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.

The life history of 21 breast cancers.

Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We developed algorithms to decipher this narrative and applied them to 21 breast cancers. Mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. Every tumor has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.

Mutational processes molding the genomes of 21 breast cancers.

All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis," was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed.

Massive genomic rearrangement acquired in a single catastrophic event during cancer development.

Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. Using next-generation sequencing, we characterize a phenomenon, which we term chromothripsis, whereby tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. Rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. These genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe. The stamp of chromothripsis can be seen in at least 2%-3% of all cancers, across many subtypes, and is present in ∼25% of bone cancers. We find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. This phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer.

The Cancer Research UK Stratified Medicine Programme as a model for delivering personalised cancer care.

Genomic screening is routinely used to guide the treatment of cancer patients in many countries. However, several multi-layered factors make this effort difficult to deliver within a clinically relevant timeframe. Here we share the learnings from the CRUK-funded Stratified Medicine Programme for advanced NSCLC patients, which could be useful to better plan future studies.

Outbreaks of Adenovirus-associated Respiratory Illness on 5 College Campuses in the United States, 2018-2019.

BACKGROUND: Human adenoviruses (HAdVs) are commonly associated with acute respiratory illness. HAdV outbreaks are well documented in congregate military training settings, but less is known about outbreaks on college campuses. During fall 2018 and spring 2019, 5 United States (US) colleges reported increases in HAdV-associated respiratory illness. Investigations were performed to better understand HAdV epidemiology in this setting. METHODS: A case was defined as a student at one of the 5 colleges, with acute respiratory illness and laboratory-confirmed HAdV infection during October 2018-December 2018 or March-May 2019. Available respiratory specimens were typed by HAdV type-specific real-time polymerase chain reaction assays, and for a subset, whole genome sequencing was performed. We reviewed available medical records and cases were invited to complete a questionnaire, which included questions on symptom presentation, social history, and absenteeism. RESULTS: We identified 168 HAdV cases. Median age was 19 (range, 17-22) years and 102 cases (61%) were male. Eleven cases were hospitalized, 10 with pneumonia; 2 cases died. Among questionnaire respondents, 80% (75/94) missed ≥ 1 day of class because of their illness. Among those with a type identified (79%), HAdV types 4 and 7 were equally detected, with frequency of each varying by site. Genome types 4a1 and 7d were identified, respectively, by whole genome sequence analysis. CONCLUSIONS: HAdV respiratory illness was associated with substantial morbidity and missed class time among young, generally healthy adults on 5 US college campuses. HAdVs should be considered a cause of respiratory illness outbreaks in congregate settings such as college campuses.

Infrared Thermography for Measuring Elevated Body Temperature: Clinical Accuracy, Calibration, and Evaluation.

Infrared thermographs (IRTs) implemented according to standardized best practices have shown strong potential for detecting elevated body temperatures (EBT), which may be useful in clinical settings and during infectious disease epidemics. However, optimal IRT calibration methods have not been established and the clinical performance of these devices relative to the more common non-contact infrared thermometers (NCITs) remains unclear. In addition to confirming the findings of our preliminary analysis of clinical study results, the primary intent of this study was to compare methods for IRT calibration and identify best practices for assessing the performance of IRTs intended to detect EBT. A key secondary aim was to compare IRT clinical accuracy to that of NCITs. We performed a clinical thermographic imaging study of more than 1000 subjects, acquiring temperature data from several facial locations that, along with reference oral temperatures, were used to calibrate two IRT systems based on seven different regression methods. Oral temperatures imputed from facial data were used to evaluate IRT clinical accuracy based on metrics such as clinical bias (Δcb), repeatability, root-mean-square difference, and sensitivity/specificity. We proposed several calibration approaches designed to account for the non-uniform data density across the temperature range and a constant offset approach tended to show better ability to detect EBT. As in our prior study, inner canthi or full-face maximum temperatures provided the highest clinical accuracy. With an optimal calibration approach, these methods achieved a Δcb between ±0.03 °C with standard deviation (σΔcb) less than 0.3 °C, and sensitivity/specificity between 84% and 94%. Results of forehead-center measurements with NCITs or IRTs indicated reduced performance. An analysis of the complete clinical data set confirms the essential findings of our preliminary evaluation, with minor differences. Our findings provide novel insights into methods and metrics for the clinical accuracy assessment of IRTs. Furthermore, our results indicate that calibration approaches providing the highest clinical accuracy in the 37-38.5 °C range may be most effective for measuring EBT. While device performance depends on many factors, IRTs can provide superior performance to NCITs.

The Epidemiology of Noise Sensitivity in New Zealand.

BACKGROUND: Sensitivity to noise, or nuisance sounds that interrupt relaxation and task-related activities, has been shown to vary significantly across individuals. The current study sought to uncover predictors of noise sensitivity, focussing on possible social and cultural determinants, including social position, education, ethnicity, gender, and the presence of an illness. METHOD: Data were collected from 746 New Zealand adults residing in 6 areas differentiated by social position. Participants responded to questions probing personal characteristics, noise sensitivity, illness, neighbourhood problems, and noise annoyance. It was hypothesized that those in high-deprivation areas and/or experiencing illness report higher levels of noise sensitivity. RESULTS: Approximately 50 and 10% of the participants reported being moderately or very noise sensitive, respectively. Significant predictors of noise sensitivity included age, length of residence, level of social deprivation, and self-reported illness. CONCLUSION: There is evidence of social determinants of noise sensitivity, including social position and residential factors.

Factors in Accessing Routine Health Care: Mental Health and Postpartum Mothers.

OBJECTIVES: One strategy proposed to decrease the maternal mortality and morbidity in the United States is to increase the rate which new mothers access routine postpartum care. Using Missouri's Pregnancy Risk Assessment Monitoring System (MO PRAMS) data, this retrospective study analyzed whether a self-reported history of depressive symptoms during the postpartum period was associated with a decreased rate of accessing the postpartum care visit (PPCV). METHODS: Data were collected on 7,357 new mothers who completed the Missouri PRAMS survey between 2009-2014. New mothers, in the Missouri's registry of birth certificates who have given birth in the last 2-4 months, were randomly selected for inclusion in the survey. A mixed-mode survey method with a prescribed protocol for data collection was utilized. RESULTS: Fourteen percent of the respondents (1,093 new mothers) reported symptoms associated with postpartum depression. A logistic regression analysis showed that among these women a weak association was found between not accessing routine PPCV and the report of depressive symptoms (p=.0254; OR=1.344 with 95%CI=1.037-1.741). This association is a new finding. CONCLUSIONS: The study finds a weakly negative association between self-reported symptoms of postpartum depression and accessing routine postpartum care. As this is a new finding, further research is needed for verification of this association.

The landscape of cancer genes and mutational processes in breast cancer.

All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.

Health-related quality of life is impacted by proximity to an airport in noise-sensitive people.

INTRODUCTION: The aim of the study was to determine whether those who are noise sensitive are more adversely affected by airport noise than those who are not noise sensitive. PARTICIPANTS AND METHODS: One area was very close to Wellington International Airport and the other was distant from the airport and any other major sources of noise such as motorways and railways. Noise sensitivity was self-rated on a three-point scale as follows: non-noise sensitive, moderately noise sensitive, or highly noise sensitive. Statistical analysis consisted of analyses of variance using the domains of the WHOQOL score with the year, area (airport or the control), and noise sensitivity as covariates. RESULTS: Noise-sensitive people were found to have a significantly poorer HRQOL than others when they lived near an airport, but not when they lived in the control area. The same effect was present at both of the time points investigated, suggesting that it is a general finding. DISCUSSION: This finding is consistent with similar studies using the WHOQOL-BREF for investigating noise from road traffic, suggesting consistency in effect across transport noise sources.

The patterns and dynamics of genomic instability in metastatic pancreatic cancer.

Pancreatic cancer is an aggressive malignancy with a five-year mortality of 97-98%, usually due to widespread metastatic disease. Previous studies indicate that this disease has a complex genomic landscape, with frequent copy number changes and point mutations, but genomic rearrangements have not been characterized in detail. Despite the clinical importance of metastasis, there remain fundamental questions about the clonal structures of metastatic tumours, including phylogenetic relationships among metastases, the scale of ongoing parallel evolution in metastatic and primary sites, and how the tumour disseminates. Here we harness advances in DNA sequencing to annotate genomic rearrangements in 13 patients with pancreatic cancer and explore clonal relationships among metastases. We find that pancreatic cancer acquires rearrangements indicative of telomere dysfunction and abnormal cell-cycle control, namely dysregulated G1-to-S-phase transition with intact G2-M checkpoint. These initiate amplification of cancer genes and occur predominantly in early cancer development rather than the later stages of the disease. Genomic instability frequently persists after cancer dissemination, resulting in ongoing, parallel and even convergent evolution among different metastases. We find evidence that there is genetic heterogeneity among metastasis-initiating cells, that seeding metastasis may require driver mutations beyond those required for primary tumours, and that phylogenetic trees across metastases show organ-specific branches. These data attest to the richness of genetic variation in cancer, brought about by the tandem forces of genomic instability and evolutionary selection.

A small-cell lung cancer genome with complex signatures of tobacco exposure.

