Evaluation of cell-free DNA approaches for multi-cancer early detection

被引：162

作者：

Jamshidi, Arash ^{[1
]}

Liu, Minetta C. ^{[2
,18
]}

Klein, Eric A. ^{[3
]}

Venin, Oliver ^{[1
]}

Hubbell, Earl ^{[1
]}

Beausang, John F. ^{[1
]}

Gross, Samuel ^{[1
]}

Melton, Collin ^{[1
]}

Fields, Alexander P. ^{[1
]}

Liu, Qinwen ^{[1
]}

Zhang, Nan ^{[1
]}

Fung, Eric T. ^{[1
]}

Kurtzman, Kathryn N. ^{[1
]}

Amini, Hamed ^{[1
]}

Betts, Craig ^{[1
,19
]}

Civello, Daniel ^{[1
,20
]}

Freese, Peter ^{[1
,21
]}

Calef, Robert ^{[1
]}

Davydov, Konstantin ^{[1
,22
]}

Fayzullina, Saniya ^{[1
]}

Hou, Chenlu ^{[1
]}

Jiang, Roger ^{[1
]}

Jung, Byoungsok ^{[1
]}

Tang, Susan ^{[1
,23
]}

Demas, Vasiliki ^{[24
]}

Newman, Joshua ^{[1
]}

Sakarya, Onur ^{[1
]}

Scott, Eric ^{[1
]}

Shenoy, Archana ^{[1
]}

Shojaee, Seyedmehdi ^{[1
]}

Steffen, Kristan K. ^{[1
]}

Nicula, Virgil ^{[1
]}

Chien, Tom C. ^{[1
]}

Bagaria, Siddhartha ^{[1
]}

Hunkapiller, Nathan ^{[1
]}

Desai, Mohini ^{[1
]}

Dong, Zhao ^{[1
]}

Richards, Donald A. ^{[4
]}

Yeatman, Timothy J. ^{[5
,6
]}

Cohn, Allen L. ^{[7
]}

Thiel, David D. ^{[8
]}

Berry, Donald A. ^{[9
]}

Tummala, Mohan K. ^{[10
]}

MCIntyre, Kristi ^{[11
]}

Sekeres, Mikkael A. ^{[12
]}

Bryce, Alan ^{[13
]}

Aravanis, Alexander M. ^{[14
]}

V. Seiden, Michael ^{[1
,15
]}

Swanton, Charles ^{[16
,17
]}

机构：

[1] GRAIL LLC, Menlo Pk, CA 94025 USA

[2] Mayo Clin, Dept Oncol, Rochester, MN 55905 USA

[3] Cleveland Clin, Cleveland, OH 44103 USA

[4] Texas Oncol, Tyler, TX 75702 USA

[5] Gibbs Canc Ctr & Res Inst, Spartanburg, SC 29303 USA

[6] Univ Utah, Dept Surg, Salt Lake City, UT 84112 USA

[7] Rocky Mt Canc Ctr, Denver, CO 80218 USA

[8] Mayo Clin Florida, Dept Urol, Jacksonville, FL 32224 USA

[9] Univ Texas MD Anderson Canc Ctr, Dept Biostat, Houston, TX 77030 USA

[10] Mercy Clin Canc Ctr, Springfield, MO 65804 USA

[11] TOPA Dallas Presbyterian, Dallas, TX 75231 USA

[12] Univ Miami, Sylvester Canc Ctr, Miami, FL 33136 USA

[13] Mayo Clin, Phoenix, AZ 85054 USA

[14] Illumina Inc, San Diego, CA 92122 USA

[15] US Oncol Res, The Woodlands, TX 77380 USA

[16] Francis Crick Inst, London NW1 1AT, England

[17] UCL Canc Inst, CRUK Lung Canc Ctr Excellence, London WC1E 6DD, England

[18] Natera Inc, Austin, TX 78753 USA

[19] Cellanome Inc, Palo Alto, CA 94303 USA

[20] Loyal Cellular Longev Inc, Menlo Pk, CA 94025 USA

[21] Meta, Menlo Pk, CA 94025 USA

[22] Aurora Innovat Inc, Mountain View, CA 94043 USA

[23] Strateos Inc, Menlo Pk, CA 94025 USA

[24] Tesseract Hlth, Guilford, CT 06437 USA

来源：

CANCER CELL | 2022年 / 40卷 / 12期

关键词：

CIRCULATING TUMOR DNA; LIQUID BIOPSY; PLASMA; VALIDATION; SURVIVAL; FRACTION;

D O I：

10.1016/j.ccell.2022.10.022

中图分类号：

R73 [肿瘤学];

学科分类号：

100214 ;

摘要：

In the Circulating Cell-free Genome Atlas (NCT02889978) substudy 1, we evaluate several approaches for a circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED) test by defining clinical limit of detection (LOD) based on circulating tumor allele fraction (cTAF), enabling performance compar-isons. Among 10 machine-learning classifiers trained on the same samples and independently validated, when evaluated at 98% specificity, those using whole-genome (WG) methylation, single nucleotide var-iants with paired white blood cell background removal, and combined scores from classifiers evaluated in this study show the highest cancer signal detection sensitivities. Compared with clinical stage and tumor type, cTAF is a more significant predictor of classifier performance and may more closely reflect tumor biology. Clinical LODs mirror relative sensitivities for all approaches. The WG methylation feature best predicts cancer signal origin. WG methylation is the most promising technology for MCED and informs development of a targeted methylation MCED test.

引用

页码：1537 / +

页数：26

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