Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project
Abstrak
Abstract Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to provide an enriched set of known indels that would be more translationally relevant by focusing on additional cancer related regions. A thorough manual review process completed by 42 reviewers, two advisors, and a judging panel of three researchers significantly enriched the known indel set by an additional 516 indels. The extended benchmarking indel set has a large range of variant allele frequencies (VAFs), with 87% of them having a VAF below 20% in reference Sample A. The reference Sample A and the indel set can be used for comprehensive benchmarking of indel calling across a wider range of VAF values in the lower range. Indel length was also variable, but the majority were under 10 base pairs (bps). Most of the indels were within coding regions, with the remainder in the gene regulatory regions. Although high confidence can be derived from the robust study design and meticulous human review, this extensive indel set has not undergone orthogonal validation. The extended benchmarking indel set, along with the indels in the previously published known-positive set, was the truth set used to benchmark indel calling pipelines in a community challenge hosted on the precisionFDA platform. This benchmarking indel set and reference samples can be utilized for a comprehensive evaluation of indel calling pipelines. Additionally, the insights and solutions obtained during the manual review process can aid in improving the performance of these pipelines.
Penulis (60)
Binsheng Gong
Dan Li
Yifan Zhang
Rebecca Kusko
Samir Lababidi
Zehui Cao
Mingyang Chen
Ning Chen
Qiaochu Chen
Qingwang Chen
Jiacheng Dai
Qiang Gan
Yuechen Gao
Mingkun Guo
Gunjan Hariani
Yujie He
Wanwan Hou
He Jiang
Garima Kushwaha
Jian-Liang Li
Jianying Li
Yulan Li
Liang-Chun Liu
Ruimei Liu
Shiming Liu
Edwin Meriaux
Mengqing Mo
Mathew Moore
Tyler J. Moss
Quanne Niu
Ananddeep Patel
Luyao Ren
Nedda F. Saremi
Erfei Shang
Jun Shang
Ping Song
Siqi Sun
Brent J. Urban
Danke Wang
Shangzi Wang
Zhining Wen
Xiangyi Xiong
Jingcheng Yang
Lihui Yin
Chao Zhang
Ruolan Zhang
Ambica Bhandari
Wanshi Cai
Agda Karina Eterovic
Dalila B. Megherbi
Tieliu Shi
Chen Suo
Ying Yu
Yuanting Zheng
Natalia Novoradovskaya
Renee L. Sears
Leming Shi
Wendell Jones
Weida Tong
Joshua Xu
Format Sitasi
Akses Cepat
- Tahun Terbit
- 2024
- Sumber Database
- DOAJ
- DOI
- 10.1038/s41598-024-57439-7
- Akses
- Open Access ✓