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0751 Improvement in Sleepiness with Once-Nightly Sodium Oxybate in People with Narcolepsy Type 1 and Narcolepsy Type 2: A Specialty Pharmacy Data Analysis
Meskill, Sarah, Herpel, Laura, Thorpy, Michael, Ruoff, Chad, Carino, Diana, BUYSMAN, ERIN, Vu, Michelle, Abaluck, Brian, Gudeman, Jennifer , Ruoff, Chad , Ruoff, Chad M , Meskill, Sarah, Herpel, Laura Bogan, Buysman, Erin K. , Abaluck, Brian

SLEEPJ | May 9, 2026 | Volume: 49 | Issue: Supplement_1 | Pages: A335-A335

10.1093/sleep/zsag091.0750 Get It

Abstract Introduction Once-nightly sodium oxybate (ON-SXB; LUMRYZ™) is approved to treat excessive daytime sleepiness (EDS) or cataplexy in patients ≥7 years of age with narcolepsy. Findings from 2 studies have demonstrated improvements in objective and subjective EDS with ON-SXB in patients with narcolepsy type 1 (NT1) or 2 (NT2) (NCT02720744, NCT06792708). To evaluate the effect of ON-SXB on EDS in a larger, more diverse narcolepsy patient population, changes in Epworth Sleepiness Scale (ESS) score were analyzed using specialty pharmacy data. Methods Demographic/clinical data were collected from Optum Frontier Therapies pharmacy for adults with NT1 or NT2 with ≥1 filled ON-SXB prescription, ≥1 ON-SXB clinical assessment, and ≥1 follow-up ESS score (6/1/2023-9/30/2024). ESS total scores were assessed at baseline and at each follow-up assessment after ON-SXB initiation. ESS assessment participation was voluntary. Data were analyzed descriptively and stratified by narcolepsy subtype. Results Of 452 patients identified, 195 had ≥1 follow-up ESS score and reported narcolepsy type (NT1, n=123 [63%; mean age, 38.6 years; female, 69%]; NT2, n=72 [37%; mean age, 40.7 years; female, 74%]). More patients with NT1 vs NT2 (72% vs 58%) had any prior oxybate use. Baseline concomitant stimulant/wake-promoting agent use was 58% and 64% for NT1 and NT2, respectively. Mean (SD) ESS total scores at baseline were 12.1 (5.7) and 12.2 (5.3) for patients with NT1 and NT2, respectively; 31% of NT1 and 33% of NT2 had severe EDS. For both subtypes, mean (SD) ESS scores were within the normal EDS range (≤10) by the first follow-up (median time, 52 days; NT1, 10.0 [5.5]; NT2, 9.6 [4.8]). At first follow-up, more than half of patients in the NT1 (55%) and NT2 (54%) subgroups achieved normal levels (ESS total score ≤10) of sleepiness, while 20% of NT1 patients and 10% of NT2 patients had severe EDS. Mean (SD) change from baseline in ESS score was -2.1 (4.3) and -2.6 (5.3) in the NT1 and NT2 subgroups, respectively. Conclusion In this real-world dataset, both NT1 and NT2 patients quickly experienced clinically meaningful improvements in ESS score after initiating ON-SXB. These results support ON-SXB as an effective EDS treatment, regardless of narcolepsy subtype. Support (if any) Avadel Pharmaceuticals
0695 Demographics and Comorbidities of Patients with Narcolepsy: A Propensity Score–Matched Cohort Study
Soltis, Marjorie, Lipford, Melissa, Smither, Allison, Gudeman, Jennifer

