Digital Commons Network^™

K-Mer Analysis Of Long-Read Alignment Pileups For Structural Variant Genotyping, Adam C English, Fabio Cunial, Ginger A Metcalf, Richard A Gibbs, Fritz J Sedlazeck

Faculty, Staff and Students Publications

Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes. Benchmarking against the latest SV datasets shows kanpig achieves a single-sample genotyping concordance of 82.1%, significantly outperforming existing tools, which average 66.3%. We explore kanpig's use for multi-sample projects by testing on 47 genetically diverse samples and find kanpig accurately genotypes complex loci (e.g. SVs neighboring other SVs), and produces higher genotyping concordance than other tools. Kanpig requires only 43 seconds to process a single sample's 20x …

Bright And Photostable Yellow Fluorescent Proteins For Extended Imaging, Jihwan Lee, Shujuan Lai, Shuyuan Yang, Shiqun Zhao, Francisco A Blanco, Anne C Lyons, Raquel Merino-Urteaga, John F Ahrens, Nathan A Nguyen, Haixin Liu, Zhuohe Liu, Gerard G Lambert, Nathan C Shaner, Liangyi Chen, Kimberley F Tolias, Jin Zhang, Taekjip Ha, François St-Pierre

Faculty, Staff and Students Publications

Fluorescent proteins are indispensable molecular tools for visualizing biological structures and processes, but their limited photostability restricts the duration of dynamic imaging experiments. Yellow fluorescent proteins (YFPs), in particular, photobleach rapidly. Here, we introduce mGold2s and mGold2t, YFPs with up to 25-fold greater photostability than mVenus and mCitrine, two commonly used YFPs, while maintaining comparable brightness. These variants were identified using a high-throughput pooled single-cell platform, simultaneously screening for high brightness and photostability. Compared with our previous benchmark, mGold, the mGold2 variants display a ~4-fold increase in photostability without sacrificing brightness. mGold2s and mGold2t extend imaging durations across diverse modalities, …

Evaluating The Efficacy Of Focused Ultrasound In Neurological Disorders And Malignancy, Kennedi Henke, Ryan Takens, Heidi Smith, Andrea Crew

Celebration of Research

Focused Ultrasound (FUS) is an emerging therapeutic strategy for neurological diseases, including Parkinson’s disease, Alzheimer’s disease, and brain tumors. Despite advancements in conventional treatments, challenges such as invasive procedures, limited drug delivery across the blood-brain barrier (BBB), and declining long-term efficacy necessitate novel approaches. FUS offers non-invasive neuroablation, BBB modulation, and enhanced drug delivery, positioning it as a promising alternative to traditional therapies. This review examines the clinical evidence on FUS’s role in tumor reduction, tremor management, and amyloid plaque reduction, highlighting its benefits, challenges, and future potential in neurological disease treatment.

Angiotensin Converting Enzyme Inhibitor Induced Angioedema (Acei-Ae): Emergency Department Treatments, Logan Held, Marcus Blankenspoor, Kristine Her, Jolene Harris

Celebration of Research

Angiotensin Converting Enzyme Inhibitor Induced Angioedema (ACEI-AE) is the acute swelling of the upper airway in patients who are currently or were formerly taking Angiotensin Converting Enzyme Inhibitors (ACEIs) for control of primary hypertension. Though emergency department presenting signs and symptoms have overlap with angioedema associated with anaphylaxis, there are key differences, including the absence of urticaria or hypotension and history of ACEI use, that can guide clinicians in identifying the underlying cause of the angioedema and initiate appropriate treatment. Due to its differing pathophysiology, ACEI-AE must be treated uniquely with Tranexamic Acid (TXA) and Fresh Frozen Plasma (FFP) to …

Safety And Efficacy Of 112 Mg Intranasal Esketamine In Patients With Treatment-Resistant Depression: A Retrospective Observational Study From Outpatient Community Clinics, Kirsten Brinkmeier, Michael Kritzer, Brandon Doan, Cecilia Li, Nicholas Mischel

