Assessing the Accuracy of Variant Detection in Cost-Effective Gene Panel Testing by Next-Generation Sequencing

Abstract Purpose: This study aimed to evaluate the significance of Next-generation sequencing (NGS)-based gene panel testing in resectable colorectal cancers (CRC)s by analyzing real-world data collected prospectively from patients. Methods: Patients with CRC who underwent surgery from July 2018 to February 2020 at our institution were included, and correlations between various NGS data and clinicopathological findings were evaluated. Results: Overall, 107 patients were included in this study. The tumor stage was I in 28 cases (26.2%), II in 40 cases (37.4%), III in 32 cases (29.9%), and IV in 7 cases (6.5%). Actionable gene alterations were found in 97.2% of the cases. Co-alteration analysis suggested that either TP53- or APC-related alterations were more frequently found in early-stage tumors (stage I). The copy number alteration count was significantly lower in right side colon tumors than in tumors in other locations (P < 0.05). Homologous recombination deficiency (HRD) was more often identified in stage IV tumors than in stage I or II tumors (P < 0.05). Moreover, high HRD status was suggested to be useful for identifying high-risk stage II tumors (P < 0.05). Conclusion: In this study, real-world NGS data represented the biological features of CRCs. HRD was identified as a useful result of gene panel testing with novel utility in clinical practice.

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Next Generation Sequencing and Multi-Gene Panel Testing: Implications for the Oncology Nurse

Seminars in Oncology Nursing ◽

10.1016/j.soncn.2017.02.007 ◽

2017 ◽

Vol 33 (2) ◽

pp. 208-218 ◽

Cited By ~ 3

Author(s):

Patricia A. Kelly

Keyword(s):

Next Generation Sequencing ◽

Gene Panel ◽

Next Generation ◽

Oncology Nurse ◽

Panel Testing ◽

Gene Panel Testing ◽

Generation Sequencing

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Utility of multi-gene panel testing with next generation sequencing in women with endometrial cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.5588 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. 5588-5588

Author(s):

Jing-Yi Chern ◽

Nigel Madden ◽

Jessica Lee ◽

Deanna Gerber ◽

Anna Cantor ◽

...

Keyword(s):

Next Generation Sequencing ◽

Family History ◽

Gynecologic Cancer ◽

Gene Mutations ◽

Gene Panel ◽

Next Generation ◽

Mmr Genes ◽

Panel Testing ◽

Gene Panel Testing ◽

Generation Sequencing

5588 Background: Lynch syndrome (LS) accounts for 2-6% of all endometrial cancers (EC), and women with a germline mutation in the mismatch repair (MMR) genes ( MLH1, MSH2, MSH6, and PMS2) have an average lifetime risk of EC of 40%. As with breast and ovarian cancer syndromes, there are likely other genes implicated in the development of EC outside of the MMR genes. Multi-gene panel testing (MGPT) with next generation sequencing (NGS) allows for simultaneous analysis of numerous genes.We sought to evaluate the characteristics and incidence of gene mutations in women with newly diagnosed EC. Methods: We conducted a review of EC patients diagnosed from 6/2013 to 12/2016 who had MGPT at our institution. Demographics, family history, genetic testing results, and tumor characteristics were collected and analyzed using χ2 tests. Results: Of the 129 patients who had MGPT, 13 (10%) had a mutation and only 5 (38%) were in patients < 50 years old. The median age of EC diagnosis is 55 (31-100) years and median BMI = 27.5 (21-59). Majority were stage 1, 76 (59%) and grade 1, 50 (39%). Patients with additional primary cancers, breast or colon were not more likely to have a mutation. However, patients with a family history of gynecologic cancer were more likely to have a mutation identified, 10 (77%) mutation vs no mutation 34 (29%), p = 0.003. Among all patients tested, 8 (6%) had a mutation in LS genes, and 6 (5%) had mutations in other genes ( BRCA1, BRCA2, RAD51C, MUTYH, CHEK2); 1 (0.8%) had both MSH2 and CHEK2 mutation. Three patients had prior testing for breast cancer; 2 were found to have a BRCA1/ 2 mutation and the other was on Tamoxifen and BRCA negative. IHC was performed on 7 of 13 patients, and 5 (71%) had a loss of MMR protein expression. Variants of uncertain significance were noted in 35/129 (27%) of patients tested. Conclusions: Majority of EC patients with a mutation detected with NGS were > age 50. We identified additional new mutations in non-LS genes including, CHEK2, RAD51C, and MUYTH with MGPT. These accounted for 29% of the mutations and would have not been not detected using classic LS gene testing. These genes are implicated in breast, ovary or colon cancer. MGPT testing is feasible and useful in identifying additional actionable gene mutations.

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Next‐generation sequencing through multi‐gene panel testing for diagnosis of hereditary ichthyosis in Chinese

Clinical Genetics ◽

10.1111/cge.13704 ◽

2020 ◽

Vol 97 (5) ◽

pp. 770-778 ◽

Cited By ~ 1

Author(s):

Ruhong Cheng ◽

Jianying Liang ◽

Yue Li ◽

Jia Zhang ◽

Cheng Ni ◽

...

Keyword(s):

Next Generation Sequencing ◽

Gene Panel ◽

Next Generation ◽

Panel Testing ◽

Gene Panel Testing ◽

Generation Sequencing

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Targeted next generation sequencing with an extended gene panel does not impact variant detection in mitochondrial diseases

BMC Medical Genetics ◽

10.1186/s12881-018-0568-y ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Morgane Plutino ◽

Annabelle Chaussenot ◽

Cécile Rouzier ◽

Samira Ait-El-Mkadem ◽

Konstantina Fragaki ◽

...

Keyword(s):

Next Generation Sequencing ◽

Mitochondrial Diseases ◽

Gene Panel ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Variant Detection ◽

Generation Sequencing

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Clinical Validity of Next-Generation Sequencing Multi-Gene Panel Testing for Detecting Pathogenic Variants in Patients With Hereditary Breast-Ovarian Cancer Syndrome

Annals of Laboratory Medicine ◽

10.3343/alm.2020.40.2.148 ◽

2020 ◽

Vol 40 (2) ◽

pp. 148-154 ◽

Cited By ~ 6

Author(s):

Jaeeun Yoo ◽

Gun Dong Lee ◽

Jee Hae Kim ◽

Seung Nam Lee ◽

Hyojin Chae ◽

...

Keyword(s):

Ovarian Cancer ◽

Next Generation Sequencing ◽

Next Generation ◽

Clinical Validity ◽

Cancer Syndrome ◽

Hereditary Breast Ovarian Cancer ◽

Panel Testing ◽

Pathogenic Variants ◽

Gene Panel Testing ◽

Generation Sequencing

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An interlaboratory study of complex variant detection

10.1101/218529 ◽

2017 ◽

Cited By ~ 3

Author(s):

Stephen E Lincoln ◽

Justin M Zook ◽

Shimul Chowdhury ◽

Shazia Mahamdallie ◽

Andrew Fellowes ◽

...

Keyword(s):

Next Generation Sequencing ◽

Validation Studies ◽

Cost Effective ◽

Interlaboratory Study ◽

Next Generation ◽

Variant Detection ◽

Synthetic Controls ◽

Next Generation Sequencing Ngs ◽

Uniform Assessment ◽

Generation Sequencing

ABSTRACTNext-generation sequencing (NGS) is widely used and cost-effective. Depending on the specific methods, NGS can have limitations detecting certain technically challenging variant types even though they are both prevalent in patients and medically important. These types are underrepresented in validation studies, hindering the uniform assessment of test methodologies by laboratory directors and clinicians. Specimens containing such variants can be difficult to obtain; thus, we evaluated a novel solution to this problem in which a diverse set of technically challenging variants was synthesized and introduced into a known genomic background. This specimen was sequenced by 7 laboratories using 10 different NGS workflows. The specimen was compatible with all 10 workflows and presented biochemical and bioinformatic challenges similar to those of patient specimens. Only 10 of 22 challenging variants were correctly identified by all 10 workflows, and only 3 workflows detected all 22. Many, but not all, of the sensitivity limitations were bioinformatic in nature. We conclude that Synthetic controls can provide an efficient and informative mechanism to augment studies with technically challenging variants that are difficult to obtain otherwise. Data from such specimens can facilitate inter-laboratory methodologic comparisons and can help establish standards that improve communication between clinicians and laboratories.

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Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

Journal of International Medical Research ◽

10.1177/0300060520967778 ◽

2020 ◽

Vol 48 (12) ◽

pp. 030006052096777

Author(s):

Peisong Chen ◽

Xuegao Yu ◽

Hao Huang ◽

Wentao Zeng ◽

Xiaohong He ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ion Torrent ◽

Next Generation ◽

Large Deletions ◽

Different Types ◽

Variant Detection ◽

Polymerase Chain ◽

Next Generation Sequencing Ngs ◽

Accuracy And Repeatability ◽

Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

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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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