Medicine and Health Sciences Commons^™

Identification Of Dual Strn-Ntrk2 Rearrangements In A High Grade Sarcoma, With Good Clinical Response To First-Line Larotrectinib Therapy, Ruihe Lin, Atrayee Basu Mallick, Zi-Xuan Wang, Phd, Scot Andrew Brown, Bo Lu, Md, Wei Jiang

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: Among the three NTRK genes, NTRK2 possesses a tremendous structural complexity and involves tumorigenesis of several types of tumors. To date, only STRN and RBPMS are identified in the fusion with NTRK2 in adult soft tissue tumors. More recently, the highly selective Trk tyrosine kinases inhibitors, including larotrectinib and entrectinib, have shown significant efficacy for treating tumors harboring NTRK fusions and were approved by FDA.

CASE PRESENTATION: We report a case of sarcoma in a 35-year-old female harboring two STRN-NTRK2 gene fusions, with a good clinical response to first-line larotrectinib treatment. Core biopsy of the 16.5 cm gluteal mass …

An Evaluation Of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology, Hon S. Ip, Sarah Uhm, Mary Lea Killian, Mia K. Torchetti

USDA Wildlife Services: Staff Publications

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing …

The Detection Of Periodic Reemergence Events Of Sars-Cov-2 Delta Strain In Communities Dominated By Omicron, Claire E. Westcott, Kevin J. Sokoloski, Eric C. Rouchka, Julia H. Chariker, Rochelle H. Holm, Ray A. Yeager, Joseph B. Moore Iv, Erin M. Elliott, Daymond Talley, Aruni Bhatnagar

Faculty Scholarship

Despite entering an endemic phase, SARS-CoV-2 remains a significant burden to public health across the global community. Wastewater sampling has consistently proven utility to understanding SARS-CoV-2 prevalence trends and genetic variation as it represents a less biased assessment of the corresponding communities. Here, we report that ongoing monitoring of SARS-CoV-2 genetic variation in samples obtained from the wastewatersheds of the city of Louisville in Jefferson county Kentucky has revealed the periodic reemergence of the Delta strain in the presence of the presumed dominant Omicron strain. Unlike previous SARS-CoV-2 waves/emergence events, the Delta reemergence events were geographically restricted in the community …

Next-Generation Sequencing Supports Targeted Antibiotic Treatment For Culture Negative Orthopedic Infections, Ravina Kullar, Emanuele Chisari, James Snyder, Christopher Cooper, Javad Parvizi, Jason Sniffen

Rothman Institute Faculty Papers

The isolation of an infective pathogen can be challenging in some patients with active, clinically apparent infectious diseases. Despite efforts in the microbiology lab to improve the sensitivity of culture in orthopedic implant-associated infections, the clinically relevant information often falls short of expectations. The management of peri-prosthetic joint infections (PJI) provides an excellent example of the use and benefits of newer diagnostic technologies to supplement the often-inadequate yield of traditional culture methods as a substantial percentage of orthopedic infections are culture-negative. Next-generation sequencing (NGS) has the potential to improve upon this yield. Bringing molecular diagnostics into practice can provide critical …

Germline Mutations In Patients With Early-Onset Prostate Cancer., Tang Tang, Xintao Tan, Ze Wang, Shuo Wang, Yapeng Wang, Jing Xu, Xiajie Wei, Dianzheng Zhang, Qiuli Liu, Jun Jiang

PCOM Scholarly Papers

Objective: To investigate the inherited mutations and their association with clinical features and treatment response in young-onset prostate cancer patients.

Method: Targeted gene sequencing on 139 tumor susceptibility genes was conducted with a total of 24 patients diagnosed with PCa under the age of 63 years old. Meanwhile, the related clinical information of those patients is collected and analyzed.

Results: Sixty-two germline mutations in 45 genes were verified in 22 patients.