Medical Student Research Symposium

This retrospective study examined the safety and efficacy of 56, 84, and 112 mg intranasal (IN) esketamine via medical record review of 24 patients with treatment resistant depression (TRD). Doses ranged from 56 mg to 112 mg and were titrated across sessions to maximize individual response while considering tolerability. Treatment response was defined by reduction in average Patient Health Questionnaire-9 (PHQ-9) scores. Tolerability was defined by blood pressures at baseline, 40 minutes after, and 2 hours after drug administration. Patients ranged from 19 to 60 years old (average 38.87), and 15 (62.5%) were female. Patients received an average of 1 …

Evaluating Engagement In Health Care And Substance Use Disorder Services Among People Who Use Drugs, Tiffany Mckenney, Kevin Cobty, Divya Boorle, Julie Gleason-Comstock

Medical Student Research Symposium

An urban community-based organization conducted a study to examine demographics of individuals who use drugs and their approaches to risk reduction. A substantial proportion reported encountering significant barriers to accessing substance use disorder (SUD) services.

In collaboration with a state survey, the community organization recruited a convenience sample of individuals who actively used drugs, examining substance use patterns, healthcare access, and barriers to SUD services. Community health workers facilitated outreach efforts, focusing on harm reduction engagement, and healthcare access.

Data were collected from 55 individuals. 51% identified as male, 48% as female, and 2% as LGBTQIA+. 67% identified as White/Caucasian, …

The Effect Of Abdominal Insufflation On Transversus Abdominis Plane (Tap) Block Efficacy In Laparoscopic Gynecologic Surgery, Hussein A. Bazzi, Justin Hruska M.D., Christopher Kliethermes M.D., Anne Thomas, Wael Saasouh M.D.

Medical Student Research Symposium

Introduction:

Approximately 15 million laparoscopic procedures are performed annually worldwide, with 4.8 million (32%) occurring in the United States. Laparoscopy is widely used for procedures such as bilateral tubal sterilizations, hysterectomies, and treatments for endometriosis and adhesions. During gynecologic laparoscopic surgeries, the abdomen is inflated with pressurized carbon dioxide for surgical visualization. Pain management typically involves a transversus abdominis plane (TAP) block, which provides intermediate postoperative pain relief (lasting 12–24 hours). This study evaluates the efficacy of TAP blocks performed during insufflation to improve postoperative pain outcomes compared to the traditional technique.

Methods:

This patient-blinded study included female gynecologic patients …

Complications Of Breast Reconstruction: Does The Area Deprivation Index Predict Risk?, Andrew Hannoudi, Noah M. Atisha, Amolak S. Jhand, Kinan Sawar, Dunya M. Atisha

Medical Student Research Symposium

INTRODUCTION: Despite mandated post-mastectomy reconstruction coverage since the Women’s Health and Cancer Rights Act (1998), vulnerable populations may be prone to breast reconstruction complications. The Area Deprivation Index (ADI) reflects neighborhood socioeconomic status utilizing US census data. This study investigates ADI's relationship to breast reconstruction complications.
METHODS: A retrospective study of immediate pre-pectoral direct-to-implant reconstruction patients at a metropolitan healthcare system from 2018-2022 was conducted. Patients were stratified by ADI: <50th percentile (ADI=1-5) and ≥50th percentile (ADI=6-10). Demographics, medical history, treatment history, and postoperative outcomes were compared. Descriptive statistics identified differences between ADI groups. Minor complications were defined as incidence of hematoma, seroma, superficial wounds, full thickness necrosis, or oral antibiotic-treated cellulitis. Major complications were defined as incidence of hospital readmission or return to OR. Long-term complications were defined as incidence of capsular contracture or ≥3 revisions. Logistic regression assessed ADI’s predictive value, accounting for confounds between cohorts.
RESULTS: Of 195 patients, 147 had low ADI and 48 had high ADI. Significant differences in BMI and race were found between groups. Low ADI demonstrated higher …

Clinical Characteristics And Outcomes Of Pediatric Staphylococcal Scalded Skin Syndrome (Ssss) At An Inner-City Tertiary Care Center, Nina Kb Gust Md, Ashley Frei Bs, Rebecca M. Adams Bs, Elika Ridelman Phd, Christina Shanti Md, Ronald Thomas Phd, Jocelyn Y. Ang Md

Medical Student Research Symposium

Introduction

Staphylococcal Scalded Skin Syndrome (SSSS) is a blistering skin condition caused by a toxin-producing staphylococcus species. Epidemiologic studies on pediatric SSSS in the United States are limited, with a reported incidence of 7.67 cases per million children and 45.1 per million infants. Immature renal function, lack of protective antibodies, and increased exotoxin target desmoglein-1 are hypothesized to increase incidence in younger children. We aimed to determine clinical and microbiological characteristics of pediatric SSSS and factors that could help predict disease severity.

