-weighted images and neuropsychological tests were analyzed from a total of 75 patients undergoing cardiac surgery (70 men; mean age, 63±10 years). CMBs were identified by a neuroradiologist blinded to clinical details who independently assessed the presence and location of CMBs using standardized criteria. Results- New CMBs were identified in 76% of patients after cardiac surgery. The majority of new CMBs were located in the frontal lobe (46%) followed by the parietal lobe (15%), cerebellum (13%), occipital lobe (12%), and temporal lobe (8%). Patients with new CMBs typically began with a higher prevalence of preexisting CMBs ( P=0.02). New CMBs were associated with longer cardiopulmonary bypass times ( P=0.003), and there was a borderline association with lower percentage hematocrit ( P=0.04). Logistic regression analysis suggested a ≈2% increase in the odds of acquiring new CMBs during cardiac surgery for every minute of bypass time (odds ratio, 1.02; 95% CI, 1.00-1.05; P=0.04). Postoperative neuropsychological decline was observed in 44% of patients and seemed to be unrelated to new CMBs. Conclusions- New CMBs identified using susceptibility-weighted images were found in 76% of patients who underwent cardiac surgery. CMBs were globally distributed with the highest numbers in the frontal and parietal lobes. Our regression analysis indicated that length of cardiopulmonary bypass time and lowered hematocrit may be significant predictors for new CMBs after cardiac surgery. Clinical Trial Registration- URL: http://www.isrctn.com . Unique identifier: 66022965.

Canvas SPW: calling de novo copy number variants in pedigrees.

Motivation: Whole genome sequencing is becoming a diagnostics of choice for the identification of rare inherited and de novo copy number variants in families with various pediatric and late-onset genetic diseases. However, joint variant calling in pedigrees is hampered by the complexity of consensus breakpoint alignment across samples within an arbitrary pedigree structure. Results: We have developed a new tool, Canvas SPW, for the identification of inherited and de novo copy number variants from pedigree sequencing data. Canvas SPW supports a number of family structures and provides a wide range of scoring and filtering options to automate and streamline identification of de novo variants. Availability and implementation: Canvas SPW is available for download from https://github.com/Illumina/canvas. Contact: sivakhno@illumina.com. Supplementary information: Supplementary data are available at Bioinformatics online.

The effects of message framing and healthcare provider recommendation on adult hepatitis B vaccination: A randomized controlled trial.

Many adults in the U.S. do not receive recommended vaccines, and the research literature remains inconclusive on the best communication strategies for increasing this behavior. This study examined the association of message framing (gained-framed vs. loss-framed vs. control), and healthcare provider (HCP) recommendation (offered vs. recommended) on uptake of adult hepatitis B virus (HBV) vaccination in a high risk population using a 3 × 2 block design randomized controlled trial. Fear of shots, fear of vaccines, and perceived message framing were examined in secondary analyses. Of the 1747 participants, 47.7% (n = 833) received 0 doses of HBV vaccine, 27.8% (n = 485) received 1 dose, 10.4% received 2 doses, and 14.1% received all 3 recommended doses. There was not a significant interaction between message framing and HCP recommendation (p = .59). Mean number of doses received by the gain-framed group (m = 0.96) was not significantly different from the loss-framed group (m = 0.97, RR = 0.99, 95% CI = 0.88-1.12). However, those receiving any framing message received significantly more doses (m = 0.96) than those in the control condition (m = 0.81, RR = 1.17, 95%CI = 1.06-1.31). Participants who received a HCP recommendation received significantly more vaccine doses (m = 0.95) than those in the vaccine-offered condition (mean = 0.82, RR = 1.16, 95%CI = 1.05-1.28). These results suggest there is no difference in vaccine uptake between gain-frame and loss-frame messages, but both are better than a control message. These results also support advising HCP to provide a strong recommendation for vaccinations beyond merely offering it to patients. This study has implications for vaccine uptake beyond HBV, and can inform future research on effective vaccine communication research. Clinicaltrials.gov Identifier: NCT00739752. Registration date: August 20, 2008.

Development and preliminary validation of an instrument to enable laypersons to assess suspected side effects from medicines.

PURPOSE: Research into causality assessment tools enabling patients to assess suspected adverse drug reactions (ADRs) is limited. Supporting patients with tools could improve their confidence in discussions with health professionals and encourage reporting of suspected ADRs to regulators. This study describes development and preliminary validation of an instrument: Side Effect Patient ASsessment Tool (SE-PAST). METHODS: SE-PAST was developed from survey and interview data involving patients experiencing suspected ADRs. It included 10 statements enabling causality assessment, covering timing, additional information sources, and experiences, with four options: yes/no/don't know/not applicable. Scoring and weighting resulted in four categories of causal association: highly probable, probable, possible, unlikely. Validation involved obtaining feedback from 31 individuals experiencing an ADR. Further validation involved online distribution through patient support groups and comparison of reported symptoms to known ADRs. RESULTS: Validators found SE-PAST easy to read (31), to understand (27), and to complete (29). A total of 294 respondents completed SE-PAST online, with 98% completing eight or more causality assessment statements. Symptoms were categorised as highly probable (46; 16%), probable (80; 62%), possible (44; 15%), and unlikely (21; 7%). A total of 221 respondents identified one suspected medicine, with 95% of these reporting at least one symptom known to be an ADR. Of 227 providing feedback, 139 (61%) found SE-PAST useful, 160 (71%) felt motivated to discuss their experience with a health professional, and 136 (60%) were encouraged to report to the regulator. CONCLUSION: SE-PAST was easily completed and understood by people experiencing suspected ADRs and could be useful in encouraging patient reporting to health professionals and agencies.

AKT: ancestry and kinship toolkit.

MOTIVATION: Ancestry and Kinship Toolkit (AKT) is a statistical genetics tool for analysing large cohorts of whole-genome sequenced samples. It can rapidly detect related samples, characterize sample ancestry, calculate correlation between variants, check Mendel consistency and perform data clustering. AKT brings together the functionality of many state-of-the-art methods, with a focus on speed and a unified interface. We believe it will be an invaluable tool for the curation of large WGS datasets. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://illumina.github.io/akt CONTACTS: joconnell@illumina.com or rudy.d.arthur@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.

tHapMix: simulating tumour samples through haplotype mixtures.

MOTIVATION: Large-scale rearrangements and copy number changes combined with different modes of clonal evolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable variant calling tools and create well-calibrated benchmarks. RESULTS: We developed a new simulation framework tHapMix that enables the creation of tumour samples with different ploidy, purity and polyclonality features. It easily scales to simulation of hundreds of somatic genomes, while re-use of real read data preserves noise and biases present in sequencing platforms. We further demonstrate tHapMix utility by creating a simulated set of 140 somatic genomes and showing how it can be used in training and testing of somatic copy number variant calling tools. AVAILABILITY AND IMPLEMENTATION: tHapMix is distributed under an open source license and can be downloaded from https://github.com/Illumina/tHapMix CONTACT: sivakhno@illumina.comSupplementary information: Supplementary data are available at Bioinformatics online.

Behavior and health beliefs as predictors of HIV testing among women: a prospective study of observed HIV testing.

Much of the research examining predictors of HIV testing has used retrospective self-report to assess HIV testing. FINDINGS: therefore, may be subject to recall bias and to difficulties determining the direction of associations. In this prospective study, we administered surveys to women in community clinics to identify predictors of subsequent observed HIV testing, overcoming these limitations. Eighty-three percent were tested. In the adjusted multivariable model, being born in the U.S., perceived benefits of testing, worries about being infected with HIV, having had more than 15 lifetime sexual partners, and having had one or more casual sexual partners in the previous three months predicted acceptance of testing. Perceived obstacles to testing predicted non-acceptance. Those who had never been tested for HIV and those tested two to five years previously had greater odds of test acceptance than those who had been tested within the last year. The findings from this study with observed testing as the outcome, confirm some of the results from retrospective, self-report studies. Participants made largely rational decisions about testing, reflecting assessments of their risk and their history of HIV testing. Health beliefs are potentially modifiable through behavioral intervention, and such interventions might result in greater acceptance of testing. ABBREVIATIONS: HIV: human immunodeficiency virus; AIDS: acquired immune deficiency syndrome; CDC: Centers for Disease Control and Prevention; ACASI: audio computer-assisted self-interview; TRA: theory of reasoned action; HBM: Health Belief Model; STI: sexually transmitted infection; STD: Sexually Transmitted Disease; AOR: adjusted odds ratio; CI: confidence interval.

Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions.

MOTIVATION: Whole-genome low-coverage sequencing has been combined with linkage-disequilibrium (LD)-based genotype refinement to accurately and cost-effectively infer genotypes in large cohorts of individuals. Most genotype refinement methods are based on hidden Markov models, which are accurate but computationally expensive. We introduce an algorithm that models LD using a simple multivariate Gaussian distribution. The key feature of our algorithm is its speed. RESULTS: Our method is hundreds of times faster than other methods on the same data set and its scaling behaviour is linear in the number of samples. We demonstrate the performance of the method on both low- and high-coverage samples. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/illumina/marvin CONTACT: rarthur@illumina.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

UNLABELLED: : We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios. AVAILABILITY AND IMPLEMENTATION: Manta is released under the open-source GPLv3 license. Source code, documentation and Linux binaries are available from https://github.com/Illumina/manta. CONTACT: csaunders@illumina.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Haplotype estimation using sequencing reads.

High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called. One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases. Our method can also use existing panels of reference haplotypes. We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP). We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb. We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate. When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results. When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved.

NxTrim: optimized trimming of Illumina mate pair reads.

MOTIVATION: Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved. The Illumina Nextera Mate Pair (NMP) protocol uses a circularization-based strategy that leaves behind 38-bp adapter sequences, which must be computationally removed from the data. While 'adapter trimming' is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary. RESULTS: We present NxTrim, a tool that strives to discard as little sequence as possible from NMP reads. NxTrim makes full use of the sequence on both sides of the adapter site to build 'virtual libraries' of mate pairs, paired-end reads and single-ended reads. For bacterial data, we show that aggregating these datasets allows a single NMP library to yield an assembly whose quality compares favourably to that obtained from regular paired-end reads. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/sequencing/NxTrim

A comprehensive catalogue of somatic mutations from a human cancer genome.

All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.

Genome variation and evolution of the malaria parasite Plasmodium falciparum.

Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and genetic variation of P. falciparum is critical for understanding the evolution of drug resistance, identifying potential vaccine candidates and appreciating the effect of parasite variation on prevalence and severity of malaria in humans. Most studies of natural variation in P. falciparum have been either in depth over small genomic regions (up to the size of a small chromosome) or genome wide but only at low resolution. In an effort to complement these studies with genome-wide data, we undertook shotgun sequencing of a Ghanaian clinical isolate (with fivefold coverage), the IT laboratory isolate (with onefold coverage) and the chimpanzee parasite P. reichenowi (with twofold coverage). We compared these sequences with the fully sequenced P. falciparum 3D7 isolate genome. We describe the most salient features of P. falciparum polymorphism and adaptive evolution with relation to gene function, transcript and protein expression and cellular localization. This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum.

Adaptive reference-free compression of sequence quality scores.

MOTIVATION: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and, hence, are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full resolution. As our approach relies directly on redundancy present in the reads, it does not need a reference sequence and is, therefore, applicable to data from metagenomics and de novo experiments as well as to re-sequencing data. RESULTS: We show that a conservative smoothing strategy affecting 75% of the quality scores above Q2 leads to an overall quality score compression of 1 bit per value with a negligible effect on variant calling. A compression of 0.68 bit per quality value is achieved using a more aggressive smoothing strategy, again with a very small effect on variant calling. AVAILABILITY: Code to construct the BWT and LCP-array on large genomic data sets is part of the BEETL library, available as a github repository at git@github.com:BEETL/BEETL.git.