Exome Analysis Research Articles

Abstract B025: Integrative clinical and molecular analysis of 665 next-generation in vitro cancer models generated by the the Human Cancer Models Initiative (HCMI) for advancing precision medicine and functional drug discovery

Abstract Advancing precision medicine research relies heavily on laboratory models that accurately reflect the rich intra- and inter-patient diversity of human tumors. While large-scale resources built on historical cell lines have provided valuable insights, these models often lack the molecular diversity needed for comprehensive translational research and may undergo genetic drift in culture, reducing their fidelity. Recent advances in technologies, such as organoid culture, have improved model derivation; however, systematic pan-cancer comparisons of genomic, transcriptomic, and epigenomic integrity following long-term ex vivo expansion remain limited. Here, we report on the Human Cancer Models Initiative (HCMI), an international program that has generated and systematically characterized 665 organoid, spheroid, and cell line models derived from over 2,500 consented donors. These models have undergone comprehensive whole-genome, exome, methylome, and transcriptome analyses. The HCMI collection includes 47 unique models representing 16 rare and histologically distinct cancer subtypes, including one of a kind disease models (e.g. desmoid tumor) and greatly broadening the diversity of available cancer models. Through integrative concordance analysis, we demonstrate that 96% of the 417 analyzed models closely mirror the molecular profiles of their parental tumors. Interesting rare exceptions to this concordance include subsets of models, where cell culture media conditions, tumor stroma, or population selection appear to influence cellular characteristics. We validated observed cellular state shifts using single-cell RNA sequencing, providing insights into the impact of ex vivo culture on model integrity. We further explored the translational utility of this resource by investigating treatment exposures, post-treatment mutational signatures, and extrachromosomal DNA (ecDNA) amplifications and their potential implications on treatment resistance within these models. This community resource offers a comprehensive roadmap for capturing a broader spectrum of cancer diversity in preclinical models, ultimately supporting and advancing therapeutic discovery. Citation Format: Dina ElHarouni, Mushriq Al-Jazrawe, Seongmin Choi, Merve Dede, Toshinori Hinoue, Sean A Misek, Heeju Noh, Luca Zanella, Moony Tseng, Hayley E Francies, Priya Sridevi, Rachana Agarwal, Cindy W Kyi, Julyann Perez-Mayoral, Megan J Stine, Eva Tonsing-Carter, James M Clinton, The HCMI Network, Peter W Laird, Calvin J Kuo, Olivier Elemento, David L Spector, Andrew D Cherniack, Kyle Ellrott, Martin L Ferguson, Rameen Beroukhim, Katherine A Hoadley, Nicolas Robine, Mathew Garnett, Andrea Califano, Paul T Spellman, David A Tuveson, Keith L Ligon, Daniela S Gerhard, Louis M Staudt, Jesse Boehm. Integrative clinical and molecular analysis of 665 next-generation in vitro cancer models generated by the the Human Cancer Models Initiative (HCMI) for advancing precision medicine and functional drug discovery [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Functional and Genomic Precision Medicine in Cancer: Different Perspectives, Common Goals; 2025 Mar 11-13; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(5 Suppl):Abstract nr B025.

Glycogenosis type XI, a rare association between muscle and skin manifestations - the contribution of proteomics for the understanding of the underlying myopathology.

Glycogenosis type 11 or deficiency in lactate dehydrogenase A (LDHA) (OMIM: 612933) is an ultra-rare condition of perturbed glycogen metabolism, first described in 1980 in a Japanese patient, and quite rare outside Japan. There are very few cases described in the literature and there is limited awareness of this condition that can easily be misdiagnosed or remain undiagnosed. To report on an ultra-rare form of glycogenosis stressing the association with cutaneous features and raise awareness for this rare condition. We report a novel pathogenic variant and aim to contribute to the understanding of the myopathophysiological mechanisms of disease by proteomics. We report the clinical, histopathological, magnetic resonance, genetic and proteomic features of a 19-year-old male of North African background that presented from infancy episodes of muscle pain, contractures and high CK levels immediately after moderate to high-intensity exercise. The patient was followed for several years prior to our observation due to severe acne that involved mostly the back and was resistant to treatment. The phenotype of this patient is similar to the ones previously described with muscle and skin involvement. The MRI functional studies, interrupted at 2'30'' due to muscle pain, allowed us to confirm the presence of a metabolic disturbance of the muscles. The histological features of the muscle were quite subtle consisting mainly in rare subsarcolemmal vacuoles also identified at ultra-structural level. Immunostaining with the antibody targeting LDHA showed intracytoplasmic aggregates of the protein unlike the normal control that presented a diffuse staining. Exome analysis revealed a novel bi-allelic frameshifting deletion in exon 7 of the LDHA gene; c.766_767delGT. Proteomic findings accord with loss of functional LDHA and provide significant insights into the pathobiochemistry of the disease. Our combined data expand the current genetic landscape of LDHA-related disease, confirms the concept of a metabolic-driven vacuolar myopathy and provides insights into the biochemical nature of myopathology.

TOR1AIP2 as a candidate gene for dystonia-hemichorea/hemiballism.

TOR1AIP2 as a candidate gene for dystonia-hemichorea/hemiballism.

Use of Clinically Informed Strategies and Diagnostic Yields of Genetic Testing for Fetal Structural Anomalies Following a Non-Diagnostic Microarray Result: A Population-Based Cohort Study.

To investigate the performance of targeted gene sequencing, expanded gene panels, and selected exomes for prenatally identified fetal anomalies, after non-diagnostic microarray results. All fetal samples received for genetic testing for fetal structural anomalies in the Canadian Maritime Provinces (2014-2022) were identified. Utilization and results of NGS sequencing strategies after a non-diagnostic microarray were correlated with ultrasound findings and autopsy results. Five hundred and ninety-three cases of fetal anomalies with non-diagnostic RAD results were identified, including 319 (54%) with isolated anomalies. Diagnostic yield from the microarray was 7.5%. Sequence-based testing for 131 cases gave an overall diagnostic yield of 38% (8.4% of initial cohort). For isolated anomalies, diagnostic yield was highest in the intracranial, renal, and musculoskeletal systems (44%, 60%, 64% respectively). Appropriate targeted gene sequencing provided a diagnostic yield of 40%. With clinically indicated criteria for exome analysis, diagnostic yields were higher than when clinical information prompted use of a selected gene panel (73% vs. 27%). Expanding to an exome after a non-diagnostic gene panel had an additional diagnostic yield of 13%. Multidisciplinary review and comprehensive clinical information can inform the selection of strategies for expanded genetic testing after non-diagnostic microarray for fetal anomalies within a publicly funded health care system.

Variants of unknown significance (VUS) in DNA repair genes in Caucasian men with muscle invasive bladder cancer (MIBC): A case of “serendipity” pushing for a BC screening program.

683 Background: In 2021 we started an enhanced PCa screening in healthy Caucasian men with germline DNA repair pathogenic variants. Over 109 enrolled men, we found two naïve patients with bladder cancer (BC), but none with PCa. This observation prompted us to investigate the prevalence of germline pathogenic variants in patients with BC and suggest genetic counselling, testing and screening for healthy relatives of subject with BC. Methods: This is a prospective ongoing study aiming to detect, by exome analysis, the prevalence of germline pathogenic (PV), likely pathogenic (LPV) variants and variant of unknown significance (VUS) in patients with BC attending the urological department from January 2024. The following DNA repair genes were considered: ATM , ATR , MRE11A , BAP1 , BARD1 , BRCA1 , NBN , BRCA2 , PALB2 , BRIP1 , CHEK2 , RAD51C , FAM175A , RAD51D , GEN1 , and XRCC1 , plus mismatch repair genes MLH1 , PMS2 , MSH2 , and MSH6 . Healthy relatives (>35 years) of patients tested positive, are being offered genetic counselling, testing and finally screening for early detection of BC. Screening consists of urine analysis, urine cytology, ultrasound abdominal assessment and cystoscopy, when indicated, every year. The study is financed/supported by Associazione Italiana per la Ricerca sul Cancro (AIRC): Protocol ICH-2812, code IG 2020-ID-25027. Results: From January to March 2024, 41 patients with BC (25 non-muscle invasive, NMIBC and 16 muscle invasive, MIBC) were tested. Overall, we found 919 variants in the 20 DNA repair genes analysed, of which 385 rare (minor allele frequency <1%). No PV and LPV were identified, while 18 VUS were found in 12 patients (29.3%; mean age 66.75 SD 11.75 vs. 69.82 SD 13.71 in negative).The reported variants affected the following genes: ATM (4); ATR (3); BARD1 (3); PMS2 (2), and BRCA2 , CHEK2 , MSH6 , NBN , PALB2 , GEN1 (1 variant each). Interestingly, all variants were found in MIBC patients or HG-NMIBC, whereas no variant was observed in low-grade NMIBC (p< 0.00001, Fisher exact test). Patients with multiple variants had a significant lower age: mean age 58.16 SD 9.02 p<0.01. Conclusions: According to Merriam-Webster dictionary “serendipity” is the phenomenon of finding valuable or agreeable things not sought for. Starting from a PCa screening in healthy men, although no clearly pathogenic variants were identified in our BC cohort, we found the presence of about 30% of VUS linked to aggressive cancers and patient low age. Those findings challenge the current (no)recommendation on genetic counselling and testing in this setting and strongly support the urgent need to raise awareness of genetic risk for BC and to design effective public health promotion policies.

Case of maternal uniparental isodisomy with autosomal recessive Alport syndrome combined with congenital myasthenia and Oguchi disease.

Uniparental isodisomy (UPiD) is a genetic condition in which an individual inherits two identical copies of a chromosome, or part of a chromosome, from one parent. UPiD can result in the development of autosomal recessive disorders if the chromosome inherited from one parent has a pathogenic variant. Herein, we present a 20year-old female patient who had no significant family history including kidney, muscular, or ocular diseases. She had muscle weakness since infancy and was suspected with congenital myasthenia. She was diagnosed with Oguchi disease, a congenital condition characterized by night blindness, by an ophthalmologist. At 3years of age, hematuria was noted, and gross hematuria was occasionally observed thereafter. Exome analysis revealed homozygous variants in the COL4A4, CHRND, and SAG genes on chromosome 2, which are the causative genes of Alport syndrome, congenital myasthenic syndrome, and Oguchi disease, respectively. Array comparative genomic hybridization analysis and microsatellite analysis revealed maternal UPiD. At approximately 18years of age, she presented with proteinuria withmild kidney impairment, and kidney biopsy was performed at 20years of age. Type IV collagen α5 chain staining showed a weak but positive image in the glomerular basement membrane. However, thinning and irregular thickening of the glomerular basement membrane and reticular changes in the dense layer were observed, which were consistent with Alport syndrome. Angiotensin II receptor blocker (candesartan) was administered, and her urinary protein levels decreased. She had a homozygous missense variant, positive α5 chain staining, and a mild phenotype.

A Robust and Comprehensive Study of the Molecular and Genetic Basis of Neurodevelopmental Delay in a Sample of 3244 Patients, Evaluated by Exome Analysis in a Latin Population.

Background and Objectives: Neurodevelopmental disorders (NDDs), including developmental delay (DD), autism spectrum disorder (ASD), intellectual disability (ID), attention-deficit/hyperactivity disorder (ADHD), and specific learning disorders, affect 15% of children and adolescents worldwide. Advances in next-generation sequencing, particularly whole exome sequencing (WES), have improved the understanding of NDD genetics. Methodology: This study analyzed 3244 patients undergoing WES (single, duo, trio analyses), with 1028 meeting inclusion criteria (67% male; aged 0-50 years). Results: Pathogenic (P) or likely pathogenic (LP) variants were identified in 190 patients, achieving a diagnostic yield of 13.4% (singleton), 14% (duo), and 21.2% (trio). A total of 207 P/LP variants were identified in NDD-associated genes: 38% were missense (48 de novo), 29% frameshift (26 de novo), 21% nonsense (14 de novo), 11% splicing site (14 de novo), and 1% inframe (1 de novo). De novo variants accounted for 49.8% of cases, with 86 novels de novo variants and 27 novel non de novo variants unreported in databases like ClinVar or scientific literature. Conclusions: This is the largest study on WES in Colombian children with NDDs and one of the largest in Latino populations. It highlights WES as a cost-effective first-tier diagnostic tool in low-income settings, reducing diagnostic timelines and improving clinical care. These findings underscore the feasibility of implementing WES in underserved populations and contribute significantly to understanding NDD genetics, identifying novel variants with potential for further research and clinical applications.

Risk factors for relapse based on the molecular profiling of Japanese patients with stage II colorectal cancer.

215 Background: The association between the molecular profiles and prognosis of Stage II colorectal cancer (CRC) remains unclear. This study aimed to evaluate the long-term outcomes of Stage II CRC based on the molecular profiling and to examine the risk factors for relapse. Methods: We retrospectively enrolled Japanese patients with pStage II CRC without pre- and/or postoperative adjuvant therapy and whose surgically resected specimens were evaluated using gene expression and whole exome analyses from January 2014 to December 2018. We evaluated the 5-year overall survival (OS) and relapse-free survival (RFS), and examined the risk factors for RFS. Results: We evaluated 322 patients with pStage II CRC, including 126 (39.1%) with right colon cancer, 133 (41.3%) with left colon cancer and 63 (19.6%) with rectal cancer. There were 87 patients (27.0%) with pT4, 175 (54.3%) with venous invasion, 120 (37.3%) with lymphatic invasion, and 68 (21.1%) with perineural invasion. Whole exome analyses revealed that there were 48 patients (14.9%) with MSI-High, and the presence of mutations in key genes for colorectal cancer development was as follows: APC , 245 (76.1%); TP53 , 208 (64.6%); KRAS , 134 (6.5%); PIK3CA , 64 (19.9%); FBXW7 , 27 (8.4%); and BRAF , 21 (6.5%). The 5-year OS and RFS rates were 98.0% and 90.7%, respectively. According to the consensus molecular subtype (CMS) classification based on gene expression, 76 patients (23.6%) had CMS4 and a significantly lower RFS than the other patients (5-year RFS: 83.8% vs. 92.9%, p=0.017). The independent risk factors for RFS were perineural invasion (Hazard ratio [HR] 5.316, p<0.001) and CMS4 (HR 2.399, p=0.020). Conclusions: Molecular profiling of Stage II CRC to assess the risk factors for relapse may contribute to the indication and drug selection for postoperative adjuvant chemotherapy and lead to personalized treatment to improve prognosis.

Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL

Chronic lymphocytic leukemia is a malignant lymphoproliferative disorder for which primary or acquired drug resistance represents a major challenge. To investigate the underlying molecular mechanisms, we generate a mouse model of ibrutinib resistance, in which, after initial treatment response, relapse under therapy occurrs with an aggressive outgrowth of malignant cells, resembling observations in patients. A comparative analysis of exome, transcriptome and proteome of sorted leukemic murine cells during treatment and after relapse suggests alterations in the proteasome activity as a driver of ibrutinib resistance. Preclinical treatment with the irreversible proteasome inhibitor carfilzomib administered upon ibrutinib resistance prolongs survival of mice. Longitudinal proteomic analysis of ibrutinib-resistant patients identifies deregulation in protein post-translational modifications. Additionally, cells from ibrutinib-resistant patients effectively respond to several proteasome inhibitors in co-culture assays. Altogether, our results from orthogonal omics approaches identify proteasome inhibition as potentially attractive treatment for chronic lymphocytic leukemia patients resistant or refractory to ibrutinib.

Discontiguous recurrences of IDH-wildtype glioblastoma share a common origin with the initial tumor and are frequently hypermutated

Glioblastoma is the deadliest primary brain tumor, largely due to inevitable recurrence of the disease after treatment. While most recurrences are local, patients rarely present with a new discontiguous focus of glioblastoma. Little is currently known about the genetic profile of discontiguous recurrences. In our institutional database, we identified 22 patients with targeted exome sequencing of pairs of initial and recurrent IDH-wildtype glioblastoma. Recurrences were classified as contiguous or discontiguous based on the presence or absence of T2 FLAIR signal connection to the initial site of disease on MRI. Exome analysis revealed shared driver and passenger mutations between discontiguous recurrences and initial tumors, supporting a common origin. Discontiguous recurrences were more likely to be hypermutated compared to contiguous recurrences (p = 0.038). Analysis of 2 glioblastoma cases with discontiguous recurrence at a collaborating institution also exhibited hypermutation. In conclusion, discontiguous glioblastoma recurrences share a common origin with the initial tumor and are more likely to be hypermutated than contiguous recurrences.

Clinical follow-up of 2 families with glomerulopathy caused by COQ8B gene variants and literature review.

Primary coenzyme Q10 (CoQ10) deficiency is an autosomal recessive genetic disease caused by mitochondrial dysfunction. Variants in Coenzyme Q8B (COQ8B) can cause primary CoQ10 deficiency. COQ8B-related glomerulopathy is a recently recognized glomerular disease that most often presents as steroid-resistant nephrotic syndrome (SRNS) in childhood. The disease often progresses to kidney failure and the renal histopathology is most commonly focal segmental glomerulosclerosis (FSGS). Four SRNS cases (2 females and 2 males) from 2 unrelated families who were followed clinically for nearly 3 years. Clinical exome testing and analyses were performed by MyGenostics Laboratory in China to evaluate unexplained proteinuria given the strong family history of glomerular disease and histologic evidence of SRNS. Pathogenic variants were identified in COQ8B in the exome studies and confirmed by direct sequencing. Clinical exome sequencing revealed biallelic variants of the COQ8B gene in 2 families. In the Family 1, the oldest of three affected siblings died of renal failure at 11 years of age. Based on the results of genetic testing which identified a homozygous variant of COQ8B, the other two affected siblings with mild proteinuria and normal renal function were treated with CoQ10 oral supplementation at an early stage. Coenzyme Q10 treatment was effective in reducing proteinuria levels in both patients from Family 1 over the first 6 months and the two patients still have low-level proteinuria and normal renal function at nearly three years. In Family 2, clinical exome sequencing revealed a compoundheterozygous variants of COQ8B in a patient with biopsy- proven FSGS. His disease was unresponsive to prior treatment with glucocorticoids and cyclosporine. Oral CoQ10 was initiated based on his genetic diagnosis and was it was effective in reducing proteinuria over the first 5 months months of therapy. However after 1 year, his disease progressed tokidney failure. Kidney transplantation was performed at 5 years of age and his condition has been stable without rejection and no recurrence of disease. COQ8B gene variant-related glomerulopathy often presents as SRNS without obvious extrarenal manifestations. The histopathology is mainly FSGS and follows an autosomal recessive mode of inheritance. Some patients may benefit from early coenzyme Q10 supplementation. For patients whose disease progresses to kidney failure, kidney transplantation can be an effective treatment. For children with unexplained proteinuria and abnormal renal function, genetic testing should be performed early in the course of disease to guide therapy where possible and improve prognosis.

Nerve Enlargement in Patients with INF2 Variants Causing Peripheral Neuropathy and Focal Segmental Glomerulosclerosis.

Background: Charcot-Marie-Tooth (CMT) disease is an inherited peripheral neuropathy primarily involving motor and sensory neurons. Mutations in INF2, an actin assembly factor, cause two diseases: peripheral neuropathy CMT-DIE (MIM614455) and/or focal segmental glomerulosclerosis (FSGS). These two phenotypes arise from the progressive degeneration affecting podocytes and Schwann cells. In general, nerve enlargement has been reported in 25% of the demyelinating CMT subtype (CMT1), while little is known about the CMT-DIE caused by INF2 variants. Methods: To characterize the peripheral nerve phenotype of INF2-related CMT, we studied the clinical course, imaging, histology, and germline genetic variants in two unrelated CMT-DIE patients. Results: Patient 1 (INF2 p.Gly73Asp) and patient 2 (p.Val108Asp) first noticed walking difficulties at 10 to 12 years old. Both of them were electrophysiologically diagnosed with demyelinating neuropathy. In patient 2, the sural nerve biopsy revealed an onion bulb formation. Both patients developed nephrotic syndrome almost simultaneously with CMT and progressed into renal failure at the age of 16 to 17 years. Around the age of 30 years, both patients manifested multiple hypertrophy of the trunk, plexus, and root in the cervical, brachial, lumbosacral nerves, and cauda equina. The histology of the cervical mass in patient 2 revealed Schwannoma. Exome analysis showed that patient 2 harbors a germline LZTR1 p.Arg68Gly variant, while patient 1 has no schwannomatosis-related mutations. Conclusions: Peripheral neuropathy caused by INF2 variants may lead to the development of multifocal hypertrophy with age, likely due to the initial demyelination and subsequent Schwann cell proliferation. Schwannoma could co-occur when the tissues attain additional hits in schwannomatosis-related genes (e.g., LZTR1).

Exome Sequencing of Fetuses With Intracranial Hemorrhage Unravels Novel Causative Genes and an Extreme Genetic Heterogeneity

ABSTRACTObjectiveFetal intracranial hemorrhage (FICH) is a rare and potentially deleterious condition. Fetal alloimmune thrombocytopenia and pathogenic variations in COL4A1/A2 genes are well‐recognized causes of FICH. However, pathogenic COL4A1/A2 variations are identified in only 20% of fetuses referred for FICH after excluding other known causes, leaving the majority unexplained and making genetic counseling difficult. Our main aim was to identify novel genes associated with FICH.MethodExome sequencing was performed on 113 unrelated fetuses (35 trios, 3 families and 75 probands) after negative COL4A1/A2 testing and exclusion of known risk factors. Exome analysis incorporated several strategies including analyses of de novo and biallelic variants, and a collapsing gene‐based burden test approach.ResultsNine individuals (8%) had a pathogenic or likely pathogenic variant identified. Additionally, 14 fetuses had a suspicious variant identified in a candidate gene. Causative genes involved platelet production, hemostasis (MPL, MECOM, PROC), endothelial cell adhesion (ESAM), and mitochondrial metabolism (ATP5PO, COQ2, PDHA1). These findings suggest that FICH may result from a broader range of genetic abnormalities beyond previously known COL4A1/A2 gene mutations.ConclusionFICH is characterized by extreme genetic heterogeneity with various pathways involved, underscoring the importance of exome‐wide analyses to fully understand its causes.

Two cases of Perry disease (Perry syndrome) in the same family with normal 123I-metaiodobenzylguanidine (MIBG) myocardial scintigraphy

This study investigated two cases. Case 1 involves a 53-year-old man who suffered from sleep apnea syndrome at age 48. Moreover, he was involved in a rear-end collision while driving and was admitted to the hospital at age. He exhibited impaired consciousness, postural tremors, and bradykinesia in the upper extremities. Subsequently, he was managed on a ventilator due to unexplained alveolar hypoventilation. Case 2 is his younger sister, a 46-year-old woman, who was being treated for depression and began to show signs of parkinsonism around age 43. The metaiodobenzylguanidine (MIBG) myocardial scintigraphy results were normal in both cases. Given that their father was also managed on a ventilator due to unexplained alveolar hypoventilation, exome analyses were performed. Both were found to have a previously reported heterozygous mutation (p.Y78C) in the DCTN1 gene and were diagnosed with Perry disease. Although MIBG myocardial scintigraphy is a useful test for diagnosing Perry disease, it is important to note that there are cases where it may yield normal results.

Multiomic Sequencing of Intermediate- to High-Risk Cutaneous Squamous Cell Carcinoma Identifies Critical Genes and Expression Patterns Associated with Disease and Poor Outcomes.

Multiomic Sequencing of Intermediate- to High-Risk Cutaneous Squamous Cell Carcinoma Identifies Critical Genes and Expression Patterns Associated with Disease and Poor Outcomes.

P686: Opportunistic screening for broad range of clinically relevant secondary findings: Outcomes of exome analysis in the Incidental Genomics RCT

P686: Opportunistic screening for broad range of clinically relevant secondary findings: Outcomes of exome analysis in the Incidental Genomics RCT

Metabolic Tumor Volume Assessed by 18F FDG-PET CT Scan as a Predictive Biomarker for Immune Checkpoint Blockers in Advanced NSCLC and Its Biological Correlates.

This study aimed to explore metabolic tumor volume (MTV) as assessed by 18F-fluorodeoxyglucose positron emission tomography-computed tomography (18F-FDG-PET/CT) and understand its biological meaning in patients with non-small cell lung cancer (NSCLC) exposed to immune checkpoint blockers (ICB). In this study, patients with advanced NSCLC and a positive PET scan within 42 days of first-line treatment were enrolled in 11 institutions across four countries. Total MTV (tMTV) was analyzed, with a 42% maximum standardized uptake value threshold. Survival was analyzed according to high tMTV (≥median). Plasma proteomic profile, whole exome, transcriptome, and other analyses were performed on monocentric cohorts to explore its biological correlates. Of the 518 patients included, 167 received ICBs, 257 had chemotherapy plus ICBs, and 94 had chemotherapy. Median tMTV was 99 cm3. Median overall survival (OS) for patients with high tMTV treated with ICBs was 11.4 vs. 29.6 months (P < 0.0012) for those with low tMTV. In patients who received chemotherapy-ICB, tMTV did not correlate with OS (P = 0.099). In patients with programmed death-ligand 1 (PD-L1) ≥1% and high tMTV, chemotherapy-ICB combination was associated with longer OS compared with ICBs alone (20 vs. 11.4 months; P = 0.026), while no survival differences were observed in the low tMTV group. High tMTV correlated (and its detrimental effect seems to be driven) with a specific proteomic profile and increase in genomic instability. Our analysis indicates high tMTV is linked to an increase in systemic inflammation, specific cytokines production, and chromosomal instability. tMTV may serve as one of the biomarkers to select the best upfront strategy in patients with PD-L1-positive advanced NSCLC.