SLEEPJ | May 9, 2026 | Volume: 49 | Issue: Supplement_1 | Pages: A310-A310

10.1093/sleep/zsag091.0694 Get It

Abstract Introduction Narcolepsy is a rare, chronic sleep disorder associated with decreased quality of life and multiple comorbid conditions, including sleep-related and psychiatric or mood disorders. This study used aggregate electronic health record (EHR) data to characterize the demographics and comorbidities of patients with narcolepsy. Methods An EHR-based search identified first-time Duke Health patients between January 1, 2012, and March 31, 2024. Included patients had ≥1 narcolepsy-specific ICD-9 (347.*) and ICD-10 (G47.4*) codes and ≥1 disease-supportive statement in clinical notes, identified using a natural language processing algorithm. A control cohort was propensity-matched for birth year, age at first institutional encounter, sex, race, number of diagnosis code instances, and mortality. Common comorbidities were compared and ranked between cohorts by odds ratio (OR). Statistical significance was determined using a chi-squared test; P values were corrected for multiple comparisons using Bonferroni correction. Results Within the EHR database of 2,617,188 patients, 1659 patients with a narcolepsy diagnosis were identified (mean age at first presentation, 32.4 years; white, 69%; female, 69%); the propensity-matched control cohort included 1659 patients (mean age at first presentation, 32.3 years; white, 69%; female, 69%). Comorbidities that occurred statistically significantly more frequently (all P< 0.0001) among the narcolepsy vs control cohort (OR [95% CI]) included sleep disorders: sleep-related movement disorders (26.26 [10.71-64.40]), hypersomnia (16.56 [12.54-21.87]), and circadian rhythm sleep disorders (15.43 [6.73-35.38]); psychiatric or mood disorders: posttraumatic stress disorder (3.08 [2.10-4.52]), attention deficit hyperactivity disorder (2.90 [2.28-3.68]), and depression (2.66 [2.27-3.11]); and pain disorders: trigeminal neuralgia (6.63 [2.80-15.70]), fibromyalgia (5.30 [3.58-7.85]), and chronic pain syndrome (3.37 [2.46-4.61]). Postural orthostatic tachycardia syndrome occurred statistically significantly more frequently (P< 0.0001) in the narcolepsy vs control cohort (7.24 [3.59-14.61]). Conclusion Consistent with prior EHR research, sleep, psychiatric, mood, and pain disorders were among the most frequently reported comorbidities of patients with narcolepsy. The results of this analysis of real-world demographic and clinical information of patients with narcolepsy may further inform clinicians of the most relevant concomitant disease states to consider when evaluating potential therapies. Support (if any) Avadel Pharmaceuticals
0722 Demographic and Clinical Characteristics of People Receiving Once-Nightly Sodium Oxybate Treatment: A Specialty Pharmacy Data Analysis
Ruoff, Chad, Thorpy, Michael, Herpel, Laura, Meskill, Sarah, Vu, Michelle, BUYSMAN, ERIN, Carino, Diana, Abaluck, Brian, Gudeman, Jennifer , Ruoff, Chad , Ruoff, Chad M , Herpel, Laura Bogan, Meskill, Sarah, Buysman, Erin K. , Abaluck, Brian

