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SEQC2 Article Collection

The MicroArray and Sequencing Quality Control (MAQC/SEQC) consortium helps with improving microarray and next-generation sequencing technologies and their application. Sequencing Quality Control Phase 2 (SEQC2) is the fourth project of MAQC that performs analytical validation of NGS applications. The specific aims are developing quality metrics for reproducible NGS results, benchmarking bioinformatics methods for whole genome sequencing and targeted gene sequencing towards the development of standard data analysis protocols, and measuring the impact of experimental and bioinformatic variables on the generation and analysis of NGS data. 

Genome Biology is happy to publish these companion articles to the project.

  1. Structural variants (SVs) are a major source of human genetic diversity and have been associated with different diseases and phenotypes. The detection of SVs is difficult, and a diverse range of detection meth...

    Authors: Zhichao Liu, Ruth Roberts, Timothy R. Mercer, Joshua Xu, Fritz J. Sedlazeck and Weida Tong
    Citation: Genome Biology 2022 23:68

    The Author Correction to this article has been published in Genome Biology 2022 23:198

  2. Next-generation sequencing (NGS) can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis. However, the human genome contains many polymorphic, low-comple...

    Authors: Andre L. M. Reis, Ira W. Deveson, Bindu Swapna Madala, Ted Wong, Chris Barker, Joshua Xu, Niall Lennon, Weida Tong and Tim R. Mercer
    Citation: Genome Biology 2022 23:19
  3. Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-b...

    Authors: Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Konstantinos Karagiannis, Malcolm Moos, Sean Smith, Luis Santana-Quintero, Chunlin Xiao, Michael Colgan, Huixiao Hong, Marghoob Mohiyuddin and Wenming Xiao
    Citation: Genome Biology 2022 23:12
  4. Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging.

    Authors: Michael M. Khayat, Sayed Mohammad Ebrahim Sahraeian, Samantha Zarate, Andrew Carroll, Huixiao Hong, Bohu Pan, Leming Shi, Richard A. Gibbs, Marghoob Mohiyuddin, Yuanting Zheng and Fritz J. Sedlazeck
    Citation: Genome Biology 2021 22:347
  5. Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other dis...

    Authors: Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W. Langhorst, V. K. Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M. Greally…
    Citation: Genome Biology 2021 22:332

    The Author Correction to this article has been published in Genome Biology 2022 23:76

    The Author Correction to this article has been published in Genome Biology 2021 22:350

  6. Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference...

    Authors: Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd A. Richmond, Donald J. Johann Jr, Halil Bisgin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee Scott Basehore, Anne Bergstrom Lucas…
    Citation: Genome Biology 2021 22:111

    The Research to this article has been published in Genome Biology 2021 22:109

  7. Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and ...

    Authors: Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabón-Peña, Zhihong Zhang, Kevin Lai, Wanshi Cai, Jennifer S. LoCoco, Eric Lader, Todd A. Richmond, Vinay K. Mittal, Liang-Chun Liu, Donald J. Johann Jr…
    Citation: Genome Biology 2021 22:109

    The Research to this article has been published in Genome Biology 2021 22:111