Mitochondrial DNA variant detection in over 6,500 rare disease families by the systematic analysis of exome and genome sequencing data resolves undiagnosed cases.

Variants in the mitochondrial genome (mtDNA) cause a diverse collection of mitochondrial diseases and have extensive phenotypic overlap with Mendelian diseases encoded on the nuclear genome. The mtDNA is often not specifically evaluated in patients with suspected Mendelian disease, resulting in overlooked diagnostic variants. Using dedicated pipelines to address the technical challenges posed by the mtDNA - circular genome, variant heteroplasmy, and nuclear misalignment - single nucleotide variants, small indels, and large mtDNA deletions were called from exome and genome sequencing data, in addition to RNA-sequencing when available. A cohort of 6,660 rare disease families were analyzed (5,625 genetically undiagnosed, 84%) from the Genomics Research to Elucidate the Genetics of Rare diseases (GREGoR) Consortium as well as other rare disease cohorts. Diagnostic mtDNA variants were identified in 10 previously genetically undiagnosed families (one large deletion, eight reported pathogenic variants, one novel pathogenic variant). In one additional undiagnosed proband, the detection of >900 heteroplasmic variants provided functional evidence of pathogenicity to a novel de novo variant in the nuclear gene POLG (DNA polymerase gamma), responsible for mtDNA replication and repair. mtDNA variant calling from data generated by exome and genome sequencing for nuclear variant analysis resulted in a genetic diagnosis or detection of a candidate variant for 0.4% of undiagnosed families affected by a broad range of rare diseases.

Clinical and genetic description of patients with chronic granulomatous disease in a pediatric hospital

Chronic granulomatous disease is a congenital immune disorder characterized by increased susceptibility to fungal and bacterial infections and dysregulated inflammation. It is caused by defects in the NADPH oxidase and EROS protein. To characterize clinically and genetically four patients with chronic granulomatous disease at the Hospital Infantil de México Federico Gómez. Patients diagnosed with chronic granulomatous disease by the dihydrorhodamine oxidase technique were molecularly and genetically characterized by measuring NADPH oxidase subunit expression and exome sequencing and analysis. The different clinical variables were obtained from clinical files, and each case was described. We described four male patients with chronic granulomatous disease: two with pathogenic variants in CYBB, one with CYBB and adjacent genes deleted, and one without p47phox expression. Mothers of the three patients with mutated CYBB were carriers. All three cases with CYBB had severe and recurrent infections in addition to Calmette-Guérin bacillus infection as the initial manifestation. The autosomal recessive case of p47phox deficiency had the mildest clinical presentation. Deleting CYBB and several contiguous genes was associated with a poor prognosis. None of the patients received hematopoietic stem cell transplantation. Chronic granulomatous disease, secondary to pathogenic variants in CYBB was the most common in these Mexican patients. The carrier mothers should be followed clinically because of the potential risk of inflammatory, autoimmune, and infectious manifestations. One of the first manifestations was Calmette-Guérin bacillus infection, and in countries such as Mexico, where this vaccine is administered, cases with any type of adverse reaction should be evaluated to rule out chronic granulomatous disease.

Comprehensive genomic characterization of hematologic malignancies at a pediatric tertiary care center.

Despite the increasing availability of comprehensive next generation sequencing (NGS), its role in characterizing pediatric hematologic malignancies remains undefined. We describe findings from comprehensive genomic profiling of hematologic malignancies at a pediatric tertiary care center. Patients enrolled on a translational research protocol to aid in cancer diagnosis, prognostication, treatment, and detection of cancer predisposition. Disease-involved samples underwent exome and RNA sequencing and analysis for single nucleotide variation, insertion/deletions, copy number alteration, structural variation, fusions, and gene expression. Twenty-eight patients with hematologic malignancies were nominated between 2018-2021. Eighteen individuals received both germline and somatic sequencing; two received germline sequencing only. Germline testing identified patients with cancer predisposition syndromes and non-cancer carrier states. Fifteen patients (15/18, 83%) had cancer-relevant somatic findings. Potential therapeutic targets were identified in seven patients (7/18, 38.9%); three (3/7, 42.9%) received targeted therapies and remain in remission an average of 47 months later.