Cancer is driven by mutation. Worldwide, tobacco smoking is the principal lifestyle exposure that causes cancer, exerting carcinogenicity through >60 chemicals that bind and mutate DNA. Using massively parallel sequencing technology, we sequenced a small-cell lung cancer cell line, NCI-H209, to explore the mutational burden associated with tobacco smoking. A total of 22,910 somatic substitutions were identified, including 134 in coding exons. Multiple mutation signatures testify to the cocktail of carcinogens in tobacco smoke and their proclivities for particular bases and surrounding sequence context. Effects of transcription-coupled repair and a second, more general, expression-linked repair pathway were evident. We identified a tandem duplication that duplicates exons 3-8 of CHD7 in frame, and another two lines carrying PVT1-CHD7 fusion genes, indicating that CHD7 may be recurrently rearranged in this disease. These findings illustrate the potential for next-generation sequencing to provide unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with cancer.

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes.

Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.

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.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

Multiple somatic rearrangements are often found in cancer genomes; however, the underlying processes of rearrangement and their contribution to cancer development are poorly characterized. Here we use a paired-end sequencing strategy to identify somatic rearrangements in breast cancer genomes. There are more rearrangements in some breast cancers than previously appreciated. Rearrangements are more frequent over gene footprints and most are intrachromosomal. Multiple rearrangement architectures are present, but tandem duplications are particularly common in some cancers, perhaps reflecting a specific defect in DNA maintenance. Short overlapping sequences at most rearrangement junctions indicate that these have been mediated by non-homologous end-joining DNA repair, although varying sequence patterns indicate that multiple processes of this type are operative. Several expressed in-frame fusion genes were identified but none was recurrent. The study provides a new perspective on cancer genomes, highlighting the diversity of somatic rearrangements and their potential contribution to cancer development.

Single-cell paired-end genome sequencing reveals structural variation per cell cycle.

The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis.

Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns.

Chronic lymphocytic leukemia is characterized by relapse after treatment and chemotherapy resistance. Similarly, in other malignancies leukemia cells accumulate mutations during growth, forming heterogeneous cell populations that are subject to Darwinian selection and may respond differentially to treatment. There is therefore a clinical need to monitor changes in the subclonal composition of cancers during disease progression. Here, we use whole-genome sequencing to track subclonal heterogeneity in 3 chronic lymphocytic leukemia patients subjected to repeated cycles of therapy. We reveal different somatic mutation profiles in each patient and use these to establish probable hierarchical patterns of subclonal evolution, to identify subclones that decline or expand over time, and to detect founder mutations. We show that clonal evolution patterns are heterogeneous in individual patients. We conclude that genome sequencing is a powerful and sensitive approach to monitor disease progression repeatedly at the molecular level. If applied to future clinical trials, this approach might eventually influence treatment strategies as a tool to individualize and direct cancer treatment.

The effect of the Missouri WISEWOMAN program on control of hypertension, hypercholesterolemia, and elevated blood glucose among low-income women.

INTRODUCTION: The Well-Integrated Screening and Evaluation for Women Across the Nation (WISEWOMAN) public health program is designed to reduce the risk of heart disease and stroke among low-income, underinsured or uninsured women through clinical screenings, risk factor assessment, and lifestyle interventions. We assessed the effect of the Missouri WISEWOMAN program on the control of high blood pressure, total cholesterol, and blood glucose levels. METHODS: We calculated the proportion of participants (N = 1,130) with abnormal blood pressure, total cholesterol, or blood glucose levels at an initial screening visit who gained control at a follow-up visit 11 to 18 months later during a 7-year period from June 30, 2005, to June 29, 2012. We used logistic regression to identify sociodemographic characteristics and other factors associated with achieving control. RESULTS: Many WISEWOMAN participants gained control of their blood pressure (41.2%), total cholesterol (24.7%), or blood glucose levels (50.0%). After controlling for sociodemographic factors, smoking status, weight status, medication use, and number of lifestyle interventions, nondiabetic women with stage II hypertension (adjusted odds ratio [AOR] = 0.36, 95% confidence interval [CI] = 0.21-0.60) and diabetic women with stage I (AOR = 0.54, 95% CI = 0.32-0.92) and stage II (AOR = 0.23, 95% CI = 0.07-0.77) hypertension were less likely to achieve control of their blood pressure than nondiabetic women with stage I hypertension. Women aged 45 to 64, women with less than a high school education, women who were obese in the initial visit, women who gained 7% or more of their weight, and women who did not participate in any lifestyle intervention sessions were significantly less likely to achieve total cholesterol control than their counterparts. CONCLUSION: The Missouri WISEWOMAN program helps many participants achieve control of blood pressure, total cholesterol, and blood glucose levels; the lifestyle intervention is likely to help participants control total cholesterol. More efforts are needed for women with diabetes and stage II hypertension to achieve blood pressure control.