ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens.

High-throughput CRISPR-Cas9 knockout screens are widely used to evaluate gene essentiality in cancer research. Here we introduce a probabilistic modeling framework, Analysis of CRISPR-based Essentiality (ACE), that accounts for multiple sources of variation in CRISPR-Cas9 screens and enables new statistical tests for essentiality. We show using simulations that ACE is effective at predicting both absolute and differential essentiality. When applied to publicly available data, ACE identifies known and novel candidates for genotype-specific essentiality, including RNA m6-A methyltransferases that exhibit enhanced essentiality in the presence of inactivating TP53 mutations. ACE provides a robust framework for identifying genes responsive to subtype-specific therapeutic targeting.

Statistical Learning of Unfamiliar Sounds as Trajectories Through a Perceptual Similarity Space.

In typical statistical learning studies, researchers define sequences in terms of the probability of the next item in the sequence given the current item (or items), and they show that high probability sequences are treated as more familiar than low probability sequences. Existing accounts of these phenomena all assume that participants represent statistical regularities more or less as they are defined by the experimenters-as sequential probabilities of symbols in a string. Here we offer an alternative, or possibly supplementary, hypothesis. Specifically, rather than identifying or labeling individual stimuli discretely in order to predict the next item in a sequence, we need only assume that the participant is able to represent the stimuli as evincing particular similarity relations to one another, with sequences represented as trajectories through this similarity space. We present experiments in which this hypothesis makes sharply different predictions from hypotheses based on the assumption that sequences are learned over discrete, labeled stimuli. We also present a series of simulation models that encode stimuli as positions in a continuous two-dimensional space, and predict the next location from the current location. Although no model captures all of the data presented here, the results of three critical experiments are more consistent with the view that participants represent trajectories through similarity space rather than sequences of discrete labels under particular conditions.

Standard Fixed-Schedule Methadone Taper Versus Symptom-Triggered Methadone Approach for Treatment of Neonatal Opioid Withdrawal Syndrome.

OBJECTIVES: We compared hospitalization outcomes in infants with neonatal opioid withdrawal syndrome (NOWS) treated with a novel symptom-triggered methadone approach (STMA) versus a fixed-schedule methadone taper (FSMT). METHODS: This was a single-center quality-improvement study of infants pharmacologically treated for NOWS. Outcomes were compared over time by using statistical process control charts and between the baseline FSMT (July 2016-November 2017) and intervention STMA (December 2017-May 2018) groups, including median hospital length of stay (LOS), methadone treatment days, total milligrams of methadone, and need for adjunctive agents. RESULTS: There were 48 infants in the FSMT group and 28 in the STMA group. Infants treated with STMA had a median LOS of 10.5 days (interquartile range [IQR] 10.5) versus 17.0 days (IQR 3.9; P = .003) in the FSMT group, with a 9.2-day difference in methadone treatment days (2.5 [IQR 9.0] vs 11.7 [IQR 4.0]; P = .0001), meeting criteria for statistical process control special cause variation. The average number of symptom-triggered doses was 2.1 (SD 1.0). Six infants in the STMA group were converted to FSMT after failing a trial of STMA. Infants successfully treated with the STMA (N = 22) had a median LOS of 10.0 days (IQR 4.0) compared with 17.0 (IQR 3.9) in the baseline FSMT group (P < .0001). CONCLUSIONS: STMA was associated with a significant reduction in median LOS and amount of methadone treatment. A symptom-triggered approach to NOWS may reduce LOS and medication exposure.

Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.

