Detection of de novo copy number deletions from targeted sequencing of trios

Jack M. Fu; Elizabeth J. Leslie; Alan F. Scott; Jeffrey C. Murray; Mary L. Marazita; Terri H. Beaty; Robert B. Scharpf; Ingo Ruczinski

doi:10.1093/bioinformatics/bty677

Detection of de novo copy number deletions from targeted sequencing of trios

Jack M. Fu, Elizabeth J. Leslie, Alan F. Scott, Jeffrey C. Murray, Mary L. Marazita, Terri H. Beaty, Robert B. Scharpf, Ingo Ruczinski

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

Motivation: De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. Results: We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability.

Original language	English (US)
Pages (from-to)	571-578
Number of pages	8
Journal	Bioinformatics
Volume	35
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/bty677
State	Published - Feb 15 2019

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bty677

Cite this

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title = "Detection of de novo copy number deletions from targeted sequencing of trios",

abstract = "Motivation: De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. Results: We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability.",

author = "Fu, {Jack M.} and Leslie, {Elizabeth J.} and Scott, {Alan F.} and Murray, {Jeffrey C.} and Marazita, {Mary L.} and Beaty, {Terri H.} and Scharpf, {Robert B.} and Ingo Ruczinski",

note = "Funding Information: This work was supported by the National Institutes of Health (NIH) grant R03 DE-02579 to IR and RBS. Data collection was supported by NIH grants R01-DE016148 to MLM and R37-DE008559 to JCM. Sequencing of the oral cleft trios was supported by NIH grant U01 HG-005925 to JCM. Publisher Copyright: {\textcopyright} 2018. Published by Oxford University Press. All rights reserved.",

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AU - Fu, Jack M.

AU - Leslie, Elizabeth J.

AU - Scott, Alan F.

AU - Murray, Jeffrey C.

AU - Marazita, Mary L.

AU - Beaty, Terri H.

AU - Scharpf, Robert B.

AU - Ruczinski, Ingo

N1 - Funding Information: This work was supported by the National Institutes of Health (NIH) grant R03 DE-02579 to IR and RBS. Data collection was supported by NIH grants R01-DE016148 to MLM and R37-DE008559 to JCM. Sequencing of the oral cleft trios was supported by NIH grant U01 HG-005925 to JCM. Publisher Copyright: © 2018. Published by Oxford University Press. All rights reserved.

PY - 2019/2/15

Y1 - 2019/2/15

N2 - Motivation: De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. Results: We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability.

AB - Motivation: De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. Results: We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability.

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Detection of de novo copy number deletions from targeted sequencing of trios

Abstract

ASJC Scopus subject areas

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