A5008982001- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Mitochondrial Function and Pathology
- Genetic Neurodegenerative Diseases
- Genomics and Rare Diseases
- DNA Repair Mechanisms
- Cytomegalovirus and herpesvirus research
- Amyotrophic Lateral Sclerosis Research
- Genetics and Neurodevelopmental Disorders
- Prenatal Screening and Diagnostics
- Mycobacterium research and diagnosis
- Transplantation: Methods and Outcomes
- Neurogenetic and Muscular Disorders Research
- Healthcare Policy and Management
- Molecular Junctions and Nanostructures
- Genetic factors in colorectal cancer
- RNA modifications and cancer
- Corneal surgery and disorders
- Adenosine and Purinergic Signaling
- Bacterial Identification and Susceptibility Testing
- Cultural and Sociopolitical Studies
- Laser-Matter Interactions and Applications
- Immune Cell Function and Interaction
- Genomics and Chromatin Dynamics
- Ovarian cancer diagnosis and treatment
Pacific Biosciences (United States)
2018-2025
Quest Diagnostics (United States)
2013
Alameda Hospital
2011
University of Chicago
1968
ABSTRACT Real-time PCR methods with primers and a probe targeting conserved regions of the bacterial 16S ribosomal DNA (rDNA) revealed larger amount rDNA in blood specimens from healthy individuals than matched reagent controls. However, origins identities these blood-associated sequences remain obscure.
Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most like the C9orf72 'GGGGCC' (G4C2) that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, too long to sequence using short-read sequencing technologies. It is unclear whether long-read technologies can traverse these long, challenging expansions. Here, we demonstrate two technologies, Pacific Biosciences' (PacBio) Oxford Nanopore Technologies' (ONT),...
In this paper we present a formal theory of photochemical fragmentation reactions for the case that intramolecular energy transfer is importance. The zero-order spectrum molecule assumed to consist discrete level in resonance with dense set levels belonging another electric manifold, which turn translational continuum representing molecular fragmentation. exact eigenstates system are computed formally and shown be resonant scattering states. Explicit formulas derived probability being...
Abstract A repeat expansion mutation in the C9orf72 gene is leading known genetic cause of FTD and ALS. The C9orf72- ALS/FTD field has been plagued by a lack reliable tools to monitor this genomic locus its RNA protein products. We have validated assays that quantify pathobiology at DNA, levels using knock-out human iPSC lines as controls. Here we show single-molecule sequencing can accurately measure faithfully report on changes what traditionally hard sequence region. This particular value...
To examine the length of a hexanucleotide expansion in C9orf72, which represents most frequent genetic cause frontotemporal lobar degeneration and motor neuron disease, we employed targeted amplification-free long-read sequencing technology: No-Amp sequencing. In our cross-sectional study, assessed cerebellar tissue from 28 well-characterized C9orf72 carriers. We obtained 3507 on-target circular consensus reads, 814 bridged repeat (23%). Importantly, observed significant correlation between...
Abstract The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, first to be explicitly consented for public dissemination genomic data cell lines. Here, we describe comprehensive dataset from individual, HG008, including DNA an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor line (HG008-T) normal cells duodenal tissue (HG008-N-D) (HG008-N-P). come thirteen whole...
Amplification of a CAG trinucleotide motif (CTG18.1) within the TCF4 gene has been strongly associated with Fuchs Endothelial Corneal Dystrophy (FECD). Nevertheless, small minority clinically unaffected elderly patients who have expanded CTG18.1 sequences identified. To test hypothesis that expansions in these are protected from FECD because they interruptions repeats, we utilized combination an amplification-free, long-read sequencing method and new target-enrichment sequence analysis tool...
Abstract Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to diverse mechanisms by which genetic variants cause disease. To address this, we developed synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, enables accurate single-nucleotide, insertion-deletion, structural variant calling diploid de novo genome assembly, permits simultaneous elucidation haplotype-resolved CpG methylation, chromatin accessibility,...
Unlike classical HLA class I genes, MR1 is assumed to have limited polymorphic positions. We developed a specific PCR assay and sequenced 56 DNA samples from cells with diverse set of genotypes. In this relatively small panel we found six allele groups encoding for different proteins. The two most frequent in had frequency 71% (MR1*01) 25% (MR1*02), respectively. Moreover, the contained many intronic SNPs silent variants, individual containing up 15 heterozygous data presented here...
Abstract Tumor evolution is a highly heterogeneous process where multiple oncogenic pathways can lead to host defense evasion. Advancements in genome sequencing are allowing us better understand these processes and their impact. However, critical genomic variations that could be pivotal the development of tumors may have remained undetected due technological constraints short-read sequencing. PacBio HiFi generates accurate (>99.9%) long reads (>15 kb) with native...
STR-PCR is limited in its utility for screening and monitoring of donors recipients double cord transplants, given inherent lack sensitivity the presence stutter artifacts which obscure potentially informative alleles. If markers are identified each individual a transplant, manual execution algorithm quantification individuals quite time-consuming. To simplify these analyses, we designed multiplexed system RUO assays software enabling instantaneous marker identification post-PCR. We employ...
Assessing engraftment kinetics and monitoring potential rejection/relapse events requires assay systems which not only have the ability to distinguish closely-matched individuals, but also accurately precisely determine relative levels of host recipient cells present in mixtures two. The current standard practice – use forensic identity kits fulfills need for finding unique genetic markers between its be applied a quantitative fashion is extremely limited. Use qPCR assays software designed...
The commonly used engraftment monitoring method of short tandem repeat (STR) amplification following allogeneic hematopoietic stem cell transplantation (HSCT) is hampered by several shortcomings affecting sensitivity, accuracy, reproducibility, and results interpretation. In an effort to provide a better solution, we have developed truly quantitative, real-time PCR method. Real-time technology ideally suited for this application because it highly sensitive quantitatively much more accurate...