Low Allele Frequency Variants Identified on Germline Multi-Gene Panel Testing for Cancer Predisposition Can Suggest the Presence of Constitutional Mosaicism Article Swipe
A. Rodríguez
,
Linda M. Polfus
,
Brittany Bychkovsky
,
Beth Souders
,
Aleix Prat
,
Bárbara Adamo
,
Judy E. Garber
,
Carolyn Horton
,
Huma Q. Rana
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1158/1078-0432.ccr-24-4105
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1158/1078-0432.ccr-24-4105
Purpose: Enabled by advancements in next-generation sequencing for hereditary cancer conditions, low allele frequency variants (LAFV) are detected by testing laboratories. This study describes the frequency and clinical factors associated with LAFVs and reports results of follow-up testing when available. Experimental Design: This retrospective study analyzed LAFV cases identified through multi-gene panel testing (MGPT) at a single high-volume germline genetic testing laboratory. LAFVs were defined as variant allele frequencies (VAF) between 10% and 30% as confirmed by Sanger sequencing. Comparative analyses were conducted between pathogenic variants with a VAF of 30% to 60% (inferred heterozygous) and LAFV cohorts. Clinical characteristics were analyzed using descriptive statistics and logistic regression models. Ancillary testing was performed on alternative specimens or family members to determine whether LAFVs were due to constitutional mosaicism. Results: Among 363,405 individuals undergoing MGPT, 965 (1.8%) had variants with a VAF between 10% and 30%. Sanger sequencing confirmed 463 (0.1%) as LAFVs. Among the confirmed LAFVs, 262 (57.6%) were classified as pathogenic variants. The LAFV cohort compared with the control heterozygous cohort was significantly older, with a higher proportion of individuals >50 years (84.1% vs. 54.9%; P < 0.001). LAFVs were present in the following genes: TP53 (110; 64.7%), NF1 (23; 13.5%), CHEK2 (13; 7.6%), ATM (12; 7.1%), and BRCA1 (4; 2.4%). Ancillary testing performed on 62 cases with LAFVs confirmed 17.7% (11/62) as constitutional mosaicism. Conclusions: LAFVs were infrequently detected in MGPT, representing 0.8% of the total variants and 0.1% of total tested. Ancillary testing is needed to understand the origins and clinical implications of LAFVs in patients and families.
Related Topics
Concepts
Sanger sequencing
Genetic testing
Germline
CHEK2
Genetics
Allele
Allele frequency
Minor allele frequency
Cancer
Medicine
Germline mutation
Biology
Oncology
Internal medicine
Gene
DNA sequencing
Mutation
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1158/1078-0432.ccr-24-4105
- https://aacrjournals.org/clincancerres/article-pdf/doi/10.1158/1078-0432.CCR-24-4105/3597364/ccr-24-4105.pdf
- OA Status
- hybrid
- Cited By
- 1
- References
- 59
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4409680237
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4409680237Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1158/1078-0432.ccr-24-4105Digital Object Identifier
- Title
-
Low Allele Frequency Variants Identified on Germline Multi-Gene Panel Testing for Cancer Predisposition Can Suggest the Presence of Constitutional MosaicismWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-04-21Full publication date if available
- Authors
-
A. Rodríguez, Linda M. Polfus, Brittany Bychkovsky, Beth Souders, Aleix Prat, Bárbara Adamo, Judy E. Garber, Carolyn Horton, Huma Q. RanaList of authors in order
- Landing page
-
https://doi.org/10.1158/1078-0432.ccr-24-4105Publisher landing page
- PDF URL
-
https://aacrjournals.org/clincancerres/article-pdf/doi/10.1158/1078-0432.CCR-24-4105/3597364/ccr-24-4105.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
-
https://aacrjournals.org/clincancerres/article-pdf/doi/10.1158/1078-0432.CCR-24-4105/3597364/ccr-24-4105.pdfDirect OA link when available
- Concepts
-
Sanger sequencing, Genetic testing, Germline, CHEK2, Genetics, Allele, Allele frequency, Minor allele frequency, Cancer, Medicine, Germline mutation, Biology, Oncology, Internal medicine, Gene, DNA sequencing, MutationTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
1Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 1Per-year citation counts (last 5 years)
- References (count)
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59Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.with | 31, 87, 139, 168, 176, 219 |
| abstract_inverted_index.(110; | 198 |
| abstract_inverted_index.(VAF) | 70 |
| abstract_inverted_index.17.7% | 222 |
| abstract_inverted_index.Among | 130, 153 |
| abstract_inverted_index.BRCA1 | 210 |
| abstract_inverted_index.CHEK2 | 203 |
| abstract_inverted_index.LAFVs | 32, 63, 123, 190, 220, 228, 257 |
| abstract_inverted_index.MGPT, | 134, 233 |
| abstract_inverted_index.cases | 48, 218 |
| abstract_inverted_index.panel | 52 |
| abstract_inverted_index.study | 23, 45 |
| abstract_inverted_index.total | 238, 243 |
| abstract_inverted_index.using | 103 |
| abstract_inverted_index.years | 183 |
| abstract_inverted_index.(0.1%) | 150 |
| abstract_inverted_index.(1.8%) | 136 |
| abstract_inverted_index.(84.1% | 184 |
| abstract_inverted_index.(LAFV) | 16 |
