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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
Journal article   Open access   Peer reviewed

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

Michael F Murray, Tune H Pers, Paz P Polak, Soumya Raychaudhuri, Heidi L Rehm, Rachel Soemedi, Nathan O Stitziel, Sara Vestecka, Jochen Supper, Claudia Gugenmus, …
Genome biology, Vol.15(3), R53
03/25/2014
DOI: 10.1186/gb-2014-15-3-r53
PMCID: PMC4073084
PMID: 24667040
url
https://doi.org/10.1186/gb-2014-15-3-r53View
Published (Version of record) Open Access

Abstract

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
 Databases, Genetic - standards Genetic Testing - standards Humans Genomics - standards Sequence Analysis, DNA - standards Male Myopathies, Structural, Congenital - genetics Financing, Organized Genetic Testing - methods Heart Defects, Congenital - genetics Peer Review, Research Genomics - economics Female Heart Defects, Congenital - diagnosis Myopathies, Structural, Congenital - diagnosis Genetic Testing - economics Sequence Analysis, DNA - economics Genomics - methods Child Sequence Analysis, DNA - methods

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