Methods

A retrospective chart review was performed for admitted patients under 18 years old diagnosed with SSSS from …

Socioeconomic Disparities And Challenges In Urban Detroit: Predicting Loss To Follow-Up After Treatment For Intracranial Aneurysms, Hailey Yasmine Rizk, Noah Goldberger, Jared Reese, Pouya Entezami

Medical Student Research Symposium

Intracranial aneurysmal subarachnoid hemorrhages (aSAH) can cause debilitating acute and chronic symptoms, and loss-to-follow-up (LTF) is a prominent issue affecting longitudinal care. Higher rates of follow-up have been correlated with better outcomes, and this study sought to identify disparities in the urban Detroit patient population and factors that may predispose patients to not receiving post-hospitalization care.

This retrospective study identified 352 patients with ruptured aSAH from 2013-2024 treated within a metro-Detroit hospital system. LTF was defined as lack of follow-up imaging >500 days post-discharge. Patient demographics and socioeconomic variables were reviewed, and Chi-square and Fisher’s tests were utilized to determine …

Socioeconomic And Demographic Factors In Genetic Testing Utilization Among Advanced Prostate Cancer Patients: A Retrospective Single-Institution Study, Alexandra T. Skowron Ms, Karen Childers, Courtney M. Rose Ms, Kyle C. Mcelyea Md, Avery K. Supernois Bs, Yousuf Hussain, Mohammed Baseer Ms, Sunita Ghosh Phd, Clara Hwang Md

Medical Student Research Symposium

Introduction

Germline genetic testing in patients with advanced prostate cancer (PCa) is underutilized. Socioeconomic and demographic factors are hypothesized to affect low rates of testing, but causality has not been established. This single institution, retrospective study aimed to understand what barriers may affect germline genetic testing for PCa patients.

Methods

The Henry Ford Health (HFH) tumor registry was queried for new diagnoses of stage 3, 4A and 4B PCa from 2017-2022. Census tract levels were assigned using patient addresses and neighborhood-based geocoding was completed for Median household income (gMHI) and Social vulnerability index (SVI). gMHI and SVI were divided into …

Variation In Treatment Recommendations For Low-Risk Prostate Cancer: A Focus On Active Surveillance Across Physician Specialties, Sinyu Yang B.S., Tiffany Chu B.S., Cathryn Bock Ph.D, Jinping Xu M.D.

Medical Student Research Symposium

Prostate cancer (PC) is the second leading cause of cancer-related death in men globally, with 1 in 8 men in the US diagnosed during their lifetime. For Low-Risk Prostate Cancer (LRPC), management options include Watchful Waiting (WW), Active Surveillance (AS), or curative treatments such as prostatectomy or radiation. While curative treatments can have significant long-term side effects like urinary incontinence and sexual dysfunction, AS is less invasive and preferred due to fewer adverse effects. However, variations in physician training may lead to differing recommendations, potentially causing confusion or frustration for patients consulting multiple specialists. This study investigates whether treatment recommendations—AS, …

Clinical And Imaging Correlates Of Cognitive Impairment Patterns In Early Unilateral Brain Injury Associated With Sturge-Weber Syndrome, Halah Keramane, Csaba Juhasz Md, Phd, Michael E. Behen Phd, Aimee Luat Md

Medical Student Research Symposium

Background: Sturge-Weber syndrome (SWS) is a rare neurocutaneous disease characterized by cerebral venous malformations leading to early damage of affected brain regions. Clinical symptoms include seizures, motor and cognitive impairment. Most SWS patients have unilateral brain involvement, and previous studies reveal substantial neurological plasticity in some of them. Some children with left-hemispheric damage demonstrate, paradoxically, preserved verbal functions and reduced nonverbal functions (a “crowding” effect), suggesting contralateral functional reorganization from damaged cortical regions. We evaluated the incidence as well as clinical and imaging correlates of such functional reorganization/crowding.

Methods: Forty-six patients (age: 2.5-24 years) with unilateral SWS underwent neurocognitive evaluations …

Intranasal Delivery Of Human Olfactory Stem Cells In Sci Treatment, Muhammad Dawood Tarar, Alexander Hayes, Camera Dockery, Alexander Weiss, Marwa Elgirsg, Medha Guduguntla, Jean Peduzzi-Nelson

Medical Student Research Symposium

Background:

Olfactory stem cells hold great promise as a treatment for neural injury and disease. Two types of stem cells are known to be present in the olfactory mucosa – basal epithelial cells and mesenchymal cells in the lamina propria. Basal epithelial cells, under stimulation of mesenchymal cells, are known to differentiate into neurons^1,2. Among other immunomodulatory functions³, mesenchymal cells are also observed to differentiate into neurons. Improvement with olfactory stem cells is observed in various animal models, including head injury⁴, nerve repair^5,6, and Alzheimer’s disease⁷. The purpose of this …

Canary In The Carpal Tunnel: A Pilot Study Of The Value Of The Screening For Amyloidosis In Carpal Tunnel Syndrome, Trevor Ruesch, Nevil Khurana, Logan Hansen Md, Katiya Barkho, Julia Malewicz, Charles Day Md

Medical Student Research Symposium

Introduction/Purpose:

Transthyretin amyloidosis occurs in two forms, hereditary transthyretin amyloidosis (hATTR), and wild-type ATTR (wtATTR)². Amyloidosis can result in restrictive cardiomyopathy presenting as heart failure with preserved ejection fraction (HFpEF)⁴. A growing body of evidence demonstrates that amyloidosis may be underdiagnosed and can be caught earlier in the disease course⁵. The proteins causing amyloidosis can also deposit into various tissues including the carpal tunnel leading to carpal tunnel syndrome ².

In this pilot study, we propose that early detection of amyloid via a biopsy of the transverse carpal ligament or tenosynovium in the …

Stopping The Cirrhosis: An International Review Of Hep C Screening In Prisons And Jails From 2004-2023, Anastasia Sahu Bs, Jack Spurlock Ba, Mhs, Eliza Beal Md

Medical Student Research Symposium

Background: As of 2023, HCV prevalence in state prisons in the United States was 9 times higher than the general population¹. Without treatment, 20% of people with HCV will develop cirrhosis, and some estimate that 70% of hepatocellular carcinoma (HCC) cases arise from cirrhosis or advanced fibrosis². Despite the high prevalence in prisons, the US does not have nationally standardized Hep C screening in correctional facilities. The goal of this study is to investigate different models of existing programs in prisons internationally. Understanding these models will inform Hep C screening in US prisons on a state …

Pulling The Trigger On Patient Care: A Comparison Of Asc And Hopd Settings For Trigger Finger Release, Carinne M. Jarvis, Nooraldin Kamalaldin, Hunter Cohn, Meet S. Patel, Charles S. Day

Medical Student Research Symposium

Introduction

There is an increased focus on balancing cost-effectiveness with positive patient outcomes. Trigger finger release (TFR) offers an opportunity to compare its value in a hospital outpatient department (HOPD) versus an ambulatory surgical center (ASC). We hypothesized that TFR performed in an ASC provides greater value.

Methods

Time-Driven Activity-Based Costing (TDABC) was used to collect cost data for each procedure. Steps in the patient care pathway were timed, and costs were categorized as:

• Direct Variable: Staff salaries, supplies

• Direct Fixed: Facility, utilities

• Indirect: Administration, marketing

Changes in PROMIS Pain Interference (PI) and Upper Extremity (UE) from pre-operative to three …

Synergistic Surgical Strategies: A Comparative Analysis Of Combined Carpal Tunnel And Trigger Finger Release, Diana Kernen Ba, Clayton Kramm Bs, Meet Patel Bs, Trae Hill Bs, Carter Dunaway Bs, Charles S. Day Md, Mba

Medical Student Research Symposium

Introduction:

Since 1980, U.S. healthcare spending has outpaced GDP growth, while lagging outcomes, highlighting the need to evaluate cost-effectiveness of treating Trigger Finger Release (TFR) and Carpal Tunnel Release (CTR) simultaneously or sequentially.