| abstract_inverted_index.(MGPT) | 54 |
| abstract_inverted_index.2.4%). | 212 |
| abstract_inverted_index.54.9%; | 186 |
| abstract_inverted_index.7.1%), | 208 |
| abstract_inverted_index.7.6%), | 205 |
| abstract_inverted_index.LAFVs, | 156 |
| abstract_inverted_index.LAFVs. | 152 |
| abstract_inverted_index.Sanger | 78, 146 |
| abstract_inverted_index.allele | 13, 68 |
| abstract_inverted_index.cancer | 10 |
| abstract_inverted_index.cohort | 166, 172 |
| abstract_inverted_index.family | 118 |
| abstract_inverted_index.genes: | 196 |
| abstract_inverted_index.higher | 178 |
| abstract_inverted_index.needed | 248 |
| abstract_inverted_index.older, | 175 |
| abstract_inverted_index.single | 57 |
| abstract_inverted_index.(11/62) | 223 |
| abstract_inverted_index.(57.6%) | 158 |
| abstract_inverted_index.0.001). | 189 |
| abstract_inverted_index.13.5%), | 202 |
| abstract_inverted_index.363,405 | 131 |
| abstract_inverted_index.64.7%), | 199 |
| abstract_inverted_index.Design: | 42 |
| abstract_inverted_index.Enabled | 2 |
| abstract_inverted_index.between | 71, 84, 142 |
| abstract_inverted_index.control | 170 |
| abstract_inverted_index.defined | 65 |
| abstract_inverted_index.factors | 29 |
| abstract_inverted_index.genetic | 60 |
| abstract_inverted_index.members | 119 |
| abstract_inverted_index.models. | 109 |
| abstract_inverted_index.origins | 252 |
| abstract_inverted_index.present | 192 |
| abstract_inverted_index.reports | 34 |
| abstract_inverted_index.results | 35 |
| abstract_inverted_index.tested. | 244 |
| abstract_inverted_index.testing | 20, 38, 53, 61, 111, 214, 246 |
| abstract_inverted_index.through | 50 |
| abstract_inverted_index.variant | 67 |
| abstract_inverted_index.whether | 122 |
| abstract_inverted_index.&lt; | 188 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Clinical | 99 |
| abstract_inverted_index.Purpose: | 1 |
| abstract_inverted_index.Results: | 129 |
| abstract_inverted_index.analyses | 81 |
| abstract_inverted_index.analyzed | 46, 102 |
| abstract_inverted_index.clinical | 28, 254 |
| abstract_inverted_index.cohorts. | 98 |
| abstract_inverted_index.compared | 167 |
| abstract_inverted_index.detected | 18, 231 |
| abstract_inverted_index.germline | 59 |
| abstract_inverted_index.logistic | 107 |
| abstract_inverted_index.patients | 259 |
| abstract_inverted_index.variants | 15, 86, 138, 239 |
| abstract_inverted_index.(inferred | 94 |
| abstract_inverted_index.Ancillary | 110, 213, 245 |
| abstract_inverted_index.conducted | 83 |
| abstract_inverted_index.confirmed | 76, 148, 155, 221 |
| abstract_inverted_index.describes | 24 |
| abstract_inverted_index.determine | 121 |
| abstract_inverted_index.families. | 261 |
| abstract_inverted_index.follow-up | 37 |
| abstract_inverted_index.following | 195 |
| abstract_inverted_index.frequency | 14, 26 |
| abstract_inverted_index.performed | 113, 215 |
| abstract_inverted_index.specimens | 116 |
| abstract_inverted_index.variants. | 163 |
| abstract_inverted_index.&gt;50 | 182 |
| abstract_inverted_index.associated | 30 |
| abstract_inverted_index.available. | 40 |
| abstract_inverted_index.classified | 160 |
| abstract_inverted_index.hereditary | 9 |
| abstract_inverted_index.identified | 49 |
| abstract_inverted_index.mosaicism. | 128, 226 |
| abstract_inverted_index.multi-gene | 51 |
| abstract_inverted_index.pathogenic | 85, 162 |
| abstract_inverted_index.proportion | 179 |
| abstract_inverted_index.regression | 108 |
| abstract_inverted_index.sequencing | 7, 147 |
| abstract_inverted_index.statistics | 105 |
| abstract_inverted_index.undergoing | 133 |
| abstract_inverted_index.understand | 250 |
| abstract_inverted_index.Comparative | 80 |
| abstract_inverted_index.alternative | 115 |
| abstract_inverted_index.conditions, | 11 |
| abstract_inverted_index.descriptive | 104 |
| abstract_inverted_index.frequencies | 69 |
| abstract_inverted_index.high-volume | 58 |
| abstract_inverted_index.individuals | 132, 181 |
| abstract_inverted_index.laboratory. | 62 |
| abstract_inverted_index.sequencing. | 79 |
| abstract_inverted_index.Conclusions: | 227 |
| abstract_inverted_index.Experimental | 41 |
| abstract_inverted_index.advancements | 4 |
| abstract_inverted_index.heterozygous | 171 |
| abstract_inverted_index.implications | 255 |
| abstract_inverted_index.infrequently | 230 |
| abstract_inverted_index.representing | 234 |
| abstract_inverted_index.heterozygous) | 95 |
| abstract_inverted_index.laboratories. | 21 |
| abstract_inverted_index.retrospective | 44 |
| abstract_inverted_index.significantly | 174 |
| abstract_inverted_index.constitutional | 127, 225 |
| abstract_inverted_index.characteristics | 100 |
| abstract_inverted_index.next-generation | 6 |
| cited_by_percentile_year.max | 95 |
| cited_by_percentile_year.min | 91 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 9 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/16 |
| sustainable_development_goals[0].score | 0.75 |
| sustainable_development_goals[0].display_name | Peace, Justice and strong institutions |
| citation_normalized_percentile.value | 0.88296807 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |