PCR duplicate proportion estimation and consequences for DNA copy number calculations

Andy Lynch; Mike Smith; Matthew Eldridge; Simon Tavaré

doi:10.1007/978-3-031-12766-3_18

PCR duplicate proportion estimation and consequences for DNA copy number calculations

Andy Lynch^*
, Mike Smith
, Matthew Eldridge
, Simon Tavaré

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

The volume of DNA in a sequencing experiment is often amplified by PCR, leading to the possibility that the same original DNA fragment will be sequenced twice - a ‘PCR duplicate’. Sometimes indistinguishable from these are multiple sequences arising from identical but independent molecules, which can lead to an over-estimation of the PCR duplicate proportion. The PCR duplicate proportion, and other measures derived from it, are important statistics for quality assurance, experimental design, and interpretation of sequencing experiments. Here we provide a full likelihood basis for a combinatorial approach using heterozygous SNPs as implemented in our R package, and demonstrate the efficacy of the approach. We also discuss the association with DNA copy number, and demonstrate the impact on a question of inferring mitochondrial DNA copy number that has recently been a feature of several high-profile cancer studies. This is explored through a simulation study.

Original language	English
Title of host publication	Recent developments in statistics and data science
Subtitle of host publication	SPE2021, Évora, Portugal, October 13–16
Editors	Regina Bispo, Lígia Henriques-Rodrigues, Russell Alpizar-Jara, Miguel de Carvalho
Place of Publication	Cham
Publisher	Springer
Pages	259-279
Number of pages	21
Volume	398
ISBN (Electronic)	9783031127663
ISBN (Print)	9783031127656
DOIs	https://doi.org/10.1007/978-3-031-12766-3_18
Publication status	Published - 29 Nov 2022
Event	XXV Congress of the Portuguese Statistical Society - Online, Évora, Portugal Duration: 13 Oct 2021 → 16 Oct 2021 Conference number: 25 http://www.spe2021.uevora.pt/en/inicio-english/

Publication series

Name	Springer proceedings in mathematics & statistics
Volume	398
ISSN (Print)	2194-1009
ISSN (Electronic)	2194-1017

Conference

Conference	XXV Congress of the Portuguese Statistical Society
Abbreviated title	SPE
Country/Territory	Portugal
City	Évora
Period	13/10/21 → 16/10/21
Internet address	http://www.spe2021.uevora.pt/en/inicio-english/

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Whole-genome sequencing
DNA copy number
Likelihood
Quality control
Mitochondria
Cancer

Access to Document

10.1007/978-3-031-12766-3_18

SPE_Paper_Resubmission
Copyright © 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG. This work has been made available online in accordance with publisher policies or with permission. Permission for further reuse of this content should be sought from the publisher or the rights holder. This is the author created accepted manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at https://doi.org/10.1007/978-3-031-12766-3_18.
Accepted author manuscript, 2.82 MB

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Lynch, A., Smith, M., Eldridge, M., & Tavaré, S. (2022). PCR duplicate proportion estimation and consequences for DNA copy number calculations. In R. Bispo, L. Henriques-Rodrigues, R. Alpizar-Jara, & M. de Carvalho (Eds.), Recent developments in statistics and data science: SPE2021, Évora, Portugal, October 13–16 (Vol. 398, pp. 259-279). (Springer proceedings in mathematics & statistics; Vol. 398). Springer. https://doi.org/10.1007/978-3-031-12766-3_18

Lynch, Andy ; Smith, Mike ; Eldridge, Matthew et al. / PCR duplicate proportion estimation and consequences for DNA copy number calculations. Recent developments in statistics and data science: SPE2021, Évora, Portugal, October 13–16. editor / Regina Bispo ; Lígia Henriques-Rodrigues ; Russell Alpizar-Jara ; Miguel de Carvalho. Vol. 398 Cham : Springer, 2022. pp. 259-279 (Springer proceedings in mathematics & statistics).

@inproceedings{dfc56c925ffc44d4a8abba1a749c4b5d,

title = "PCR duplicate proportion estimation and consequences for DNA copy number calculations",

abstract = "The volume of DNA in a sequencing experiment is often amplified by PCR, leading to the possibility that the same original DNA fragment will be sequenced twice - a {\textquoteleft}PCR duplicate{\textquoteright}. Sometimes indistinguishable from these are multiple sequences arising from identical but independent molecules, which can lead to an over-estimation of the PCR duplicate proportion. The PCR duplicate proportion, and other measures derived from it, are important statistics for quality assurance, experimental design, and interpretation of sequencing experiments. Here we provide a full likelihood basis for a combinatorial approach using heterozygous SNPs as implemented in our R package, and demonstrate the efficacy of the approach. We also discuss the association with DNA copy number, and demonstrate the impact on a question of inferring mitochondrial DNA copy number that has recently been a feature of several high-profile cancer studies. This is explored through a simulation study.",

keywords = "Whole-genome sequencing, DNA copy number, Likelihood, Quality control, Mitochondria, Cancer",

author = "Andy Lynch and Mike Smith and Matthew Eldridge and Simon Tavar{\'e}",

year = "2022",

month = nov,

day = "29",

doi = "10.1007/978-3-031-12766-3\_18",

language = "English",

isbn = "9783031127656",

volume = "398",

series = "Springer proceedings in mathematics \& statistics",

publisher = "Springer",

pages = "259--279",

editor = "Regina Bispo and L{\'i}gia Henriques-Rodrigues and Russell Alpizar-Jara and \{de Carvalho\}, Miguel",

booktitle = "Recent developments in statistics and data science",

address = "Netherlands",

note = "XXV Congress of the Portuguese Statistical Society, SPE ; Conference date: 13-10-2021 Through 16-10-2021",

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}

Lynch, A, Smith, M, Eldridge, M & Tavaré, S 2022, PCR duplicate proportion estimation and consequences for DNA copy number calculations. in R Bispo, L Henriques-Rodrigues, R Alpizar-Jara & M de Carvalho (eds), Recent developments in statistics and data science: SPE2021, Évora, Portugal, October 13–16. vol. 398, Springer proceedings in mathematics & statistics, vol. 398, Springer, Cham, pp. 259-279, XXV Congress of the Portuguese Statistical Society, Évora, Portugal, 13/10/21. https://doi.org/10.1007/978-3-031-12766-3_18

PCR duplicate proportion estimation and consequences for DNA copy number calculations. / Lynch, Andy; Smith, Mike; Eldridge, Matthew et al.
Recent developments in statistics and data science: SPE2021, Évora, Portugal, October 13–16. ed. / Regina Bispo; Lígia Henriques-Rodrigues; Russell Alpizar-Jara; Miguel de Carvalho. Vol. 398 Cham: Springer, 2022. p. 259-279 (Springer proceedings in mathematics & statistics; Vol. 398).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - PCR duplicate proportion estimation and consequences for DNA copy number calculations

AU - Lynch, Andy

AU - Smith, Mike

AU - Eldridge, Matthew

AU - Tavaré, Simon

N1 - Conference code: 25

PY - 2022/11/29

Y1 - 2022/11/29

N2 - The volume of DNA in a sequencing experiment is often amplified by PCR, leading to the possibility that the same original DNA fragment will be sequenced twice - a ‘PCR duplicate’. Sometimes indistinguishable from these are multiple sequences arising from identical but independent molecules, which can lead to an over-estimation of the PCR duplicate proportion. The PCR duplicate proportion, and other measures derived from it, are important statistics for quality assurance, experimental design, and interpretation of sequencing experiments. Here we provide a full likelihood basis for a combinatorial approach using heterozygous SNPs as implemented in our R package, and demonstrate the efficacy of the approach. We also discuss the association with DNA copy number, and demonstrate the impact on a question of inferring mitochondrial DNA copy number that has recently been a feature of several high-profile cancer studies. This is explored through a simulation study.

AB - The volume of DNA in a sequencing experiment is often amplified by PCR, leading to the possibility that the same original DNA fragment will be sequenced twice - a ‘PCR duplicate’. Sometimes indistinguishable from these are multiple sequences arising from identical but independent molecules, which can lead to an over-estimation of the PCR duplicate proportion. The PCR duplicate proportion, and other measures derived from it, are important statistics for quality assurance, experimental design, and interpretation of sequencing experiments. Here we provide a full likelihood basis for a combinatorial approach using heterozygous SNPs as implemented in our R package, and demonstrate the efficacy of the approach. We also discuss the association with DNA copy number, and demonstrate the impact on a question of inferring mitochondrial DNA copy number that has recently been a feature of several high-profile cancer studies. This is explored through a simulation study.

KW - Whole-genome sequencing

KW - DNA copy number

KW - Likelihood

KW - Quality control

KW - Mitochondria

KW - Cancer

UR - https://doi.org/10.1007/978-3-031-12766-3

UR - http://doi.org/10.5281/zenodo.6257577

U2 - 10.1007/978-3-031-12766-3_18

DO - 10.1007/978-3-031-12766-3_18

M3 - Conference contribution

SN - 9783031127656

VL - 398

T3 - Springer proceedings in mathematics & statistics

SP - 259

EP - 279

BT - Recent developments in statistics and data science

A2 - Bispo, Regina

A2 - Henriques-Rodrigues, Lígia

A2 - Alpizar-Jara, Russell

A2 - de Carvalho, Miguel

PB - Springer

CY - Cham

T2 - XXV Congress of the Portuguese Statistical Society

Y2 - 13 October 2021 through 16 October 2021

ER -

Lynch A, Smith M, Eldridge M, Tavaré S. PCR duplicate proportion estimation and consequences for DNA copy number calculations. In Bispo R, Henriques-Rodrigues L, Alpizar-Jara R, de Carvalho M, editors, Recent developments in statistics and data science: SPE2021, Évora, Portugal, October 13–16. Vol. 398. Cham: Springer. 2022. p. 259-279. (Springer proceedings in mathematics & statistics). Epub 2022 Nov 28. doi: 10.1007/978-3-031-12766-3_18

PCR duplicate proportion estimation and consequences for DNA copy number calculations

Abstract

Publication series

Conference

UN SDGs

Keywords

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