Citations

We developed a generally applicable method, CRISPR/Cas9-targeted long-read sequencing (CTLR-Seq), to resolve, haplotype-specifically, the large and complex regions in the human genome that had been previously impenetrable to sequencing analysis, such as large segmental duplications (SegDups) and their associated genome rearrangements. CTLR-Seq combines in vitro Cas9-mediated cutting of the genome and pulse-field gel electrophoresis to isolate intact large (i.e., up to 2,000 kb) genomic regions that encompass previously unresolvable genomic sequences. These targets are then sequenced (amplification-free) at high on-target coverage using long-read sequencing, allowing for their complete sequence assembly. We applied CTLR-Seq to the SegDup-mediated rearrangements that constitute the boundaries of, and give rise to, the 22q11.2 Deletion Syndrome (22q11DS), the most common human microdeletion disorder. We then performed de novo assembly to resolve, at base-pair resolution, the full sequence rearrangements and exact chromosomal breakpoints of 22q11.2DS (including all common subtypes). Across multiple patients, we found a high degree of variability for both the rearranged SegDup sequences and the exact chromosomal breakpoint locations, which coincide with various transposons within the 22q11.2 SegDups, suggesting that 22q11DS can be driven by transposon-mediated genome recombination. Guided by CTLR-Seq results from two 22q11DS patients, we performed three-dimensional chromosomal folding analysis for the 22q11.2 SegDups from patient-derived neurons and astrocytes and found chromosome interactions anchored within the SegDups to be both cell type-specific and patient-specific. Lastly, we demonstrated that CTLR-Seq enables cell-type specific analysis of DNA methylation patterns within the deletion haplotype of 22q11DS.

Mixed invasive ductal and lobular carcinoma (MDLC) is a rare histologic subtype of breast cancer displaying both E-cadherin positive ductal and E-cadherin negative lobular morphologies within the same tumor, posing challenges with regard to anticipated clinical management. It remains unclear whether these distinct morphologies also have distinct biology and risk of recurrence. Our spatially resolved transcriptomic, genomic, and single-cell profiling revealed clinically significant differences between ductal and lobular tumor regions including distinct intrinsic subtype heterogeneity – e.g., MDLC with triple-negative breast cancer (TNBC) or basal ductal and estrogen receptor positive (ER+) luminal lobular regions, distinct enrichment of cell cycle arrest/senescence and oncogenic (ER and MYC ) signatures, genetic and epigenetic CDH1 inactivation in lobular but not ductal regions, and single-cell ductal and lobular subpopulations with unique oncogenic signatures further highlighting intraregional heterogeneity. Altogether, we demonstrated that the intratumoral morphological/histological heterogeneity within MDLC is underpinned by intrinsic subtype and oncogenic heterogeneity which may result in prognostic uncertainty and therapeutic dilemma.

Abstract Background The PALLAS trial investigated the addition of palbociclib to standard adjuvant endocrine therapy reduces breast cancer recurrence. This pre-specified analysis was conducted to determine whether adjuvant palbociclib benefited patients diagnosed with lower risk stage IIA disease compared to those with higher stage disease. Methods PALLAS was an international, multicenter, randomized, open-label, phase III trial, representing a public-private partnership between Pfizer, the Austrian Breast Cancer Study Group and, the U.S. ALLIANCE Foundation. Patients diagnosed with stage II-III, hormone-receptor-positive, HER2/neu negative breast cancer who were within 12 months of diagnosis, and had completed all definitive therapy aside from endocrine therapy, which was started within 6 months prior to study entry. All patients were required to submit a formalin-fixed paraffin-embedded (FFPE) tumor block. Patients were randomly assigned 1:1 to receive standard adjuvant endocrine therapy (of physicians’ choice) for at least 5 years with or without 2 years of Palbociclib, administered orally at a starting dose of 125 mg daily, given for 21 days followed by a 7-day break. Results A total of 5,796 patients with HR+/HER2- early breast cancer (including 1,010 with stage IIA) were enrolled. Median follow-up was 50 months for stage IIA patients and 43.1 months overall. In the stage IIA cohort, four-year iDFS in the palbociclib arm was 92.9% versus 92.1% for ET alone (HR 0.75, 95%CI 0.48–1.19, p = 0.23). There was no differential benefit by histologic grade, chemotherapy receipt, age, or anatomic/clinical risk. Additionally, no benefit to palbociclib was seen in this cohort in invasive breast cancer-free survival (iBCFS), locoregional relapse-free survival (LRFS), distant relapse-free survival (DRFS), or overall survival (OS). For the stage IIB/III patients, 4-year iDFS was 85.3% for palbociclib + ET versus 83.6% for ET alone (HR 0.91, 95% CI 0.77–1.07, p = 0.24). Conclusions and Relevance: While there were substantial differences in outcome for stage IIA versus IIB/III patients at 4 years of follow-up, the addition of 2 years of palbociclib did not improve outcomes for patients, regardless of stage. Trial Registration: The study was registered on Clinicaltrials.gov on July 31, 2015, and was assigned the clinical trial number (NCT02513394).

