A comprehensive next generation sequencing tissue assay for Asian-prevalent cancers—Analytical validation and performance evaluation with clinical samples Article Swipe
Cedric Chuan Young Ng
,
Sandy Lim
,
Abner Herbert Lim
,
Nur Diyana Md Nasir
,
Jingxian Zhang
,
Vikneswari Rajasegaran
,
Jing Yi Lee
,
Jessica Sook Ting Kok
,
Aye Aye Thike
,
Johnathan Xiande Lim
,
Ruifen Weng
,
Sidney Yee
,
Yukti Choudhury
,
Jason Yongsheng Chan
,
Puay Hoon Tan
,
Min‐Han Tan
,
Bin Tean Teh
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3389/fmolb.2022.963243
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3389/fmolb.2022.963243
Introduction: A well-validated diagnostic assay with curated biomarkers complements clinicopathological factors to facilitate early diagnosis and ensure timely treatment delivery. This study focuses on an Asian-centric cancer diagnostic assay designed and thoroughly validated against commercially available standard references and a cohort of over 200 clinical specimens spanning 12 diverse Asian-centric cancer types. Methods: The assay uses hybrid-capture probes capable of profiling DNA aberrations from 572 cancer-related genes and 91 RNA fusion partners. The panel can detect clinically-tractable biomarkers such as microsatellite instability (MSI) and tumor mutation burden (TMB). Results: Analytical evaluation demonstrated 100% specificity and 99.9% sensitivity within a ≥5% VAF limit of detection (LoD) for SNV/Indels. RNA-based fusion features an LoD of ≥5 copies per nanogram input when evaluated against commercial references. Excellent linearity and concordance were observed when benchmarking against orthogonal methods in identifying MSI status, TMB scores and RNA fusions. Actionable genetic alterations were identified in 65% of the clinical samples. Conclusion: These results demonstrate a molecular diagnostic assay that accurately detects genomic alterations and complex biomarkers. The data also supports an excellent performance of this assay for making critical diagnoses and well-informed therapeutic decisions in Asian prevalent cancers.
Related Topics
Concepts
Concordance
Computational biology
Indel
Biology
Fusion gene
Microsatellite instability
Oncology
Bioinformatics
Medicine
Gene
Genetics
Microsatellite
Genotype
Allele
Single-nucleotide polymorphism
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fmolb.2022.963243
- OA Status
- gold
- Cited By
- 7
- References
- 40
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4296734196
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4296734196Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.3389/fmolb.2022.963243Digital Object Identifier
- Title
-
A comprehensive next generation sequencing tissue assay for Asian-prevalent cancers—Analytical validation and performance evaluation with clinical samplesWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-09-21Full publication date if available
- Authors
-
Cedric Chuan Young Ng, Sandy Lim, Abner Herbert Lim, Nur Diyana Md Nasir, Jingxian Zhang, Vikneswari Rajasegaran, Jing Yi Lee, Jessica Sook Ting Kok, Aye Aye Thike, Johnathan Xiande Lim, Ruifen Weng, Sidney Yee, Yukti Choudhury, Jason Yongsheng Chan, Puay Hoon Tan, Min‐Han Tan, Bin Tean TehList of authors in order
- Landing page
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https://doi.org/10.3389/fmolb.2022.963243Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.3389/fmolb.2022.963243Direct OA link when available
- Concepts
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Concordance, Computational biology, Indel, Biology, Fusion gene, Microsatellite instability, Oncology, Bioinformatics, Medicine, Gene, Genetics, Microsatellite, Genotype, Allele, Single-nucleotide polymorphismTop concepts (fields/topics) attached by OpenAlex
- Cited by
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7Total citation count in OpenAlex
- Citations by year (recent)
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2025: 3, 2024: 3, 2023: 1Per-year citation counts (last 5 years)
- References (count)
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40Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.fusion | 70, 108 |
| abstract_inverted_index.making | 181 |
| abstract_inverted_index.probes | 57 |
| abstract_inverted_index.scores | 139 |
| abstract_inverted_index.timely | 17 |