Methods:

36 Patients were recruited: 12 CTR and 12 TFR patients comprised the sequential cohort, while 12 patients who underwent simultaneous CTR and TFR comprised the simultaneous cohort. Costs were calculated utilizing time-dependent activity-based costing (TDABC), activity-based costing (ABC), and insurance claims data. Procedural times were tracked and multiplied by personnel per-minute salaries to determine direct variable labor costs. Direct variable costs for supplies and direct fixed …

Characterizing Kmt2d In Endometrial Cancer, Katherine R. Davanzo

Medical Student Research Symposium

Endometrial cancer is rising in incidence in the United States, notably among premenopausal women. This increase and the trend of delayed childbearing warrant the need for further advancement in fertility-sparing treatment for endometrial cancer. A gene left widely unexplored in its possible clinical utility as a target for fertility-sparing treatment is KMT2D, a lysine-specific methyltransferase and tumor suppressor. Preliminary gene set enrichment analysis on a 12Z endometriotic epithelial cell line identified TIMP3 as a gene that is possibly regulated by KMT2D expression. TIMP3 encodes an irreversible inhibitor of matrix metalloproteinases (MMPs), a well-recognized class of proteins as contributing to the …

The Role Of Churches In Enhancing Cancer Screening Adherence: A Focus On Faith-Based Health Literacy Among African American Women, Miranda I. Goodson, Genevieve Murray

Medical Student Research Symposium

Background: It is estimated that cancer is the second leading cause of death for African American women in the United States. One study revealed that Black women have a 1 in 3 chance of developing cancer with a 1 in 6 chance of mortality. Research has shown a lower breast cancer screening adherence among women in cultural minorities and faith-based communities. The importance of spirituality and religion as an influential factor on Black community members’ beliefs about health and medicine must be considered as churches are pillars of social support within Black American communities.

Methods: A search for studies about …

Is There A Difference In Effectiveness Between Nonoperative Treatments For Modified Garcia-Elias Scapholunate Ligament Injuries Stages 1 And 2?, Michelle Yi, Minie Zhang, Lucas Kopp, Charles S. Day

Medical Student Research Symposium

Introduction

Scapholunate interosseous ligament (SLIL) injuries result from falling on an outstretched hand. Studies have assessed the effectiveness of non-operative treatments, but none has compared different non-operative treatments. We analyze the effectiveness of casting and bracing/splinting based on patient reported outcomes (PRO).

Methods

Chart review was conducted on 1150 possible SLIL injury patients from 5 orthopaedic hand surgeons from a Midwestern, tertiary-care academic hospital system between 2021 and 2024. Two patient cohorts were divided based on treatment. PROs obtained were PROMIS Upper Extremity (UE) and Pain Interference (PI) pre-treatment and 2-3 months after. Patient improvement was calculated as difference between …

Implications Of Glyphosate-Based Herbicides On The Female Reproductive System And Reproductive Outcomes, Alexandra Stone, Olivia G. Camp Ms, David Bai Md, Awoniyi Awonuga, Husam M. Abu-Soud

Medical Student Research Symposium

Background

Glyphosate-based herbicides (GBHs) are the most widely used herbicides in the United States, accounting for 19% of estimated global use. Although the Environmental Protection Agency has reaffirmed that the active ingredient glyphosate (GLY) is safe for humans, recent studies on exposure have suggested an association with cancer, metabolic disorders, endocrine disruption and infertility, and Alzheimer’s and Parkinson’s disease. Recently, we have shown that GLY exposure deteriorates metaphase II oocyte quality through zinc deficiency, ROS accumulation, and chromosome disruption. In this work, we review the mechanisms of GLY toxicity in the female reproductive tract and discuss the potential clinical implications …

