Sequencing Quality Control 2

The Sequencing Quality Control 2 (SEQC2/MAQC-IV) project provides resources to aid sequencing reproducibility and highlights factors that can guide platform and software choice.

The MicroArray Quality Control consortium—a 16-year international effort led by the FDA and involving hundreds of scientists from academia, industry and government—helped make genomic medicine a reality.

Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing.

Tumor–normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking ‘tumor-only’ or ‘matched tumor–normal’ analyses.

A comprehensive comparison of 20 single-cell RNA-seq datasets derived from the two cell lines analyzed using six preprocessing pipelines, eight normalization methods and seven batch-correction algorithms derived from four different sequencing platforms at different centers.

Reliable detection of mutations below 0.5% variant allele frequency remains a key challenge for circulating tumor DNA sequencing assays.

Next-generation sequencing platforms are benchmarked using human, bacterial and metagenomics reference materials.