Conclusion: Mutations in DRGs are more prevalent in early-onset PCa with advanced clinical stages, and these patients had shorter progression-free survival. ADT Combined with either radiotherapy or chemotherapy may …

Prognostic Implications Of Epidermal And Platelet-Derived Growth Factor Receptor Alterations In 2 Cohorts Of Idh, Iyad Alnahhas, Appaji Rayi, Maria Del Pilar Guillermo Prieto Eibl, Shirley Ong, Pierre Giglio, Vinay Puduvalli

Department of Neurology Faculty Papers

Background: Glioblastoma remains a deadly brain cancer with dismal prognosis. Genetic alterations, including IDH mutations, 1p19q co-deletion status and MGMT promoter methylation have been proven to be prognostic and predictive to response to treatment in gliomas. In this manuscript, we aimed to correlate other mutations and genetic alterations with various clinical endpoints in patients with IDH-wild-type (IDHwt) glioblastoma.

Methods: We compiled a comprehensive clinically annotated database of IDHwt GBM patients treated at the Ohio State University Wexner Medical Center for whom we had mutational data through a CLIA-certified genomic laboratory. We then added data that is publicly available from Memorial …

The Genetic Landscape Of Neurodegenerative And Cerebrovascular Disease Phenotypes., Allison A. Dilliott

Electronic Thesis and Dissertation Repository

Neurodegenerative diseases are progressive, incurable conditions characterized by neuronal degeneration and protein aggregation, resulting in cognitive decline and/or motor dysfunction. Over half a million Canadians are affected with these diseases, and the number of cases is expected to rise as the aging population grows and average lifespans continue to increase. There are currently no curative treatments, and only few therapeutics are available to target disease symptoms or slow disease progression. Further, diagnosis can be challenging, relying on clinical features that are often highly heterogeneous between patients. Gaining a greater understanding of the full spectrum of genetic factors contributing to these …

Genetic Approaches For The Study Of Complex Human Diseases, Julieta Lazarte

Electronic Thesis and Dissertation Repository

The field of human genetics has evolved from its initial narrow focus on single-gene Mendelian disorders, which largely affect children, to our current understanding that for most diseases there is continuum of rare to common variants which can exert a range of phenotypic effects. Despite advances in sequencing capabilities and our overall understanding of diseases, there remains a large proportion of heritability unexplained. Through the use of next-generation sequencing technologies and DNA microarray, I have explored a spectrum of genetic variations from rare, single and structural variants to common variants in individuals with i) “lone” atrial fibrillation; ii) familial hypercholesterolemia; …

Next-Generation Sequencing In The Diagnosis Of Rare Pediatric Sinonasal Tumors., Atif A. Ahmed, Divya Vundamati, Midhat Farooqi, Elena Repnikova, Timothy Zinkus, Maxine Hetherington, Lorien Paulson

Manuscripts, Articles, Book Chapters and Other Papers

The diagnosis of desmoid fibromatosis or other spindle cell tumors in the sinonasal region is very rare in children and needs to be thoroughly confirmed with immunohistochemical and/or molecular tests. We report 2 patients with such rare tumors and describe the use of next-generation sequencing in their evaluation. A 3-year-old female had a 4.4-cm midline nasal cavity mass involving the bony septum and extending into the base of the skull bilaterally. The moderate cellular fibroblastic proliferation revealed areas of thick keloid-like collagen bands and other areas with myxoid edematous stroma. Deep targeted sequencing identified a novel G34V mutation in the

Variant-Specific Inflation Factors For Assessing Population Stratification At The Phenotypic Variance Level, Tamar Sofer, Xiuwen Zheng, Cecelia A. Laurie, Stephanie M. Gogarten, Jennifer A. Brody, Matthew P. Conomos, Joshua C. Bis, Timothy A. Thornton, Adam Szpiro, Joanne E. Curran, Michael Mahaney

School of Medicine Publications and Presentations

In modern Whole Genome Sequencing (WGS) epidemiological studies, participant-level data from multiple studies are often pooled and results are obtained from a single analysis. We consider the impact of differential phenotype variances by study, which we term 'variance stratification'. Unaccounted for, variance stratification can lead to both decreased statistical power, and increased false positives rates, depending on how allele frequencies, sample sizes, and phenotypic variances vary across the studies that are pooled. We develop a procedure to compute variant-specific inflation factors, and show how it can be used for diagnosis of genetic association analyses on pooled individual level data from …

Robust, Flexible, And Scalable Tests For Hardy-Weinberg Equilibrium Across Diverse Ancestries, Alan M. Kwong, Thomas W. Blackwell, Jonathon Lefaive, Mariza De Andrade, John Barnard, Kathleen C. Barnes, John Blangero

School of Medicine Publications and Presentations

Traditional Hardy-Weinberg equilibrium (HWE) tests (the χ2 test and the exact test) have long been used as a metric for evaluating genotype quality, as technical artifacts leading to incorrect genotype calls often can be identified as deviations from HWE. However, in datasets comprised of individuals from diverse ancestries, HWE can be violated even without genotyping error, complicating the use of HWE testing to assess genotype data quality. In this manuscript, we present the Robust Unified Test for HWE (RUTH) to test for HWE while accounting for population structure and genotype uncertainty, and evaluate the impact of population heterogeneity and genotype …

Sequencing Of 53,831 Diverse Genomes From The Nhlbi Topmed Program, Daniel Taliun, Daniel N. Harris, Michael D. Kessler, Jedidiah Carlson, John Blangero, Joanne E. Curran, Michael C. Mahaney, Harald H. H. Goring, Ravindranath Duggirala, Juan M. Peralta

School of Medicine Publications and Presentations

The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and …

Clinical Utility Of Molecular Profiling In Recurrent Glioblastoma Multiforme, Rebecca P. Bystrom, Pavalan Selvam, Jens Rueter, Honey Reddi, Christine Lu-Emerson

Journal of Maine Medical Center

Introduction: Glioblastoma multiforme (GBM) is the most common and aggressive primary malignant brain tumor found in adults. GBM has limited therapeutic options. Initial tumor sampling establishes the histopathologic diagnosis, identifies prognostic and therapeutic biomarkers, and provides an opportunity for molecular profiling. By contrast, the utility of repeat tumor sampling and molecular profiling in recurrent GBM is not well established.

Clinical Findings: We present a 69-year-old woman with GBM whose tumor recurred after standard treatment with temozolomide (TMZ) and concurrent radiation, followed by adjuvant TMZ. This patient had a methylated O6-methylguanine-DNA methyltransferase (MGMT) promoter, which ordinarily predicts a favorable response to …

Population Genomic Transformations Induced By Isolation Of Wild Bird Avian Influenza Viruses (Orthomyxoviridae) In Embryonated Chicken Eggs, Matthew W. Hopken, Antoinette J. Piaggio, K. L. Pabilonia, James Pierce, Theodore Anderson, Courtney Pierce, Zaid Abdo

USDA Wildlife Services: Staff Publications

Isolation and cultivation of wild-type viruses in model organism cells or tissues is standard practice in virology. Oftentimes, the virus host species is distantly related to the species from which the culture system was developed. Thus, virus culture in these tissues and cells basically constitutes a host jump, which can lead to genomic changes through genetic drift and/or adaptation to the culture system. We directly sequenced 70 avian influenza virus (Orthomyxoviridae) genomes from oropharyngeal/cloacal swabs collected from wild bird species and paired virus isolates propagated from the same samples following isolation in specific-pathogen-free embryonated chicken eggs. The data were analyzed …

Genome-Wide Dna Methylation Profiling In Human Breast Tissue By Illumina Truseq Methyl Capture Epic Sequencing And Infinium Methylationepic Beadchip Microarray, Nan Lin, Jinpeng Liu, James Castle, Jun Wan, Aditi Shendre, Yunlong Liu, Chi Wang, Chunyan He

Markey Cancer Center Faculty Publications

A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall, there …

Capturing Functional Epigenomes For Insight Into Metabolic Diseases., Fiona Allum, Elin Grundberg

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Metabolic diseases such as obesity are known to be driven by both environmental and genetic factors. Although genome-wide association studies of common variants and their impact on complex traits have provided some biological insight into disease etiology, identified genetic variants have been found to contribute only a small proportion to disease heritability, and to map mainly to non-coding regions of the genome. To link variants to function, association studies of cellular traits, such as epigenetic marks, in disease-relevant tissues are commonly applied.

SCOPE OF THE REVIEW: We review large-scale efforts to generate genome-wide maps of coordinated epigenetic marks and …

Complex Oncological Decision-Making Utilizing Fast-And-Frugal Trees In A Community Setting-Role Of Academic And Hybrid Modeling., Ravi Salgia, Isa Mambetsariev, Tingting Tan, Amanda Schwer, Daryl Pearlstein, Hazem Chehabi, Angel Baroz, Jeremy Fricke, Rebecca Pharaon, Hannah Romo, Thomas Waddington, Razmig Babikian, Linda Buck, Prakash Kulkarni, Mary Cianfrocca, Benjamin Djulbegovic, Sumanta K Pal

Articles, Abstracts, and Reports

Non-small cell lung cancer is a devastating disease and with the advent of targeted therapies and molecular testing, the decision-making process has become complex. While established guidelines and pathways offer some guidance, they are difficult to utilize in a busy community practice and are not always implemented in the community. The rationale of the study was to identify a cohort of patients with lung adenocarcinoma at a City of Hope community site (n = 11) and utilize their case studies to develop a decision-making framework utilizing fast-and-frugal tree (FFT) heuristics. Most patients had stage IV (N = 9, 81.8%) disease …

Spectrum Of Germline Cancer Susceptibility Gene Mutations In Turkish Colorectal Cancer Patients: A Single Center Study, Haktan Bağiş Erdem, Taha Bahsi̇

Turkish Journal of Medical Sciences

Background/aim: Quarter of colorectal cancer patients have a family history and 6% of these comprise hereditary cancer syndromes. For developing national health strategies for genetic screening, it is crucial to determine the spectrum of damaging alterations in causative genes and to describe frequent founder mutations. Materials and methods: One hundred and thirty six unrelated colorectal cancer cases were investigated. Qiagen large hereditary cancer panel and Hereditary Cancer Solution v1.1 panel were used for sequencing. The sequencing process was performed on the Illumina MiSeq system. The data analyses were performed on QIAGEN Clinical Insight (QCITM) Analyze software and Sophia DDM software. …

Hypotrichosis With Juvenile Macular Dystrophy: Combination Of Whole-Genome Sequencing And Genome-Wide Homozygosity Mapping Identifies A Large Deletion In Cdh3 Initially Undetected By Whole-Exome Sequencing-A Lesson From Next-Generation Sequencing., Amir Hossein Saeidian, Hassan Vahidnezhad, Leila Youssefian, Soheila Sotudeh, Meisam Sargazi, Sirous Zeinali, Jouni Uitto

Department of Dermatology and Cutaneous Biology Faculty Papers

BACKGROUND: Hypotrichosis with juvenile macular dystrophy (HJMD) is an autosomal recessive disorder characterized by abnormal growth of scalp hair and juvenile macular degeneration leading to blindness. We have explored the genetic basis of HJMD in a large consanguineous family with 12 affected patients, 1-76 years of age, with characteristic phenotypes.

METHODS: We first applied genome-wide homozygosity mapping to 10 affected individuals for linkage analysis to identify the genomic region of the defective gene. All affected individuals shared a 7.2 Mb region of homozygosity on chromosome 16q21-22.3, which harbored 298 genes, including CDH3, previously associated with HJMD. However, whole-exome sequencing (WES) …

Exome Sequencing Of 20,791 Cases Of Type 2 Diabetes And 24,440 Controls, Jason Flannick, Josep M. Mercader, Christian Fuchsberger, Miriam S. Udler, Anubha Mahajan, Jennifer Wessel, Gil Atzmon, John Blangero, Ravindranath Duggirala, Benjamin Glaser

School of Medicine Publications and Presentations

Protein-coding genetic variants that strongly affect disease risk can yield relevant clues to disease pathogenesis. Here we report exome-sequencing analyses of 20,791 individuals with type 2 diabetes (T2D) and 24,440 non-diabetic control participants from 5 ancestries. We identify gene-level associations of rare variants (with minor allele frequencies of less than 0.5%) in 4 genes at exome-wide significance, including a series of more than 30 SLC30A8 alleles that conveys protection against T2D, and in 12 gene sets, including those corresponding to T2D drug targets (P = 6.1 × 10−3) and candidate genes from knockout mice (P = 5.2 × …

Improving The Genetic Diagnosis Of Familial Hypercholesterolemia, Michael Iacocca

Electronic Thesis and Dissertation Repository

Familial hypercholesterolemia (FH) is a genetic disorder of severely elevated low-density lipoprotein (LDL) cholesterol that is widely underdiagnosed and undertreated. To improve the identification of FH and initiate timely and appropriate treatment strategies, genetic testing is becoming increasingly offered worldwide as a central part of diagnosis. I describe three main ways providing a genetic diagnosis in FH can be improved. First, next-generation sequencing (NGS)-based approaches can be used to reliably identify large-scale variant types known as copy number variations (CNVs) in the LDL receptor gene (LDLR); second, NGS methodology can be further applied to extend CNV screening to …

Clinical Genome Sequencing In An Unbiased Pediatric Cohort., Isabelle Thiffault, Emily G. Farrow, Lee Zellmer, Courtney D. Berrios, Neil Miller, Margaret Gibson, Raymond Caylor, Janda L. Jenkins, Deb Faller, Sarah E. Soden, Carol J. Saunders

Manuscripts, Articles, Book Chapters and Other Papers

PURPOSE: We report for the first time, the use of clinical genome sequencing (GS) in an unbiased pediatric cohort. We describe the clinical validation, patient metrics, ordering patterns, results, reimbursement, and physician retrieval of results for the first consecutive 80 cases.

METHODS: Clinical GS was performed for both inpatients and outpatients undergoing etiologic evaluations. Results were reported in the electronic medical record. Evidence of report retrieval by clinicians and whether interpretation was concordant with laboratory report was obtained through retrospective chart review.

RESULTS: Twenty definitive diagnoses were made in 19 patients (24%; n = 80). Except for two partial gene …

Next-Generation Sequencing Of Hiv-1 Single Genome Amplicons, Gustavo H. Kijak, Eric Sanders-Buell, Phuc Pham, Elizabeth A. Harbolick, Celina Oropeza, Anne Marie O'Sullivan, Meera Bose, Charmagne G. Beckett, Mark Milazzo, Merlin L. Robb, Sheila A. Peel, Paul T. Scott, Nelson L. Michael, Adam W. Armstrong, Jerome H. Kim, David Brett-Major, Sodsai Tovanabutra

Journal Articles: Epidemiology

The analysis of HIV-1 sequences has helped understand the viral molecular epidemiology, monitor the development of antiretroviral drug resistance, and design candidate vaccines. The introduction of single genome amplification (SGA) has been a major advancement in the field, allowing for the characterization of multiple sequences per patient while preserving linkage among polymorphisms in the same viral genome copy. Sequencing of SGA amplicons is performed by capillary Sanger sequencing, which presents low throughput, requires a high amount of template, and is highly sensitive to template/primer mismatching. In order to meet the increasing demand for HIV-1 SGA amplicon sequencing, we have developed …

Improved Reference Genome For The Domestic Horse Increases Assembly Contiguity And Composition, Theodore S. Kalbfleisch, Edward S. Rice, Michael S. Depriest Jr., Brian P. Walenz, Matthew S. Hestand, Joris R. Vermeesch, Brendan L. O'Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E Mccue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Richard E. Green, Donald C. Miller, Douglas F. Antczak, James N. Macleod

Maxwell H. Gluck Equine Research Center Faculty Publications

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of …

Genetic Determinants Underlying Rare Diseases Identified Using Next-Generation Sequencing Technologies, Rosettia Ho

Electronic Thesis and Dissertation Repository

Rare disorders affect less than one in 2000 individuals, placing a huge burden on individuals, families and the health care system. Gene discovery is the starting point in understanding the molecular mechanisms underlying these diseases. The advent of next-generation sequencing has accelerated discovery of disease-causing genetic variants and is showing numerous benefits for research and medicine. I describe the application of next-generation sequencing, namely LipidSeq™ ‒ a targeted resequencing panel for the identification of dyslipidemia-associated variants ‒ and whole-exome sequencing, to identify genetic determinants of several rare diseases. Utilization of next-generation sequencing plus associated bioinformatics led to the discovery of …

Extracellular Vesicle Rnas Reflect Placenta Dysfunction And Are A Biomarker Source For Preterm Labour., Shannon Fallen, David Baxter, Xiaogang Wu, Taek-Kyun Kim, Oksana Shynlova, Min Young Lee, Kelsey Scherler, Stephen Lye, Leroy Hood, Kai Wang

Articles, Abstracts, and Reports

Preterm birth (PTB) can lead to lifelong complications and challenges. Identifying and monitoring molecular signals in easily accessible biological samples that can diagnose or predict the risk of preterm labour (PTL) in pregnant women will reduce or prevent PTBs. A number of studies identified putative biomarkers for PTL including protein, miRNA and hormones from various body fluids. However, biomarkers identified from these studies usually lack consistency and reproducibility. Extracellular vesicles (EVs) in circulation have gained significant interest in recent years as these vesicles may be involved in cell-cell communication. We have used an improved small RNA library construction protocol and …

Telomerase Reverse Transcriptase Promoter Alterations Across Cancer Types As Detected By Next-Generation Sequencing: A Clinical And Molecular Analysis Of 423 Patients., Maria Schwaederle, Nithya Krishnamurthy, Gregory A Daniels, David E Piccioni, Santosh Kesari, Paul T Fanta, Richard B Schwab, Sandip P Patel, Barbara A Parker, Razelle Kurzrock

Articles, Abstracts, and Reports

BACKGROUND: Telomerase reverse transcriptase (TERT) promoter mutations that may affect telomerase activity have recently been described in human malignancies. The purpose of this study was to investigate the clinical correlates of TERT promoter abnormalities in a large cohort of patients with diverse cancers.

METHODS: This study analyzed TERT promoter alterations and clinical characteristics of 423 consecutive patients for whom molecular testing by next-generation sequencing was performed between August 2014 and July 2015.

RESULTS: Of the 423 patients, 61 (14.4%) had TERT promoter mutations, and this placed TERT promoter alterations among the most prevalent aberrations after tumor protein 53 (TP53; 39%) …

Corrigendum: Identification Of The Cftr C.1666a > G Mutation In Hereditary Inclusion Body Myopathy Using Next-Generation Sequencing Analysis, Yan Lu, Yu-Wei Da, Yong-Biao Zhang, Xin-Gang Li, Min Wang, Li Di, Mi Pang, Lin Lei

Research outputs 2014 to 2021

A Corrigendum on Identification of the CFTR c.1666A>G Mutation in Hereditary Inclusion Body Myopathy Using Next-Generation Sequencing Analysis

by Lu, Y., Da, Y.-W., Zhang, Y.-B., Li, X.-G., Wang, M., Di, L., et al. (2018). Front. Neurosci. 12:329. doi: 10.3389/fnins.2018.00329

An error was found in the first and second sentence of the original article's abstract.

Applications Of Next-Generation Sequencing And Functional Genomics In Translational Medicine, Andrew Hardigan

All ETDs from UAB

The development of next-generation sequencing (NGS) technologies has led to unparalleled advances in our understanding of the genetic basis of disease, evolution, and genetic and genomic regulation. Building on the advances made in the Human Genome Project and more recent efforts such as the Encylopedia of DNA Elements (ENCODE) and the Roadmap Epigenomics Project, whole-genome and whole-exome sequencing (WGS/WES) and a wide variety of NGS-enabled functional assays are bridging the gap between scientific discovery and clinical medicine. This trend towards genomically informed “bench-to-bedside” translational medicine is driven in large part by the sharply decreasing costs for NGS in both clinical …

Identification Of Prognostic Cancer Biomarkers Through The Application Of Rna-Seq Technologies And Bioinformatics, Nathan Wong

McKelvey School of Engineering Theses & Dissertations

MicroRNAs (miRNAs) are short single-stranded RNAs that function as the guide sequence of the post-transcriptional regulatory process known as the RNA-induced silencing complex (RISC), which targets mRNA sequences for degradation through complementary binding to the guide miRNA. Changes in miRNA expression have been reported as correlated with numerous biological processes, including embryonic development, cellular differentiation, and disease manifestation. In the latter case, dysregulation has been observed in response to infection by human papillomavirus (HPV), which has also been established as both oncogenic in cervical cancers and oropharyngeal cancers and favorable for overall patient survival after tumor formation. The identification of …