The Application of Control Materials for Ongoing Quality Management of Next-Generation Sequencing in a Clinical Genetic Laboratory

Next-generation sequencing (NGS) has played an important role in detecting genetic variants with pathologic and therapeutic potential. The advantages of NGS, such as high-throughput sequencing capacity and massively parallel sequencing, have a significant impact on realization of genetic profiling in clinical genetic laboratories. These changes have enabled clinicians to execute precision medicine in diagnosis, prognosis, and treatment for patients. However, to adapt targeted gene panels in diagnostic use, analytical validation and ongoing quality control should be implemented and applied with both practical guidelines and appropriate control materials. Several guidelines for NGS quality control recommend usage of control materials such as HapMap cell lines, synthetic DNA fragments, and genetically characterized cell lines; however, specifications or applications of such usage are insufficient to guideline method development. This review focuses on what factors should be considered before control material selection for NGS assay and practical methods of how they could be developed in clinical genetic laboratories. This review also provides the detailed sources of critical information related to control materials.

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CCMG practice guideline: laboratory guidelines for next-generation sequencing

Journal of Medical Genetics ◽

10.1136/jmedgenet-2019-106152 ◽

2019 ◽

Vol 56 (12) ◽

pp. 792-800 ◽

Cited By ~ 5

Author(s):

Stacey Hume ◽

Tanya N Nelson ◽

Marsha Speevak ◽

Elizabeth McCready ◽

Ron Agatep ◽

...

Keyword(s):

Next Generation Sequencing ◽

Clinical Laboratory ◽

Massively Parallel Sequencing ◽

Clinical Genetics ◽

Next Generation ◽

Clinical Genetic ◽

Inherited Disorders ◽

Laboratory Service ◽

Clinical Laboratories ◽

Generation Sequencing

PurposeThe purpose of this document is to provide guidance for the use of next-generation sequencing (NGS, also known as massively parallel sequencing or MPS) in Canadian clinical genetic laboratories for detection of genetic variants in genomic DNA and mitochondrial DNA for inherited disorders, as well as somatic variants in tumour DNA for acquired cancers. They are intended for Canadian clinical laboratories engaged in developing, validating and using NGS methods.Methods of statement developmentThe document was drafted by the Canadian College of Medical Geneticists (CCMG) Ad Hoc Working Group on NGS Guidelines to make recommendations relevant to NGS. The statement was circulated for comment to the CCMG Laboratory Practice and Clinical Practice committees, and to the CCMG membership. Following incorporation of feedback, the document was approved by the CCMG Board of Directors.DisclaimerThe CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada and should not be considered to be inclusive of all information laboratories should consider in the validation and use of NGS for a clinical laboratory service.

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Contamination Assessment for Cancer Next-Generation Sequencing: Method Development and Clinical Implementation

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2020-0679-oa ◽

2021 ◽

Author(s):

Yvonne Y. Li ◽

Ryan J. Schmidt ◽

Danielle K. Manning ◽

Yonghui Jia ◽

Fei Dong

Keyword(s):

Quality Control ◽

Next Generation Sequencing ◽

Method Development ◽

Control Measure ◽

Next Generation Sequencing Data ◽

Molecular Diagnostic ◽

Next Generation ◽

Contamination Assessment ◽

Clinical Cancer ◽

Generation Sequencing

Context.— The presence of allogeneic contamination impacts clinical reporting in cancer next-generation sequencing specimens. Although consensus guidelines recommend the identification of contaminating DNA as a part of quality control, implementation of contamination assessment methods in clinical molecular diagnostic laboratories has not been reported in the literature. Objective.— To develop and implement a method to assess allogeneic contamination in clinical cancer next-generation sequencing specimens. Design.— We describe a method to detect contamination based on the evaluation of single-nucleotide polymorphic sites from tumor-only specimens. We validate this method and apply it to a large cohort of cancer sequencing specimens. Results.— Identification of specimen contamination is validated via in silico and in vitro mixtures, and reference range and reproducibility are established in a panel of normal specimens. The algorithm accurately detects an episode of systemic contamination due to reagent impurity. We prospectively apply this algorithm across 7571 clinical cancer specimens from a targeted next-generation sequencing panel, in which 262 specimens (3.5%) are predicted to be affected by greater than 5% contamination. Conclusions.— Allogeneic contamination can be inferred from intrinsic cancer next-generation sequencing data without paired normal sequencing. The adoption of this approach can be useful as a quality control measure for laboratories performing clinical next-generation sequencing.

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Next-Generation Sequencing: An Emerging Tool for Drug Designing

Current Pharmaceutical Design ◽

10.2174/1381612825666190911155508 ◽

2019 ◽

Vol 25 (31) ◽

pp. 3350-3357 ◽

Cited By ~ 1

Author(s):

Pooja Tripathi ◽

Jyotsna Singh ◽

Jonathan A. Lal ◽

Vijay Tripathi

Keyword(s):

Next Generation Sequencing ◽

High Throughput ◽

Large Scale ◽

Massively Parallel Sequencing ◽

Genomic Research ◽

Biological Research ◽

Next Generation ◽

Human Welfare ◽

Drug Designing ◽

Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

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Applying Ancestry and Sex Computation as a Quality Control Tool in Targeted Next-Generation Sequencing

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqv098 ◽

2016 ◽

Vol 145 (3) ◽

pp. 308-315 ◽

Cited By ~ 4

Author(s):

Patrick C. Mathias ◽

Emily H. Turner ◽

Sheena M. Scroggins ◽

Stephen J. Salipante ◽

Noah G. Hoffman ◽

...

Keyword(s):

Quality Control ◽

Next Generation Sequencing ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Quality Control Tool ◽

Generation Sequencing ◽

Control Tool

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Next-generation sequencing in the clinical genetic screening of patients with pheochromocytoma and paraganglioma

Endocrine Connections ◽

10.1530/ec-13-0009 ◽

2013 ◽

Vol 2 (2) ◽

pp. 104-111 ◽

Cited By ~ 32

Author(s):

Joakim Crona ◽

Alberto Delgado Verdugo ◽

Dan Granberg ◽

Staffan Welin ◽

Peter Stålberg ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genetic Screening ◽

Bioinformatics Analysis ◽

Cost Effective ◽

Susceptibility Genes ◽

Next Generation ◽

Clinical Genetic ◽

Cost Effective Method ◽

Agilent Sureselect ◽

Generation Sequencing

BackgroundRecent findings have shown that up to 60% of pheochromocytomas (PCCs) and paragangliomas (PGLs) are caused by germline or somatic mutations in one of the 11 hitherto known susceptibility genes: SDHA, SDHB, SDHC, SDHD, SDHAF2, VHL, HIF2A (EPAS1), RET, NF1, TMEM127 and MAX. This list of genes is constantly growing and the 11 genes together consist of 144 exons. A genetic screening test is extensively time consuming and expensive. Hence, we introduce next-generation sequencing (NGS) as a time-efficient and cost-effective alternative.MethodsTumour lesions from three patients with apparently sporadic PCC were subjected to whole exome sequencing utilizing Agilent Sureselect target enrichment system and Illumina Hi seq platform. Bioinformatics analysis was performed in-house using commercially available software. Variants in PCC and PGL susceptibility genes were identified.ResultsWe have identified 16 unique genetic variants in PCC susceptibility loci in three different PCC, spending less than a 30-min hands-on, in-house time. Two patients had one unique variant each that was classified as probably and possibly pathogenic: NF1 Arg304Ter and RET Tyr791Phe. The RET variant was verified by Sanger sequencing.ConclusionsNGS can serve as a fast and cost-effective method in the clinical genetic screening of PCC. The bioinformatics analysis may be performed without expert skills. We identified process optimization, characterization of unknown variants and determination of additive effects of multiple variants as key issues to be addressed by future studies.

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Lavage of the Uterine Cavity for Molecular Detection of Müllerian Duct Carcinomas: A Proof-of-Concept Study

Journal of Clinical Oncology ◽

10.1200/jco.2015.61.3083 ◽

2015 ◽

Vol 33 (36) ◽

pp. 4293-4300 ◽

Cited By ~ 43

Author(s):

Elisabeth Maritschnegg ◽

Yuxuan Wang ◽

Nina Pecha ◽

Reinhard Horvat ◽

Els Van Nieuwenhuysen ◽

...

Keyword(s):

Next Generation Sequencing ◽

Tumor Tissue ◽

Massively Parallel Sequencing ◽

Uterine Cavity ◽

Mullerian Duct ◽

Next Generation ◽

Benign Lesions ◽

Cavity Detection ◽

Müllerian Duct ◽

Generation Sequencing

Purpose Type II ovarian cancer (OC) and endometrial cancer (EC) are generally diagnosed at an advanced stage, translating into a poor survival rate. There is increasing evidence that Müllerian duct cancers may exfoliate cells. We have established an approach for lavage of the uterine cavity to detect shed cancer cells. Patients and Methods Lavage of the uterine cavity was used to obtain samples from 65 patients, including 30 with OC, five with EC, three with other malignancies, and 27 with benign lesions involving gynecologic organs. These samples, as well as corresponding tumor tissue, were examined for the presence of somatic mutations using massively parallel sequencing (next-generation sequencing) and, in a subset, singleplex analysis. Results The lavage technique could be applied successfully, and sufficient amounts of DNA were obtained in all patients. Mutations, mainly in TP53, were identified in 18 (60%) of 30 lavage samples of patients with OC using next-generation sequencing. Singleplex analysis of mutations previously determined in corresponding tumor tissue led to further identification of six patients. Taken together, in 24 (80%) of 30 patients with OC, specific mutations could be identified. This also included one patient with occult OC. All five analyzed lavage specimens from patients with EC harbored mutations. Eight (29.6%) of 27 patients with benign lesions tested positive for mutations, six (75%) as a result of mutations in the KRAS gene. Conclusion This study proved that tumor cells from ovarian neoplasms are shed and can be collected via lavage of the uterine cavity. Detection of OC and EC and even clinically occult OC was achieved, making it a potential tool of significant promise for early diagnosis.

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FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology

Precision Cancer Medicine ◽

10.21037/pcm-21-29 ◽

2021 ◽

Vol 0 ◽

pp. 0-0

Author(s):

Dan Li ◽

Rebecca Kusko ◽

Baitang Ning ◽

Weida Tong ◽

Donald J. Johann Jr ◽

...

Keyword(s):

Quality Control ◽

Next Generation Sequencing ◽

Precision Oncology ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications

Genes ◽

10.3390/genes9090429 ◽

2018 ◽

Vol 9 (9) ◽

pp. 429 ◽

Cited By ~ 38

Author(s):

Daniela Barros-Silva ◽

C. Marques ◽

Rui Henrique ◽

Carmen Jerónimo

Keyword(s):

Dna Methylation ◽

Next Generation Sequencing ◽

High Throughput Sequencing ◽

Epigenetic Modification ◽

Response To Therapy ◽

Next Generation ◽

Sequencing Technologies ◽

Prognosis And Prediction ◽

Novel Biomarkers ◽

Generation Sequencing

DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.

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