DNA N6-adenine methylation (6mA) has recently been described in diverse eukaryotes, spanning unicellular organisms to metazoa. Here, we report a DNA 6mA methyltransferase complex in ciliates, termed MTA1c. It consists of two MT-A70 proteins and two homeobox-like DNA-binding proteins and specifically methylates dsDNA. Disruption of the catalytic subunit, MTA1, in the ciliate Oxytricha leads to genome-wide loss of 6mA and abolishment of the consensus ApT dimethylated motif. Mutants fail to complete the sexual cycle, which normally coincides with peak MTA1 expression. We investigate the impact of 6mA on nucleosome occupancy in vitro by reconstructing complete, full-length Oxytricha chromosomes harboring 6mA in native or ectopic positions. We show that 6mA directly disfavors nucleosomes in vitro in a local, quantitative manner, independent of DNA sequence. Furthermore, the chromatin remodeler ACF can overcome this effect. Our study identifies a diverged DNA N6-adenine methyltransferase and defines the role of 6mA in chromatin organization.

Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms.

BACKGROUND: Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even "third generation" sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly. RESULTS: We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall. CONCLUSIONS: This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.

The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged, although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available, with nearly 20,000 variants present, most of which were missed by short-read sequencing. Surrounding the important ERBB2 oncogene (also known as HER2), we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the genome and sheds new light on the complex mechanisms involved in cancer genome evolution.

Quality improvement initiative to improve inpatient outcomes for Neonatal Abstinence Syndrome.

OBJECTIVES: To improve Neonatal Abstinence Syndrome (NAS) inpatient outcomes through a comprehensive quality improvement (QI) program. DESIGN: Inclusion criteria were opioid-exposed infants ≥36 weeks. QI methodology including stakeholder interviews and plan-do-study-act (PDSA) cycles were utilized. We compared pre- and post-intervention NAS outcomes after a QI initiative that included: A non-pharmacologic care bundle, function-based assessments consisting of symptom prioritization and then the "Eat, Sleep, Console" (ESC) Tool; and a switch to methadone for pharmacologic treatment. RESULTS: Pharmacologic treatment decreased from 87.1 to 40.0%; adjunctive agent use from 33.6 to 2.4%; hospitalization length from a mean 17.4 to 11.3 days, and opioid treatment days from 16.2 to 12.7 (p < 0.001 for all). Total hospital charges decreased from $31,825 to $20,668 per infant. Parental presence increased from 55.6 to 75.8% (p < 0.0001). No adverse events were noted. CONCLUSIONS: A comprehensive QI program focused on non-pharmacologic care, function-based assessments, and methadone resulted in significant sustained improvements in NAS outcomes. These findings have important implications for establishing potentially better practices for opioid-exposed newborns.

Virologic and immunologic outcomes in HIV-infected Cambodian children after 18 months of highly active antiretroviral therapy (HAART).

This observational cohort study was conducted among HIV-infected, antiretroviral therapy (ART) naive children in Phnom Penh, Cambodia, to evaluate the feasibility and efficacy of highly active antiretroviral therapy (HAART) delivered using a modified directly observed therapy (MDOT) protocol. From August 2004 to March 2006, 26 children were enrolled and started on a first-line HAART regimen, which was continued for 18 months. The study included a directly observed therapy phase (months 1-3) and a medication self-administration phase (months 4-18). CD4 percentage (CD4%) and HIV-1 RNA plasma viral load (PVL) were measured at baseline and at months 6, 12, and 18. At baseline, the median age was 5.5 years (range: 13 months-12 years), the median CD4% was 4, and the median PVL was 7.5x10(5) copies/ml. At 18 months, 23 (88%) children were alive and participating in the study. Of these children, 20 (87%) had a PVL <400 copies/ml and 12 (52%) had PVL < 50 copies/ml. The median CD4% increased to 23, while the median change in height-for-weight z-score was 0.64. Genotypic resistance typing in 2 children with PVL > 400 copies/ml at 18 months demonstrated mutations associated with resistance to lamivudine (M184V) and non-nucleoside reverse transcriptase inhibitors (Y181C and G190A). The virologic and immunologic outcomes achieved in this study compare favorably with those reported by other pediatric HIV treatment programs worldwide. The study results suggest that MDOT may be effective for HAART administration in limited-resource settings like Cambodia.