Renal autotransplant as a definitive treatment for nutcracker syndrome: A multicenter retrospective study.

Objective: Nutcracker syndrome is a rare condition that involves mechanical compression of the left renal vein, leading to chronic and debilitating left flank pain. The etiology of the pain is misdiagnosed frequently, and patients usually require long-term opioid use to manage their pain. Multiple therapeutic options for nutcracker syndrome have been described in the literature but the reports are limited by small numbers of patients, and the lack of convincing data demonstrating consistently improved outcomes.

DNA N-gram analysis framework (DNAnamer): A generalized N-gram frequency analysis framework for the supervised classification of DNA sequences.

In 1948, Claude Shannon published a mathematical system describing the probabilistic relationships between the letters of a natural language and their subsequent order or syntax structure. By counting unique, reoccurring sequences of letters called N-grams, this language model was used to generate recognizable English sentences from N-gram frequency probability tables. More recently, N-gram analysis methodologies have been successfully applied to address many complex problems in a variety of domains, from language processing to genomics.

An evaluation of the organ procurement and transplantation network's expanded post-transplant performance metrics.

On July 14, 2022, the Organ Procurement and Transplantation Network's (OPTN) Membership and Professional Standards Committee (MPSC) approved bylaws including two new post-transplant performance evaluation metrics, the 90-day (90D) and 1-year conditional on the 90-day (1YC90D) graft survival hazard ratio (HR). These metrics have replaced the previous 1-year (1Y) unconditional, post-transplant graft survival HR and are used to nationally rank and identify programs for MPSC review. The MPSC's policies have major implications for all transplant programs, providers, and patients across the United States.

A comparative study of structural variant calling in WGS from Alzheimer's disease families.

Detecting structural variants (SVs) in whole-genome sequencing poses significant challenges. We present a protocol for variant calling, merging, genotyping, sensitivity analysis, and laboratory validation for generating a high-quality SV call set in whole-genome sequencing from the Alzheimer's Disease Sequencing Project comprising 578 individuals from 111 families. Employing two complementary pipelines, Scalpel and Parliament, for SV/indel calling, we assessed sensitivity through sample replicates (N = 9) with in silico variant spike-ins.

Patient years lost due to cytomegalovirus serostatus mismatching in the scientific registry of transplant recipients.

Background: The cytomegalovirus (CMV) mismatch rate in deceased donor kidney transplant (DDKT) recipients in the US remains above 40%. Since CMV mismatching is common in DDKT recipients, the cumulative effects may be significant in the context of overall patient and graft survival. Our primary objective was to describe the short- and long-term risks associated with high-risk CMV donor positive/recipient negative (D+/R-) mismatching among DDKT recipients with the explicit goal of deriving a mathematical mismatching penalty.

Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects.

Structural variations (SVs) are important contributors to the genetics of numerous human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due to challenges in accurately detecting SVs. Here, we analyzed whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (ADSP, N=16,905 subjects) and identified 400,234 (168,223 high-quality) SVs.

Reassessing the survival benefit of deceased donor liver transplantation: retrospective cohort study.

Introduction: Currently in the United States, deceased donor liver transplant (DDLT) allocation priority is based on the model for end-stage liver disease including sodium (MELD-Na) score. The United Network for organ sharing's 'Share-15' policy states that candidates with MELD-Na scores of 15 or greater have priority to receive local organ offers compared to candidates with lower MELD-Na scores. Since the inception of this policy, major changes in the primary etiologies of end-stage liver disease have occurred and previous assumptions need to be recalibrated.

A model for calculating the long-term estimated post-transplant survival of deceased donor liver transplant patients.

Background: The estimated long-term survival (EPTS) score is used for kidney allocation. A comparable prognostic tool to accurately quantify EPTS benefit in deceased donor liver transplant (DDLT) candidates is nonexistent.

Methods: Using the Scientific Registry of Transplant Recipients (SRTR) database, we developed, calibrated, and validated a nonlinear regression equation to calculate liver-EPTS (L-EPTS) for 5- and 10-year outcomes in adult DDLT recipients.

Preliminary safety and efficacy of laser stricturotomy for treatment of refractory biliary anastomotic strictures following liver transplantation.

Biliary anastomotic stricture (BAS) is a frequent complication of liver transplantation and is associated with reduced graft survival and patient morbidity. Existing treatments for BAS involve dilation of the stricture though placement of 1 or more catheters for 6 to 24 months yielding limited effectiveness in transplant patients. In this case series, we present preliminary safety and efficacy of a novel percutaneous laser stricturotomy treatment in a cohort of 5 posttransplant patients with BAS refractory to long-term large bore catheterization.

Survival Benefit of Living-Donor Liver Transplant.

Importance: Despite the acceptance of living-donor liver transplant (LDLT) as a lifesaving procedure for end-stage liver disease, it remains underused in the United States. Quantification of lifetime survival benefit and the Model for End-stage Liver Disease incorporating sodium levels (MELD-Na) score range at which benefit outweighs risk in LDLT is necessary to demonstrate its safety and effectiveness.

Objective: To assess the survival benefit, life-years saved, and the MELD-Na score at which that survival benefit was obtained for individuals who received an LDLT compared with that for individuals who remained on the wait list.

Erosion of Gene Co-expression Networks Reveal Deregulation of Immune System Processes in Late-Onset Alzheimer's Disease.

We have applied a novel and integrative analysis framework for next-generation sequencing (NGS) data to 503 human subjects provided by the Religious Orders Study and Memory and Aging Project (ROSMAP) to examine changes in transcriptomic organization and common variants in association with late-onset Alzheimer's disease (LOAD). Our framework identified seven reproducible, co-regulated modules after quality control (QC), clinical segregation, preservation filtering, and functional ontology analysis. These modules were specifically enriched in several innate and adaptive immune system processes, the synaptic vesicle cycle, and Hippo signaling.

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed "consensus calling," to combine genotype calls from both pipelines into a single high-quality set.

Integrated Systems Approach Reveals Sphingolipid Metabolism Pathway Dysregulation in Association with Late-Onset Alzheimer's Disease.

Late-onset Alzheimer's disease (LOAD) and age are significantly correlated such that one-third of Americans beyond 85 years of age are afflicted. We have designed and implemented a pilot study that combines systems biology approaches with traditional next-generation sequencing (NGS) analysis techniques to identify relevant regulatory pathways, infer functional relationships and confirm the dysregulation of these biological pathways in LOAD. Our study design is a most comprehensive systems approach combining co-expression network modeling derived from RNA-seq data, rigorous quality control (QC) standards, functional ontology, and expression quantitative trait loci (eQTL) derived from whole exome (WES) single nucleotide variant (SNV) genotype data.

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.

Unlabelled: We implemented a high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA-DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer-target gene relationships.

Availability And Implementation: This software package is designed to run on high-performance computing clusters with Oracle Grid Engine. The source code is freely available under the MIT license for academic and nonprofit use.