Dataset Information

Assessing aneuploidy with repetitive element sequencing.

ABSTRACT: We report a sensitive PCR-based assay called Repetitive Element AneupLoidy Sequencing System (RealSeqS) that can detect aneuploidy in samples containing as little as 3 pg of DNA. Using a single primer pair, we amplified ?350,000 amplicons distributed throughout the genome. Aneuploidy was detected in 49% of liquid biopsies from a total of 883 nonmetastatic, clinically detected cancers of the colorectum, esophagus, liver, lung, ovary, pancreas, breast, or stomach. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% in these eight cancer types, while only 1% of 812 healthy controls scored positive.

SUBMITTER: Douville C

PROVIDER: S-EPMC7060727 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Publications

Assessing aneuploidy with repetitive element sequencing.

Douville Christopher C Cohen Joshua D JD Ptak Janine J Popoli Maria M Schaefer Joy J Silliman Natalie N Dobbyn Lisa L Schoen Robert E RE Tie Jeanne J Gibbs Peter P Goggins Michael M Wolfgang Christopher L CL Wang Tian-Li TL Shih Ie-Ming IM Karchin Rachel R Lennon Anne Marie AM Hruban Ralph H RH Tomasetti Cristian C Bettegowda Chetan C Kinzler Kenneth W KW Papadopoulos Nickolas N Vogelstein Bert B

Proceedings of the National Academy of Sciences of the United States of America 20200219 9

We report a sensitive PCR-based assay called Repetitive Element AneupLoidy Sequencing System (RealSeqS) that can detect aneuploidy in samples containing as little as 3 pg of DNA. Using a single primer pair, we amplified ∼350,000 amplicons distributed throughout the genome. Aneuploidy was detected in 49% of liquid biopsies from a total of 883 nonmetastatic, clinically detected cancers of the colorectum, esophagus, liver, lung, ovary, pancreas, breast, or stomach. Combining aneuploidy with somatic ...[more]

PMID: 32075918

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Project description:Background: There is a current lack of any composite measure for the effective tracking and monitoring of clinical change in individuals exposed to repetitive head impacts (RHI). The aim of this study is to create a composite instrument for the purposes of detecting change over time in cognitive and behavioral function in individuals exposed to RHI. Methods: The data to derive the composite instrument came from the Professional Fighters Brain Health Study (PFBHS), a longitudinal study of active and retired professional fighters [boxers and mixed martial arts (MMA) fighters] and healthy controls. Participants in the PFBHS underwent assessment on an annual basis that included computerized cognitive testing and behavioral questionnaires. Multivariate logistic regression models were employed to compare active fighters (n = 117) with controls (n = 22), and retired fighters (n = 26) with controls to identify the predictors that could be used to differentiate the groups over time. In a second step, linear discriminant analysis was performed to derive the linear discriminant coefficients for the three groups by using the predictors from the two separate logistic regression models. Results: The composite scale is a weighted linear value of 12 standardized scores consisting of both current and yearly change scores in domains including: processing speed, choice reaction time, semantic fluency, letter fluency, and Barrett Impulsiveness Scale. Because the weighting of values differed between active and retired fighters, two versions emerged. The mean and standard deviation ratio (MSDR) showed that the new index had better sensitivity compared to the individual measures, with the ratio of MSDR of the new index to that of the existing measures of at least 1.84. Conclusion: With the increasing need for tools to follow individuals exposed to RHI and the potential of clinical trials on the horizon for CTE, the RHICI is poised to serve as an initial approach to a composite clinical measure.

Dataset Information

Assessing aneuploidy with repetitive element sequencing.

Publications

Assessing aneuploidy with repetitive element sequencing.

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