Custom Pediatric Oncology Next-Generation Sequencing Panel Identifies Somatic Mosaicism in Archival Tissue and Enhances Targeted Clinical Care

Cancer Biology ◽

Health Care Policy ◽

Clinical Care ◽

Dynamic Environment ◽

Investigational Drug ◽

Next Generation ◽

Genomic Alterations ◽

Clinical Annotation ◽

Next-generation sequencing (NGS)–based technology has lowered the cost of cancer testing for genomic alterations and is now commercially available from a growing number of diagnostic laboratories. However, laboratories vary in the methodologies underlying their tests, the types and numbers of genomic alterations covered by the test, and the clinical annotation of the sequencing findings. Determining the value of NGS tests is dependent on whether it is used to support clinical trials or as a part of routine clinical care at a time when both the investigational drug pipeline and the list of U.S. Food and Drug Administration–approved or Compendium-listed therapeutics is in a high state of flux. Reimbursement policy for NGS testing by the Centers for Medicare & Medicaid is evolving as the value of NGS testing becomes more clearly defined for specific clinical situations. Patient care and clinical decisions-making are dependent on the oncologist’s knowledge of when NGS testing has value. Here, we review principles and practice for NGS testing in this dynamic confluence of technology, cancer biology, and health care policy.

Therapeutic impact and timing of gastrointestinal malignancy genomic profiling: A single-institution experience.

Journal of Clinical Oncology ◽

10.1200/jco.2016.34.4_suppl.584 ◽

2016 ◽

Vol 34 (4_suppl) ◽

pp. 584-584

Author(s):

Kristin Lynn Koenig ◽

Jarred Burkart ◽

Sameh Mikhail ◽

Christina Sing-Ying Wu ◽

Anne M. Noonan ◽

...

Keyword(s):

Clinical Trials ◽

Targeted Therapies ◽

Clinical Care ◽

Comprehensive Cancer Center ◽

Genomic Profiling ◽

Next Generation ◽

Wild Type ◽

Genomic Alterations ◽

584 Background: Tumor genomic profiling has become critical in the identification of targeted therapeutic options for patients (pts) with advanced malignancies. Mutational frequencies and their therapeutic importance vary among tumor types. This analysis was undertaken to characterize the landscape of genomic alterations in gastrointestinal (GI) malignancies found in a large academic institutional practice, and to determine the frequency of alteration-specific targeted therapy selection based on genomic profiling. Methods: Adult pts with GI malignancies presenting to the Ohio State University Comprehensive Cancer Center oncology clinics were offered next generation sequencing through FoundationOne testing as part of routine clinical care. Institutional review board approval was obtained to retrospectively analyze results from FoundationOne testing performed between 2012 and 2015. Results: 265 pts with GI malignancies underwent successful genomic profiling. 1205 genomic alterations were found, with an average of 4.5 per tumor (range 0-20); 365 (30%) of these were potentially actionable and most often found in colorectal or gastroesophageal tumors. 14 pts (5.3%) had actionable alterations in MET, CDKN2A/B, FGFR2, KRAS, BRAF, or NF2 that led to enrollment in genotype-directed clinical trials or off label use of targeted therapies beyond standard of care. Pt performance status at the time of genomic alteration identification was a significant factor in precluding genotype-directed therapy. One variant of unknown significance involving FGFR2 identified at initial testing subsequently became actionable and led to pt enrollment on a clinical trial. One pt with rectal cancer was found to have a KRAS wild-type and BRAF mutant primary but KRAS mutant and BRAF wild-type liver metastasis. Conclusions: Genomic profiling of GI malignancies through next generation sequencing is feasible and can lead to genotype-directed therapy selection; however, it should be considered early in the pt’s course to optimize use of targeted therapies through clinical trials. Consideration should be given to serial tumor testing to identify emerging genomic alterations for optimal therapy selection.

Next-generation sequencing discloses a nonsense mutation in the dystrophin gene from long preserved dried umbilical cord and low-level somatic mosaicism in the proband mother

Journal of Human Genetics ◽

10.1038/jhg.2015.157 ◽

2016 ◽

Vol 61 (4) ◽

pp. 351-355 ◽

Cited By ~ 6

Author(s):

Mariko Taniguchi-Ikeda ◽

Yasuhiro Takeshima ◽

Tomoko Lee ◽

Masahiro Nishiyama ◽

Hiroyuki Awano ◽

...

