Feasibility Of Whole-genome Sequencing Research Articles

Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil.

In this pilot study, we aimed to evaluate the feasibility of whole genome sequencing (WGS) as a first-tier diagnostic test for infants hospitalized in neonatal intensive care units in the Brazilian healthcare system. The cohort presented here results from a joint collaboration between private and public hospitals in Brazil considering the initiative of a clinical laboratory to provide timely diagnosis for critically ill infants. We performed trio (proband and parents) WGS in 21 infants suspected of a genetic disease with an urgent need for diagnosis to guide medical care. Overall, the primary indication for genetic testing was dysmorphic syndromes (n = 14, 67%) followed by inborn errors of metabolism (n = 6, 29%) and skeletal dysplasias (n = 1, 5%). The diagnostic yield in our cohort was 57% (12/21) based on cases that received a definitive or likely definitive diagnostic result from WGS analysis. A total of 16 pathogenic/likely pathogenic variants and 10 variants of unknown significance were detected, and in most cases inherited from an unaffected parent. In addition, the reported variants were of different types, but mainly missense (58%) and associated with autosomal diseases (19/26); only three were associated with X-linked diseases, detected in hemizygosity in the proband an inherited from an unaffected mother. Notably, we identified 10 novel variants, absent from public genomic databases, in our cohort. Considering the entire diagnostic process, the average turnaround time from enrollment to medical report in our study was 53 days. Our findings demonstrate the remarkable utility of WGS as a diagnostic tool, elevating the potential of transformative impact since it outperforms conventional genetic tests. Here, we address the main challenges associated with implementing WGS in the medical care system in Brazil, as well as discuss the potential benefits and limitations of WGS as a diagnostic tool in the neonatal care setting.

Clinical utility of whole genome sequencing in hematological neoplasms.

7028 Background: Hematological neoplasms are often characterized by acute onset and rapid disease progression. Cytogenetics, FISH, SNP arrays, targeted DNA and RNA sequencing are performed to inform diagnosis, risk stratification and guide treatment decisions. Whole genome sequencing (WGS) offers the opportunity to comprehensively characterize all putative biomarkers in a single assay. However, a limitation in current WGS implementation is the requirement for a germline sample, as sources of control tissue are frequently contaminated with leukemic cells resulting in false negative calls. Methods: To evaluate the clinical utility and feasibility of WGS in the diagnostic work up of leukemias, we analyzed 57 B-cell acute lymphoblastic leukemia (B-ALL) from the UKALL14 trial (NCT01085617) with no informative biomarkers at diagnosis. WGS analysis was performed on the leukemic sample and a matching control sample (with minimal residual disease level of <1%). Using this dataset, we trained the development of an unmatched (uWGS) analytical workflow (Isabl) for a tumor only WGS study. This workflow was validated across 20 hematologic neoplasms (12 B-ALL, 6 AML and 2 T-ALL). Results: Among the 57 cases, 5 failed QC owing to low tumor content (<25%). Of the remaining 52, putative biomarkers of clinical relevance were identified by WGS in 69% (36/52). These included delineation of aberrant karyotypes where conventional chromosome banding failed (4/52), the detection of newly described fusion genes (such as IGH-DUX4 and EP300-ZNF384 in 21/52) and recurrent gene mutations (i.e. PAX5 P80R, ZEB2 H1038R in 11/52). uWGS workflow in our training dataset captured 86% of biomarkers identified in the matched analysis (3/3 ploidy, 21/22 fusion and 7/11 coding). Concordance between the matched and uWGS workflow for arm-level and focal copy number alterations (CNAs), structural variants (SVs) and annotated hotspot mutations were 94%, 84%, 83% and 100% respectively. Independent validation of the uWGS workflow across 20 myeloid and lymphoid neoplasms, recapitulated all clinically reported biomarkers (14/15 CNAs, 16/16 SVs) as well as captured two novel findings not previously detected in two B-ALL patients, to include a focal deletion in BTG1 and the fusion gene P2RY8-CRLF2, as well as a NOTCH1 translocation in T-ALL. Conclusions: Our findings demonstrate that comprehensive WGS allows for the detection of the same biomarkers as a range of clinical assays using a single test, as well as the opportunity to discover novel clinical and research findings to support future correlative research and biomarker development. Additionally, we developed and validated an uWGS workflow that allows WGS analysis of hematopoietic neoplasms at diagnosis, enabling detection and reporting of clinically relevant biomarkers.

Feasibility of whole-genome sequencing in routine clinical practice.