SLEEPJ | May 9, 2026 | Volume: 49 | Issue: Supplement_1 | Pages: A321-A322

10.1093/sleep/zsag091.0721 Get It

Abstract Introduction Once-nightly sodium oxybate (ON-SXB [LUMRYZ™]) is approved to treat excessive daytime sleepiness (EDS) or cataplexy in patients ≥7 years of age with narcolepsy. Real-world demographic/clinical characteristics and treatment adherence in patients with narcolepsy who received ON-SXB from a specialty pharmacy were assessed. Methods Baseline demographic/clinical data were collected from Optum Frontier Therapies pharmacy for patients with ≥1 filled ON-SXB prescription, ≥1 ON-SXB-related clinical assessment, and baseline Epworth Sleepiness Scale (ESS) score from 6/1/2023-9/30/2024. Adherence (≥80% of days covered) was assessed for patients with ≥3 months of ON-SXB use. Data were stratified by narcolepsy subtype (narcolepsy type 1 [NT1] and 2 [NT2] when available) and prior oxybate use (transitioned from prior oxybate therapy to ON-SXB ≤30 days of index [switch]/were oxybate-naive or discontinued oxybate >30 days before index [not-on-oxybate]). Data were analyzed descriptively. Results 452 patients were identified (NT1, 55%; NT2, 37%; NT unknown, 9%; switch, 40%; not-on-oxybate, 60% [oxybate-naive, n=147/271]). Mean (range) age was 38.9 (16.0-88.0) years. Most patients were female (68%) and had commercial insurance (78%). Overall, 67% of patients had prior oxybate use (NT1, 72% [n=179/247]; NT2, 59% [n=98/166]; switch, 100%; not-on-oxybate, 46% [n=124/271]); for these patients, the most common oxybate (65%) was mixed-salt oxybates (NT1, 61%; NT2, 70%; switch, 61%; not-on-oxybate, 70%). Overall, 64% of patients used stimulants/wake-promoting agents (WPAs) (NT1, 64%; NT2, 65%; switch, 60%; not-on-oxybate, 67%). Overall, the mean (SD) baseline ESS score was 12.0 ([5.5]; NT1, 11.7 [5.5]; NT2, 12.5 [5.3]; switch, 11.0 [5.7]; not-on-oxybate, 12.7 [5.3]). At baseline, 29% of patients experienced severe EDS (ESS score ≥16: NT1, 26%; NT2, 30%; switch, 20%; not-on-oxybate, 34%). Of 269 patients with ON-SXB use ≥3 months, 84% (NT1, 84%; NT2, 89%; switch, 94%; not-on-oxybate, 76%) demonstrated adherence. Conclusion Patients not on an oxybate had the highest baseline ESS scores and proportion with severe EDS, despite greater stimulant/WPA utilization. Patients with NT1 used oxybates more frequently than those with NT2 despite those with NT2 having higher baseline ESS scores and a greater proportion having severe EDS, suggesting oxybates merit earlier consideration in patients with NT2. Most patients demonstrated ON-SXB adherence, indicating they would likely receive full therapeutic benefit. Support (if any) Avadel Pharmaceuticals
Addressing the needs of nano-rare patients: the n-Lorem experience
Crooke, Stanley T. , Glass, Sarah, Gleeson, Joseph G, Mignon, Laurence, Skourti-Stathaki, Konstantina , Douville, Julie , Knutsen, Megan, Pu, He, Bain, Jennifer M, Berry-Kravis, Elizabeth , Kim-McManus, Olivia, Eichler, Florian , Chung, Wendy K, Nagy, Amanda, Kaufmann, Horacio, Gonzalez-Duarte, Alejandra, Oskarsson, Björn, McCourt, Emily A. , Berry‐Kravis, Elizabeth , Nagy, Amanda , Leung, Nelson , Kaufmann, Horacio , Gleeson, Joseph G. , Mignon, Laurence, Bain, Jennifer , Shneider, Neil A. , McManus, Olivia Kim , Chung, Wendy K. , González-Duarte, Alejandra

Nucleic Acids Research | May 8, 2026 | Volume: 54 | Issue: 10 | Pages: No page available

10.1093/nar/gkag504 | PMID 42227334 Get It

Abstract Patients with extremely rare pathogenic variants pose unique challenges to current healthcare systems. Nano-rare mutations have been defined as mutations with a known prevalence of <30 patients worldwide, but because of the small fraction of humans who have undergone genetic testing, neither the precise prevalence of individual mutations nor the total prevalence of patients with nano-rare mutations is known. n-Lorem is a non-profit founded in 2020 with the mission of equitably discovering, developing, and providing bespoke experimental antisense oligonucleotides (ASOs) for free, for life, to patients with nano-rare mutations that are amenable to ASO treatment. In this perspective, we provide an overview of the n-Lorem processes and systems, the characteristics of the first 329 patients who have applied for treatment for whom initial assessment was completed and suitability for ASO treatment determined, and a summary of the results of ASO treatment for patients treated to date. Detailed data on individual patients and the overall clinical safety and tolerability profiles of the ASOs for which there are clinical data are the subjects of other manuscripts.
Monogenic and Polygenic Contributions to Cardiomyopathy and Heart Failure Across Diverse Populations
Pereira, Naveen, Tan, Jia W. , Dikilitas, Ozan , Figueiral, Marta , Tan-Arroyo, Jennifer , Olson, Rory, Srinivas, Akshatha, (227567), Yao Xiao, Venettozzi, Marcella, Vairo, Filippo Pinto e, Schaid, DJ, Klee, Eric W., Dikilitas, Ozan , Olson, Rory J. , Panwar, Deepak, Cao, Jenny , Srinivas, Akshatha, Klee, Eric W.

No container title available | May 8, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.21203/rs.3.rs-9581360/v1 Get It

Abstract Pathogenic variants in cardiomyopathy genes confer substantial disease risk, yet clinical penetrance varies widely. The population-level prevalence, age-specific penetrance, and the extent to which polygenic susceptibility modifies disease risk across diverse ancestries remain poorly defined. This population-based cohort study leveraged genome sequencing and linked electronic health record data from the All of Us Research Program (n=414,830). This study found that P/LP variants in cardiomyopathy-associated genes were present in 0.91% of participants (95% CI, 0.88%–0.94%), with similar prevalence across ancestry groups. Compared with non-carriers, variant carriers had significantly higher odds of all-cause heart failure (ACHF, OR, 2.58; 95% CI, 2.31–2.89), non-ischemic heart failure (NIHF, OR, 2.74; 95% CI, 2.42–3.10), and non-ischemic cardiomyopathy (NICM, OR, 4.99; 95% CI, 4.44–5.63). Among carriers, by age 50 years, 24.5% (95% CI, 14.5%–33.4%) developed ACHF, 17.2% (95% CI, 8.8%–24.8%) developed NIHF, and 30.1% (95% CI, 19.5%–40.2%) developed NICM. Higher polygenic risk for heart failure was independently associated with increased risk of ACHF (OR, 1.81; 95% CI, 1.74–1.89), NIHF (OR, 1.66; 95% CI, 1.58–1.75), and NICM (OR, 1.69; 95% CI, 1.59–1.80). Among carriers with elevated polygenic risk, odds of disease were substantially higher than among non-carriers at average polygenic risk (ACHF: OR, 4.71; 95% CI, 4.17–5.32; NIHF: OR, 4.56; 95% CI, 3.99–5.22; NICM: OR, 8.51; 95% CI, 7.44–9.73). Results showed that P/LP variants in cardiomyopathy genes were relatively common in this large, ancestrally diverse cohort, and conferred increased risk of cardiomyopathy and HF, with incomplete but clinically meaningful penetrance. Polygenic risk for HF independently and additively increased disease risk across ancestries. Integrating both may improve risk stratification and enable more precise, equitable care.
Cardiovascular, Renal, and Hepatic Biomarkers Outside Guideline-Recommended Thresholds: Prevalence and Determinants in Type 1 Diabetes
Lucove, Jaime C. , CORNELIUS, EMILEE M., Nguyen, Huyen T., Shah, Viral N., Sherr, J L, Kudva, Yogish C., Carlson, Anders L., Wolf, Wendy A. , Shah, Viral N. , Sherr, Jennifer L , Kudva, Yogish C. , Carlson, Anders L.

Diabetes Technology & Therapeutics | May 8, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.1177/15209156261444998 | PMID 42098923 Get It

Introduction: The objective of the study was to evaluate the prevalence of cardiovascular, renal, and hepatic biomarkers that fall outside guideline-based thresholds in adults with type 1 diabetes (T1D), and to identify demographic and clinical factors associated with these biomarkers. Methods: This observational study linked data on 2,923 adults with T1D from the T1D Exchange Registry and NorstellaLinQ’s laboratory data (2022–2023). Prevalence of biomarkers outside guideline-recommended thresholds was calculated. Generalized estimating equations (GEE) were used to model associations with age, sex, race/ethnicity, insurance, T1D duration, body mass index (BMI), and hemoglobin A1c (HbA1c), while accounting for within-subject correlation due to repeated measures. Results: Elevated low-density lipoprotein (LDL) cholesterol (≥70 mg/dL, above the recommended goal for individuals with diabetes at high risk for atherosclerotic cardiovascular disease) was common (80.2%), as were overweight (33.8%) and obesity (30.3%). Additional findings included high total cholesterol (≥200 mg/dL, 22.6%), low high-density lipoprotein (HDL) cholesterol (<40 mg/dL males, <50 mg/dL females, 13.4%), elevated urinary albumin-to-creatinine ratio (≥30 mg/g, 13.0%), reduced estimated glomerular filtration rate (<60 mL/min/1.73 m 2 , 6.2%), and elevated fibrosis-4 index (FIB-4) (≥1.3, 14.4%). In adjusted GEE models, higher HbA1c was significantly associated with increased odds of abnormal cardiovascular and renal biomarkers across most measures. Male sex and BMI were linked to lower HDL cholesterol, while older age was strongly associated with elevated FIB-4. Conclusion: Obesity and elevated LDL cholesterol are highly prevalent in adults with T1D, indicating substantial cardiometabolic risk. The lack of outcome trials in this population underscores the need for studies to evaluate strategies to improve weight and lipid management and thereby reduce cardiovascular and renal risk in adults with T1D.
Macrophage metabolism directs regenerative versus fibrotic healing through BMP signaling in the mouse digit tip
Liu, Siqi, Ramesh, Madhumidha, Raymond, Charlotte, Carleton, John, Tower, Robert , Tower, Robert J , Simkin, Jennifer , Sammarco, Mimi C. , Su, Ni , Carleton, John, Le, Anne , Trostle, Alexander J. , Simkin, Jennifer

No container title available | May 7, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.64898/2026.05.04.722661 | PMID 42146602 Get It

ABSTRACT Macrophages play a central role in determining the outcomes of healing, coordinating regeneration in some injuries and scar formation in others. In both cases, this coordination involves the cross-talk between macrophages and surrounding cells. But what drives the different cross-communication pathways to determine healing outcomes is not well known. In this study, we make use of the mouse digit tip amputation model, in which an amputation through the third phalangeal element (P3) is able to completely regenerate whereas an amputation through the second phalangeal element (P2) forms a scar. We identify a population of macrophages that is specific to the P3 regenerating digit. By integrating single-cell RNAseq, spatial transcriptomics, and metabolomic analyses, we show that this population localizes specifically to the growing bone front, express BMP ligands that drive downstream BMP activation in neighboring osteoblasts and is governed by a two-part metabolic switch involving increased fatty acid oxidation coupled with reduced glycolytic activity. This spatially restricted, BMP-expressing macrophage population is entirely absent in the scar-forming P2 injury, and our data indicate that environmental conditions unique to the regenerating digit are responsible for its emergence. Together these findings identify a regeneration-specific macrophage signaling center for patterned bone formation and suggest that targeting the metabolic conditions that drive this population could improve the efficacy of regenerative therapies.
The Epidemiology of Young-Onset Barrett’s Esophagus in the United States
Vasireddy, Anila R. , Chandar, Apoorva K., Maravillas, Mart A., Perez, Jaime A., Perneth, Sandra L. Algarin, Leggett, Cadman L. , Katzka, David A. , Iyer, Prasad G. , Kamboj, Amrit K. , Vasireddy, Anila , Algarin Perneth, Sandra L, Kamboj, A K , Leggett, Cadman L , Chandar, Apoorva K., Maravillas, Mart Andrew , Kolb, Jennifer M. , Gaddam, Srinivas

Journal of Clinical Gastroenterology | May 7, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.1097/mcg.0000000000002394 | PMID 42095766 Get It

Introduction: Young-onset esophageal adenocarcinoma (EAC) often presents at advanced stages and is associated with poor outcomes. We aimed to examine the epidemiology of young-onset Barrett’s esophagus (BE) using the TriNetX database. Methods: Young-onset BE patients (age 18 to younger than 50 y) with esophagogastroduodenoscopy (EGD) within 1 year before index BE diagnosis between 2014 and 2023 were included. Negative binomial regression was used to evaluate incident-time trends, and logistic regression to assess for independent predictors of young-onset BE. Results: BE diagnosis was present in 76,691 (3.3%) of 2,337,786 patients that underwent EGD, of which 14,120 (18%) had prevalent young-onset BE. BE dysplasia/EAC was present in 6% of young-onset patients at initial diagnosis. Conventional BE risk factors also predicted young-onset BE: GERD (OR=2.4), White race (OR=2.4), male sex (OR=2.2), smoking (OR=1.2), and obesity (OR=1.1). Each additional risk factor increased the probability of BE prevalence by 74% in young patients versus 54% in older patients. The prevalence of young-onset BE was 4.5% with GERD and ≥3 additional risk factors, and 2.3% when ≥3 risk factors were present. Discussion: Young-onset BE accounts for 18% of all BE cases, demonstrates a striking 6% rate of dysplasia/neoplasia at initial diagnosis, and has a prevalence of 4.5% in those with GERD and ≥3 risk factors. These findings suggest that young-onset BE is an important patient population that merits further study. Additional studies are necessary to study the cost-effectiveness of BE screening in younger patients with multiple risk factors.
A complete human pancreatic cancer genome
Wagner, Justin , Keskus, Ayse G. , Oshima, Keisuke K. , Ranallo-Benavidez, T. Rhyker , McDaniel, Jennifer , Šikić, Mile , Lin, Dehui , Paulin, Luis F. , Sedlazeck, Fritz J. , Munding, Elizabeth M., Sanborn, JZ, Carroll, Andrew, Hassaine, Rayan, Cameron, Daniel, Catreux, Severine , Lee, Yeonghun , Murray, Lisa , Truong, Sean , Zimin, Aleksey V. , Cross, Erin , McGowan, Matthew , Vernich, Michael, Liss, Andrew S., Kocher, Jean-Pierre, Stephens, Zachary, Ahmad, Tanveer, Bryant, Asher , Dwarshuis, Nathan , Thibaud-Nissen, Francoise, Antipov, Dmitry, Koren, Sergey, Phillippy, Adam, Jain, Miten , Wenger, Aaron M. , Eacker, Stephen, Sahraeian, Sayed Mohammad Ebrahim, Boutros, Paul C., Patel, Yash, McConnell, Joseph , Borchers, Matthew , Gerton, Jennifer L. , Kostos, Paxton, Benjamin, Hila, Mootor, Mohammed Faizal Eeman , Xu, Yuan , Asri, Mobin , Miga, Karen H. , Park, Jimin , Paten, Benedict , Choi, Jae Young , Nguyen, L. , Robinson, Dan R. , Vo, Josh N. , Murtaza, Ghulam , Mason, Christopher E. , Cheng, Haoyu, Xiao, Chunlin , English, Adam C , Sedlazeck, Fritz J , Sanborn, J Zachary , Carroll, Andrew , Chang, Pi-Chuan , Cook, Daniel E , Shafin, Kishwar , de Ligt, Joep , Cameron, Daniel , Catreux, Severine , Lee, Yeonghun , Murray, Lisa , Truong, Sean , Brueffer, Christian , Cross, Erin , McGowan, Matthew , Vernich, Michael , Liss, Andrew S , Kocher, Jean-Pierre A , Stephens, Zachary , He, Hua-Jun , He, Zhiyong , Olson, Nathan D , Narzisi, Giuseppe , Jain, Miten , Wenger, Aaron M , Boutros, Paul C , Patel, Yash , Yamaguchi, Takafumi N , McConnell, Joseph , Gerton, Jennifer L , Guarracino, Andrea , Jehangir, Maryam , Mootor, Mohammed Faizal Eeman , Xu, Yuan , Miga, Karen H , Park, Jimin , Paten, Benedict , Luo, Ruibang , Zheng, Zhenxian , Choi, Jae Young , Nguyen, Linh , Vats, Pankaj , Gao, Shenghan , Murtaza, Ghulam , Mason, Christopher E , Barthel, Floris P , Xiao, Chunlin , Logsdon, Glennis A , Kolmogorov, Mikhail , Zook, Justin M , Keskus, Ayse , Ranallo-Benavidez, T Rhyker , Paulin, Luis F. , Sanborn, John Z., Ahmad, Tanveer, Thibaud‐Nissen, Françoise , Antipov, Dmitry , Koren, Sergey , Phillippy, Adam M. , Musunuri, Rajeeva , Eacker, Stephen M. , Yamaguchi, Takafumi N. , Jehangir, Maryam , Benjamin, Hila

No container title available | May 6, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.64898/2026.05.01.722316 | PMID 42146349 Get It

Summary Cancer genome sequencing is essential for understanding tumor evolution and advancing precision medicine. 1 However, reference gaps and germline variants obscure detection of small and large somatic variants and methylation in repetitive regions. 1–3 It is common for tumor cells to gain or lose chromosome arms due to somatic structural changes that occur inside highly repetitive satellite DNA sequences in the centromeres. 4 To identify the full spectrum of somatic variants, including complex rearrangements, we construct and curate near-complete, haplotype-resolved assemblies of the most recent common ancestor of an early-passage broadly-consented hypodiploid pancreatic cancer cell line and matched normal tissues. The tumor assembly completely recapitulates all 35 tumor chromosomes observed with karyotyping, with multiple translocation-induced hybrid chromosomes. The hybrid chromosomes contain putative functional dicentric and fused centromeres, nested foldback inversions causing 14 breakpoints with a haplotype switch in a single event, and centromeric satellite tandem duplications up to 136 kbp. Direct comparison of tumor and normal assembly haplotypes uncovers >7,000 variants altering >1 Mbp of sequence in repetitive regions that have been hidden by reference gaps and germline variants. 44 % of somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures and kataegis/omikli clusters. Most somatic LINE insertions originate from two hypomethylated non-reference germline LINE insertions, highlighting their impact on insertion mutation burden. These assemblies demonstrate that centromeric, acrocentric, and telomeric regions conventionally excluded from analysis harbor extensive somatic and epigenetic changes. Resolving complete tumor genomes enables a deeper understanding of cancer structural plasticity and the endpoints of breakage-fusion-bridge cycles. These assembled, curated paired normal-tumor benchmarks will serve as a critical foundation for developing future algorithms to characterize the most intractable regions of cancer genomes.