The Role Of Age, Experience, And Physical Fitness In Technical Performance In Karate: An Observational Analysis, Rui Miguel Silva, Joaquim Ferreira, Georgian Badicu, Jarosław Muracki, Beata Pożarowszczyk-Kuczko, Adam Kawczyński

Baltic Journal of Health and Physical Activity

Background: This study aimed to investigate the relationships between age, experience, anthropometric measures, physical fitness, and the quality of technical performance in karate practitioners. We conducted an observational cross-sectional study with 53 federated karate athletes, aged 5 to 55, affiliated with the Youth Karate Association Portugal. The participants were divided into age and experience groups to assess differences in anthropometric measures (body mass, height, BMI) and physical fitness (strength, power, flexibility). The technical performance of four specific karate techniques – kizami, gyaku zuki, mawashi geri, and ura mawashi geri – was evaluated using a custom-designed technical evaluation …

The Relationship Between Fear Avoidance Beliefs And Low Back Pain In Crossfit Participants, Kyle Flaten

Doctorate in Kinesiology

This study aimed to examine the relationships between fear avoidance, low back pain (LBP), and disability in CrossFit (CF) participants in the greater Twin Cities area in Minnesota with correlations between the Oswestry Disability Index (ODI), the Roland Morris Disability Questionnaire (RMDQ), and Fear Avoidance Belief Questionnaire for physical activity (FABQpa). 151 CF participants voluntarily completed the survey, including demographic information, LBP characteristics, the ODI, the RMDQ, and the FABQpa. Results showed that for CF participants with current LBP, duration had a large effect on fear avoidance (ɲ = .519 and ɲ2 = .269), and for those who reported a …

Hif Regulates Multiple Translated Endogenous Retroviruses: Implications For Cancer Immunotherapy, Qinqin Jiang, David A Braun, Karl R Clauser, Vijyendra Ramesh, Nitin H Shirole, Joseph E Duke-Cohan, Nancy Nabilsi, Nicholas J Kramer, Cleo Forman, Isabelle E Lippincott, Susan Klaeger, Kshiti M Phulphagar, Vipheaviny Chea, Nawoo Kim, Allison P Vanasse, Eddy Saad, Teagan Parsons, Melissa Carr-Reynolds, Isabel Carulli, Katarina Pinjusic, Yijia Jiang, Rong Li, Sudeepa Syamala, Suzanna Rachimi, Eva K Verzani, Jonathan D Stevens, William J Lane, Sabrina Y Camp, Kevin Meli, Melissa B Pappalardi, Zachary T Herbert, Xintao Qiu, Paloma Cejas, Henry W Long, Sachet A Shukla, Eliezer M Van Allen, Toni K Choueiri, L Stirling Churchman, Jennifer G Abelin, Cagan Gurer, Gavin Macbeath, Richard W Childs, Steven A Carr, Derin B Keskin, Catherine J Wu, William G Kaelin

Faculty, Staff and Student Publications

Clear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is considered immunogenic because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor. An earlier case report described a ccRCC patient who was cured by an allogeneic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERV), ERVE-4. We report that ERVE-4 is one of many ERVs that are induced by HIF, translated …

Breaking The Synaptic Vesicle Cycle: Mechanistic Insights Into Presynaptic Dysfunctions In Epilepsy, Kevin Jiang, Lu-Tang Yang, Mingshan Xue

Duncan NRI Faculty and Staff Publications

Synaptic dysfunction is a hallmark of many neurological disorders including epilepsy. An increasing number of epilepsy-causing pathogenic variants are being identified in genes encoding presynaptic proteins that affect every step of the synaptic vesicle cycle, from vesicle loading, tethering, docking, priming, calcium sensing, fusing, to recycling. These different molecular dysfunctions result in converging impairment of presynaptic neurotransmitter release, yet lead to diverse epileptic disorders. This review focuses on representative monogenic epileptic disorders caused by pathogenic variants of key presynaptic proteins involved in different stages of the synaptic vesicle cycle: SYN1 (vesicle pool regulation), STXBP1 (vesicle docking, priming, and fusion), and …

