CfDNA from cancer patients ofter show a trio of peaks products of mono-, di- and tri-nucleosome fragments. We usually repair and make liberaries directly without enriching for smallest peak (we believe ctDNA is in all three peaks). When we do matching normal samples we do shear lymphocyte DNA to 150-200 bp and libraries look great an de sequencing as well, better than cfDNA obviously. This different in insert sizes surely affects the library complexity, quality, capture efficiency and therefore sequencing (on target versus off target, sequencing bias etc) What do you guys think about shearing the cfDNA to 150-200 bp as done for normal?
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