We consider the problem of reducing the time that healthcare professionals need to understand the patient’s medical history through the next generation of biomedical decision support. This problem is societally important because it has the potential to improve healthcare quality and patient outcomes. However, navigating electronic health records (EHR) is challenging due to high patient-doctor ratios, potentially long medical histories, urgency of treatment for some medical conditions, and patient variability. The current EHR systems provide only a longitudinal view of patient medical history, which is time-consuming to browse, and doctors often need to engage nurses, residents, and others for initial analysis. To overcome this limitation, we envision an alternative spatial representation of patient histories (e.g., electronic health records) and other biomedical data in the form of Atlas-EHR. Just like Google Maps, which allows a global, national, regional, and local view, Atlas-EHR can start with an overview of the patient’s anatomy and history before drilling down to spatially anatomical subsystems, their individual components, or subcomponents. Atlas-EHR presents a compelling opportunity for spatial computing since healthcare is almost a fifth of the US economy. However, traditional spatial computing designed for geographic use cases (e.g., navigation, land survey, and mapping) faces many hurdles in the biomedical domain. This article presents several open research questions under this theme in five broad areas of spatial computing.

Background: Stroke guideline statements are important references for clinicians due to the rapidly evolving nature of treatments. Guideline statements should be informed by up-to-date systematic reviews (SRs) and meta-analyses (MAs) because they provide the highest level of evidence. To investigate the utilization of SRs/MAs in stroke management guidelines, we conducted a literature review of guidelines and extracted relevant information regarding SRs/MAs. Methods: A literature review was conducted in PubMed with supplementation using the Trip medical database with the term “stroke” as the target population, followed by using the filter “guidelines”. We extracted the number of included SRs/MAs, the years of publication, the country of origin, and other characteristics of interest. Descriptive statistics were generated using the R software version 4.2.1. Results: We included 27 guideline statements. The median number of overall SRs or MAs within the guidelines was 4.0 (interquartile range [IQR] = 2–9). For MAs only, the median number included in the guidelines was 3.0 (IQR = 2.0–5.5). Canadian guidelines had the oldest citations, with a median gap of 12.0 (IQR = 5.2–18.0) years for the oldest citation, followed by European (median = 12; IQR = 9.5–13.5) and US (median = 10.0; IQR = 5.2–16) guidelines. Conclusions: Stroke guideline writing groups and issuing bodies should devote greater effort to the inclusion of up-to-date SRs/MAs in their guideline statements so that clinicians can reference recent data with the highest level of evidence.

Abstract INTRODUCTION Tau‐positron emission tomography (PET) outcome data of patients with Alzheimer's disease (AD) cannot currently be meaningfully compared or combined when different tracers are used due to differences in tracer properties, instrumentation, and methods of analysis. METHODS Using head‐to‐head data from five cohorts with tau PET radiotracers designed to target tau deposition in AD, we tested a joint propagation model (JPM) to harmonize quantification (units termed “CenTauR” [CTR]). JPM is a statistical model that simultaneously models the relationships between head‐to‐head and anchor point data. JPM was compared to a linear regression approach analogous to the one used in the amyloid PET Centiloid scale. RESULTS A strong linear relationship was observed between CTR values across brain regions. Using the JPM approach, CTR estimates were similar to, but more accurate than, those derived using the linear regression approach. DISCUSSION Preliminary findings using the JPM support the development and adoption of a universal scale for tau‐PET quantification. Highlights Tested a novel joint propagation model (JPM) to harmonize quantification of tau PET. Units of common scale are termed “CenTauRs”. Tested a Centiloid‐like linear regression approach. Using five cohorts with head‐to‐head tau PET, JPM outperformed linearregressionbased approach. Strong linear relationship was observed between CenTauRs values across brain regions.