Use Of Genome Sequencing Research Articles

Universal newborn screening using genome sequencing: early experience from the GUARDIAN study.

For more than 20 years there has been speculation about a future in which newborns are routinely screened at birth for genetic disorders using genome sequencing, but prospective large-scale studies assessing this vision have only recently begun. Genome sequencing may provide a means of expanding the scope of conditions included in newborn screening programs and improving the positive predictive value of traditional newborn screening. However, the use of genome sequencing for newborn screening has also raised concerns including acceptability, equity, and scalability. By reviewing the initial results of the GUARDIAN study and contrasting them with other pilot studies investigating the use of genome sequencing for large-scale newborn screening, we highlight how the lessons learned from these studies are shaping the future for the implementation of truly universal and equitable newborn genomic screening.

Genome Sequencing After Exome Sequencing in Pediatric Epilepsy

This cohort study examined the yield and use of genome sequencing after nondiagnostic exome sequencing for pediatric patients with unexplained epilepsy between August 2018 and May 2023.

STUDY OF SOMATIC AND GERMINAL MUTATIONS IN ARTERIOVENOUS MALFORMATIONS OF THE BRAIN USING WHOLE EXOME SEQUENCING

Rare vascular lesions known as brain arteriovenous malformations (bAVMs) are caused by shunts between cerebral arteries and veins that do not involve the capillary bed. The majority of bAVMs do not cause any symptoms, however some can be controlled by seizures and result in potentially fatal brain hemorrhages. Over the past ten years, significant advancements in our understanding of bAVM pathogenesis have been accomplished, primarily through the use of genome sequencing and biomolecular analysis. An autosomal dominant vascular disorder called Hereditary Hemorrhagic Telangiectasia (HHT, also known as Rendu-Osler-Weber Syndrome) affects about 1 in 5000 people globally and is associated with about 5% of brain AVMs, while the remaining 95% are due to sporadic mutations. The major aim of the project is to investigate genetic causes of sporadic forms of AVMs in the brain by means of whole-exome sequencing of tissues with AVM lesions and blood samples. Analysis of somatic mutations will broaden the understanding of AVM pathogenesis. This study was carried out in accordance with the Declaration of Helsinki's tenets and approved by the National Center of Biotechnology 's ethics committee (№9, 7 November 2023, ) Astana). Based on clinical data, the age range of the patients at the onset of the disease also encompassed 25 to 40 years. To confirm the diagnosis, MRI and CAG data were used to validate the diagnosis. Each patient completed a specially designed questionnaire with medical information (such as age of debut and type of course) and demographic data (such as age, gender, and nationality). Three patients were classified as having a Spetzler-Martin grade II, while one patient was categorized as grade III. The sizes of arteriovenous malformations (AVMs) varied from 0 to 3 mm in one patient (grade II) to 3 to 6 mm in three patients (grades II-III). AVM tissue specimens were obtained during clinically necessary procedures. Brain AVM tissues were collected during surgery, which involved trepanation and excision of the AVM. Blood samples were also collected from these patients. Both DNA and RNA were isolated from these tissue and blood samples for subsequent exome sequencing an. Qubit 2.0 fluorometer was employed for more precise determination of DNA concentration, given that the nucleic acids will be utilized in future whole exome sequencing analysis. Whole exome sequencing was performed on six samples (blood and tissue) by Novaseq 6000 (Illumina). The annotated results were analyzed for the presence of single-nucleotide polymorphisms (SNP) and insertion-deletion mutations (Indels) between DNAs from the AVM tissue sample and blood. The GATK workflow was used for the analysis and annotation of the raw data, and vcf files were generated. Then, the variants were filtered for a quality ≥ 30 in Excel 1st blood 117554, 1st tissue 114715; 2nd blood 112972, 2nd tissue 116022; 3rd blood 112859, 3rd tissue 117168 and genotype differences between tissue and blood DNA samples 1st blood 114512, 1st tissue 111682; 2nd blood 110614, 2nd tissue 111982; 3rd blood 110564, 3rd tissue 112805. After selecting only non-synonymous, frameshift insertions and deletions variants with different genotypes in the blood and tissue samples, 1st blood 279, 1st tissue 277; 2nd blood 279, 2nd tissue 271; 3rd blood 275, 3rd tissue 268 variations were observed. Analysis of whole-exome data continues.