| abstract_inverted_index.types. | 51 |
| abstract_inverted_index.within | 97 |
| abstract_inverted_index.against | 33, 120, 131 |
| abstract_inverted_index.capable | 58 |
| abstract_inverted_index.complex | 168 |
| abstract_inverted_index.curated | 6 |
| abstract_inverted_index.detects | 164 |
| abstract_inverted_index.diverse | 48 |
| abstract_inverted_index.factors | 10 |
| abstract_inverted_index.focuses | 22 |
| abstract_inverted_index.genetic | 144 |
| abstract_inverted_index.genomic | 165 |
| abstract_inverted_index.methods | 133 |
| abstract_inverted_index.results | 156 |
| abstract_inverted_index.status, | 137 |
| abstract_inverted_index.Methods: | 52 |
| abstract_inverted_index.Results: | 88 |
| abstract_inverted_index.cancers. | 191 |
| abstract_inverted_index.clinical | 44, 152 |
| abstract_inverted_index.critical | 182 |
| abstract_inverted_index.designed | 29 |
| abstract_inverted_index.features | 109 |
| abstract_inverted_index.fusions. | 142 |
| abstract_inverted_index.mutation | 85 |
| abstract_inverted_index.nanogram | 116 |
| abstract_inverted_index.observed | 128 |
| abstract_inverted_index.samples. | 153 |
| abstract_inverted_index.spanning | 46 |
| abstract_inverted_index.standard | 36 |
| abstract_inverted_index.supports | 173 |
| abstract_inverted_index.Excellent | 123 |
| abstract_inverted_index.RNA-based | 107 |
| abstract_inverted_index.available | 35 |
| abstract_inverted_index.decisions | 187 |
| abstract_inverted_index.delivery. | 19 |
| abstract_inverted_index.detection | 103 |
| abstract_inverted_index.diagnoses | 183 |
| abstract_inverted_index.diagnosis | 14 |
| abstract_inverted_index.evaluated | 119 |
| abstract_inverted_index.excellent | 175 |
| abstract_inverted_index.linearity | 124 |
| abstract_inverted_index.molecular | 159 |
| abstract_inverted_index.partners. | 71 |
| abstract_inverted_index.prevalent | 190 |
| abstract_inverted_index.profiling | 60 |
| abstract_inverted_index.specimens | 45 |
| abstract_inverted_index.treatment | 18 |
| abstract_inverted_index.validated | 32 |
| abstract_inverted_index.Actionable | 143 |
| abstract_inverted_index.Analytical | 89 |
| abstract_inverted_index.accurately | 163 |
| abstract_inverted_index.biomarkers | 7, 77 |
| abstract_inverted_index.commercial | 121 |
| abstract_inverted_index.diagnostic | 3, 27, 160 |
| abstract_inverted_index.evaluation | 90 |
| abstract_inverted_index.facilitate | 12 |
| abstract_inverted_index.identified | 147 |
| abstract_inverted_index.orthogonal | 132 |
| abstract_inverted_index.references | 37 |
| abstract_inverted_index.thoroughly | 31 |
| abstract_inverted_index.Conclusion: | 154 |
| abstract_inverted_index.SNV/Indels. | 106 |
| abstract_inverted_index.aberrations | 62 |
| abstract_inverted_index.alterations | 145, 166 |
| abstract_inverted_index.biomarkers. | 169 |
| abstract_inverted_index.complements | 8 |
| abstract_inverted_index.concordance | 126 |
| abstract_inverted_index.demonstrate | 157 |
| abstract_inverted_index.identifying | 135 |
| abstract_inverted_index.instability | 81 |
| abstract_inverted_index.performance | 176 |
| abstract_inverted_index.references. | 122 |
| abstract_inverted_index.sensitivity | 96 |
| abstract_inverted_index.specificity | 93 |
| abstract_inverted_index.therapeutic | 186 |
| abstract_inverted_index.benchmarking | 130 |
| abstract_inverted_index.commercially | 34 |
| abstract_inverted_index.demonstrated | 91 |
| abstract_inverted_index.Asian-centric | 25, 49 |
| abstract_inverted_index.Introduction: | 0 |
| abstract_inverted_index.well-informed | 185 |
| abstract_inverted_index.cancer-related | 65 |
| abstract_inverted_index.hybrid-capture | 56 |
| abstract_inverted_index.microsatellite | 80 |
| abstract_inverted_index.well-validated | 2 |
| abstract_inverted_index.clinicopathological | 9 |
| abstract_inverted_index.clinically-tractable | 76 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 89 |
| corresponding_author_ids | https://openalex.org/A5036351512, https://openalex.org/A5039053890 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 17 |
| corresponding_institution_ids | https://openalex.org/I4210137145 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.6399999856948853 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.67424996 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |