Trial reportCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology2015
The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology.
Trial report in Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Divergent Genomic Drivers in Benign-Appearing Lung Precursors and Their Synchronous Carcinomas.Cancers · 2026Article
- Unlocking uterine biology at home: a validated system for DNA, RNA, and microbial analysis from menstrual effluence.medRxiv : the preprint server for health sciences · 2025Article
- Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses.BMC genomics · 2024Article
- A polygenic score associated with fracture risk in breast cancer patients treated with aromatase inhibitors.NPJ breast cancer · 2024Article
- Sample Collection Methods in Upper Gastrointestinal Research.Journal of Korean medical science · 2023Review
- Direct RNA Nanopore Sequencing of SARS-CoV-2 Extracted from Critical Material from Swabs.Life (Basel, Switzerland) · 2022Article
- A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples.iScience · 2021Article
- Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders.BMC medical genomics · 2021Article
- Whole-genome sequencing data of Kazakh individuals.BMC research notes · 2021Article
- Schizophrenic Psychosis Symptoms in a Background of Mild-To-Moderate Carnitine Palmitoyltransferase II Deficiency: A Case Report.Reports (MDPI) · 2020Article
- Quality of whole genome sequencing from blood versus saliva derived DNA in cardiac patients.BMC medical genomics · 2020Article
- Measuring coverage and accuracy of whole-exome sequencing in clinical context.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Article
- Comparison of SureSelect and Nextera Exome Capture Performance in Single-Cell Sequencing.Human heredity · 2018Article
- A framework for the estimation of the proportion of true discoveries in single nucleotide variant detection studies for human data.PloS one · 2018Article
- Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing.BMC medical genomics · 2016Article
- The minimal amount of starting DNA for Agilent's hybrid capture-based targeted massively parallel sequencing.Scientific reports · 2016Article
- Recommendations on Collecting and Storing Samples for Genetic Studies in Hearing and Tinnitus Research.Ear and hearingArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
backgroundWhole-exome sequencing (WES) has recently emerged as an appealing approach to systematically study coding variants. However, the requirement for a large amount of high-quality DNA poses a barrier that may limit its application in large cancer epidemiologic studies. We evaluated the performance of WES with low input amount and saliva DNA as an alternative source material.
methodsFive breast cancer patients were randomly selected from the Pathways Study. From each patient, four samples, including 3 μg, 1 μg, and 0.2 μg blood DNA and 1 μg saliva DNA, were aliquoted for library preparation using the Agilent SureSelect Kit and sequencing using Illumina HiSeq2500. Quality metrics of sequencing and variant calling, as well as concordance of variant calls from the whole exome and 21 known breast cancer genes, were assessed by input amount and DNA source.
resultsThere was little difference by input amount or DNA source on the quality of sequencing and variant calling. The concordance rate was about 98% for single-nucleotide variant calls and 83% to 86% for short insertion/deletion calls. For the 21 known breast cancer genes, WES based on low input amount and saliva DNA identified the same set variants in samples from a same patient.
conclusionsLow DNA input amount, as well as saliva DNA, can be used to generate WES data of satisfactory quality. IMPACT: Our findings support the expansion of WES applications in cancer epidemiologic studies where only low DNA amount or saliva samples are available.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.