Genome sequencing differentiates a paracentric inversion from a balanced insertion enabling more accurate preimplantation genetic testing.

Distinguishing paracentric inversions (PAIs) from chromosomal insertions has traditionally relied on fluorescent insitu hybridization (FISH) techniques, but recent advancements in high-throughput sequencing have enabled the use of genome sequencing for such differentiation. In this study, we present a 38-year-old male carrier of a paracentric inversion on chromosome 2q, inv (2)(q31.2q34), whose partner experienced recurrent miscarriages. FISH analysis confirmed the inversion, and genome sequencing was employed for detailed characterization. Preimplantation genetic testing (PGT) revealed that all assessed embryos were balanced, consistent with the low risk of unbalanced offspring associated with PAIs. While PAI carriers traditionally exhibit low risk of producing unbalanced offspring, exceptions exist due to crossover events within the inversion loop. Although the sample size was limited, the findings align with existing sperm study data, supporting the rare occurrence of unbalanced progeny in PAI carriers. This study highlights the possibility of characterizing PAIs using genome sequencing to enable correct reproductive counseling and PGT decisions. Detailed characterization of a PAI is crucial for understanding potential outcomes and guiding PGT strategies, as accurate knowledge of the inversion size is essential for appropriate method selection in PGT. Given the very low risk of unbalanced offspring in PAI carriers, routine PGT may not be warranted but should be considered in specific cases with a history of unbalanced progeny or recurrent miscarriages. This study contributes to our understanding of PAI segregation and its implications for reproductive outcomes.

Annotating microbial functions with ProkFunFind.

Analyzing microbial genomes has become an essential part of microbiology research, giving valuable insights into the functions and evolution of microbial species. Identifying genes of interest and assigning putative annotations to those genes is a central task in genome analysis, and a plethora of tools and approaches have been developed for this task. The ProkFunFind tool was developed to bridge the gap between these various annotation approaches, providing a flexible and customizable search approach to annotate microbial functions. ProkFunFind is designed around hierarchical definitions of biological functions, where individual genes can be identified using heterogeneous search terms consisting of sequences, profile hidden Markov models, protein domains, and orthology groups. This flexible and customizable search approach allows for searches to be tailored to specific biological functions, and the search results are output in multiple formats to facilitate downstream analyses. The utility of the ProkFunFind search tool was demonstrated through its application in searching for bacterial flagella, which are complex organelles composed of multiple genes. Overall, ProkFunFind provides an accessible and flexible way to integrate multiple types of annotation and sequence data while annotating biological functions in microbial genomes.IMPORTANCEGenome sequencing and analysis are increasingly important parts of microbiology, providing a way to predict metabolic functions, identify virulence factors, and understand the evolution of microbes. The expanded use of genome sequencing has also brought an abundance of search and annotation methods, but integrating the information from these different methods can be challenging and is often done through ad hoc approaches. To bridge the gap between different types of annotations, we developed ProkFunFind, a flexible and customizable search tool incorporating multiple search approaches and annotation types to annotate microbial functions. We demonstrated the utility of ProkFunFind by searching for gene clusters encoding flagellar genes using a combination of different annotation types and searches. Overall, ProkFunFind provides a reproducible and flexible way to identify gene clusters of interest, facilitating the meaningful analysis of new and existing microbial genomes.

Systematic review of the uptake and outcomes from returning secondary findings to adult participants in research genomic testing.

The increasing use of genomic sequencing in research means secondary findings (SF) is more frequently detected and becoming a more pressing issue for researchers. This is reflected by the recent publication of multiple guidelines on this issue, calling for researchers to have a plan for managing SF prior to commencing their research. A deeper understanding of participants' experiences and outcomes from receiving SF is needed to ensure that the return of SF is conducted ethically and with adequate support. This review focuses on the uptake and outcomes of receiving actionable SF for research participants. This review included studies from January 2010 to January 2023. Databases searched included Medline, Embase, PsycINFO, and Scopus. Of the 3903 studies identified, 29 were included in the analysis. The uptake of SF ranged between 20% and 97%, and outcomes were categorized into psychological, clinical, lifestyle and behavioral, and family outcomes. The results indicate there is minimal psychological impact from receiving SF. Almost all participants greatly valued receiving SF. These findings highlight considerations for researchers when returning results, including the importance of involving genetic health professionals in consenting, results return process, and ensuring continuity of care by engaging healthcare providers.

Rapid identification of primary atopic disorders (PAD) by a clinical landmark-guided, upfront use of genomic sequencing.

Primary atopic disorders (PAD) are monogenic disorders caused by pathogenic gene variants encoding proteins that are key for the maintenance of a healthy skin barrier and a well-functioning immune system. Physicians face the challenge to find single, extremely rare PAD patients/families among the millions of individuals with common allergic diseases. We describe case scenarios with signature PAD. We review the literature and deduct specific clinical red flags for PAD detection. They include a positive family history and/or signs of pathological susceptibility to infections, immunodysregulation, or syndromic disease. Results of conventional laboratory and most immunological lab studies are not sufficient to make a definitive diagnosis of PAD. In the past, multistep narrowing of differential diagnoses by various immunological and other laboratory tests led to testing of single genes or gene panel analyses, which was a time-consuming and often unsuccessful approach. The implementation of whole-genomic analyses in the routine diagnostics has led to a paradigm shift. Upfront genome-wide analysis by whole genome sequencing (WGS) will shorten the time to diagnosis, save patients from unnecessary investigations, and reduce morbidity and mortality. We propose a rational, clinical landmark-based approach for deciding which cases pass the filter for carrying out early WGS. WGS result interpretation requires a great deal of caution regarding the causal relationship of variants in PAD phenotypes and absence of proof by adequate functional tests. In case of negative WGS results, a re-iteration attitude with re-analyses of the data (using the latest data base annotation)) may eventually lead to PAD diagnosis. PAD, like many other rare genetic diseases, will only be successfully managed, if physicians from different clinical specialties and geneticists interact regularly in multidisciplinary conferences.

The Impact of Genomic Sequencing on Veterinary Diagnostics

Genomic sequencing has revolutionized veterinary diagnostics by providing a comprehensive understanding of an animal's genetic makeup and its implications for health and disease. By unraveling genetic variations and disease markers, genomic sequencing enables precise and early diagnoses of inherited diseases, infectious diseases, and cancer in animals. It empowers veterinarians to tailor treatment approaches based on an animal's genomic data, including targeted therapies and personalized medicine. Genomic sequencing also enhances disease surveillance, aids in breeding programs, and improves disease prevention strategies. However, the use of genomic sequencing in veterinary diagnostics raises ethical considerations, such as informed consent, privacy, and data ownership. Challenges include data privacy and security, interpretation of complex genomic data, and ensuring accessibility to genomic sequencing technologies. Emerging trends, including expanded genomic databases, integration of multi-omics approaches, and the implementation of artificial intelligence and machine learning, offer new opportunities for improved diagnoses and treatment outcomes. In conclusion, genomic sequencing has a profound impact on veterinary diagnostics, enabling precise diagnoses, personalized treatment approaches, and advancements in breeding programs and disease prevention.

The motivation and process for developing a consortium-wide time and motion study to estimate resource implications of innovations in the use of genome sequencing to inform patient care.

Costs of implementing genomic testing innovations extend beyond the cost of sequencing, affecting personnel and infrastructure for which little data are available. We developed a time and motion (T&M) study within the Clinical Sequencing Evidence-Generating Research (CSER) consortium to address this gap, and herein describe challenges of conducting T&M studies within a research consortium and the approaches we developed to overcome them. CSER investigators created a subgroup to carry out the T&M study (authors). We describe logistical and administrative challenges associated with resource use data collection across heterogeneous projects conducted in real-world clinical settings, and our solutions for completing this study and harmonizing data across projects. We delineate processes for feasible data collection on workflow, personnel, and resources required to deliver genetic testing innovations in each CSER project. A critical early step involved developing detailed project-specific process flow diagrams of innovation implementation in projects' clinical settings. Analyzing diagrams across sites, we identified common process-step themes, used to organize project-specific data collection and cross-project analysis. Given the heterogeneity of innovations, study design, and workflows, which affect resources required to deliver genetic testing innovations, flexibility was necessary to harmonize data collection. Despite its challenges, this heterogeneity provides rich insights about variation in clinical processes and resource implications for implementing genetic testing innovations.

