Enhanced detection of circulating tumor DNA by fragment size analysis

Florent Mouliere, Dineika Chandrananda, Anna M Piskorz, Elizabeth K Moore, James Morris, Lise Barlebo Ahlborn, Richard Mair, Teodora Goranova, Francesco Marass, Katrin Heider, Jonathan C M Wan, Anna Supernat, Irena Hudecova, Ioannis Gounaris, Susana Ros, Mercedes Jimenez-Linan, Javier Garcia-Corbacho, Keval Patel, Olga Østrup, Suzanne Murphy & 17 others Matthew D Eldridge, Davina Gale, Grant D Stewart, Johanna Burge, Wendy N Cooper, Michiel S van der Heijden, Charles E Massie, Colin Watts, Pippa Corrie, Simon Pacey, Kevin M Brindle, Richard D Baird, Morten Mau-Sørensen, Christine A Parkinson, Christopher G Smith, James D Brenton, Nitzan Rosenfeld

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95% of cases and more than fourfold enrichment in >10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC <0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA.

Original languageEnglish
JournalScience Translational Medicine
Volume10
Issue number466
DOIs
Publication statusPublished - 7 Nov 2018

Cite this

Mouliere, F., Chandrananda, D., Piskorz, A. M., Moore, E. K., Morris, J., Ahlborn, L. B., ... Rosenfeld, N. (2018). Enhanced detection of circulating tumor DNA by fragment size analysis. Science Translational Medicine, 10(466). https://doi.org/10.1126/scitranslmed.aat4921
Mouliere, Florent ; Chandrananda, Dineika ; Piskorz, Anna M ; Moore, Elizabeth K ; Morris, James ; Ahlborn, Lise Barlebo ; Mair, Richard ; Goranova, Teodora ; Marass, Francesco ; Heider, Katrin ; Wan, Jonathan C M ; Supernat, Anna ; Hudecova, Irena ; Gounaris, Ioannis ; Ros, Susana ; Jimenez-Linan, Mercedes ; Garcia-Corbacho, Javier ; Patel, Keval ; Østrup, Olga ; Murphy, Suzanne ; Eldridge, Matthew D ; Gale, Davina ; Stewart, Grant D ; Burge, Johanna ; Cooper, Wendy N ; van der Heijden, Michiel S ; Massie, Charles E ; Watts, Colin ; Corrie, Pippa ; Pacey, Simon ; Brindle, Kevin M ; Baird, Richard D ; Mau-Sørensen, Morten ; Parkinson, Christine A ; Smith, Christopher G ; Brenton, James D ; Rosenfeld, Nitzan. / Enhanced detection of circulating tumor DNA by fragment size analysis. In: Science Translational Medicine. 2018 ; Vol. 10, No. 466.
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title = "Enhanced detection of circulating tumor DNA by fragment size analysis",
abstract = "Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95{\%} of cases and more than fourfold enrichment in >10{\%} of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC <0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA.",
author = "Florent Mouliere and Dineika Chandrananda and Piskorz, {Anna M} and Moore, {Elizabeth K} and James Morris and Ahlborn, {Lise Barlebo} and Richard Mair and Teodora Goranova and Francesco Marass and Katrin Heider and Wan, {Jonathan C M} and Anna Supernat and Irena Hudecova and Ioannis Gounaris and Susana Ros and Mercedes Jimenez-Linan and Javier Garcia-Corbacho and Keval Patel and Olga {\O}strup and Suzanne Murphy and Eldridge, {Matthew D} and Davina Gale and Stewart, {Grant D} and Johanna Burge and Cooper, {Wendy N} and {van der Heijden}, {Michiel S} and Massie, {Charles E} and Colin Watts and Pippa Corrie and Simon Pacey and Brindle, {Kevin M} and Baird, {Richard D} and Morten Mau-S{\o}rensen and Parkinson, {Christine A} and Smith, {Christopher G} and Brenton, {James D} and Nitzan Rosenfeld",
note = "Copyright {\circledC} 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.",
year = "2018",
month = "11",
day = "7",
doi = "10.1126/scitranslmed.aat4921",
language = "English",
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journal = "Science Translational Medicine",
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Mouliere, F, Chandrananda, D, Piskorz, AM, Moore, EK, Morris, J, Ahlborn, LB, Mair, R, Goranova, T, Marass, F, Heider, K, Wan, JCM, Supernat, A, Hudecova, I, Gounaris, I, Ros, S, Jimenez-Linan, M, Garcia-Corbacho, J, Patel, K, Østrup, O, Murphy, S, Eldridge, MD, Gale, D, Stewart, GD, Burge, J, Cooper, WN, van der Heijden, MS, Massie, CE, Watts, C, Corrie, P, Pacey, S, Brindle, KM, Baird, RD, Mau-Sørensen, M, Parkinson, CA, Smith, CG, Brenton, JD & Rosenfeld, N 2018, 'Enhanced detection of circulating tumor DNA by fragment size analysis' Science Translational Medicine, vol. 10, no. 466. https://doi.org/10.1126/scitranslmed.aat4921