Keyword(s):

Umbilical Cord ◽

Nonsense Mutation ◽

Somatic Mosaicism ◽

Dystrophin Gene ◽

Next Generation ◽

Low Level ◽

Incorporation of Next-Generation Sequencing into Routine Clinical Care to Direct Treatment of Head and Neck Squamous Cell Carcinoma

Clinical Cancer Research ◽

10.1158/1078-0432.ccr-15-2314 ◽

2016 ◽

Vol 22 (12) ◽

pp. 2939-2949 ◽

Cited By ~ 27

Author(s):

Nicole G. Chau ◽

Yvonne Y. Li ◽

Vickie Y. Jo ◽

Guilherme Rabinowits ◽

Jochen H. Lorch ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Head And Neck ◽

Squamous Cell ◽

Clinical Care ◽

Neck Squamous Cell Carcinoma ◽

Next Generation ◽

Routine Clinical Care ◽

Somatic mosaicism in a Cornelia de Lange syndrome patient withNIPBLmutation identified by different next generation sequencing approaches

Clinical Genetics ◽

10.1111/cge.12333 ◽

2014 ◽

Vol 86 (6) ◽

pp. 595-597 ◽

Cited By ~ 10

Author(s):

C. Baquero-Montoya ◽

M.C. Gil-Rodríguez ◽

D. Braunholz ◽

M.E. Teresa-Rodrigo ◽

C. Obieglo ◽

...

Keyword(s):

Somatic Mosaicism ◽

Cornelia De Lange Syndrome ◽

Syndrome Patient ◽

Next Generation ◽

Cornelia De Lange ◽

Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants

Clinical Chemistry ◽

10.1373/clinchem.2015.249623 ◽

2016 ◽

Vol 62 (4) ◽

pp. 647-654 ◽

Cited By ~ 88

Author(s):

Tyler F Beck ◽

James C Mullikin ◽

Leslie G Biesecker ◽

Keyword(s):

Sanger Sequencing ◽

Large Scale ◽

Best Practice ◽

Clinical Care ◽

Systematic Evaluation ◽

Next Generation ◽

Current Standard ◽

Ngs Data ◽

Abstract BACKGROUND Next-generation sequencing (NGS) data are used for both clinical care and clinical research. DNA sequence variants identified using NGS are often returned to patients/participants as part of clinical or research protocols. The current standard of care is to validate NGS variants using Sanger sequencing, which is costly and time-consuming. METHODS We performed a large-scale, systematic evaluation of Sanger-based validation of NGS variants using data from the ClinSeq® project. We first used NGS data from 19 genes in 5 participants, comparing them to high-throughput Sanger sequencing results on the same samples, and found no discrepancies among 234 NGS variants. We then compared NGS variants in 5 genes from 684 participants against data from Sanger sequencing. RESULTS Of over 5800 NGS-derived variants, 19 were not validated by Sanger data. Using newly designed sequencing primers, Sanger sequencing confirmed 17 of the NGS variants, and the remaining 2 variants had low quality scores from exome sequencing. Overall, we measured a validation rate of 99.965% for NGS variants using Sanger sequencing, which was higher than many existing medical tests that do not necessitate orthogonal validation. CONCLUSIONS A single round of Sanger sequencing is more likely to incorrectly refute a true-positive variant from NGS than to correctly identify a false-positive variant from NGS. Validation of NGS-derived variants using Sanger sequencing has limited utility, and best practice standards should not include routine orthogonal Sanger validation of NGS variants.

Review of Clinical Next-Generation Sequencing

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2016-0501-ra ◽

2017 ◽

Vol 141 (11) ◽

pp. 1544-1557 ◽

Cited By ~ 87

Author(s):

Sophia Yohe ◽

Bharat Thyagarajan

Keyword(s):

Clinical Care ◽

Cost Effective ◽

Next Generation ◽

Inherited Disorders ◽

Academic Center ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Context.— Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. Objective.— To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. Data Sources.— The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. Conclusions.— The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.

Comparison of KRAS mutation analysis of colorectal cancer samples by standard testing and next-generation sequencing

Journal of Clinical Pathology ◽

10.1136/jclinpath-2014-202405 ◽

2014 ◽

Vol 67 (9) ◽

pp. 764-767 ◽

Cited By ~ 21

Author(s):

Nishi Kothari ◽

Michael J Schell ◽

Jamie K Teer ◽

Timothy Yeatman ◽

David Shibata ◽

...

Keyword(s):

Colorectal Cancer ◽

Clinical Laboratory ◽

Clinical Care ◽

Next Generation ◽

Illumina Platform ◽

Kras Mutations ◽

Standard Testing ◽

Next Generation Sequencing Ngs ◽

AimsBased on KRAS testing, the subset of patients with metastatic colorectal cancer (CRC) that could benefit from anti-EGFR therapy can be better delineated. Though KRAS testing has become significantly more prevalent over the last few years, methods for testing remain heterogeneous and discordance has been reported between methods.MethodsIn this study, we examined a CRC patient population and compared KRAS testing done in Clinical Laboratory Improvement Amendments (CLIA) approved laboratories as part of standard clinical care and by next-generation sequencing (NGS) using the Illumina platform. Discordances were further evaluated with manual review of the NGS testing.ResultsOut of 468 CRC patient samples, 77 had KRAS testing done by both CLIA assay and NGS. There were concordant results between testing methodologies in 74 out of 77 patients, or 96% (95% CI 89% to 99%). There were three patient samples that showed discordant results between the two methods of testing. Upon further investigation of the NGS results for the three discordant cases, one sample showed a low level of the mutation seen in the standard testing, one sample showed low tumour fraction and a third did not show any evidence of the mutation that was found with the standard assay. Five patients had KRAS mutations not typically tested with standard testing.ConclusionsOverall there was a high concordance rate between NGS and standard testing for KRAS. However, NGS revealed mutations that are not tested for with standard KRAS assays that might have clinical impact with regards to the role for anti-EGFR therapy.

Clinical application of cell-free next-generation sequencing for infectious diseases at a tertiary children’s hospital

BMC Infectious Diseases ◽

10.1186/s12879-021-06292-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Julianne Wilke ◽

Nanda Ramchandar ◽

Christopher Cannavino ◽

Alice Pong ◽

Adriana Tremoulet ◽

...

Keyword(s):

Infectious Diseases ◽

Clinical Application ◽

Clinical Care ◽

Next Generation ◽

Children's Hospital ◽

Percent Agreement ◽

Children’S Hospital ◽

The Impact ◽

Abstract Background Children affected by infectious diseases may not always have a detectable infectious etiology. Diagnostic uncertainty can lead to prolonged hospitalizations, inappropriately broad or extended courses of antibiotics, invasive diagnostic procedures, and difficulty predicting the clinical course and outcome. Cell-free plasma next-generation sequencing (cfNGS) can identify viral, bacterial, and fungal infections by detecting pathogen DNA in peripheral blood. This testing modality offers the ability to test for many organisms at once in a shotgun metagenomic approach with a rapid turnaround time. We sought to compare the results of cfNGS to conventional diagnostic test results and describe the impact of cfNGS on clinical care in a diverse pediatric population at a large academic children’s hospital. Methods We performed a retrospective chart review of hospitalized subjects at a tertiary pediatric hospital to determine the diagnostic yield of cfNGS and its impact on clinical care. Results We describe the clinical application of results from 142 cfNGS tests in the management of 110 subjects over an 8-month study period. In comparison to conventional testing as a reference standard, cfNGS was found to have a positive percent agreement of 89.6% and negative percent agreement of 52.3%. Furthermore, 32.4% of cfNGS results were directly applied to make a clinical change in management. Conclusions We demonstrate the clinically utility of cfNGS in the management of acutely ill children. Future studies, both retrospective and prospective, are needed to clarify the optimal indications for testing.

672. Diagnosis of Rocky Mountain Spotted Fever Using Plasma Metagenomic Next-Generation Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab466.869 ◽

2021 ◽

Vol 8 (Supplement_1) ◽

pp. S438-S438

Author(s):

Leslie Chiang ◽

Nanda Ramchandar ◽

Nicole Coufal ◽

Lauge Farnaes ◽

Jennifer Foley

Keyword(s):

Clinical Care ◽

Spotted Fever ◽

Panel Member ◽

Rocky Mountain ◽

Next Generation ◽

Rocky Mountain Spotted Fever ◽

Rickettsia Rickettsii ◽

Serologic Testing ◽

Abstract Background Rocky mountain spotted fever (RMSF), caused by Rickettsia rickettsii, incurs significant morbidity and mortality, especially in children. Early in the course of illness, standard diagnostic tests are of limited sensitivity, and diagnosis is often based on clinical symptoms and local epidemiology. The diagnosis can be missed in areas where RMSF is not endemic, and a delay in initiation of therapy may lead to poor clinical outcomes. Plasma metagenomic next-generation sequencing (mNGS), with turnaround times approaching 48 hours, may be a useful adjunctive tool in the diagnosis of RMSF. Methods We describe four children hospitalized with RMSF between January 1, 2017 to May 15, 2021 at a tertiary children’s hospital in southern California. All had plasma mNGS and rickettsial serologic testing as part of clinical care. Results mNGS detected Rickettsia rickettsii in all 4 patients. Only 2 subjects had positive serologic testing initially and required repeat testing in the convalescent stage to confirm RMSF. The mean turnaround time for mNGS was 2.75 days, which was comparable to serologic testing. Antibiotic therapy was changed in three subjects as a result of the plasma mNGS result. Conclusion Plasma mNGS may be a useful diagnostic modality early in the disease course of RMSF. Disclosures Lauge Farnaes, MD, PhD, Cardea Bio (Advisor or Review Panel member)IDbyDNA (Employee)