Gang Cheng

Background: Circulating cell-free DNA (cfDNA) detection for non-invasive diagnosis requires higher sensitivity and accuracy due to the low circulating tumor DNA (ctDNA) content. Many methods have been developed to improve detection of ctDNA, including ultra-deep sequencing or enrichment of shorter cfDNA fragments, such as those in the range of 90–150 bp. Methods: Here, we developed a method for single-stranded DNA (ssDNA) library preparation with a large proportion of magnetic beads to enrich the shorter cfDNA fragments. We aimed to determine if this could increase the ctDNA content and thus improve the sensitivity of ctDNA detection by testing the method in blood samples from patients with advanced cancers (non-small cell lung cancers, esophageal squamous cell carcinoma, cholangiocarcinoma, colorectal cancer and liver cancer). Results: This method was able to obtain shorter cfDNA both in commercial cfDNA references and real world clinical cfDNA samples. Plasmid simulation experiments showed that using a large proportion of magnetic beads to construct the library could obtain more ctDNA derived from shorter-fragment plasmids, which could significantly improve the detection of ctDNA especially in the low-variant allele frequency sample. In real-world clinical samples, this method may be able to increase the opportunity to obtain alteration reads from short fragments, which was important to low frequency detection. Conclusions: The ssDNA library preparation with large proportion of magnetic beads could increase the opportunity to obtain alteration reads from short fragments, which is crucial for low variant allele frequency detection.

The identification and interpretation of germline BRCA1/2 variants becomes increasingly important in breast and ovarian cancer treatment. However, there is no comprehensive analysis of the germline BRCA1/2 variants in Chinese population. Here we performed a systematic review and meta‐analysis on such variants from 94 publications. A total of 2128 BRCA1/2 variant records were extracted, including 601 from BRCA1 and 632 from BRCA2. 414, 734, 449, 307 were also recorded in the BIC, ClinVar, ENIGMA and UMD databases, respectively, and 579 variants were newly reported. Subsequent analysis showed that the overall germline BRCA1/2 pathogenic variant frequency was 5.7% and 21.8% in Chinese breast and ovarian cancer, respectively. Populations with high‐risk factors exhibited higher pathogenic variant percentage. Furthermore, the variant profile in Chinese is distinctive from that in other ethnic groups with no distinct founder pathogenic variants. We also tested our in‐house ACMG‐guided pathogenicity interpretation procedure for Chinese BRCA1/2 variants. Our results achieved a consistency of 91.2%‐97.6% (5‐grade classification) or 98.4%‐100% (2‐grade classification) with public databases. In conclusion, this study represents the first comprehensive meta‐analysis of Chinese BRCA1/2 variants and validates our in‐house pathogenicity interpretation procedure, thereby providing guidance for further PARP inhibitor development and companion diagnostics in Chinese population.