Enhanced detection of circulating tumor DNA by fragment size analysis. / Mouliere, Florent; Chandrananda, Dineika; Piskorz, Anna M; Moore, Elizabeth K; Morris, James; Ahlborn, Lise Barlebo; Mair, Richard; Goranova, Teodora; Marass, Francesco; Heider, Katrin; Wan, Jonathan C M; Supernat, Anna; Hudecova, Irena; Gounaris, Ioannis; Ros, Susana; Jimenez-Linan, Mercedes; Garcia-Corbacho, Javier; Patel, Keval; Østrup, Olga; Murphy, Suzanne; Eldridge, Matthew D; Gale, Davina; Stewart, Grant D; Burge, Johanna; Cooper, Wendy N; van der Heijden, Michiel S; Massie, Charles E; Watts, Colin; Corrie, Pippa; Pacey, Simon; Brindle, Kevin M; Baird, Richard D; Mau-Sørensen, Morten; Parkinson, Christine A; Smith, Christopher G; Brenton, James D; Rosenfeld, Nitzan.

In: Science Translational Medicine, Vol. 10, No. 466, 07.11.2018.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Enhanced detection of circulating tumor DNA by fragment size analysis

AU - Mouliere, Florent

AU - Chandrananda, Dineika

AU - Piskorz, Anna M

AU - Moore, Elizabeth K

AU - Morris, James

AU - Ahlborn, Lise Barlebo

AU - Mair, Richard

AU - Goranova, Teodora

AU - Marass, Francesco

AU - Heider, Katrin

AU - Wan, Jonathan C M

AU - Supernat, Anna

AU - Hudecova, Irena

AU - Gounaris, Ioannis

AU - Ros, Susana

AU - Jimenez-Linan, Mercedes

AU - Garcia-Corbacho, Javier

AU - Patel, Keval

AU - Østrup, Olga

AU - Murphy, Suzanne

AU - Eldridge, Matthew D

AU - Gale, Davina

AU - Stewart, Grant D

AU - Burge, Johanna

AU - Cooper, Wendy N

AU - van der Heijden, Michiel S

AU - Massie, Charles E

AU - Watts, Colin

AU - Corrie, Pippa

AU - Pacey, Simon

AU - Brindle, Kevin M

AU - Baird, Richard D

AU - Mau-Sørensen, Morten

AU - Parkinson, Christine A

AU - Smith, Christopher G

AU - Brenton, James D

AU - Rosenfeld, Nitzan

N1 - Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

PY - 2018/11/7

Y1 - 2018/11/7

N2 - Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95% of cases and more than fourfold enrichment in >10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC <0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA.

AB - Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95% of cases and more than fourfold enrichment in >10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC <0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA.

U2 - 10.1126/scitranslmed.aat4921

DO - 10.1126/scitranslmed.aat4921

M3 - Article

VL - 10

JO - Science Translational Medicine

JF - Science Translational Medicine

SN - 1946-6234

IS - 466

ER -