De Novo Variants In Cdkl1 And Cdkl2 Are Associated With Neurodevelopmental Symptoms, Ali H Bereshneh, Jonathan C Andrews, Daniel F Eberl, Guney Bademci, Nicholas A Borja, Stephanie Bivona, Wendy K Chung, Shinya Yamamoto, Michael F Wangler, Shane Mckee, Mustafa Tekin, Hugo J Bellen, Oguz Kanca

Duncan NRI Faculty and Staff Publications

The CDKL (cyclin-dependent kinase-like) family consists of five members in humans, CDKL1-5, that encode serine-threonine kinases. The only member that has been associated with a Mendelian disorder is CDKL5, and variants in CDKL5 cause developmental and epileptic encephalopathy type 2 (DEE2). Here, we study four de novo variants in CDKL2 identified in five individuals, including three unrelated probands and monozygotic twins. These individuals present with overlapping symptoms, including global developmental delay, intellectual disability, childhood-onset epilepsy, dyspraxia, and speech deficits. We also identified two individuals with de novo missense variants in CDKL1 in the published Deciphering Developmental Disorders (DDD) and GeneDx …

Open Access Dataset And Common Data Model For Pulse Oximeter Performance Data, Nicholas Fong, Michael S Lipnick, Ella Behnke, Yu Chou, Seif Elmankabadi, Lily Ortiz, Christopher S Almond, Isabella Auchus, Garrett W Burnett, Ronald Bisegerwa, Desireé R Conrad, Carolyn M Hendrickson, Shubhada Hooli, Robert Kopotic, Gregory Leeb, Daniel Martin, Eric D Mccollum, Ellis P Monk, Kelvin L Moore, Leonid Shmuylovich, J Brady Scott, An-Kwok Ian Wong, Tianyue Zhou, Romain Pirracchio, Philip E Bickler, John Feiner, Tyler J Law

Faculty, Staff and Students Publications

The OpenOximetry Dataset stores clinical and lab pulse oximetry data. It supports measurements of arterial oxygen saturation (SaO2) by arterial blood gas co-oximetry and pulse oximetry (SpO2), alongside processed and unprocessed photoplethysmography (PPG) data and other metadata. This includes skin color measurements, finger diameter, vital signs (e.g., arterial blood pressure, end-tidal carbon dioxide), and arterial blood gas parameters (e.g., acid-base balance, hemoglobin concentration). All data, from desaturation studies to clinical trials, are collected prospectively to ensure accuracy. A common data model and standardized protocols for consistent archival and interpretation ensure consistent data archival and interpretation. The dataset aims to facilitate …

Clinical Validation Of Rna Sequencing For Mendelian Disorder Diagnostics, Sen Zhao, Kristina Macakova, Jefferson C Sinson, Hongzheng Dai, Jill Rosenfeld, Gladys E Zapata, Shenglan Li, Patricia A Ward, Christiana Wang, Chunjing Qu, Becky Maywald, Brendan Lee, Christine Eng, Pengfei Liu

Faculty, Staff and Students Publications

Despite rapid advancements in clinical sequencing, over half of diagnostic evaluations still lack definitive results. RNA sequencing (RNA-seq) has shown promise in research settings for bridging this gap by providing essential functional data for accurate interpretation of diagnostic sequencing results. However, despite advanced research pipelines, clinical translation of diagnostic RNA-seq has not yet been realized. We have developed and validated a clinical diagnostic RNA-seq test for individuals with suspected genetic disorders who have existing or concurrent comprehensive DNA diagnostic testing. This diagnostic RNA-seq test processes RNA samples from fibroblasts or blood and derives clinical interpretations based on the analytical detection …

"I Know Who I Am": Draw-And-Tell Conversations With Gender-Creative Children, Eline Leemans Lenne

Dissertations and Theses

A growing number of children identify in various gender-creative ways, likely due to broader social awareness and affirmation of transgenderism. Gender-creative children face higher risks for adverse social, academic, mental health, and healthcare outcomes compared to non-transgender peers. Support from loved ones along with guidance from pediatric providers can mitigate poor outcomes and ensure that gender-creative children live healthy and happy lives. Young gender-creative children's perspectives about the aforementioned topics are markedly absent from the literature, which instead highlights adolescent and adult proxy perspectives.

In this participatory arts-based study anchored by a constructivist epistemology and informed by post-structuralist, queer, and …