CAPP-Seq Targeted Sequencing and Analysis

Targeted capture and sequencing analysis of all samples was performed using CAPP-Seq (17 (link)). We employed a 302-kb CAPP-Seq selector targeting 771 noncontiguous regions of the human genome, spanning 276 genes (18 (link)). A maximum of 32 ng DNA was input into sequencing library preparation. For plasma and BAL fluid samples with less than 32 ng of isolated cell-free DNA (cfDNA), all the extracted cfDNA was used for library preparation, down to a minimum of 16 ng. Samples were sequenced using 2 × 100 or 2 × 150 reads on an Illumina HiSeq 2500 or 4000. Sequencing data were processed using a previously described bioinformatics pipeline (12, 17 (link)). SNVs and indels were genotyped in all samples (17 (link)).

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Nair V.S., Hui A.B., Chabon J.J., Esfahani M.S., Stehr H., Nabet B.Y., Zhou L., Chaudhuri A.A., Benson J., Ayers K., Bedi H., Ramsey M., Van Wert R., Antic S., Lui N., Backhus L., Berry M., Sung A.W., Massion P.P., Shrager J.B., Alizadeh A.A, & Diehn M. (2022). Genomic Profiling of Bronchoalveolar Lavage Fluid in Lung Cancer. Cancer Research, 82(16), 2838-2847.

Publication 2022

HiSeq 2500 or 4000

A dna Cell free dna Genes Human genome Indels Library Plasma

Corresponding Organization : Stanford University

Other organizations : Vanderbilt University, California Institute for Regenerative Medicine

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Variable analysis

independent variables

Targeted capture and sequencing analysis of all samples was performed using CAPP-Seq
We employed a 302-kb CAPP-Seq selector targeting 771 noncontiguous regions of the human genome, spanning 276 genes

dependent variables

SNVs and indels were genotyped in all samples

control variables

A maximum of 32 ng DNA was input into sequencing library preparation
For plasma and BAL fluid samples with less than 32 ng of isolated cell-free DNA (cfDNA), all the extracted cfDNA was used for library preparation, down to a minimum of 16 ng
Samples were sequenced using 2 × 100 or 2 × 150 reads on an Illumina HiSeq 2500 or 4000
Sequencing data were processed using a previously described bioinformatics pipeline

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