Use of genome sequencing to resolve differences in gradient diffusion and agar dilution antimicrobial susceptibility testing performance of Neisseria gonorrhoeae isolates in Alberta, Canada.

Agar dilution is the gold standard method for phenotypic antimicrobial susceptibility testing (AST) for Neisseria gonorrhoeae. However, this method is laborious and requires expertise, so laboratories that perform N. gonorrhoeae AST may choose alternative methods such as disk diffusion and gradient diffusion. In this study, we retrospectively compare the performance of gradient diffusion to agar dilution for 2,394 unique N. gonorrhoeae isolates identified in Alberta from 2017 to 2020 against azithromycin, cefixime, ceftriaxone, ciprofloxacin, penicillin, and tetracycline. Genome sequencing was utilized to resolve discrepancies between AST methods, detect antimicrobial resistance markers, and identify trends between error rates and sequence types (STs) of isolates. Over 90% of N. gonorrhoeae isolates were susceptible to azithromycin, cefixime, and ceftriaxone, whereas decreased susceptibility was observed for ciprofloxacin, penicillin, and tetracycline. Categorical (CA) and essential agreement (EA) was poorest between the two methods for penicillin (CA: 86.02%; EA: 77.69%) and tetracycline (CA: 47.22%; EA: 55.96%); however, the low CA was primarily attributed to minor errors. Antimicrobial agents with errors outside of acceptable limits included azithromycin (very major error: 18.42%; major error: 7.73%) and tetracycline (very major error: 6.17%). Genome sequencing on a subset of isolates resolved 30.3% of the azithromycin major errors and confirmed the azithromycin or tetracycline very major errors. Significant associations between certain STs and error types for azithromycin and tetracycline were also identified. Overall, gradient diffusion compared well to agar dilution for cefixime, ceftriaxone, and ciprofloxacin, and genome sequencing was identified as a useful tool to arbitrate discrepant susceptibility testing results between gradient diffusion and agar dilution for N. gonorrhoeae.

Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater – a study in District East, Karachi, Pakistan

Wastewater-based surveillance is used to track the temporal patterns of the SARS-CoV-2 virus in communities. Viral RNA particle detection in wastewater samples can indicate an outbreak within a catchment area. We describe the feasibility of using a sewage network to monitor SARS-CoV-2 trend and use of genomic sequencing to describe the viral variant abundance in an urban district in Karachi, Pakistan. This was among the first studies from Pakistan to demonstrate the surveillance for SARS-CoV-2 from a semi-formal sewage system. Four sites draining into the Lyari River in District East, Karachi, were identified and included in the current study. Raw sewage samples were collected early morning twice weekly from each site between June 10, 2021 and January 17, 2022, using Bag Mediated Filtration System (BMFS). Secondary concentration of filtered samples was achieved by ultracentrifugation and skim milk flocculation. SARS-CoV-2 RNA concentrations in the samples were estimated using PCR (Qiagen ProMega kits for N1 & N2 genes). A distributed-lag negative binomial regression model within a hierarchical Bayesian framework was used to describe the relationship between wastewater RNA concentration and COVID-19 cases from the catchment area. Genomic sequencing was performed using Illumina iSeq100. Among the 151 raw sewage samples included in the study, 123 samples (81.5%) tested positive for N1 or N2 genes. The average SARS-CoV-2 RNA concentrations in the sewage samples at each lag (1-14 days prior) were associated with the cases reported for the respective days, with a peak association observed on lag day 10 (RR: 1.15; 95% Credible Interval: 1.10-1.21). Genomic sequencing showed that the delta variant dominated till September 2022, while the omicron variant was identified in November2022. Wastewater-based surveillance, together with genomic sequencing provides valuable information for monitoring the community temporal trend of SARS-CoV-2. PATH, Bill & Melinda Gates Foundation, and Global Innovation Fund.

Use of genome sequencing to hunt for cryptic second-hit variants: analysis of 31 cases recruited to the 100 000 Genomes Project

BackgroundCurrent clinical testing methods used to uncover the genetic basis of rare disease have inherent limitations, which can lead to causative pathogenic variants being missed. Within the rare disease arm...

Are We Ready for Whole Population Genomic Sequencing of Asymptomatic Newborns?

The introduction of genomic sequencing technologies into routine newborn screening programs in some form is not only inevitable but also already occurring in some settings. The question is therefore not "if" but "when and how" genomic newborn screening (GNBS) should be implemented. In April 2022, the Centre for Ethics of Paediatric Genomics held a one-day symposium exploring ethical issues relating to the use of genomic sequencing in a range of clinical settings. This review article synthesises the panel discussion and presents both the potential benefits of wide-scale implementation of genomic newborn screening, as well as its practical and ethical issues, including obtaining appropriate consent, and health system implications. A more in-depth understanding of the barriers associated with implementing genomic newborn screening is critical to the success of GNBS programs, both from a practical perspective and also in order to maintain public trust in an important public health initiative.

Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program.

Copy number variations (CNVs) play a significant role in human disease. While chromosomal microarray has traditionally been the first-tier test for CNV detection, use of genome sequencing (GS) is increasing. We report the frequency of CNVs detected with GS in a diverse pediatric cohort from the NYCKidSeq program and highlight specific examples of its clinical impact. A total of 1052 children (0-21 years) with neurodevelopmental, cardiac, and/or immunodeficiency phenotypes received GS. Phenotype-driven analysis was used, resulting in 183 (17.4%) participants with a diagnostic result. CNVs accounted for 20.2% of participants with a diagnostic result (37/183) and ranged from 0.5 kb to 16 Mb. Of participants with a diagnostic result (n = 183) and phenotypes in more than one category, 5/17 (29.4%) were solved by a CNV finding, suggesting a high prevalence of diagnostic CNVs in participants with complex phenotypes. Thirteen participants with a diagnostic CNV (35.1%) had previously uninformative genetic testing, of which nine included a chromosomal microarray. This study demonstrates the benefits of GS for reliable detection of CNVs in a pediatric cohort with variable phenotypes.

A multi-center natural history study of precision-based genomics in prostate cancer (PC).

TPS5121 Background: With genomic-based therapies approved for advanced PC, there has been a substantial rise in the clinical use of genomic sequencing. In addition to identifying actionable targets, there is a long list of less common ‘tail’ alterations in metastatic PC with unclear prognostic or predictive significance. We hypothesize that integrative clinico-genomic studies of uncommon subgroups of PC, defined based on a molecular biomarker of low-prevalence or based on an exceptional clinical outcome to therapy, can lead to the identification of new predictive and resistance biomarkers and will accelerate the development of precision medicine strategies for patients with PC. Methods: This is a multi-institutional prospective observational study for longitudinal collection of clinical and genomic data from participants (prts) with distinct molecular alterations of interest and/or exceptional phenotypes. The primary objectives are: 1) to define the natural history of men with select molecular alterations and/or exceptional clinical responses, 2) to establish a biospecimen repository for extensive molecular analyses to study the biology of PC and mediators of therapeutic response and resistance. Exploratory objectives include: 1) understanding the impact of co-occurring genomics alterations and other molecular alterations on the natural history of PC in these defined subsets, 2) identifying biologic mechanisms of exceptional response, primary and secondary resistance, and tracking evolutionary patterns that occur during acquired resistance. Eligible prts have a diagnosis of PC with known germline and/or somatic variants in PIK3A, PIK3CB, and/or AKT, PALB2, BRIP1, RAD50, RAD51, RAD54, RB1, SPOP, Wnt/B-catenin pathway, MMR genes ( MLH1, MSH2, MSH6, PMS2), EPCAM and/or TMB-high (as defined by TMB ≥ 10 mut/Mb). Any platform for genomic testing is acceptable and data is collected centrally. Prts deemed exceptional responders (with or without mutational aberrations) are defined as those with a complete response or a confirmed partial response of any duration of time to systemic therapies or any response of exceptional duration (particularly with therapies targeting PARP, the androgen receptor, and/or immunotherapies). Data including demographic, disease characteristics, treatment outcomes including response to therapies, and survival are collected along with other pathologic, radiographic, and molecular/genomic data. Correlative sample collection includes archival primary and metastatic biopsy specimens and prospective collection of blood for future analyses. This study will provide insights into the significance of individual and co-occurring alterations and will help establish a path forward for the expansion of drug indications for PC patients with rare variants. 37 prts have been accrued with an accrual ceiling of 2000 prts. Clinical trial information: NCT04706663 .

DeMAG predicts the effects of variants in clinically actionable genes by integrating structural and evolutionary epistatic features

Despite the increasing use of genomic sequencing in clinical practice, the interpretation of rare genetic variants remains challenging even in well-studied disease genes, resulting in many patients with Variants of Uncertain Significance (VUSs). Computational Variant Effect Predictors (VEPs) provide valuable evidence in variant assessment, but they are prone to misclassifying benign variants, contributing to false positives. Here, we develop Deciphering Mutations in Actionable Genes (DeMAG), a supervised classifier for missense variants trained using extensive diagnostic data available in 59 actionable disease genes (American College of Medical Genetics and Genomics Secondary Findings v2.0, ACMG SF v2.0). DeMAG improves performance over existing VEPs by reaching balanced specificity (82%) and sensitivity (94%) on clinical data, and includes a novel epistatic feature, the ‘partners score’, which leverages evolutionary and structural partnerships of residues. The ‘partners score’ provides a general framework for modeling epistatic interactions, integrating both clinical and functional information. We provide our tool and predictions for all missense variants in 316 clinically actionable disease genes (demag.org) to facilitate the interpretation of variants and improve clinical decision-making.

Expanding the Australian Newborn Blood Spot Screening Program using genomic sequencing: do we want it and are we ready?

Since the introduction of genome sequencing in medicine, the factors involved in deciding how to integrate this technology into population screening programs such as Newborn Screening (NBS) have been widely debated. In Australia, participation in NBS is not mandatory, but over 99.9% of parents elect to uptake this screening. Gauging stakeholder attitudes towards potential changes to NBS is vital in maintaining this high participation rate. The current study aimed to determine the knowledge and attitudes of Australian parents and health professionals to the incorporation of genomic sequencing into NBS programs. Participants were surveyed online in 2016 using surveys adapted from previous studies. The majority of parents (90%) self-reported some knowledge of NBS, with 77% expressing an interest in NBS using the new technology. This was significantly lower than those who would utilise NBS using current technologies (99%). Although, many health professionals (62%) felt that new technologies should currently not be used as an adjunct to NBS, 79% foresaw the use of genomic sequencing in NBS by 2026. However, for genomic sequencing to be considered, practical and technical challenges as well as parent information needs were identified including the need for accurate interpretation of data; pre-and post-test counselling; and appropriate parental consent and opt-out process. Therefore, although some support for implementing genomic sequencing into Australian NBS does exist, there is a need for further investigation into the ethical, social, legal and practical implications of introducing this new technology as a replacement to current NBS methods.

A deep intronic TCTN2 variant activating a cryptic exon predicted by SpliceRover in a patient with Joubert syndrome.

The recent introduction of genome sequencing in genetic analysis has led to the identification of pathogenic variants located in deep introns. Recently, several new tools have emerged to predict the impact of variants on splicing. Here, we present a Japanese boy of Joubert syndrome with biallelic TCTN2 variants. Exome sequencing identified only a heterozygous maternal nonsense TCTN2 variant (NM_024809.5:c.916C >T, p.(Gln306Ter)). Subsequent genome sequencing identified a deep intronic variant (c.1033+423G>A) inherited from his father. The machine learning algorithms SpliceAI, Squirls, and Pangolin were unable to predict alterations in splicing by the c.1033+423G>A variant. SpliceRover, a tool for splice site prediction using FASTA sequence, was able to detect a cryptic exon which was 85-bp away from the variant and within the inverted Alu sequence while SpliceRover scores for these splice sites showed slight increase (donor) or decrease (acceptor) between the reference and mutant sequences. RNA sequencing and RT-PCR using urinary cells confirmed inclusion of the cryptic exon. The patient showed major symptoms of TCTN2-related disorders such as developmental delay, dysmorphic facial features and polydactyly. He also showed uncommon features such as retinal dystrophy, exotropia, abnormal pattern of respiration, and periventricular heterotopia, confirming these as one of features of TCTN2-related disorders. Our study highlights usefulness of genome sequencing and RNA sequencing using urinary cells for molecular diagnosis of genetic disorders and suggests that database of cryptic splice sites predicted in introns by SpliceRover using the reference sequences can be helpful in extracting candidate variants from large numbers of intronic variants in genome sequencing.

