Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease

The core software used as part of the Karius test is described in the Clinical-grade microbial cfDNA sequencing for infectious disease section in Methods, under the sub-sections Sequence data processing and alignment, Microorganism abundance estimation and Pathogen detection. The open source software includes the following external tools: bcl2fastq v2.17.1.14, Trimmomatic v0.32, Bowtie v2.2.4 and BLAST v2.2.30. A description of all open source code is included in Methods and further details are available on request. The proprietary portions of the code are not available.

The data that support the findings of this study are available from the corresponding author on request. Sequencing data that support the finding of this study (with human reads removed) have been deposited in NCBI SRA and can be accessed with the BioProject identifier PRJNA507824.

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The authors would like to thank S. Sinha for assistance with the preparation of the manuscript, as well as H. Quach, R. Davila, S. Madan, V. Baichwal, C. Ho, H. Seng, R. Aquino, A. Parham, R. Mann, I. Brown, P. Callagy, A. Visweswaran, C. Keller, C. Bucsit and A. Araya for their contributions to these validation studies.

Author notes

1. These authors contributed equally: Timothy A. Blauwkamp, Simone Thair, Judith C. Wilber, Samuel Yang.

Affiliations

1. Karius, Inc., Redwood City, CA, USA

• Timothy A. Blauwkamp

• , Michael J. Rosen

• , Lily Blair

• , Martin S. Lindner

• , Igor D. Vilfan

• , Trupti Kawli

• , Fred C. Christians

• , Shivkumar Venkatasubrahmanyam

• , Gregory D. Wall

• , Anita Cheung

• , Zoë N. Rogers

• , Galit Meshulam-Simon

• , Liza Huijse

• , Sanjeev Balakrishnan

• , Desiree Hollemon

• , David K. Hong

• , Marla Lay Vaughn

• , Mickey Kertesz

• , Sivan Bercovici

•  & Judith C. Wilber

2. Department of Emergency Medicine, Stanford University, Palo Alto, CA, USA

• Simone Thair

• , James V. Quinn

•  & Samuel Yang

Contributions

S.T., M.J.R., L.B., M.S.L., I.D.V., T.K., F.C.C., S.V., G.D.W., A.C., Z.N.R., G.M.-S., L.H., S.Balakrishnan, J.V.Q., D.H., D.K.H. and M.L.V. designed and carried out experiments, analysed data and summarized the results. T.A.B., S.T., M.L.V., M.K., S.Bercovici, J.C.W. and S.Y. analysed data and supervised the work. T.A.B., S.Bercovici, S.T., D.H. and D.K.H. wrote the paper.

Competing interests

This study was funded by Karius, Inc. and describes the validation of a product developed by Karius, Inc. All authors (excepting S.T., J.V.Q. and S.Y.) are current or former employees and/or share -holders of Karius, Inc. This does not alter our adherence to Nature Microbiology policies on sharing data and materials.

Corresponding author

Correspondence to Timothy A. Blauwkamp.

1. Supplementary Information

   Supplementary Figures 1–9, Supplementary Tables 1–4 and Supplementary Table 8.

2. Reporting Summary

3. Supplementary Table 5

   Subjects with definite and probable infections identified by NGS.

4. Supplementary Table 6

   Aetiology of infection for patients with positive NGS results adjudicated as possible.

5. Supplementary Table 7

   Subjects with ‘unlikely’ infections identified by NGS.