3013 Background: In the next few years numerous drugs will be approved for defined genomic targets, most of these in a tumor agnostic manner. Identifying patients who can benefit from this is critical for the future success of precision medicine, ideally using a single comprehensive test to detect all possible biomarkers. The WIDE study (WGS Implementation in standard cancer Diagnostics for Every cancer patient) aimed to evaluate the feasibility, clinical validity (primary endpoints) and added value (secondary endpoint) of clinical grade Whole Genome Sequencing (cWGS) in routine clinical practice. Methods: cWGS was prospectively performed on 1,200 consecutive patients with (suspected) metastatic cancer. Tumor material was obtained during routine clinical procedures for both Standard-Of-Care (SOC) and cWGS. Next to securing a high quality specimen for SOC diagnostics, multiple frozen sections per patient were evaluated to identify the sample most suitable for WGS. cWGS was conducted independently of, but in parallel with SOC diagnostics, which included SOC molecular diagnostics (Moldx) for 48% of patients. cWGS and MolDx results were compared and discussed in a dedicated tumor board. Additional tests for resolving discordances were applied when needed. Results: cWGS was successfully performed in 69% (841/1217) of samples with a technical success rate of 97% (841/871). An insufficient amount of tumor cells ( < 20%) was the main reason for not completing cWGS (25%, 310/1217). cWGS turn-around-time (TAT), due to continuous improvements to the clinical procedure and cWGS pipeline over the course of the study, decreased to 10 working days. A total of 856 genomic biomarkers identified by SOC MolDx could be compared to cWGS results. Initial analyses of discordances revealed an error rate of 2.1% (18/856) for cWGS compared to a 1.0% (8/856) error rate for SOC Moldx. After optimizing cWGS and SOC pipelines based on these findings, error rates dropped to 0.6% (5/856) and 0.7% (6/856) for cWGS and SOC MolDx, respectively. Overall, cWGS identified clinically actionable (routine practice and experimental) biomarkers in 71% of all patients tested. Compared to SOC MolDx, cWGS identified one or more additional clinically actionable biomarkers in 54% (446/832) of patients. Interestingly, in patients who were not tested by SOC MolDx, actionable variants were identified by cWGS in 54% (153/282). Conclusions: The WIDE study has shown that cWGS is feasible in routine clinical practice in a comprehensive cancer center setting, using tumor material obtained during routine procedures. Furthermore, cWGS showed added value by identifying one or more additional clinically actionable biomarkers in 54% of patients including patients who had not received SOC Moldx. These outcomes have led to the successful adoption of cWGS at the Netherlands Cancer Institute as part of routine care, which will further facilitate precision medicine for cancer patients.

Prediction of treatment outcomes for multidrug-resistant tuberculosis by whole-genome sequencing

Whole-genome sequencing (WGS) has been proposed to be a powerful tool to predict drug resistance for antitubercular drugs. However, the feasibility of WGS in predicting final treatment outcomes for multidrug-resistant tuberculosis (MDR-TB) patients remains unclear PATIENTS AND METHODS: In this prospective observational study conducted from January 2014 to September 2016, MDR-TB patients were enrolled consecutively. Genotypic drug sensitivity testing was performed via WGS using culture isolates. Patients were followed for two years to determine the treatment outcomes. Multivariate analysis was used to identify the association between information provided by WGS and the final treatment outcomes RESULTS: A total of 123 patients with MDR-TB were included in this study. The overall favorable treatment outcome rate was 60.2%. Multivariate analysis showed that independent risk factors associated with unfavorable treatment outcome including high-level moxifloxacin phenotypic resistance (OR, 4.362; 95%CI, 1.364-13.950; p=0.013), cycloserine phenotypic resistance (OR, 7.457; 95%CI, 1.644-33.819; p=0.009), mutations causing high-level fluoroquinolones resistance (OR, 3.947; 95%CI, 1.195-13.034; p=0.024), and ethA mutation (OR, 3.817; 95% CI, 1.154-12.823; p=0.028). WGS costs for each patient are ¥450 ($63), and the average turnaround time was one week CONCLUSIONS: In summary, WGS showed promising feasibility in predicting treatment outcomes for MDR-TB patients within a clinically relevant time frame.

The Dialogue Between Social Environments and the Genome

The relationship between innate, inborn inherited properties and the environment, particularly the social environment, has been one of the most contentious topics in human intellectual discourse for many generations. This discussion touches upon foundational moral and philosophical questions that define who we are, and is therefore highly emotionally loaded. This agelong discussion has been reinvigorated in recent times by leapfrog progress in genetic research and the emerging dominant dogma in biology that genotypes determine physical as well as behavioral phenotypes. The sequencing of the human genome and the increasing feasibility of whole genome sequencing raised hopes that the vast majority of human disorders and interindividual variation in health and behavior will be explained by interindividual variations in DNA sequence. Genetic determinism has been pervasively dominant in biological sciences for the last century and beyond. Strong evidence for heritability of behavioral traits has paved a path for these concepts into social and behavioral sciences as well.