Clinical impact of mutations in driver oncogenes and TP53/RB1 in advanced prostate cancer.

263 Background: Prostate cancer (PCa) is characterized by considerable genetic heterogeneity, and complex genomic features may influence prognosis and treatment response. We created a database of aggressive PCa that integrates comprehensive genomic sequencing with detailed clinical outcomes to better understand the optimal use of genomic sequencing. Methods: From 4/2005-7/2021, PCa cancer patients older than 18 years of age underwent tissue collection for tumoral RNA-sequencing and tumor/normal whole exome sequencing at our institution (HUM00046018, HUM00048105, HUM00067928, SU2C). Genomic and transcriptomic sequencing data was processed using Turnkey Precision Oncology. Genetic alterations, including ETS fusions, SPOP, FOXA1 class 1, and CDK12 mutations, as well as TP53 and RB1 mutations were analyzed. Clinical data was collected from 05/2021-01/2022, and clinical associations (metastasis free survival (MFS), time to castrate resistant prostate cancer (CRPC), and overall survival (OS)) were determined. Results: Data was available for 325 men. Median follow up from diagnosis was 106 months (IQR, 90-121), median age at diagnosis was 61 (IQR, 54-67), and most (91%) presented with PCa adenocarcinoma (n=292/325). At diagnosis, 51% (n=165) had localized, 5% (n=18) had clinical node positive, and 40% (n=128) had de-novo M1 disease. At time of tissue sampling, 87% (n=283) had metastatic disease, and 59% (n=192) were castrate resistant. Established PCa driver mutations included 140 ETS fusions (49%), 26 SPOP mutations (9%), 22 FOXA1 class 1 mutations (8%), and 15 (5%) CDK12 mutations. For men with localized disease at diagnosis (n=197/325), ETS fusion was associated with improved MFS (HR: 0.55; 95% CI: 0.37-0.81), time to CRPC (HR: 0.53; 0.35-0.80), and OS (HR: 0.56; 0.35-0.89). SPOP mutations were also associated with improved prognosis in this population (n=197/325): MFS (HR: 0.45; 0.24-0.84), time to CRPC (HR: 0.36; 0.18-0.73), and OS (HR: 0.46; 0.21-0.99). TP53 mutations were identified in 38% (n=122) of all patients and were associated with worse OS from the time of biopsy after adjusting for PCa castration state and disease spread at biopsy (HR: 2.2; 1.7-2.9, p<0.001). RB1 mutations were identified in 12% (n=40; 24/40 also TP53 mutants). OS from the time of biopsy was worse in the presence of dual TP53/RB1 mutants when compared to TP53 or RB1 mutants alone, independent of the disease state at time of biopsy (HR, 4.3; 95%CI: 2.7-7.0). Conclusions: In a cohort of aggressive PCa, oncogenic driver mutations were associated with significant differences in prognosis. ETS fusions and SPOP mutations correlated with improved outcomes for men with localized disease at presentation. TP53 loss was associated with worse prognosis, as was the combination with RB1 loss, across the disease spectrum. Future efforts will focus on correlating sensitivity to PCa treatments with genetic alterations throughout the disease course.

Uncovering Carpal Tunnel Syndrome Risk through Genetics: A Path to Early Prevention

Carpal Tunnel Syndrome (CTS) is a common disorder that affects the hand, caused by compression of the median nerve at the wrist. Despite its prevalence and impact on individuals, the underlying biological mechanisms of CTS remain poorly understood. Moreover, there is a lack of strategies for identifying individuals at risk for CTS in order to prevent its development. In recent years, the use of genome sequencing, genetic analysis, and genome-wide association studies (GWAS) has revealed several genetic factors that may be associated with CTS, including specific genes and gene loci. A Genetic Risk Score (GRS) that incorporates these findings could potentially be used to predict the likelihood of developing CTS and enable earlier identification and prevention of the condition. GWAS has already demonstrated a correlation between CTS severity and a GRS composed of 13 susceptibility loci. Further research on the development of a more comprehensive GRS for CTS could potentially reduce the overall burden of this disorder.